Difference between revisions of "Computational Chemistry II"

Latest revision as of 12:33, 28 March 2019

These are additional computational activities...

Calculation

optimize and vibrational frequency

3.8088e-4 H = 1 kJ/mol

Calculation

optimize energy first using B#LYP/6-31G(d)

then do NMR calculation using optimized geometry

view NMR setting TMS shift to 0.0.

13C NMR

1H NMR

Construct the following structure (R=H)

alt text

Submit a job Energy Optimization/HF/Routine

Determine how well this level of calculation matches the values from the crystal structure.

@@ Line 1: / Line 1: @@
 These are additional computational activities...
+[http://iron.monmsci.net/~webmo/cgi-bin/webmo/login.cgi WebMO 18.0]
+===Computation of Thermodynamic Data===
+Calculation
+:optimize and vibrational frequency
+.8088e-4 H = 1 kJ/mol
+====Heat of Combustion====
+http://homepages.gac.edu/~anienow/CHE-371a/Labs/Heats%20of%20Formation.pdf
+====pKa====
+https://www.uow.edu.au/~adamt/Trevitt_Research/Links_files/pKa%20workshop%20slides.pdf
+[[File:Screen Shot 2018-04-26 at 1.49.55 PM.png|400px]]
+[[File:Screen Shot 2018-04-26 at 1.43.56 PM.png|400px]]
+===NMR Computations===
+:https://en.wikipedia.org/wiki/Tetramethylsilane
+:https://en.wikipedia.org/wiki/Chemical_shift
+Calculation
+:optimize energy first using B#LYP/6-31G(d)
+:then do NMR calculation using optimized geometry
+:view NMR setting TMS shift to 0.0.
+::13C NMR
+::1H NMR
+===Peptide Bond===
+Construct the following structure (R=H)
+{|
+|[[File:IMG_1082.jpg|600px|thumb|left|alt text]]
+|}
+Submit a job Energy Optimization/HF/Routine
+Determine how well this level of calculation matches the values from the crystal structure.
+===Visualizing Protein Structure===
+[https://www.youtube.com/watch?v=wiKyOF-pGw4 PyMol for Beginners]