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Computer Modeling of Organic Compounds Flipbook PDF
Computer Modeling of Organic Compounds Molecular Modeling of Organic Compounds Kinetic Control vs. Thermodynamic Control
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11/30/2012
Computer Modeling of Organic Compounds
Molecular Modeling of Organic Compounds Kinetic Control vs. Thermodynamic Control
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Thermodynamic Control Consider a reaction in which reactants A
and B can react to form either product C or product D through two different reaction pathways (mechanisms).
C
A + B
D
If the reaction conditions are such that both
forward and reverse reactions are proceeding at a good rate, an equilibrium will be established between C and D.
Thermodynamic Control (Cont.) C
A + B
D
When an equilibrium is established between
C and D (all four reactions proceeding at reasonable rate), the ratio of C to D is controlled by the difference in stability (energy content) of C and D. This system is said to be under thermodynamic control. Determining the lowest energy product will allow prediction of the major product.
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Calculation of Product Energies To calculate the energy of an organic molecule,
we first use the computer to calculate the lowest energy 3-dimensional structure (Geometry Optimization) using molecular mechanics methods. We then recalculate the optimum geometry using more complex semi-empirical methods. Make sure you follow this two-step procedure for each calculation.
Product Energies (Cont.) One of the properties calculated by the semi-
empirical method is the heat of formation. This is the energy difference between the structure and the isolated individual atoms. Heat of formation is normally negative (product more stable than atoms). We can use the calculated heats of formation to compare energies of different products, and thus predict the major product under equilibrium conditions.
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Kinetic Control C
A + B
D
In some cases, the reverse reactions to
convert C and D back to A and B are much slower than the forward reactions. Under these conditions, the ratio of C to D will be controlled only by the relative rates of the reactions forming them (kinetics), and the reaction is said to be under kinetic control.
Kinetic Control (Cont.) Under conditions of kinetic control, the
ratio of products can be predicted if we know the relative energies of the two transition states. Transition state energies are much harder to calculate than energies of products or reactive intermediates since transition states are not at an energy minimum! We are not going to calculate TS energies today.
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Kinetic Control (Cont.) In today’s exercise we are going to study a
reaction in which a single carbocation intermediate can react at two different sites to give different products.
C A + B
I+ D
Kinetic Control (Cont.) C A + B
I+ D
In this case, we can make a prediction that
the site that possesses the greatest positive charge will react faster. We can use the computer (semi-emperical methods) to calculate the charge at the two sites.
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Experimental Procedure (Cont.) You will work in pairs. One person should
operate the computer; the other one should be reading the instructions to the operator. The computers are already set up in lab to begin the experiment. You do not need to check out a bin today.
Lab Reports Your lab report will consist of the Pre-lab
page, the Worksheet, and Post-lab Questions from the website. There will be no post-lab write-up.
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Camphor Reduction Product Today you will also need to analyze the product from the borohydride reduction of camphor. You will need to weigh your product, obtain an IR spectrum, and take a melting point of your product. MelTemps are at the back bench only. Do not handle chemicals around the computers
Camphor Reduction Product Student workers are available to help you take an infrared spectrum of your product. Some students need to take care of finishing last week’s experiment before finishing today’s computer experiment in order to avoid a waiting line at the IR spectrometers or MelTemps.
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