Computational Chemistry Exercise: cis, trans Temperature
Dependence of a Copper(II) glycine Complex
Part 1: Reaction Pathway analysis via semi-empirical
calculations
Chemical reactions forming chiral complexes often have different energy pathways. The
two stable chiral products of the bis-Copper(II) glycine complex formation produces an
intermediate that can form two different transition states, leading to the formation of two
different chiral products. The amount of product formed depends on the energy
relationship between all of the species in the reaction pathway.
Figure 1. Reaction pathways for Cu(II) glycine cis and trans products
The two products are labeled K (kinetic) and T (thermal) and have a common
intermediate, but has an Ea for T that is higher than for K. Furthermore, The total energy
change of the product T is much higher than for K so that the backward reaction energy
barrier for K is less (to the intermediate, I) than for T. This means that at moderate
temperatures, K forms more readily than T, producing this particular product in
abundance. This occurs even though the product K is higher in energy than T (final
energy).
If the reaction is run at a temperature where there is an energy Et(K) available, but not
Et(T), then there is enough energy for the back reaction of K to occur, but not for T.
Since Et(K) is larger than the EaT, then any K that forms can back-react to the
intermediate and re-form as T, but T cannot back react, and a preponderance of T forms
at the expense of K.
Since Et(K) and Et(T) are not known, the reaction cannot be driven to a particular
product. However, if the reaction is run at sufficiently high temperatures, so that at least
Et (T) is available, then all reaction pathways can be accessed ( both T and K can backreact to form the intermediate) and the product distribution depends on the
thermodynamic stability of the products K and T. Since T is lower in final energy than K,
the thermodynamic product is the predominant one under these conditions.
Procedure: Open ChemDraw on the PC and open the file cis_glycine.cd3. This is the
beginning structure for the complex of one steric conformation. Select the Analyze menu
bar and then select compute properties. There will be a set of parameters displayed on a
menu:
select a minimum of Total energy, torsional energy, bend energy, stretch energy, and the
dipole moment as parameters to calculate.
Run the computation and record the results. Repeat the experiment with the second
compound (trans) and then compare the values for each parameter determined.
Determine the stability (at room temperature) of the isomers from the tabulated data.
Predict the predominant isomer produced at room temperature.
Symmetry Analysis
Determine the symmetry point group of each isomer. From the appropriate symmetry
table, determine the number of IR bands for each complex. Assign the predicted bands
asymmetric and symmetric for the cis isomer (M-N and M-O), and asymmetric for the
trans isomer. Assign the peaks on the IR spectra provided and compare them with your
predicted assignments. Can you differentiate between the complexes based on the IR
spectra?
cis and trans structures
cis-[Cu(gly)2].H2O
0
0.5
1
1.5
2
2.5
4000
3500
3000
2500
2000
1500
1000
500
1500
1000
500
trans-[Cu(gly)2].H2O
0.5
1
1.5
4000
3500
3000
2500
2000