Full metadata
Title
Calculating infrared spectra of proteins and other organic molecules based on normal modes
Description
The goal of this theoretical study of infrared spectra was to ascertain to what degree molecules may be identified from their IR spectra and which spectral regions are best suited for this purpose. The frequencies considered range from the lowest frequency molecular vibrations in the far-IR, terahertz region (below ~3 THz or 100 cm-1) up to the highest frequency vibrations (~120 THz or 4000 cm-1). An emphasis was placed on the IR spectra of chemical and biological threat molecules in the interest of detection and prevention. To calculate IR spectra, the technique of normal mode analysis was applied to organic molecules ranging in size from 8 to 11,352 atoms. The IR intensities of the vibrational modes were calculated in terms of the derivative of the molecular dipole moment with respect to each normal coordinate. Three sets of molecules were studied: the organophosphorus G- and V-type nerve agents and chemically related simulants (15 molecules ranging in size from 11 to 40 atoms); 21 other small molecules ranging in size from 8 to 24 atoms; and 13 proteins ranging in size from 304 to 11,352 atoms. Spectra for the first two sets of molecules were calculated using quantum chemistry software, the last two sets using force fields. The "middle" set used both methods, allowing for comparison between them and with experimental spectra from the NIST/EPA Gas-Phase Infrared Library. The calculated spectra of proteins, for which only force field calculations are practical, reproduced the experimentally observed amide I and II bands, but they were shifted by approximately +40 cm-1 relative to experiment. Considering the entire spectrum of protein vibrations, the most promising frequency range for differentiating between proteins was approximately 600-1300 cm-1 where water has low absorption and the proteins show some differences.
Date Created
2012
Contributors
- Mott, Adam J (Author)
- Rez, Peter (Thesis advisor)
- Ozkan, Banu (Committee member)
- Shumway, John (Committee member)
- Thorpe, Michael (Committee member)
- Vaiana, Sara (Committee member)
- Arizona State University (Publisher)
Topical Subject
Resource Type
Extent
ix, 119 p. : ill. (some col.)
Language
eng
Copyright Statement
In Copyright
Primary Member of
Peer-reviewed
No
Open Access
No
Handle
https://hdl.handle.net/2286/R.I.15193
Statement of Responsibility
by Adam J. Mott
Description Source
Retrieved on August 2, 2013
Level of coding
full
Note
thesis
Partial requirement for: Ph.D., Arizona State University, 2012
bibliography
Includes bibliographical references (p. 111-119)
Field of study: Physics
System Created
- 2012-08-24 06:32:06
System Modified
- 2021-08-30 01:45:09
- 3 years 2 months ago
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