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My research lies in Theoretical Chemistry, specifically in computing the electronic properties of molecules and how they react. Reaction mechanisms are the pathways that atoms take when similar molecules rearrange. I am presently exploring the mechanisms in which groups of atoms rearrange in a reaction called the [1,4] shift, which is important in the synthesis of organic compounds containing nitrogen, oxygen, or sulfur atoms. My longer range plans include the question of complexity in chemistry and chemical synthesis.
The graph gives the results for a "simple" organic reaction that becomes "complex" and "complicated":
(The H atom in the middle of the starting molecule somehow gets over to the upper right side of the molecule,
and the right-hand pentagon becomes a hexagon. The "product" molecule on the right is then formed.)
An atom can't just "pop" off one side, go flying through space, and re-attach itself to an atom on the other side of a molecule.
An H atom usually moves step-by-step. The H atom breaks its bond to one atom and moves to a neighboring atom where it forms a new bond.
But which path does it go in that molecule on the left?
Does it go around the edge of the left-hand pentagon or around the edge of the right-hand pentagon, or straight between the two pentagons to the middle N atom and continue on its way to one of the CN's?
At what point during all this H popping does the new bond form, turning the pentagon into a hexagon?
When an atom breaks a bond, it costs energy. When the atom forms a new bond on the neighboring atom, energy is released. This is just like walking up a hill and coming down the other side.
In Quantum Chemistry and "Structure&Bonding" courses, we learn to calculate the energy of a molecule in a valley (where all the atoms are attached to each other in one way) and the mountain top (where the bond between two atoms is broken) and follow the way the atoms "go down-hill" and re-attach themselves to give a new molecule in its energy valley.
but wait! There's more we can do.
It's just like for us... "The higher the mountain, the more time it takes us to get over it."
For atoms... "The higher in energy the top is from the molecule in the valley, the slower will be the reaction."
We can answer our question about which path the H atom takes. All we have to do is calculate the energy needed for each step. (Hooray for computers!)
I found out by putting all the steps in each pathway (around each pentagon, up the middle, etc) on the graph above.
In Chemical Principles we take only one peak between two valleys, look at the structure of the "reactant" molecule in the valley on the left and the "product" molecule in the valley on the right.
We learn to spot the shapes of molecules, learn how we can measure the peak height in the lab as well as on the computer. We will also see what happens when one valley is deeper than another. It turns out that the closer their energy levels are to each other, the more the two molecules will probably ping-pong back and forth and "equilibrate".
This equilibrium is what is behind how many volts a battery will have and how long the bunny will keep going, how nerve cells work, and much more that we cover in Chemical Principles.
In Organic Chemistry, two or three peaks are used. We will learn how to spot patterns that hydrogen, carbon, nitrogen, oxygen, and chlorine atoms take in reactions. We use these patterns to design more complex molecules from simple building block molecules.
In Advanced Organic Chemistry, we put together all the principles we learned (or should have learned) in the first three years of chemistry. We use them to predict that graph above and the rates and energies involved in reactions. We compare the usual patterns and predict any by-products in chemical reactions. We look at the chemistry that happens inside organic solar cells so that we can design better ones.
Above all, we learn how to argue from principle.
Click here for my presentation on Complexity in Chemistry.
(If your search engine brought you here when you typed in (Edmond)Burke and complexity,
let me disappoint you further by informing you that Science has moved on from conservative systems to emergent ones.)
Click here for some images of the Na cation at various positions above the C9H11 anion. Notice how the conjugated polyene goes through a change in its structure from flat (as taught in Organic Chemistry textbooks) to V-shaped when the Na+ moves a small distance.
Former links to my courses: (no longer readable except for Organic Chemistry)
of Modern Chemistry
General Chemistry II, for those in the Allied Heath Fields (Nursing, Physical Therapy...)
Chemical Principles II, last updated: 2011/12/26/20/01
Organic I and II, Summer '13 :last updated 2013/04/06/15/49:
Advanced Organic(AOC), Fall '10: last updated 2010/08/26/15/19:
Structure and Bonding, Spring '11 :last updated, 2011/01/177/12/52
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In 1988 I saved the trees in front of the Science Building, which were scheduled for elimination without notifying the students or faculty. When I saw the tree removal crew starting, I climbed up the tree where a worker was starting to chain-saw the upper branches and convinced him to stop. The Science Building is still bordered on two sides by locust trees (on the left of the photo). In 1980 when I arrived at Rutgers Camden, they reached just above the first floor. When I retired in 2014, they were higher than the front of the (three story) building. I have enjoyed watching them grow, almost as much as watching my 3300 students, whom I feel privileged to have taught. (Yes, I still remember every one of you and where you sat in class.)