Variational Calculation of Fine and Hyperfine Resolved Rovibronic Spectra of Diatomic Molecules

The thesis presents methods for the variational calculation of fine and hyperfine resolved rovibronic spectra of diatomic molecules, as part of the ExoMol and ExoMolHD projects. The theory of these methods has been fully discussed. The corresponding algorithms have been implemented based on previous works of the ExoMol Group. The line lists of two molecules, NO and VO has been calculated, which validates the proposed methods. Nitric oxide is one of the principal oxides of nitrogen, which plays a significant role the investigations of our atmosphere and astrophysics. Due to its importance, the radical has been investigated in numerous theoretical and experimental works. However, there is no NO ultraviolet line list in well-known databases. A major issue in generating a UV line list for NO results from the difficulty of modelling the valence-Rydberg interaction between its B2Π and C2Π states. To address the problem, a spectroscopic model has been proposed to resolve the energy structures of B2Π and C2Π coupled states. Based on the model, an accurate line list, called XABC, has been computed, which covers the pure rotational, vibrational and rovibronic spectra of 14N16O. Vanadium monoxide is also an open shell diatomic system. Its dominating isotopologue 51V16O has non-zero nuclear spin, I = 7/2. The interaction between the spin of unpaired electrons and the nuclear spin yields a very pronounced hyperfine structure. The widely used effective Hamiltonian method for hyperfine structure is not applicable to give accurate line list of VO, as the interactions between the electronic states of VO reshape its line positions and intensities. This thesis presents a variational algorithm for the calculation of hyperfine structure and spectra of diatomic molecules. The hyperfine-resolved IR spectra of VO has been computed from first principles, considering necessary nuclear hyperfine coupling curves

Line List For The Lowest Four States Of No

We computed an accurate line list, called \texttt{XABC}, for nitric oxide (NO) which covers its pure rotational, vibrational and rovibronic spectra belonging to the lowest four electronic states of NO, i.e. X\,$^2\Pi$, A\,$^2\Sigma^+$, B\,$^2\Pi$ and C\,$^2\Pi$. \texttt{XABC} is a major extension and update of the ExoMol \texttt{NOname} line list which was calculated within the X\,$^2\Pi$ state of NO. As first step we built a spectroscopic model which represents the rovibronic structure of A\,$^2\Sigma^+$, B\,$^2\Pi$, C\,$^2\Pi$ states of NO. Empirical energy levels for the three electronic states are determined using the a combination of the MARVEL procedure and \textit{ab initio} calculations, and the available experimental data are critically evaluated. {\it Ab inito} methods which deal simultaneously with the Rydberg-like A\,$^2\Sigma^+$ and C\,$^2\Pi$, and the valence B\,$^2\Pi$ state are tested. Methods of modeling the sharp avoided crossing between the B\,$^2\Pi$ and C\,$^2\Pi$states are tested. A rovibronic Hamiltonian matrix is constructed using variational nuclear motion program \textsc{Duo} whose eigenvalues are fitted to the MARVEL energy levels. The matrix also includes coupling terms obtained from the refinement of the \textit{ab initio} potential energy and spin-orbit coupling curves. Calculated and observed energy levels agree well with each other, validating the applicability of our method and providing a useful model for this open shell system. This part has been published in \textit{J. Chem. Phys.} https://doi.org/10.1063/5.0038527. A mixture of empirical and theoretical electronic transition dipole moments are used for the final calculation of NO rovibronic transitions belong to the A\,$^2\Sigma^+$ -- X\,$^2\Pi$, B\,$^2\Pi$ -- X\,$^2\Pi$ and C\,$^2\Pi$ -- X\,$^2\Pi$ which correspond to the $\gamma$, $\beta$ and $\delta$ band systems, respectively, as well as minor improvements to transitions within the X\,$^2\Pi$ ground state. Our model generates a high-accuracy NO ultraviolet line list covering the complicated regions where the B\,$^2\Pi$ -C\,$^2\Pi$ states interact. Technical details of this part are given in the \texttt{XABC} line list paper submitted to \textit{Mon. Not. Roy. Astron. Soc.}. \texttt{XABC} provides comprehensive data for $\lambda > 160$ {nm} ($\tilde{\nu} <$ 63000 cm$^{-1}$) for the analysis of atmospheric NO on Earth, Venus or Mars, other astronomical observations and applications. It is available via www.exomol.com

