[dontwanttofail]

I am taking a molecular modeling course and we are using a Software called Spartan. I don't have too much trouble with the software, but I don't understand some general concepts.

For example, say I build methane in the software.  Then I use some method that is an approximation of the Shrodinger equation, say Hartree Fock equation.  OK.  I will end up getting some energy, usually really high, that says relE, relative Energy.  My question is, what is this energy exactly?  What does it represent?  What does this value mean?  I know energy is PE + KE, so does this value truly represent that?  I mean, I know there are errors in calculations thats not what I'm asking, I'm just beweildered on what it actually means. 

I know that from taking all these energies I can find deltaH(rxn) and deltaH(form) of different molecules, but that's about it.  I know how to do those things but not why its happening

The reason I ask is because when the situation is appropriate I can use Molecular Mechanics instead of Quantum Mechanics to get some energy, but that energy value
E = stretchingE + bendingE + torsionE + non-bondinginteractionsE

so I am really confused.  I know you only use the molecular mechanics energies as comparisons (like compare the energy of cis v. trans).


PLEASE HELP ME FROM GETTING A D, THANKS!!

BTW I am a math major... can someone please kick me in the head for taking this course??

[rajan]

a good book for this is chris cramer's "computational chemistry"

hartree fock sets up a calculation that explicitly, and from first principles, calculates the energy of your molecule based on the positions of the atoms and electrons (which are generally much more difficult to define positions for than atoms). hartree fock knows what a bond is because it's a minimum energy structure, but molecular mechanics only knows what a bond is if you tell it (which is why you need to give MM connectivity information). hartree fock is variational in the way is solves the secular equation so it always gives you energies that are higher than reality. molecular mechanics gives you energies that someone has programmed to be pretty close to reality so it could be too high or too low.

as for the energy of the molecule, hartree fock misses a lot of the electron's energies (and in spite of knowing of this shortcoming, it's still useful). molecular mechanics will miss anything that newton's laws can't tell you.

this is a really broad question, but possibly the best answer is that molecular mechanics treats every molecule as a bunch of marbles (nuclei) linked by springs (bonds), and hartree fock attempts to solve quantum mechanical equations for your system after you've given it some initial positions of atoms.

as for kicking you in the head, try getting married. that way you'll always have someone there to do such things.