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Vibrational and photoionization spectroscopy of biomolecules: Aliphatic amino acid structures
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10.1063/1.2902980
/content/aip/journal/jcp/128/16/10.1063/1.2902980
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/16/10.1063/1.2902980

Figures

Image of FIG. 1.
FIG. 1.

Calculated structures for general amino acid isomers according to Ref. 11.

Image of FIG. 2.
FIG. 2.

Mass spectra for valine ionized with light with the IR laser on (red) and off (blue). Note that most mass channels increase in intensity with the IR laser on but mass channel decreases in intensity with the IR laser on. The weak feature located at 118 in the mass spectrum is assigned as the protonated valine cation, which arises from the photodissociation of the valine dimer. The gap between mass and mass does not contain features.

Image of FIG. 3.
FIG. 3.

Schematic drawing of the potential energy surfaces of the amino acid ions for a given isomer structure. Since the ionization process occurs in attoseconds and the nuclei move in femtoseconds, the vertical ionization position is the same as the ground state equilibrium position for a given conformer. This energy is apparently sufficient, in terms of excess vibrational energy in the amino acid , to surmount a barrier to a rearrangement reaction in the ion. The for this reaction then adds to the ion vibrational energy as does the vibrational excitation (IR absorption) added to the neutral amino acid in the ground state absorption experiment. This total vibrational energy in the ion can influence the population of the various fragmentation channels open to the ion. Note that these channels are not changed by the vibrational energy absorption. Nonetheless, the existing fragmentation channel can change population (positive and/or negative) due to the absorption of CH, NH, or OH vibrational energy. All the modes change the fragment intensity the same way, positive or negative.

Image of FIG. 4.
FIG. 4.

Schematic drawing of the ground structure state potential energy surface for the three lowest energy isomers for each amino acid. The barriers and IR energies are roughly to scale for the hydrogen bonding energies. The energy differences between the respective minima are of the order of a few kcal/mol and are calculational algorithm and basis set dependent (see text for further discussion of these points).

Image of FIG. 5.
FIG. 5.

The IR spectra for valine isomers observed in different fragment mass channels as indicated. The isomers identified in the figure are suggested based on the structures given in Fig. 1, the fragmentation mass channels, and the IR spectra.

Image of FIG. 6.
FIG. 6.

Mass spectra for glycine ionized with light with the IR laser on (red) and off (blue). Note that both mass channel signals 30 and 42 increase with the presence of IR radiation, while mass channels 31 and 43 seem little affected by the presence of IR radiation.

Image of FIG. 7.
FIG. 7.

The IR spectra for glycine isomers obtained in different fragment mass channels as indicated. The isomers identified in the figure are suggested based on the structure given in Fig. 1, the fragmentation mass channels, and the IR spectra.

Image of FIG. 8.
FIG. 8.

Mass spectra for leucine ionized with light with the IR laser on (red) and off (blue). Note that most mass channels increase in intensity with the IR laser on but mass channel 87 decreases in intensity with the IR laser on.

Image of FIG. 9.
FIG. 9.

The IR spectra for leucine obtained in different fragment mass channels as indicated. The isomers identified in the figure are suggested based on the structures given in Fig. 1, the fragmentation mass channels, and the IR absorption spectra.

Tables

Generic image for table
Table I.

Isomers of valine, possible IR absorption assignments, and ionization and suggested fragmentation processes under IR plus vuv radiation for each of the main lower energy conformers. Note that other rearrangements of fragments are possible.

Generic image for table
Table II.

Isomers of glycine, possible IR absorption assignments, and ionization and suggested fragmentation processes under IR plus vuv radiation for each of the main lower energy conformers. Note that other rearrangements of fragments are possible.

Generic image for table
Table III.

Isomers of leucine, possible IR absorption assignments, and ionization and suggested fragmentation processes under IR plus vuv radiation for each of the main lower energy isomers. Note that other rearrangements of fragments are possible.

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/content/aip/journal/jcp/128/16/10.1063/1.2902980
2008-04-28
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Vibrational and photoionization spectroscopy of biomolecules: Aliphatic amino acid structures
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/16/10.1063/1.2902980
10.1063/1.2902980
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