An empirical spectroscopic model for eleven electronic states of VO

Previously-determined empirical energy levels are used to construct a rovibronic model for the X 4Σ −, A′ 4Φ, A 4Π, B 4Π, C 4Σ −, D 4Δ, 1 2Δ, 1 2Σ +, 1 2Φ, 1 2Π and 2 2Π electronic states of vanadium monoxide. The spectrum of VO is characterized by many couplings and crossings between the states associated with these curves. The model is based on the use of potential energy curves, represented as extended Morse oscillators, and couplings (spin–orbit, spin–spin, angular momentum), represented by polynomials, which are tuned to the data plus an empirical allowance for spin–rotation couplings. The curves are used as input for the variational nuclear motion code Duo. For the X 4Σ −, 1 2Φ and 1 2Π states the model reproduces the observed energy to significantly better than 0.1 cm−1. For the other states the standard deviations are between 0.25 and 1.5 cm−1. Further experimental data and consideration of hyperfine effects would probably be needed to significantly improve this situation

A variational model for the hyperfine resolved spectrum of VO in its ground electronic state

A variational model for the infra-red spectrum of VO is presented which aims to accurately predict the hyperfine structure within the VO X 4Σ− electronic ground state. To give the correct electron spin splitting of the X 4Σ− state, electron spin dipolar interaction within the ground state and the spin-orbit coupling between X 4Σ− and two excited states, A 4Π and 1 2Σ+, are calculated ab initio alongside hyperfine interaction terms. Four hyperfine coupling terms are explicitly considered: Fermi-contact interaction, electron spin-nuclear spin dipolar interaction, nuclear spin-rotation interaction and nuclear electric quadrupole interaction. These terms are included as part of a full variational solution of the nuclear-motion Schrödinger equation performed using program Duo, which is used to generate both hyperfine-resolved energy levels and spectra. To improve the accuracy of the model, ab initio curves are subject to small shifts. The energy levels generated by this model show good agreement with the recently derived empirical term values. This and other comparisons validate both our model and the recently developed hyperfine modules in Duo

ExoMol molecular line lists -- XLII: Rovibronic molecular line list for the low-lying states of NO

An accurate line list, called XABC, is computed for nitric oxide which covers its pure rotational, vibrational and rovibronic spectra. A mixture of empirical and theoretical electronic transition dipole moments are used for the final calculation of $^{14}\mathrm{N}^{16}\mathrm{O}$ rovibronic \mathrm{A}\,^2\Sigma^+ -- \mathrm{X}\,^2\Pi, \mathrm{B}\,^2\Pi -- $\mathrm{X}^2\Pi$ and \mathrm{C}\,^2\Pi -- \mathrm{X}\,^2\Pi which correspond to the $\gamma$, $\beta$ and $\delta$ band systems, respectively, as well as minor improvements to transitions within the \mathrm{X}\,^2\Pi ground state. The work is a major update of the ExoMol NOname line list. It provides a high-accuracy NO ultraviolet line list covering the complicated regions where the \mathrm{B}\,^2\Pi-\mathrm{C}\,^2\Pi states interact. XABC provides comprehensive data for the lowest four doublet states of NO in the region of $\lambda > 160 ~ \mathrm{nm}$ ($\tilde{\nu} < 63~000~\mathrm{cm}^{-1}$) for the analysis of atmospheric NO on Earth, Venus or Mars, other astronomical observations and applications. The data is available via www.exomol.com.Comment: 13 pages, 14 figures, 2 table

