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On the importance of nuclear quantum motions in near edge x-ray absorption fine structure spectroscopy of molecules
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10.1063/1.3125509
/content/aip/journal/jcp/130/18/10.1063/1.3125509
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/18/10.1063/1.3125509

Figures

Image of FIG. 1.
FIG. 1.

Measured and simulated core-level spectra of -triazine (indicated top right) at the nitrogen edge, offset vertically for clarity: (a) from top to bottom: measured NEXAFS [solid (blue)] and ISEELS [dotted (yellow)] spectra in comparison with the calculated spectra using fixed nuclei (red), classical MD (black with gray error bars), and PIMD (purple with error bars). The average spectra for classical MD and PIMD are shown in darker colors with a shaded width of one standard deviation. The experimental spectra are taken from the literature and the vertical line is the experimental ionization potential (see text). (b) An enlargement of the spectral energy range 398–405 eV for PIMD, classical MD, and NEXAFS data. The PIMD results reproduce a shoulder around 400 eV, as found experimentally, unlike the classical MD results.

Image of FIG. 2.
FIG. 2.

Isosurfaces of several electronic states of -triazine from the fixed-nuclei structure without and with a core hole on the bottom most nitrogen and from a single PIMD configuration without and with a nitrogen core excitation respectively. Positive and negative phases are indicated in red and green, respectively. The excited nitrogen is always on the lowermost (blue) atom of the selected configuration. State A corresponds to spectral feature 1, state B to spectral feature 2, state C is representative of spectral feature 3, and state D is a scattering state corresponding to feature 5. Further details are given in the text.

Image of FIG. 3.
FIG. 3.

A plot of the difference in -triazine CNC bond angles, with the two relevant angles labeled in red ( and ), sampled from the classical [solid (blue)] and PIMD [dashed (red)] distributions. The PIMD data shows a significantly broader distribution than that of classical MD. The errors are of the size of the width of the lines.

Image of FIG. 4.
FIG. 4.

A plot of -triazine C-N-C-H dihedral angles, with relevant atoms labeled (1–4), sampled from classical [solid (blue)] and PIMD [dashed (red)] distributions. The PIMD data shows a significantly broader distribution than that of classical MD. The errors are of the size of the width of the lines.

Image of FIG. 5.
FIG. 5.

A plot of the glycine dihedral angle, with the relevant atoms labeled (1–4), sampled from classical [solid (blue)] and PIMD [dashed (red)] distributions. The PIMD data shows a slightly broader distribution than that of classical MD. The errors are of the size of the width of the lines. At PIMD is more intense than classical.

Image of FIG. 6.
FIG. 6.

Measured and simulated core-level spectra of glycine at the nitrogen -edge (from top to bottom): Measured NEXAFS [solid (blue)] and ISEELS [dash-dot (yellow)] spectra in comparison with the calculated spectra using fixed nuclei (red), a Boltzmann-weighted average from the four lowest energy conformers (green), classical MD (black with gray error bars), and PIMD (purple with error bars). The average spectra for classical MD and PIMD are shown in darker colors with a shaded width of one standard deviation. The experimental spectra are taken from literature and the vertical line is the experimental ionization potential (see text).

Tables

Generic image for table
Table I.

Calculated vibrational modes of -triazine listed in frequency . The molecular structure was optimized and then the vibrational modes were calculated, using the B3LYP exchange-correlation functional and a basis set. We note that the lowest energy mode corresponds to .

Generic image for table
Table II.

Calculated vibrational modes of glycine listed in both frequency and temperature (K). The molecular structure was optimized and then the vibrational modes were calculated, using the B3LYP exchange-correlation functional and a basis set. The lowest energy mode corresponds to 92.97 K, well below experimental temperature.

Generic image for table
Table III.

Summary of transition energies (eV) obtained by various methods for -triazine.

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/content/aip/journal/jcp/130/18/10.1063/1.3125509
2009-05-13
2014-04-23
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: On the importance of nuclear quantum motions in near edge x-ray absorption fine structure spectroscopy of molecules
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/18/10.1063/1.3125509
10.1063/1.3125509
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