Difference between revisions of "Comp Chem 04"
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===Today's Computational Task=== | ===Today's Computational Task=== | ||
| − | Calculate the UV-Vis spectrum for both the non-colored, form of phenolphthalein and the pink-color form of phenolphthalein. These calculations will take a significantly longer period of time than previous calculations, so i suggest that you get 2 jobs running (colorless and pink), make sure the "email notification" box is checked under the "Utilities" tab...and return to this lab activity once both of your jobs are done. | + | :''(Please note that i have not completed this task (my first job has been running for ~3 hours), but i have been able to submit jobs. Jobs with incorrectly defined structures will fail quickly).'' |
| + | |||
| + | Calculate the UV-Vis spectrum for both the non-colored, form of phenolphthalein and the pink-color form of phenolphthalein. These calculations will take a significantly longer period of time than previous calculations, so i suggest that you get 2 jobs running (colorless and pink), make sure the "email notification" box is checked under the "Utilities" tab...and return to this lab activity once both of your jobs are done...come to think of it, i am not sure the mail server is running on the iMAC Pro??? | ||
| + | |||
| + | :'''Notes on drawing dianion'''...When drawing an ion in WebMO, after cleaning up the structure, select the "adjust" tool, select the H-atom (it will turn gray), then hit delete. You specify charge when setting up the calculation. | ||
:Calculation parameters: | :Calculation parameters: | ||
| − | + | {| Border=1 | |
| − | + | |Calculation || Geometry optimization|| then Excited State and UV_vis | |
| − | + | |- | |
| − | + | |Theory/Method||Moller-Plesset 2*|| CIS | |
| − | + | |- | |
| + | |Basis Set|| Routine 6-31G(d)||Routine 6-31G(d) | ||
| + | |- | ||
| + | |Multiplicity ||Singlet||Singlet | ||
| + | |- | ||
| + | |Charge|| 0 or -2|| 0 or -2 | ||
| + | |} | ||
| + | :''*''considered a ''post-HF'' type of theory that acknowledges electron correlation. | ||
====Reporting==== | ====Reporting==== | ||
:1) Screenshots or equivalent of UV-Vis spectra for both non-colored and pink structures. | :1) Screenshots or equivalent of UV-Vis spectra for both non-colored and pink structures. | ||
| − | :2) Physical chemistry statement of why the pH>8 structure has color...look carefully at the orientation of the two phenol rings in the non-colored form...and compare this to the two phenol rings in the pink-form. | + | :2) Physical chemistry statement of why the pH>8 structure has color...look carefully at the orientation of the two phenol rings in the non-colored form...and compare this to the two phenol rings in the pink-form. Each ring is essentially a "box" with a ''λ<sub>max</sub>'' around 270 nm, but when the rings are conjugated and coplanar, the box dimension increase substantially leading to a ''λ<sub>max</sub>'' of ~ 650 nm. |
Latest revision as of 18:31, 30 April 2020
(4/30/20, bes)
Greetings...welcome to your last (sad face) Pchem II lab.
- A reminder...comp chem activities will be included on the Exam 3.
My Friend Bob2
In today's lab activity i will be using some information provided by Bob Gotwals, a current chemistry faculty member at the North Carolina School of Science and Mathematics (NCSSM). NCSSM is a residential "magnetic school" for junior and senior high school students. I first met Bob2 when i was a chemistry faculty member at NCSSM (2000-2002) and Bob2 worked at Shodor (I was told is an abbreviation for SHOrt and DORky). At that time, Bob2 was promoting computational chemistry to educators and was developing significant online "COMP CHEM" resources.
To start today's "lab" i ask you to watch the 24 min video as an overview of computational chemistry. This video will provide a general overview and provide for you a framework on where quantum mechanics works into the computation scene. Many of these slides/topics should be familiar to you...
Methods in Computational Chemistry, by Bob Gotwals
Phenolphthalein
You are all aware of the pH-dependent color change of a solution of phenolphthalein (no color to pink at ~pH 8). We can use WebMO to calculate the UV-Vis spectrum of this pH "indicator." You may see Bob2's rendition of this lab (exercise 3)...here, but i will define our specific calculation parameters below.
The chemistry is highlighted by a very nice animation of the deprotonation process on the Wikipedia site <-- go see this now.
Today's Computational Task
- (Please note that i have not completed this task (my first job has been running for ~3 hours), but i have been able to submit jobs. Jobs with incorrectly defined structures will fail quickly).
Calculate the UV-Vis spectrum for both the non-colored, form of phenolphthalein and the pink-color form of phenolphthalein. These calculations will take a significantly longer period of time than previous calculations, so i suggest that you get 2 jobs running (colorless and pink), make sure the "email notification" box is checked under the "Utilities" tab...and return to this lab activity once both of your jobs are done...come to think of it, i am not sure the mail server is running on the iMAC Pro???
- Notes on drawing dianion...When drawing an ion in WebMO, after cleaning up the structure, select the "adjust" tool, select the H-atom (it will turn gray), then hit delete. You specify charge when setting up the calculation.
- Calculation parameters:
| Calculation | Geometry optimization | then Excited State and UV_vis |
| Theory/Method | Moller-Plesset 2* | CIS |
| Basis Set | Routine 6-31G(d) | Routine 6-31G(d) |
| Multiplicity | Singlet | Singlet |
| Charge | 0 or -2 | 0 or -2 |
- *considered a post-HF type of theory that acknowledges electron correlation.
Reporting
- 1) Screenshots or equivalent of UV-Vis spectra for both non-colored and pink structures.
- 2) Physical chemistry statement of why the pH>8 structure has color...look carefully at the orientation of the two phenol rings in the non-colored form...and compare this to the two phenol rings in the pink-form. Each ring is essentially a "box" with a λmax around 270 nm, but when the rings are conjugated and coplanar, the box dimension increase substantially leading to a λmax of ~ 650 nm.