Electronic structure, bonding and stability of fumarate, maleate, and succinate dianions from X-ray spectroscopy.

The electronic structure of the fumarate, maleate, and succinate dianions in the context of their stability is determined in a joint experimental and computational study with X-ray absorption spectroscopy and resonant inelastic X-ray scattering at the O K-edge. The study reveals differences in the electronic states and molecular orbitals of the three molecules. In particular, maleate has a non-degenerate oxygen core-orbital with an energy difference of approximately 0.15 eV, visible in a two peak structure in XAS. Polarization-dependent RIXS provides information on the orientation of the occupied valence molecular orbitals with respect to the carboxylate group plane and shows a gradually increasing energy gap between the HOMO and excited π* LUMO from fumarate to maleate to succinate. We also demonstrate the energy excitation dependence of the RIXS spectra of maleate, with the total inelastic RIXS profile shifting towards higher energy loss as the detuning is increased from negative to positive values. Our findings show that maleate is less stable than fumarate and succinate due to the presence of electronic density on its HOMO orbital on the CC bond between carboxylate groups, which can lead to weaker bonding of maleate with molecules or ions.

Biosynthetic flexibility of Pseudomonas aeruginosa leads to hydroxylated 2-alkylquinolones with proinflammatory host response.

The human pathogen Pseudomonas aeruginosa produces various 4(1H)-quinolones with diverse functions. Among these, 2-nonyl-4(1H)-quinolone (NQ) and its N-oxide (NQNO) belong to the main metabolites. Their biosynthesis involves substrates from the fatty acid metabolism and we hypothesized that oxidized fatty acids could be responsible for a so far undetected class of metabolites. We developed a divergent synthesis strategy for 2'-hydroxy (2'-OH) and 2'-oxo- substituted quinolones and N-oxides and demonstrated for the first time that 2'-OH-NQ and 2'-OH-NQNO but not the corresponding 2'-oxo compounds are naturally produced by PAO1 and PA14 strains of P. aeruginosa. The main metabolite 2'-OH-NQ is produced even in concentrations comparable to NQ. Exogenous availability of ß-hydroxydecanoic acid can further increase the production of 2'-OH-NQ. In contrast to NQ, 2'-OH-NQ potently induced the cytokine IL-8 in a human cell line at 100 nм, suggesting a potential role in host immune modulation.

Wave packet theory for non-resonant x-ray emission and non-resonant Auger electron emission in molecules.

We present a time-dependent theory for non-resonant x-ray emission spectrum (XES) and normal Auger spectrum (NAS) calculation, based on a fully quantum description of nuclear dynamics using the vibrational wave packet concept. We compare two formulations of the time-dependent theory, either employing a two-time propagation scheme or using spectral integration over the electron energy continuum. We find that the latter formulation is more efficient for numerical simulations, providing a reasonable accuracy when the integration step is shorter than the lifetime broadening of the core-ionized state. We demonstrate our approach using the example of non-resonant x-ray emission from a water molecule, considering the lowest core-ionized K-1 and first core-ionized shake-up K-1V-1V1 intermediate states. These channels exemplify the developed theory on bound-bound, bound-continuum, continuum-bound, and continuum-continuum transitions. Our results suggest that the time-dependent approach is efficient for simulating XES involving dissociative states, whereas the time-independent approach, based on Franck-Condon factors, is more efficient for bound-bound transitions expressed as discrete frequency dependence in the energy domain. The methods and discussion have general applicability, including both NAS and more complex systems, such as liquid water.

Beyond iron: metal-binding activity of the Pseudomonas quinolone signal-motif.

The Pseudomonas quinolone signal (PQS) is an important quorum sensing signal controlling virulence of the human pathogen Pseudomonas aeruginosa. PQS also exhibits multiple additional biological functions for P. aeruginosa, including the trapping of ferric iron. The PQS-motif has proven as privileged structure with great potential which is why we here explored the synthesis of two different types of crosslinked dimeric PQS-motifs as potential iron chelators. These compounds indeed chelated ferric iron and produced colorful and fluorescent complexes also with other metal ions. Inspired by these results, we revisited the metal ion binding capabilities of the natural product PQS and were able to detect further metal complexes beyond ferric iron and confirm the complex stoichiometry by mass spectrometry.

