arXiv subjects

Minrui Wei

Publications and source records attributed to Minrui Wei.

9 recordsLinked to original sources

arXiv2026

Core-Level Spectroscopy Decodes Bond-Alternation Dynamics of Cyclo[18]Carbon

The advent of X-ray free-electron lasers and high-harmonic generation has made time-resolved X-ray spectroscopy a powerful tool for probing local atomic environments, yet whether localized core excitations can report on global collective distortions remains open. Cyclo[18]carbon (C$_{18}$), with its polyynic ground state (D$_\text{9h}$) and cumulenic transition state (D$_\text{18h}$), provides an ideal model to address this long-standing issue in bond-length alternation (BLA) dynamics. Mapping two-dimensional potential energy surfaces by first-principles simulations, we find that core ionization symmetrizes the ground-state double-well potential along the BLA coordinate. Our calculated X-ray spectra reveal remarkable sensitivity to bond-length variations: C1s ionization potentials vary by up to 2.4~eV across the BLA coordinate (1.1--1.4~\AA), with a 0.9~eV variation for minima predicted by different functionals, while NEXAFS $\pi^*$ peaks shift by up to 4~eV across the same coordinate. These predicted signatures provide a quantitative spectroscopy--structure dictionary for decoding transient structures in future ultrafast X-ray experiments and monitoring bond-alternation dynamics in real time.

physics.atm-clus↗

arXiv2025

Predicting Accurate X-ray Absorption Spectra for CN$^+$, CN, and CN$^-$: Insights from Multiconfigurational and Density Functional Simulations

High-resolution X-ray spectroscopy is an essential tool in X-ray astronomy, enabling detailed studies of celestial objects and their physical and chemical properties. However, comprehensive mapping of high-resolution X-ray spectra for even simple interstellar and circumstellar molecules is still lacking. In this study, we conducted systematic quantum chemical simulations to predict the C1s X-ray absorption spectra of CN$^+$, CN, and CN$^-$. Our findings provide valuable references for both X-ray astronomy and laboratory studies. We assigned the first electronic peak of CN$^+$ and CN to C1s $\rightarrow σ^*$ transitions, while the peak for CN$^-$ corresponds to a C1s $\rightarrow π^*$ transition. We explained that the two-fold degeneracy ($π^*_{xz}$ and $π^*_{yz}$) of the C1s$\rightarrowπ^*$ transitions results in CN$^-$ exhibiting a significantly stronger first absorption compared to the other two systems. We further calculated the vibronic fine structures for these transitions using the quantum wavepacket method based on multiconfigurational-level, anharmonic potential energy curves, revealing distinct energy positions for the 0-0 absorptions at 280.7 eV, 279.6 eV, and 285.8 eV. Each vibronic profile features a prominent 0-0 peak, showing overall similarity but differing intensity ratios of the 0-0 and 0-1 peaks. Notably, introducing a C1s core hole leads to shortened C-N bond lengths and increased vibrational frequencies across all species. These findings enhance our understanding of the electronic structures and X-ray spectra of carbon-nitrogen species, emphasizing the influence of charge state on X-ray absorptions.

physics.chem-ph↗

arXiv2025

Mapping Transient Structures of Cyclo[18]Carbon by Computational X-Ray Spectra

The structure of cyclo[18]carbon (C$_{18}$), whether in its polyynic form with bond length alternation (BLA) or its cumulenic form without BLA, has long fascinated researchers, even prior to its successful synthesis. Recent studies suggest a polyynic ground state and a cumulenic transient state; however, the dynamics remain unclear and lack experimental validation. This study presents a first-principles theoretical investigation of the bond lengths ($R_1$ and $R_2$) dependent two-dimensional potential energy surfaces (PESs) of C$_{18}$, concentrating on the ground state and carbon 1s ionized and excited states. We examine the potential of X-ray spectra for determining bond lengths and monitoring transient structures, finding that both X-ray photoelectron (XPS) and absorption (XAS) spectra are sensitive to these variations. Utilizing a library of ground-state minimum structures optimized with 14 different functionals, we observe that core binding energies predicted with the $ω$B97XD functional can vary by 0.9 eV (290.3--291.2 eV). Unlike the ground state PES, which predicts minima at alternating bond lengths, the C1s ionized state PES predicts minima with equivalent bond lengths. In the XAS spectra, peaks 1$π^*$ and 2$π^*$ show a redshift with increasing bond lengths along the line where $R_1 = R_2$. Additionally, increasing $R_2$ (with $R_1$ fixed) results in an initial redshift followed by a blueshift, minimizing at $R_1 = R_2$. Major peaks indicate that both 1$π^*$ and 2$π^*$ arise from two channels: C1s$\rightarrowπ^*_{z}$ (out-of-plane) and C1s$\rightarrowπ^*_{xy}$ (in-plane) transitions at coinciding energies.

