Zn K-edge X-ray Absorption Spectroscopy Dataset and Graph Neural Network Models for Aqueous ZnCl2 Solutions

Zenodo (CERN European Organization for Nuclear Research) · 2026-04-21

This dataset supports the machine learning prediction of Zn K-edge X-ray absorption spectra (XAS) from atomic structures of aqueous ZnCl₂ solutions. Atomic structures were sampled from molecular dynamics (MD) simulations using a machine learning interatomic potential (MLIP), and target XAS spectra were computed with VASP using the core-hole approach, spanning a range of ZnCl2 concentrations from 0.1 m to 30 m and solvation environments. The repository includes:- Atomic structures (PyMatGen format) and target XAS spectra - Pre-trained graph neural network (GNN) weights using an M3GNet backbone - Python source code and Jupyter notebooks for model training, inference, and interpretability analysis (Integrated Gradients, UMAP clustering) Associated publication: Chuntian Cao et al., Deciphering the Solvation Structure of Aqueous ZnCl₂ Solutions from X-ray Absorption Spectra using Interpretable Graph Neural Network, The Journal of Physical Chemistry B, 2026 (in press).

Deciphering the Solvation Structure of Aqueous ZnCl ₂ Solutions from X-ray Absorption Spectra Using the Interpretable Graph Neural Network

The Journal of Physical Chemistry B · 2026-04-28

solutions. Training data are generated from ab initio XAS calculations on molecular dynamics snapshots obtained using a machine learning interatomic potential. The GNN reproduces experimental spectra across concentrations from dilute (<0.1 m) to highly concentrated (30 m, "water-in-salt") regimes and scales efficiently to large, disordered liquid systems beyond the reach of conventional ab initio approaches. Gradient-based attribution analysis reveals that the model learns physically meaningful structure-spectrum relationships. Ligand-specific attributions reflect orbital hybridization patterns and the origin of the excitations derived from the density functional theory. Bond-length attributions recover spectral shifts consistent with multiple-scattering theory. This work bridges data-driven prediction with electronic-structure theory, establishing a general paradigm for interpretable ML that links atomic structure, electronic structure, and spectroscopic observables.

Zn K-edge X-ray Absorption Spectroscopy Dataset and Graph Neural Network Models for Aqueous ZnCl2 Solutions

Open MIND · 2026-04-21

This dataset supports the machine learning prediction of Zn K-edge X-ray absorption spectra (XAS) from atomic structures of aqueous ZnCl₂ solutions. Atomic structures were sampled from molecular dynamics (MD) simulations using a machine learning interatomic potential (MLIP), and target XAS spectra were computed with VASP using the core-hole approach, spanning a range of ZnCl2 concentrations from 0.1 m to 30 m and solvation environments. The repository includes:- Atomic structures (PyMatGen format) and target XAS spectra - Pre-trained graph neural network (GNN) weights using an M3GNet backbone - Python source code and Jupyter notebooks for model training, inference, and interpretability analysis (Integrated Gradients, UMAP clustering) Associated publication: Chuntian Cao et al., Deciphering the Solvation Structure of Aqueous ZnCl₂ Solutions from X-ray Absorption Spectra using Interpretable Graph Neural Network, The Journal of Physical Chemistry B, 2026 (in press).

Detailed Electronic Structure of Octahedral Ag Clusters Confined in Zeolite A

The Journal of Physical Chemistry C · 2025-07-17

The properties of exchanged zeolites depend on the structure–guest relationship. The abundant work accumulated over the past few years reveals gaps in knowledge about this relationship, both experimental and theoretical. We studied in detail the electronic structure of fully Ag-exchanged dehydrated zeolite LTA by first-principles calculations involving the whole unit cell, that is, a nonsimplified structural model. The use of the large stoichiometric unit cell allowed us to study the role of intrinsic disorder on the electronic structure and its spectral signatures, in addition to the modulation of the electronic structure owing to the octahedral Ag clusters confined within the sodalite cage, to evaluate its charge state and to determine the spatial extent of the modulation. In addition, differences in the electronic structure due to changes in the size and structure of the confined Ag clusters were investigated. In this way, it was determined that the density of states has varying contributions of Ag atoms in the framework and the cluster. Because the electronic structure presents variations dependent on the coordination environment and, despite the extremely low stability of zeolites under an electron microscope, recent progress in instrumentation allows us to harbor enormous expectations that studies on the electronic structure and its modulation can be started and carried out with almost no radiation damage. In this context, we evaluate the potential efficacy of electron energy-loss spectroscopy in distinguishing filled and empty sodalite cages and in sensing different Ag clusters.

