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. 2024 Oct 16;9(43):43884-43893.
doi: 10.1021/acsomega.4c07024. eCollection 2024 Oct 29.

NEXAFS Spectra Simulations of Nitrogen-Bearing Heterocycles

Ricardo R Oliveira  1 , Amanda D Torres  1 , Alexandre B Rocha  1
Affiliations

NEXAFS Spectra Simulations of Nitrogen-Bearing Heterocycles

Ricardo R Oliveira et al. ACS Omega. .

Abstract

Five-membered heterocyclic compounds containing nitrogen atoms are important biomolecule building blocks. In addition to their fundamental biological importance, these molecular structures are used in several technological applications. Consequently, it is essential to develop techniques that allow the characterization of these fundamental systems. We address this issue by performing simulations of K-edge NEXAFS spectra by applying a time-dependent density functional theory (TDDFT) and an inner-shell multiconfigurational self-consistent field (IS-MCSCF) of selected molecules. Also, vibronic coupling simulations were considered for the TDDFT computations. Surprisingly, molecular orbital binding energies do not reproduce the order of the transition energies obtained by IS-MCSCF, indicating a possible breakdown of the orbital picture concerning the NEXAFS spectrum. In general, the TDDFT and IS-MCSCF results are compatible and are in close agreement with experimental data. Moreover, vibronic coupling and vertical transition results were very similar. Finally, it is important to mention that, to the best of our knowledge, this is the first time that the IS-MCSCF method has been applied to molecular systems of this size.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
All molecules studied in this work include indole, adenine, 3-formylindole (3-FI), guanine, and protonated guanine.
Figure 2
Figure 2
Hartree–Fock (HF) orbitals, HF binding energies (BE), and the first MCSCF vertical transitions (VE) of indole carbon K-edge.
Figure 3
Figure 3
Indole K-edge vertical simulated spectra at carbon (top) and nitrogen (middle). A comparison of the vertical simulated spectra with the one obtained by considering vibronic coupling effects at the carbon edge is also shown (bottom). Simulated spectra have been obtained at two levels of theory, i.e, MCSCF and TDDFT.
Figure 4
Figure 4
Hartree–Fock (HF) orbitals, HF binding energies (BE), and first MCSCF vertical transitions (VE) of 3-formylindole (3-FI) carbon K-edge.
Figure 5
Figure 5
3-Formylindole (3-FI) vertical simulated spectra at carbon (top), nitrogen (middle), and oxygen (botton) K-edges. Simulated spectra have been obtained at two levels of theory, i.e., MCSCF (blue line) and TDDFT (red line).
Figure 6
Figure 6
Hartree–Fock (HF) orbitals, HF binding energies (BE), and first MCSCF vertical transitions (VE) of adenine carbon and nitrogen K-edges.
Figure 7
Figure 7
Adenine vertical simulated spectra at carbon (top) and nitrogen (botton) K-edges at two levels of theory: MCSCF (blue line) and TDDFT (red line).
Figure 8
Figure 8
Hartree–Fock (HF) orbitals, HF binding energies (BE), and first MCSCF vertical transitions (VE) of the guanine carbon and the nitrogen K-edges.
Figure 9
Figure 9
Guanine vertical simulated spectra at carbon (top), nitrogen (middle), and oxygen (bottom) K-edges at two levels of theory, MCSCF (blue line) and TDDFT (red line). For the oxygen K-edge spectrum, two tautomers were considered. The first band is due to the 1s orbital from the carbonyl group, but the second (experimental) band is due to the 1s orbital from the protonated oxygen in the OH group.
Figure 10
Figure 10
Guanine nitrogen K-edge simulated spectra at the TDDFT level of theory with vibronic coupling.
See this image and copyright information in PMC

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