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Lukáš Tomaník

Publications and source records attributed to Lukáš Tomaník.

2 recordsLinked to original sources

How Does Mg$^{2+}_{(aq)}$ Interact with ATP$_{(aq)}$? Biomolecular Structure through the Lens of Liquid-Jet Photoelectron Spectroscopy

Site-specific information on how adenosine triphosphate in the aqueous phase (ATP$_{(aq)}$) interacts with magnesium (Mg$^{2+}_{(aq)}$) is a prerequisite to understanding its complex biochemistry. To gather such information, we apply liquid-jet photoelectron spectroscopy (LJ-PES) assisted by electronic-structure calculations to study ATP$_{(aq)}$ solutions with and without dissolved Mg$^{2+}$. Valence photoemission data reveal spectral changes in the phosphate and adenine features of ATP$_{(aq)}$ due to interactions with the divalent cation. Chemical shifts in Mg 2p, Mg 2s, P 2p, and P 2s core-level spectra as a function of the Mg$^{2+}$/ATP concentration ratio are correlated to the formation of [MgATP]$^{-2}_{(aq)}$ and Mg$_2$ATP$_{(aq)}$ complexes, demonstrating the element-sensitivity of the technique to Mg$^{2+}$-phosphate interactions. In addition, we report and compare P 2s data from ATP$_{(aq)}$ and adenosine mono- and di-phosphate (AMP$_{(aq)}$ and ADP$_{(aq)}$, respectively) solutions, probing the electronic structure of the phosphate chain and the local environment of individual phosphate units in ATP$_{(aq)}$. Finally, we have recorded intermolecular Coulombic decay (ICD) spectra initiated by ionization of Mg 1s electrons to probe ligand exchange in the Mg$^{2+}$-ATP$_{(aq)}$ coordination environment, demonstrating the unique capabilities of ICD for revealing structural information. Our results provide an overview of the electronic structure of ATP$_{(aq)}$ and Mg$^{2+}$-ATP$_{(aq)}$ moieties relevant to phosphorylation and dephosphorylation reactions that are central to bioenergetics in living organisms.

physics.chem-ph↗

Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water

Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems unveil microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C$_8$H$_7$N), tryptophan's chromophore, in water: a strong localized $\text{N-H}\cdots\text{OH}_2$ hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of indole's electronic structure in aqueous solution. We have recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through \emph{ab initio} modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the non-equilibrium polarizable-continuum model. A two-hole electron-population analysis quantitatively describes the Auger spectra. Core-electron binding energies for nitrogen and carbon highlight the specific interaction with a hydrogen-bonded water molecule at the N-H group and otherwise nonspecific solvent interactions.

physics.chem-ph↗