Communication: Near edge x-ray absorption fine structure spectroscopy of aqueous adenosine triphosphate at the carbon and nitrogen K-edges

How Does Mg2+(aq) Interact with ATP(aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy

Liquid-jet photoemission spectroscopy (LJ-PES) allows for a direct probing of electronic structure in aqueous solutions. We show the applicability of the approach to biomolecules in a complex environment, exploring site-specific information on the interaction of adenosine triphosphate in the aqueous phase (ATP(aq)) with magnesium (Mg2+(aq)), highlighting the synergy brought about by the simultaneous analysis of different regions in the photoelectron spectrum. In particular, we demonstrate intermolecular Coulombic decay (ICD) spectroscopy as a new and powerful addition to the arsenal of techniques for biomolecular structure investigation. We apply LJ-PES assisted by electronic-structure calculations to study ATP(aq) solutions with and without dissolved Mg2+. Valence photoelectron 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 Mg2+/ATP concentration ratio are correlated to the formation of [Mg(ATP) 2]6-(aq), [MgATP]2-(aq), and [Mg2ATP](aq) complexes, demonstrating the element sensitivity of the technique to Mg2+-phosphate interactions. The most direct probe of the intermolecular interactions between ATP(aq) and Mg2+(aq) is delivered by the emerging ICD electrons following ionization of Mg 1s electrons. ICD spectra are shown to sensitively probe ligand exchange in the Mg2+-ATP(aq) coordination environment. In addition, we report and compare P 2s data from ATP(aq) and adenosine mono- and diphosphate (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). Our results provide a comprehensive view of the electronic structure of ATP(aq) and Mg2+-ATP(aq) complexes relevant to phosphorylation and dephosphorylation reactions that are central to bioenergetics in living organisms.

Effect of Protonation on the Molecular Structure of Adenosine 5'-Triphosphate: A Combined Theoretical and Near Edge X-ray Absorption Fine Structure Study

The present work combines the near edge X-ray absorption mass spectrometry of a protonated adenosine 5'-triphosphate (ATP) molecule isolated in an ion trap with (time-dependent) density functional theory calculations. Our study unravels the effect of protonation on the ATP structure and its spectral properties, providing structure-property relationships at atomistic resolution for protonated ATP (ATPH) isolated in the gas-phase conditions. On the other hand, the present C and N K-edge X-ray absorption spectra of isolated ATPH appear closely like those previously reported for solvated ATP at low pH. Therefore, the present work should be relevant for further investigation and modeling of structure-function properties of protonated adenine and ATP in complex biological environments.

Highly efficient ammonia synthesis at low temperature over a Ru-Co catalyst with dual atomically dispersed active centers

The desire for a carbon-free society and the continuously increasing demand for clean energy make it valuable to exploit green ammonia (NH3) synthesis that proceeds via the electrolysis driven Haber-Bosch (eHB) process. The key for successful operation is to develop advanced catalysts that can operate under mild conditions with efficacy. The main bottleneck of NH3 synthesis under mild conditions is the known scaling relation in which the feasibility of N2 dissociative adsorption of a catalyst is inversely related to that of the desorption of surface N-containing intermediate species, which leads to the dilemma that NH3 synthesis could not be catalyzed effectively under mild conditions. The present work offers a new strategy via introducing atomically dispersed Ru onto a single Co atom coordinated with pyrrolic N, which forms RuCo dual single-atom active sites. In this system the d-band centers of Ru and Co were both regulated to decouple the scaling relation. Detailed experimental and theoretical investigations demonstrate that the d-bands of Ru and Co both become narrow, and there is a significant overlapping of t2g and eg orbitals as well as the formation of a nearly uniform Co 3d ligand field, making the electronic structure of the Co atom resemble that of a "free-atom". The "free-Co-atom" acts as a bridge to facilitate electron transfer from pyrrolic N to surface Ru single atoms, which enables the Ru atom to donate electrons to the antibonding π* orbitals of N2, thus resulting in promoted N2 adsorption and activation. Meanwhile, H2 adsorbs dissociatively on the Co center to form a hydride, which can transfer to the Ru site to cause the hydrogenation of the activated N2 to generate N2H x (x = 1-4) intermediates. The narrow d-band centers of this RuCo catalyst facilitate desorption of surface *NH3 intermediates even at 50 °C. The cooperativity of the RuCo system decouples the sites for the activation of N2 from those for the desorption of *NH3 and *N2H x intermediates, giving rise to a favorable pathway for efficient NH3 synthesis under mild conditions.

