- Science Honors Program - Computer Modeling and Visualization in Chemistry Molecular Mechanics & Quantum Chemistry Eric Knoll Jiggling and Wiggling Feynman Lectures on Physics
Certainly no subject or field is making more progress on so many fronts at the present moment than biology, and if we were to name the most powerful assumption of all, which leads one on and on in an attempt to understand life, it is that all things are made of atoms, and that everything that living things do can be understood in terms of the jigglings and wigglings of atoms.
The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. It therefore becomes desirable that approximate practical methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation.
-- Dirac, 1929
Improper torsion (sp2)
Two new parameters:
D: dissociation energy
a: width of the potential well
An example of how force fields andm olecular mechanics are used. Molecular mechanics are used as the basis for the molecular dynamics simulations in the below movies.
Protons and neutrons make up the heavy, positive core, the NUCLEUS, which occupies a small volume of the atom.
J J Thompson in his plum pudding model. This consisted of a matrix of protons in which were embedded electrons.
Ernest Rutherford (1871 – 1937) used alpha particles to study the nature of atomic structure with the following apparatus:
Photoelectric Effect: the ejection of electrons from the surface of a substance by light; the energy of the electrons depends upon the wavelength of light, not the intensity.
DeBroglie WavelengthDeBroglie: Wave-like properties of matter.
Traveling waves vs. Standing Waves.
Atomic and Molecular Orbitals are 3-D STANDING WAVES
that have stationary states.
Schrodinger developed this theory in the 1920’s.
Example of 1-D guitar string standing wave.
Density of shading represents the probability of finding an electron at any point.
The graph shows how probability varies with distance.
Since electrons are particles that have wavelike properties, we cannot expect them to behave like point-like objects moving along precise trajectories.
Erwin Schrödinger: Replace the precise trajectory of particles by a wavefunction (ψ), a mathematical function that varies with position
Max Born: physical interpretation of wavefunctions. Probability of finding a particle in a region is proportional to ψ2.
Wavefunctions of s orbitals of higher energy have more complicated radial variation with nodes.
Boundary surface encloses surface with a > 90% probability of finding electron
(Terms from left to right)
For Polyatomic Molecules:
Valence Bond Theory: Similar to drawing Lewis structures. Orbitals for bonds are localized between the two bonded atoms, or as a lone pair of electrons on one atom. The electrons in the lone pair or bond do NOT spread out over the entire molecule.
Molecular Orbital Theory: orbitals are delocalized over the entire molecule.
Which is more correct?
1sA + 1sB
σ – bond H2
FCi = iSCi