Hydrogen bond effects in multimode nuclear dynamics of acetic acid observed via resonant x-ray scattering.

A theoretical and experimental study of the gas phase and liquid acetic acid based on resonant inelastic x-ray scattering (RIXS) spectroscopy is presented. We combine and compare different levels of theory for an isolated molecule for a comprehensive analysis, including electronic and vibrational degrees of freedom. The excitation energy scan over the oxygen K-edge absorption reveals nuclear dynamic effects in the core-excited and final electronic states. The theoretical simulations for the monomer and two different forms of the dimer are compared against high-resolution experimental data for pure liquid acetic acid. We show that the theoretical model based on a dimer describes the hydrogen bond formation in the liquid phase well and that this bond formation sufficiently alters the RIXS spectra, allowing us to trace these effects directly from the experiment. Multimode vibrational dynamics is accounted for in our simulations by using a hybrid time-dependent stationary approach for the quantum nuclear wave packet simulations, showing the important role it plays in RIXS.

Vibrational resonant inelastic X-ray scattering in liquid acetic acid: a ruler for molecular chain lengths.

Quenching of vibrational excitations in resonant inelastic X-ray scattering (RIXS) spectra of liquid acetic acid is observed. At the oxygen core resonance associated with localized excitations at the O-H bond, the spectra lack the typical progression of vibrational excitations observed in RIXS spectra of comparable systems. We interpret this phenomenon as due to strong rehybridization of the unoccupied molecular orbitals as a result of hydrogen bonding, which however cannot be observed in x-ray absorption but only by means of RIXS. This allows us to address the molecular structure of the liquid, and to determine a lower limit for the average molecular chain length.

Nuclear dynamics in resonant inelastic X-ray scattering and X-ray absorption of methanol.

We report on a combined theoretical and experimental study of core-excitation spectra of gas and liquid phase methanol as obtained with the use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). The electronic transitions are studied with computational methods that include strict and extended second-order algebraic diagrammatic construction [ADC(2) and ADC(2)-x], restricted active space second-order perturbation theory, and time-dependent density functional theory-providing a complete assignment of the near oxygen K-edge XAS. We show that multimode nuclear dynamics is of crucial importance for explaining the available experimental XAS and RIXS spectra. The multimode nuclear motion was considered in a recently developed "mixed representation" where dissociative states and highly excited vibrational modes are accurately treated with a time-dependent wave packet technique, while the remaining active vibrational modes are described using Franck-Condon amplitudes. Particular attention is paid to the polarization dependence of RIXS and the effects of the isotopic substitution on the RIXS profile in the case of dissociative core-excited states. Our approach predicts the splitting of the 2a″ RIXS peak to be due to an interplay between molecular and pseudo-atomic features arising in the course of transitions between dissociative core- and valence-excited states. The dynamical nature of the splitting of the 2a″ peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical results are in good agreement with our liquid phase measurements and gas phase experimental data available from the literature.

Ultrafast dissociation features in RIXS spectra of the water molecule.

In this combined theoretical and experimental study we report on an analysis of the resonant inelastic X-ray scattering (RIXS) spectra of gas phase water via the lowest dissociative core-excited state |1s-1O4a11. We focus on the spectral feature near the dissociation limit of the electronic ground state. We show that the narrow atomic-like peak consists of the overlapping contribution from the RIXS channels back to the ground state and to the first valence excited state |1b-114a11 of the molecule. The spectral feature has signatures of ultrafast dissociation (UFD) in the core-excited state, as we show by means of ab initio calculations and time-dependent nuclear wave packet simulations. We show that the electronically elastic RIXS channel gives substantial contribution to the atomic-like resonance due to the strong bond length dependence of the magnitude and orientation of the transition dipole moment. By studying the RIXS for an excitation energy scan over the core-excited state resonance, we can understand and single out the molecular and atomic-like contributions in the decay to the lowest valence-excited state. Our study is complemented by a theoretical discussion of RIXS in the case of isotopically substituted water (HDO and D2O) where the nuclear dynamics is significantly affected by the heavier fragments' mass.