Equation-of-Motion MLCCSD and CCSD-in-HF Oscillator Strengths and Their Application to Core Excitations

We present an implementation of equation-of-motion oscillator strengths for the multilevel CCSD (MLCCSD) model where CCS is used as the lower level method (CCS/CCSD). In this model, the double excitations of the cluster operator are restricted to an active orbital space, whereas the single excitations are unrestricted. Calculated nitrogen K-edge spectra of adenosine, adenosine triphosphate (ATP), and an ATP-water system are used to demonstrate the performance of the model. Projected atomic orbitals (PAOs) are used to partition the virtual space into active and inactive orbital sets. Cholesky decomposition of the Hartree-Fock density is used to partition the occupied orbitals. This Cholesky-PAO partitioning is cheap, scaling as O(N3), and is suitable for the calculation of core excitations, which are localized in character. By restricting the single excitations of the cluster operator to the active space, as well as the double excitations, the CCSD-in-HF model is obtained. A comparison of the two models-MLCCSD and CCSD-in-HF-is presented for the core excitation spectra of the adenosine and ATP systems.

Iron-Free Cathode Catalysts for Proton-Exchange-Membrane Fuel Cells: Cobalt Catalysts and the Peroxide Mitigation Approach

High-performance and inexpensive platinum-group-metal (PGM)-free catalysts for the oxygen reduction reaction (ORR) in challenging acidic media are crucial for proton-exchange-membrane fuel cells (PEMFCs). Catalysts based on Fe and N codoped carbon (Fe-N-C) have demonstrated promising activity and stability. However, a serious concern is the Fenton reactions between Fe²⁺ and H₂ O₂ generating active free radicals, which likely cause degradation of the catalysts, organic ionomers within electrodes, and polymer membranes used in PEMFCs. Alternatively, Co-N-C catalysts with mitigated Fenton reactions have been explored as a promising replacement for Fe and PGM catalysts. Therefore, herein, the focus is on Co-N-C catalysts for the ORR relevant to PEMFC applications. Catalyst synthesis, structure/morphology, activity and stability improvement, and reaction mechanisms are discussed in detail. Combining experimental and theoretical understanding, the aim is to elucidate the structure-property correlations and provide guidance for rational design of advanced Co catalysts with a special emphasis on atomically dispersed single-metal-site catalysts. In the meantime, to reduce H₂ O₂ generation during the ORR on the Co catalysts, potential strategies are outlined to minimize the detrimental effect on fuel cell durability.

Thermally and Magnetically Robust Triplet Ground State Diradical

High spin ( S = 1) organic diradicals may offer enhanced properties with respect to several emerging technologies, but typically exhibit low singlet triplet energy gaps and possess limited thermal stability. We report triplet ground state diradical 2 with a large singlet-triplet energy gap, Δ E_ST ≥ 1.7 kcal mol^-1, leading to nearly exclusive population of triplet ground state at room temperature, and good thermal stability with onset of decomposition at ∼160 °C under inert atmosphere. Magnetic properties of 2 and the previously prepared diradical 1 are characterized by SQUID magnetometry of polycrystalline powders, in polystyrene glass, and in other matrices. Polycrystalline diradical 2 forms a novel one-dimensional (1D) spin-1 ( S = 1) chain of organic radicals with intrachain antiferromagnetic coupling of J'/ k = -14 K, which is associated with the N···N and N···O intermolecular contacts. The intrachain antiferromagnetic coupling in 2 is by far strongest among all studied 1D S = 1 chains of organic radicals, which also makes 1D S = 1 chains of 2 most isotropic, and therefore an excellent system for studies of low-dimensional magnetism. In polystyrene glass and in frozen benzene or dibutyl phthalate solution, both 1 and 2 are monomeric. Diradical 2 is thermally robust and is evaporated under ultrahigh vacuum to form thin films of intact diradicals on silicon substrate, as demonstrated by X-ray photoelectron spectroscopy. Based on C-K NEXAFS spectra and AFM images of the ∼1.5 nm thick films, the diradical molecules form islands on the substrate with molecules stacked approximately along the crystallographic a-axis. The films are stable under ultrahigh vacuum for at least 60 h but show signs of decomposition when exposed to ambient conditions for 7 h.

