While we wait for everyone to arrive, please jot down your syntheses numbers for weeks 1 and 2. Your protocols can be picked up from the lab before you leave.
While we wait for everyone to arrive, please jot down your syntheses numbers for weeks 1 and 2. Your protocols can be picked up from the lab before you leave.
Introduction to Molecular Modeling
The 1998 Nobel Prize in Chemistry
Applications - models to explain chemical
- phenomena at the molecular level
- Protein folding
- Active sites of enzymes
Industry/Pharmaceuticals - drug mechanism and/or metabolism
- product improvement
- Avoid costly experiments
- ($, time, safety)
Objectives for today…what kind of information can you obtain from molecular modelling?
ĤΨ = εΨ Two energy forms must be accounted for:
1) Potential energy • Electrostatic attraction b/w electrons & nucleus (usual view of bonding) • Electrostatic repulsion b/w nuclei • minimize by finding equilibrium bond length 2) Kinetic energy • e- movement minimize by allowing for delocalization in a larger space (i.e. create an MO larger than the AO) Total energy is the heat of a hypothetical reaction that creates a molecule from a collection of separated nuclei and electrons.
Schrodinger equation ĤΨ = εΨ describes molecules in terms of motions and interactions of nuclei and electrons solvable for a 1-electron atom only use approximations to simplify the equations to be solved Born-Oppenheimer Approximation nuclei >>> electrons nuclear kinetic energy = 0 Hartree-Fock Approximation electrons move independently of each other In the calculation, one electron is selected and the Schrodinger equation is solved in the presence of a field (replacing individual e-e interactions) containing the remaining electrons. This is repeated for each electron until convergence.
3-21G basis set {These two functions are different because they have different exponent arguments (ζ).}
HOMO & LUMO electron pair donor/acceptor orbitals
HOMO & LUMO electron pair donor/acceptor orbitals “frontier orbitals,” important for chemical reactions
What are the limits of your chosen model? Hartree-Fock models tend to overestimate energies and underestimate bond lengths. Methods exist to correct HF calculations. IR frequencies tend to be 12% higher than experimental values. No single method is ideal for all applications. Models and basis sets are chosen based on the properties, problems, level of confidence, and practicality. Improved technology allow for advances in modeling.
Some final reminders… Do the examples in pairs and then individually do the exercises to be turned in. The updated Spartan ’08 info is on the course website. It remains largely the same as what is in your manual for ‘06. The online info contains a copy of the report to be completed. Info can be cut and pasted into the document, printed, and turned in. The department has 15 licenses, so if your calculation fails at first, try again. Pick up protocol for first synthesis before leaving!
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