Non-resonant two-photon x-ray absorption in Cu

ArXiv.org · 2025-04-15

We present a real-space Green's function theory and calculations of two-photon x-ray absorption (TPA). Our focus is on non-resonant K-shell TPA in metallic Cu, which has been observed experimentally at intense x-ray free electron laser (XFEL) sources. The theory is based on an independentparticle Green's function treatment of the Kramers-Heisenberg equation and an approximation for the sum over non-resonant intermediate states in terms of a static quadrupole transition operator. XFEL effects are modeled by a partially depleted d-band. This approach is shown to give results for K-shell TPA in quantitative agreement with XFEL experiment and with a Bethe-Salpeter Equation approach. We also briefly discuss many-body corrections and TPA sum-rules.

Time-Resolved X-Ray Spectroscopy from the Atomic Orbital Ground State Up

Physical Review X · 2025-01-23

X-ray spectroscopy has been a key method to determine ground- and excited-state properties of quantum materials with atomic specificity. Now, new x-ray facilities are opening the door to the study of pump-probe x-ray spectroscopy—specifically, time-resolved x-ray absorption (trXAS) and time-resolved resonant inelastic x-ray scattering (trRIXS). In this paper, we will present simulations of each of these spectroscopies using a time-domain full atomic multiplet, charge-transfer Hamiltonian adapted to study the properties of a generalized cluster model including a central transition-metal ion caged by ligand atoms in a planar geometry. The numerically evaluated trXAS and trRIXS cross sections for representative electron configurations <a:math xmlns:a="http://www.w3.org/1998/Math/MathML" display="inline"><a:mn>3</a:mn><a:msup><a:mi>d</a:mi><a:mn>9</a:mn></a:msup></a:math> and <c:math xmlns:c="http://www.w3.org/1998/Math/MathML" display="inline"><c:mn>3</c:mn><c:msup><c:mi>d</c:mi><c:mn>8</c:mn></c:msup></c:math> demonstrate the insights that can be obtained from charge-transfer pumping and how this nonequilibrium process affects ground- and excited-state properties. The straightforward characterization of the excitations in these systems based on our analysis of the simulations can serve as a benchmark for future experiments, as access to these time-resolved spectroscopic techniques becomes more widely available.

A formal FeIII/V redox couple in an intercalation electrode

Nature Materials · 2025-10-15 · 2 citations

Nonresonant two-photon x-ray absorption in Cu

Physical review. B./Physical review. B · 2025-06-24

Roadmap for warm dense matter physics

ArXiv.org · 2025-05-05 · 2 citations

This roadmap presents the state-of-the-art, current challenges and near future developments anticipated in the thriving field of warm dense matter physics. Originating from strongly coupled plasma physics, high pressure physics and high energy density science, the warm dense matter physics community has recently taken a giant leap forward. This is due to spectacular developments in laser technology, diagnostic capabilities, and computer simulation techniques. Only in the last decade has it become possible to perform accurate enough simulations \&amp; experiments to truly verify theoretical results as well as to reliably design experiments based on predictions. Consequently, this roadmap discusses recent developments and contemporary challenges that are faced by theoretical methods, and experimental techniques needed to create and diagnose warm dense matter. A large part of this roadmap is dedicated to specific warm dense matter systems and applications in astrophysics, inertial confinement fusion and novel material synthesis.

Efficient Variable-Time Implementation of the RT-EOM-CCSDT Approach for Core and Valence Ionization Spectral Functions

Journal of Chemical Theory and Computation · 2025-06-05 · 2 citations

The real-time equation-of-motion coupled cluster (RT-EOM-CC) method has been shown to accurately predict the core and valence photoelectron spectral functions for a variety of small to moderately sized molecular systems. Previous many-body implementations included single and double CC excitations. Here, we extend the approach to include full triples CC excitations. To reduce the computational demand of these added excitations, we have implemented a more efficient approach for the time-integrator that includes an improved solver for the recursive equations and a variable time step. The new implementation is tested by computing the core spectral function of the water molecule in a reduced active space. In this space, the RT-EOM-CCSDT results agree very well with reference full configuration interaction results, up to a renormalization factor. We also compare to the experimental core and inner valence photoelectron spectra of water using a full active space, where the triple excitations fix the issues previously observed at the RT-EOM-CCSD level.