A method for the variational calculation of hyperfine-resolved rovibronic spectra of diatomic molecules

An algorithm for the calculation of hyperfine structure and spectra of diatomic molecules based on the variational nuclear motion is presented. The hyperfine coupling terms considered are Fermi-contact, nuclear spin-electron spin dipole–dipole, nuclear spin–orbit, nuclear spin-rotation, and nuclear electric quadrupole interactions. Initial hyperfine-unresolved wave functions are obtained for a given set of potential energy curves and associated couplings by a variation solution of the nuclear-motion Schrödinger equation. Fully hyperfine-resolved parity-conserved rovibronic Hamiltonian matrices for a given final angular momentum, F, are constructed and then diagonalized to give hyperfine-resolved energies and wave functions. Electric transition dipole moment curves can then be used to generate a hyperfine-resolved line list by applying rigorous selection rules. The algorithm is implemented in Duo, which is a general program for calculating spectra of diatomic molecules. This approach is tested for NO and MgH, and the results are compared to experiment and shown to be consistent with those given by the well-used effective Hamiltonian code PGOPHER

A spectroscopic model for the low-lying electronic states of NO

The rovibronic structure of A$^2\Sigma^+$, B$^2\Pi$ and C$^2\Pi$ states of nitric oxide (NO)is studied with the aim of producing comprehensive line lists for its near ultraviolet spectrum. Empirical energy levels for the three electronic states are determined using the a combination of the empirical MARVEL procedure and ab initio calculations, and the available experimental data are critically evaluated. Abinito methods which deal simultaneously with the Rydberg-like A$^2\Sigma^+$ and C$^2\Pi$, and the valence B$^2\Pi$ state are tested. Methods of modeling the sharp avoided crossing between the B$^2\Pi$ and C$^2\Pi$ states are tested. A rovibronic Hamiltonian matrix is constructed using variational nuclear motion program DUO whose eigenvalues are fitted to the MARVEL energy levels. The matrix also includes coupling terms obtained from the refinement of the ab initio potential energy and spin-orbit coupling curves. Calculated and observed energy levels agree well with each other, validating the applicability of our method and providing a useful model for this open shell system.Comment: 14 page

In vitro activity and In vivo efficacy of Isoliquiritigenin against Staphylococcus xylosus ATCC 700404 by IGPD target.

Staphylococcus xylosus (S. xylosus) is a type of coagulase-negative Staphylococcus, which was previously considered as non-pathogenic. However, recent studies have linked it with cases of mastitis in cows. Isoliquiritigenin (ISL) is a bioactive compound with pharmacological functions including antibacterial activity. In this study, we evaluated the effect of ISL on S. xylosus in vitro and in vivo. The MIC of ISL against S. xylosus was 80 μg/mL. It was observed that sub-MICs of ISL (1/2MIC, 1/4MIC, 1/8MIC) significantly inhibited the formation of S. xylosus biofilm in vitro. Previous studies have observed that inhibiting imidazole glycerol phosphate dehydratase (IGPD) concomitantly inhibited biofilm formation in S. xylosus. So, we designed experiments to target the formation of IGPD or inhibits its activities in S. xylosus ATCC 700404. The results indicated that the activity of IGPD and its histidine content decreased significantly under 1/2 MIC (40 μg/mL) ISL, and the expression of IGPD gene (hisB) and IGPD protein was significantly down-regulated. Furthermore, Bio-layer interferometry experiments showed that ISL directly interacted with IGPD protein (with strong affinity; KD = 234 μM). In addition, molecular docking was used to predict the binding mode of ISL and IGPD. In vivo tests revealed that, ISL significantly reduced TNF-α and IL-6 levels, mitigated the destruction of the mammary glands and reversed the production of inflammatory cells in mice. The results of the study suggest that, ISL may inhibit S. xylosus growth by acting on IGPD, which can be used as a target protein to treat infections caused by S. xylosus