Solid energy calibration standards for P K-edge XANES: electronic structure analysis of PPh4Br

Relativistic Orbital-Optimized Density Functional Theory for Accurate Core-Level Spectroscopy

Core-level spectra of 1s electrons of elements heavier than Ne show significant relativistic effects. We combine advances in orbital-optimized density functional theory (OO-DFT) with the spin-free exact two-component (X2C) model for scalar relativistic effects to study K-edge spectra of third period elements. OO-DFT/X2C is found to be quite accurate at predicting energies, yielding a ∼0.5 eV root-mean-square error versus experiment with the modern SCAN (and related) functionals. This marks a significant improvement over the >50 eV deviations that are typical for the popular time-dependent DFT (TDDFT) approach. Consequently, experimental spectra are quite well reproduced by OO-DFT/X2C, sans empirical shifts for alignment. OO-DFT/X2C combines high accuracy with ground state DFT cost and is thus a promising route for computing core-level spectra of third period elements. We also explored K and L edges of 3d transition metals to identify limitations of the OO-DFT/X2C approach in modeling the spectra of heavier atoms.

Gauging aromatic conjugation and charge delocalization in the aryl silanes PhnSiH4−n (n = 0–4), with silicon K-edge XAS and TDDFT

Si K-edge X-ray absorption spectra (XAS) have been measured experimentally and calculated using time-dependent density functional theory (TDDFT) to investigate electronic structure in aryl silanes, Ph_nSiH_4−n (n = 0–4).

Scrutinizing metal-ligand covalency and redox non-innocence via nitrogen K-edge X-ray absorption spectroscopy

Nitrogen K-edge X-ray absorption spectra (XAS) were obtained for 19 transition metal complexes bearing bipyridine, ethylenediamine, ammine, and nitride ligands. Time-dependent density functional theory (TDDFT) and DFT/restricted open configuration interaction singles (DFT/ROCIS) calculations were found to predict relative N K-edge XAS peak energies with good fidelity to experiment. The average difference (|ΔE|) between experimental and linear corrected calculated energies were found to be 0.55 ± 0.05 eV and 0.46 ± 0.04 eV, respectively, using the B3LYP hybrid density functional and scalar relativistically recontracted ZORA-def2-TZVP(-f) basis set. Deconvolution of these global correlations into individual N-donor ligand classes gave improved agreement between experiment and theory with |ΔE| less than 0.4 eV for all ligand classes in the case of DFT/ROCIS. In addition, calibration method-dependent values for the N 1s → 2p radial dipole integral of 25.4 ± 1.7 and 26.8 ± 1.9 are obtained, affording means to estimate the nitrogen 2p character in unfilled frontier molecular orbitals. For the complexes studied, nitrogen covalency values correlate well to those calculated by hybrid DFT with an R 2 = 0.92 ± 0.01. Additionally, as a test case, a well-characterized PNP ligand framework (PNP = N[2-P(CHMe2)2-4-methylphenyl]2 1-) coordinated to NiII is investigated for its ability to act as a redox non-innocent ligand. Upon oxidation of (PNP)NiCl with [FeCp2](OTf) to its radical cation, [(PNP)NiCl](OTf) (OTf = triflate), a new low-energy feature emerges in the N K-edge XAS spectra. This feature is assigned as N 1s to a PNP-localized acceptor orbital exhibiting 27 ± 2% N 2p aminyl radical character, obtained using the aforementioned nitrogen covalency calibration. Combined, these data showcase a direct spectroscopic means of identifying redox-active N-donor ligands and also estimating nitrogen 2p covalency of frontier molecular orbitals in transition metal complexes.

Abiotic phosphorus recycling from adsorbed ribonucleotides on a ferrihydrite-type mineral: Probing solution and surface species

Iron (Fe) (oxyhydr)oxide minerals, which are amongst most reactive minerals in soils and sediments, are known to exhibit strong adsorption of inorganic phosphate (P_i) and organophosphate (P_o) compounds. Beyond synthetic P_o compounds, much still remains unknown about the reactivity of these minerals to transform naturally-occurring P_o compounds to P_i, particularly with respect to solution versus surface speciation of P_o hydrolysis. To investigate this reactivity with a ferrihydrite-type mineral and ribonucleotides, we employed high-resolution liquid chromatography-mass spectrometry (LC-MS), X-ray absorption near-edge structure (XANES), Fourier-transform infrared (FTIR) spectroscopy, and molecular modeling. Kinetic experiments were conducted with the mineral (1 g L^-1) reacted with adenosine monophosphate, diphosphate, or triphosphate (respectively AMP, ADP, ATP; 50 µM). Analysis of solution organic species by LC-MS implied that only adsorption occurred with AMP and ADP but both adsorption and dephosphorylation of ATP were evident. Maximum adsorption capacities per gram of mineral were 40.6 ± 0.8 µmol AMP, 35.7 ± 1.6 µmol ADP, and 10.9 ± 1.0 µmol ATP; solution dephosphorylated by-products accounted for 15% of initial ATP. Subsequent XANES analysis of the surface species revealed that 16% of adsorbed AMP and 30% of adsorbed ATP were subjected to dephosphorylation, which was not fully quantifiable from the solution measurements. Molecular simulations predicted that ADP and ATP were complexed mainly via the phosphate groups whereas AMP binding also involved multiple hydrogen bonds with the adenosine moiety; our FTIR data confirmed these binding confirmations. Our findings thus imply that specific adsorption mechanisms dictate the recycling and subsequent trapping of P_i from ribonucleotide-like biomolecules reacted with Fe (oxyhydr)oxide minerals.