Tutorials on Building and displaying molecules
Building and optimizing BF3
Building, optimizing and displaying the Lone Pair in SF4
Reacting BF3 + NH3
Building and optimizing diborane, B2H6.
Calculating Energy v.s. Distance Curves for F2 and "He2"
Calculating a bond rotation energy profile for 1,2-Dibromoethane
Plotting Molecular Orbitals
Plotting the Molecular Orbitals of Ferrocene
Ferrocene MOs using Orca / MultiWFN / Chimera
Stepwise Reaction of Ethene with Br2
Molecular fitting (Fit 2 or more molecules)
The OCTET RULE should obeyed by p-block compounds and there are very few exceptions
The Lewis Structures for PCl5,
SO2, SO3, SO42- that are often seen
in textbooks (first row) are wrong.
These systems are not hypervalent. AsMe5 is an exception
The more accurate and correct OCTET obeying structures are in the second row.
This can be examined using Electron Localization Function, ELF, and Natural Bond Orbital, NBO, analysis.
The ELF analysis uses Academic free software and there are some costs involved in NBO analysis
Bernard Silvi's TOPMOD program for
ELF calculations can be run on a Windows 10 PC
Instructions for downloading and installing Ubuntu inside Win 10 and the TOPMOD package are here.
Instructions for running TOPMOD on AsMe5 and SF6 using academic free software or Gaussian and the results are here..
ELF and NBO analysis of SO2 is described here.
Glucose Sucrose Starch Cellulose
Amino acids, Peptide bond and Proteins
Fatty acid Cholesterol Glycerides
DNA / RNA
Building Blocks of DNA / RNA
Animating Vibrations and Orbital Plots using Firefly (requires Firefly formerly PC-Gamess)
Thermal annealing of cyclohexane derivatives (requires Tinker)