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16: Biomaterials- Studies of Protein Structure by Computational Quantum Chemistry

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    CHEM 174 Physical Chemistry Laboratory II

    Biomaterials: Studies of Protein Structure by Computational Quantum Chemistry

    Introduction

    You already become familiar Spartan. In this lab you will use it to:

    1) Calculate an IR spectra of Glycine, Alanine, Leucine and Valine
    2) Calculate an IR spectra of polyglycine
    3) Examine the difference between an α-helix and a β-sheet.

    Procedure

    Part 1 Glycine Example

    Go into Spartan and select a new simulation. Click on the Peptide tab on the model entry toolbox. Click “Gly” to bring up glycine at the top of the toolbox. Click on the main screen to bring up glycine on the main model window.

    Now you need to terminate the glycine so click terminate. For simplicity on the calculate be sure that the terminate option is set to yield a neutral molecule.

    You are ready to set up the calculation. Enter calculations and choose the Hartree-Fock 3-21G model, choose single energy and click the IR box, also keep the molecule neutral. Submit the calculation under a name that you choose.

    When the calculation is complete view the IR spectra and note the IR bands that were calculated. Repeat for the other amino acids

    Compare the glycine calculation with your spectra for solid glycine from the previous laboratory and discuss in your laboratory report.

    Part 2. Triglycine

    Repeat for triglycine. Note that it would be better if the calculation was performed for a larger peptide but triglycine is already a little time consuming. You will compare this calculation with your spectra for solid collagen.

    Part 3. α-Helix and β-Sheets

    1. Use Spartan to construct a peptide with at least 20 amino acids (your choice). Transfer it to the screen as an α-helix. Save an image of the structure for your report and discuss its appearance.
    2. Use Spartan to construct the same peptide and transfer it to the screen as a β-sheet. Save an image of the structure for your report and discuss its appearance.

    Report

    Use the research journal article format.

    Discuss your results by answering the following questions in the discussion section of your report.

    • For glycine, compare the individually computed vibrational frequencies to those observed (from the previous laboratory) in your experimental spectrum.
    • Which vibrational motions produced the most intense peaks in your observed glycine spectrum? Is this consistent with the theoretical prediction?
    • Compare the theoretical frequencies of glycine to those of the other amino acids. What are the similarities and what are the differences?
    • For all the calculated spectra what can you say about the relationship between the functional groups and the absorbance peaks?
    • How many peaks can you identify as being common between the different amino acids?
    • You probably noticed that the same group (e.g. C=O stretching) in different molecules might have shifted significantly. By significantly, we mean by more than 2x the spectral resolution. Which group frequency shifted the most between your molecules? In what direction, relative to the Glycine frequencies, is the shift? (Lower energy or higher energy) Offer an explanation for this behavior.
    • Perform some statistical analysis on the vibrational frequencies of the different amino acids based on literature data (average absolute error, standard deviation, and variance).
    • What are the similarities and differences between the calculated spectra of glycine and triglycine?
    • What are the similarities and differences between the calculated spectra of glycine and your measured glycine IR?
    • What are the similarities and differences between the calculated spectra of triglycine and your measured collagen IR? Clearly the spectra will not the same but can you say anything about the trend?
    • Discuss the major differences between peptides with α-helix and β-sheet structures.
    • Overall, discuss your impressions on the utility of IR spectroscopy as a probe of protein structure: “thumbs up”, “thumbs down”, or something in between?

    Reference

    Spartan ’04 Windows: Tutorial and User’s Guide, Wavefunction, Irvine, CA, 2004, pages 102 – 105.


    16: Biomaterials- Studies of Protein Structure by Computational Quantum Chemistry is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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