Difference between revisions of "Computational Chemistry III"

Latest revision as of 13:11, 19 March 2020

A Computational Study of Polyaromatic Hydrocarbon Radical Anions.

https://en.wikipedia.org/wiki/Polycyclic_aromatic_hydrocarbon

Polyaromatic hydrocarbons are an interesting class of chemical compounds. My (bes) first publication involved benzene and naphthalene, the simplest of the aromatic/di-aromatic hydrocarbons.

Task 1

Can you find my (Bradley E. Sturgeon) Journal of Physical Chemistry publication titled, "Separation of Benzene and ²H-Substituted Benzene via Potassium Reduction"? This quick literature search is best done using our new "Web of Science" database Monmouth College recently added to its resources. Since you are most likely off campus, you will need to "authenticate" thru the main Library page found here <--right click to open in new tab. Choose the "Find" tab, then Databases, W, then "Web of Science." Now do an author search for Sturgeon, BE <-- this should return 42 results (3/18/20). Many of my listed references are "meeting abstracts" (ACS National meeting) so in order to refine the search to only my "Articles" scroll down to "Document Types," this should focus the search down to 22 results (3/18/20) or 3 pages. Navigate back to page 3...and you should find the above article. Note that this publication has been cited in other publications 31 times (3/18/20), but it has not been cited since 2012. Because Monmouth College has a digital subscription to all ACS journals (thanks to the Haldeman Library Endowment), we have access to the digital copy of the paper.

Task 2

Continuing with the literature searching...you will notice that there are multiple co-authors --> Gerald R. Stevenson, Bradley E. Sturgeon, K. Shay Vines, and Steven J. Peters. If you select the title of the article this will take you to a page with more information. Notice that the author names are hyperlinks. Investigate each author (hyperlink) and note the following information:

- current location / past locations

- alternative names

- a complete list of references.

Which of the co-authors are still active in the profession? (look at the last publication date of the references)

Where is "Steven J. Peters" currently working? (Answer: where he received his undergraduate degree, Illinois State University)

Gerald R. Stevenson was one of my two undergraduate research advisors. From the above search it looks as though GR Stevenson stopped publishing in 2005, but this is not the case. Do another author search for Stevenson, CD, then refine to include only Illinois State University and "Articles." You find an article titled,

EFFECT OF ISOTOPIC-SUBSTITUTION ON ASSOCIATION WITH THE SODIUM COUNTERION

By: STEVENSON, CD; WAGNER, EP; REITER, RC

INORGANIC CHEMISTRY Volume: 32 Issue: 11 Pages: 2480-2482 Published: MAY 26 1993

Download the article and read the footnote.

Yes, Gerald R. Stevenson is Cheryl D. Stevenson. Professor Stevenson has made great contributions to science from both the perspective of original research and the extensive amount of effort put forth to work with undergraduates to train them to be research scientist. I am currently friends with Steve Peters, both Steve and I are a product of Professor Stevenson efforts and are both very proud of it!

Task 3

Now for the chemistry...

Use WebMO/Gaussian to optimize the geometry of benzene (neutral).

- consider using the "build/fragment" menu options,

- you will notice that there is a small icon in the lefthand column of icons that is red C_6h. This means that the molecule could have some level of symmetry that is currently not in the model. You may continue with the calculation without symmetrizing, but it is good practice to cancel and then click the red icon to symmetrize the molecule,

- Calculation: Geometry Optimization,

- Theory: B3LYP,

- Basis Set: Routine: 6-31G(d),

- Charge = 0,

- Multiplicity = single <--recall Multiplicity=(# of unpaired electrons)*1/2 + 1,

- Submit.

This calculation should take less than 1 min if no one else is running jobs.

Results

1) Bond lengths, bond angle, and dihedral angles (How to measure bond lengths, angle, and dihedral angles)

- What is the average bond length for the carbon-carbon bonding?

- What is the average bond length for the carbon-hydrogen bonding?

2) Visualize Results

- Molecular Orbitals: Select the menu Calculate/Huckel/Molecular Orbitals

(click on the orbital in the list shown to visualize the orbital)

The highest occupied molecular orbital (HOMO) is doubly degenerate, orbitals 14 and 15 (ie. same energy).

The lowest unoccupied molecular orbital (LUMO) is doubly degenerate, orbitals 16 and 17 (ie. same energy).

Since the HOMO and LUMO are doubly degenerate, an electron in this energy level spends equal time in each of the two orbitals with the result being that the orbital looks more like an average of the two HOMO (14/15) / LUMO (16/17) orbitals. This can be visualized by calculating the "Electrophilic (HOMO) frontier density" and "Nucleophilic (LUMO) frontier density"...select "Properties" at the bottom of the "Orbitals" inset.

Task 4

Use WebMO/Gaussian to optimize the geometry of the benzene radical anion (bz + 1e-, ie. the result of the reduction of benzene).

- Starting with the optimized benzene (neutral) structure, click "New Job Using This Geometry,"

- NO modifications needed to the structure, so move to the "Job Options" window,

- Calculation: Geometry Optimization,

- Theory: B3LYP,

- *Basis Set: Accurate: 6-311+G(2d,p),

- *Charge = -1,

- *Multiplicity = Doublet <--recall Multiplicity=(# of unpaired electrons)*1/2 + 1,

- *Select the "Advanced" tab and enter the following into the Additional Keywords --> density=current