Tricks in organic reactions

Mitsunobu reaction: Ph3PO formed during the course of reaction entraps lots of product. After filtering the reaction mixture, warm the Ph3PO with organic solvent, e.g. ether, to recover the product.

Aqueous workup for polar compounds: Use brine (saturated NaCl solution) instead of water to avoid loss of product in aqueous layer.

Instructions to run Sparky in Mac OSX
Step 1 - Run dmg file, which also opens the terminal from X11.
Step 2 - Open Finder, Open Sparky 3.115, Right click on Sparky icon and click on “Show Package Contents”
Step 3 - Go to Contents/Resources/bin, click on any file to get the path
Step 4 - Take the path in X11 terminal to reach there and execute file by “./filename” e.g.
./vnmr2ucsf /Users/Chemist/Desktop/procpar
/Users/Chemist/Desktop/phasefile
/Users/Chemist/Desktop/filename.ucsf H H
Step 5 - filename.ucsf can be opened using sparky. Methods for Processing/Integrating/Labelling is documented in manual

Instructions to run NMRpipe in Mac OSX
Step 1 - Open terminal through X11.
Step 2 - Enter: tcsh (to move from bash shell to c shell)
Step 3 - Go to the directory cd Documents/NMRpipe
Step 4 - Then, enter: source com/nmrInit.mac.com
Step 5 - Then, enter: source dynamo/com/dynInit.com
Step 6 - Then, enter: source com/font.com
Step 7 - Then, enter: setenv NMR_CONT CORRECT_ALL (to override expiration date)
Step 8 - Then, enter: nmrDraw (to open graphics panel)

Gaussian Troubleshooting
Location Transition States: Identical Atom Ordering for QST2 or QST3 jobs
Step 1 - Open a new "Molecule Group" in Gaussview
Step 2 - Draw the reactant molecules
Step 3 - Click "Edit" and then "Copy"
Step 4 - Click "Edit" and then "Paste" and select "Add to Molecule Group"
Checkpoint: Click "View" and select "Labels" to confirm order of atoms
Step 5 - Click "View Both" in toolbar, modify the structures
Checkpoint: Optimize individual structure separately and cut-paste to the molecule group replacing the unoptimized structure
Step 6 - Submit QST2 job or repeat from Step 3 for QST3
Checkpoint: For submitting job, click "Calculate", select "Job Type", select "Optimization" and set "Optimization to a" - TS(QST2) or TS(QST3)