Soft X-ray Spectroscopy of the Amine Group: Hydrogen Bond Motifs in Alkylamine/Alkylammonium Acid-Base Pairs

We use N K-edge absorption spectroscopy to explore the electronic structure of the amine group, one of the most prototypical chemical functionalities playing a key role in acid-base chemistry, electron donor-acceptor interactions, and nucleophilic substitution reactions. In this study, we focus on aliphatic amines and make use of the nitrogen 1s core electron excitations to elucidate the roles of N-H σ* and N-C σ* contributions in the unoccupied orbitals. We have measured N K-edge absorption spectra of the ethylamine bases Et _xNH_{3- x} ( x = 0...3; Et- = C₂H₅-) and the conjugate positively charged ethylammonium cation acids Et _yNH_{4- y}⁺ ( y = 0...4; Et- = C₂H₅-) dissolved in the protic solvents ethanol and water. Upon consecutive exchange of N-H for ethyl-groups, we observe a spectral shift, a systematic decrease of the N K-edge pre-edge peak, and a major contribution in the post-edge region for the ethylamine series. Instead, for the ethylammonium ions, the consecutive exchange of N-H for ethyl groups leads to an apparent reduction of pre-edge and post-edge intensities relative to the main-edge band, without significant frequency shifts. Building on findings from our previously reported study on aqueous ammonia and ammonium ions, we can rationalize these observations by comparing calculated N K-edge absorption spectra of free and hydrogen-bonded clusters. Hydrogen bonding interactions lead only to minor spectral effects in the ethylamine series, but have a large impact in the ethylammonium ion series. Visualization of the unoccupied molecular orbitals shows the consecutive change in molecular orbital character from N-H σ* to N-C σ* in these alkylamine/alkylammonium ion series. This can act as a benchmark for future studies on chemically more involved amine compounds.

An experimental and theoretical study of adenine adsorption on Au(111)

The parallel and upright adenine phases on Au(111) were studied by photoelectron and absorption spectroscopies in combination with density functional theory calculations.

Exploring Protonation and Deprotonation Effects with Auger Electron Spectroscopy

Auger electron spectroscopy is demonstrated to be a very efficient tool to probe alterations in local chemical environment due to changes in protonation states. We show that electronic and geometric structure changes induced by protonation or deprotonation are well reflected in Auger spectra through characteristic chemical shifts and spectral shape variations. We also present evidence that Auger spectra are sensitive to relative concentrations of compounds in different protonation states. Special attention is paid to the high kinetic energy spectral regions that exhibit remarkable features resulting from core ICD-like transitions in normal species and Auger transitions in deprotonated fragments. The latter contribution was so far ignored when explaining Auger spectra of species embedded in the environment. This contribution should be reconsidered, taking into account the recently discovered possibility of ultrafast dissociation of core-ionized hydrogen-bonded systems in media.

Gas-Phase Protein Inner-Shell Spectroscopy by Coupling an Ion Trap with a Soft X-ray Beamline

C, N, and O near-edge ion yield spectroscopy of 8+ selected electrosprayed cations of cytochrome c protein (12 kDa) has been performed by coupling a linear quadrupole ion trap with a soft X-ray beamline. The photoactivation tandem mass spectra were recorded as a function of the photon energy. Photoionization of the precursor, accompanied by CO2 loss, is the dominant relaxation process, showing high photoion stability following direct or resonant photoionization. The partial ion yields extracted from recorded mass spectra show significantly different behaviors for single and double ionization channels, which can be qualitatively explained by different Auger decay mechanisms. However, the single ionization spectra reveal characteristic structures when compared to existing near-edge X-ray absorption fine structure (NEXAFS) spectra from thin films of peptides and proteins. Therefore, the present experiment opens up new avenues for near-edge X-ray spectroscopy of macromolecules in the gas phase, overcoming the radiation damage issue or the environmental effects as due to the surface, intermolecular interactions, and solvent.

Covalent hybrid of spinel manganese-cobalt oxide and graphene as advanced oxygen reduction electrocatalysts

Through direct nanoparticle nucleation and growth on nitrogen doped, reduced graphene oxide sheets and cation substitution of spinel Co(3)O(4) nanoparticles, a manganese-cobalt spinel MnCo(2)O(4)/graphene hybrid was developed as a highly efficient electrocatalyst for oxygen reduction reaction (ORR) in alkaline conditions. Electrochemical and X-ray near-edge structure (XANES) investigations revealed that the nucleation and growth method for forming inorganic-nanocarbon hybrids results in covalent coupling between spinel oxide nanoparticles and N-doped reduced graphene oxide (N-rmGO) sheets. Carbon K-edge and nitrogen K-edge XANES showed strongly perturbed C-O and C-N bonding in the N-rmGO sheet, suggesting the formation of C-O-metal and C-N-metal bonds between N-doped graphene oxide and spinel oxide nanoparticles. Co L-edge and Mn L-edge XANES suggested substitution of Co(3+) sites by Mn(3+), which increased the activity of the catalytic sites in the hybrid materials, further boosting the ORR activity compared with the pure cobalt oxide hybrid. The covalently bonded hybrid afforded much greater activity and durability than the physical mixture of nanoparticles and carbon materials including N-rmGO. At the same mass loading, the MnCo(2)O(4)/N-graphene hybrid can outperform Pt/C in ORR current density at medium overpotentials with stability superior to Pt/C in alkaline solutions.