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Dipeptide Structure Computation and Experiment

The document summarizes an experiment and computational study of the dipeptide N-Acyl-Ala-Ala-Benzyl. Infrared spectroscopy revealed two distinct structures with different environments for the NH bonds. Computational results identified two low energy structures - one with intramolecular hydrogen bonding and one with a NH-π interaction. The computed vibrational spectra matched well with the experimental infrared spectrum. Including entropy corrections, the two structures were predicted to be very close in energy at 200K, explaining the observation of both structures experimentally.

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Viorel Aldea
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43 views

Dipeptide Structure Computation and Experiment

The document summarizes an experiment and computational study of the dipeptide N-Acyl-Ala-Ala-Benzyl. Infrared spectroscopy revealed two distinct structures with different environments for the NH bonds. Computational results identified two low energy structures - one with intramolecular hydrogen bonding and one with a NH-π interaction. The computed vibrational spectra matched well with the experimental infrared spectrum. Including entropy corrections, the two structures were predicted to be very close in energy at 200K, explaining the observation of both structures experimentally.

Uploaded by

Viorel Aldea
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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DIPEPTIDE STRUCTURE:

COMPUTATION AND EXPERIMENT

Here’s a nice example of the productive interplay between experiment and

computations.1 The dipeptide N-Acyl-Ala-Ala-Benzyl was prepared and subjected

to UV and IR/UV analysis. The IR showed two separate structures with distinctly

different environments for the NH bonds: one structure showed intramolecular

hydrogen bonding while the other did not.

B97/TZVPP computations revealed two structures. The first is a linear dipeptide

with intramolecular hydrogen bonding occurring in a 5,5 relationship. (There are

actually three conformers of this but all have similar energy, only one is shown in

Figure 1.) The second structure displays a bent shape with a NH-π interaction, also

shown in Figure 1. The computed vibrational spectra for each structure matches up

well with the NH region of the experimental IR.

Figure 1. B97-D/TZVPP optimized structures of N-Acyl-Ala-Ala-Benzyl.


The authors spend a great deal of time noting that the 0 K energies predict that the

second structure, being 4 kcal mol-1 more stable, should be the only one observed.

However, since the jet cooling will likely trap the structures at their 300 K

distribution, this could account for the existence of two structures. However, when

the computations include entropy corrections, so now we’re looking at ΔG(200 K),

B97-D and MO6-2x suggest that the two structures are very close in energy. But

they caution that MP2 predicts a large energy gap unless atomic counterpoise

corrections are used to account for intramolecular basis set superposition (see

this post), a problem that appears to be much less severe with the DFT methods.

Source: http://comporgchem.com/blog/?p=1134

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