Oscail Tutorials

Molecular Modelling using Moilin

   Getting Móilín Started
       Introduction
   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.
     

    Carbohydrates
        Glucose Sucrose Starch Cellulose
    Proteins
        Amino acids, Peptide bond and Proteins
        Building Peptides
    Fats
        Fatty acid Cholesterol Glycerides
    DNA / RNA
        Building Blocks of DNA / RNA
    Firefly
        Animating Vibrations and Orbital Plots using Firefly (requires Firefly formerly PC-Gamess)
    Tinker
        Thermal annealing of cyclohexane derivatives (requires Tinker)