physics.chem-ph↗

arXiv2024

Simulating Vibrationally-Resolved X-ray Photoelectron Spectra of Flexible Molecules: Linear Alkanes C$_{n}$H$_{2n+2}$ ($n$=1-8)

We integrated full core-hole density functional theory with Franck-Condon calculations, considering Duschinsky rotation, to simulate vibrationally-resolved C1s X-ray photoelectron spectra (XPS) of eight linear alkanes, from methane to octane (C$_{n}$H$_{2n+2}$, $n$=1--8). Results align excellently with experimental absolute binding energies and profiles. The spectrum of ethane serves as a ``spectral seed'', with each longer alkane's atom-specific spectrum displaying similar characteristics, albeit with shifts and slight intensity adjustments. Detailed assignments clarify the distinct spectra in short alkanes ($n$=1--4) and their stabilization in long alkanes ($n$=5--8). Carbons are classified as central or distal (C$_1$ and C$_2$), with central carbons contributing nearly identically to the lowest-energy feature A, while distal carbons contribute to the second lowest-energy feature B (both are 0-0 transitions). Increasing molecule size adds more central carbons, enhancing feature A and weakening feature B. Our analysis identifies two dominant Franck-Condon-active vibrations: C$^*$--H stretching ($\sim$3400-3500 cm$^{-1}$) and bending ($\sim$1400-1500 cm$^{-1}$) modes. Structural analysis shows that core ionization minimally affects alkane geometry, less than in ring compounds from previous studies. This work extends our protocol from rigid ring compounds to flexible molecules, contributing to building a high-resolution theoretical XPS library and enhancing the understanding of vibronic coupling.

physics.chem-ph↗

arXiv2024

Effects of Structural Variations to X-ray Absorption Spectra of g-C$_3$N$_4$: Insights from DFT and TDDFT Simulations

X-ray absorption spectroscopy (XAS) is widely employed for structure characterization of graphitic carbon nitride (g-C$_3$N$_4$) and its composites. Nevertheless, even for pure g-C$_3$N$_4$, discrepancies in energy and profile exist across different experiments, which can be attributed to variations in structures arising from diverse synthesis conditions and calibration procedures. Here, we conducted a theoretical investigation on XAS of three representative g-C$_3$N$_4$ structures (planar, corrugated, and micro-corrugated) optimized with different strategies, to understand the structure-spectroscopy relation. Different methods were compared, including density functional theory (DFT) with the full (FCH) or equivalent (ECH) core-hole approximation, as well as the time-dependent DFT (TDDFT). FCH was responsible for getting accurate absolute absorption energy; while ECH and TDDFT aided in interpreting the spectra, through ECH-state canonical molecular orbitals (ECH-CMOs) and natural transition orbitals (NTOs), respectively. With each method, the spectra at the three structures show evident differences, which can be correlated to different individual experiments or in between. Our calculations explained the structural reason behind the spectral discrepancies among different experiments. Moreover, profiles predicted by these methods also displayed consistency, so their differences can be used as a reliable indicator of their accuracy. Both ECH-CMOs and NTO particle orbitals led to similar graphics, validating their applicability in interpreting the transitions. This work provides a comprehensive analysis of the structure-XAS relation for g-C$_3$N$_4$, provides concrete explanations for the spectral differences reported in various experiments, and offers insight for future structure dynamical and transient X-ray spectral analyses.

cond-mat.mtrl-sci↗

arXiv2024

Temperature and Tautomeric Effects in High-Resolution Oxygen 1s X-ray Photoelectron Spectroscopy of Purines and Pyrimidines

Purines and pyrimidines, crucial building blocks in biological systems, have attracted significant interest across molecular physics, biochemistry, pharmacology, and chemistry. Extensive spectroscopies have been employed for characterization, while the temperature and potential tautomeric effects can complicate the interpretation of underlying physics and chemistry. Here, we conducted first-principles simulations to analyze the vibrationally-resolved O1s X-ray photoelectron spectra of 6 common biomolecules at different temperatures, comprising 3 purine (xanthine, caffeine, and hypoxanthine) and 3 pyrimidine (thymine, 5F-uracil, and uracil) derivatives, and the tautomeric effect of hypoxanthine at varying temperatures. Using both time-independent (TI) and time-dependent (TD) methods under the Franck-Condon approximation, we obtained theoretical spectra that exhibited excellent agreement with experiments. Our analysis of these systems, all featuring carbonyl oxygens, unveiled distinctive characteristics of oxygen in N-CO-N (O2) compared to that within a N-CO-C structure (O1), showcasing higher O1s binding energy and total vibrational reorganization energy. We observed small differences in the zero-point vibration energies between the core-ionized and ground states, indicating a weak Duschinsky rotation effect. We consistently found that O1s ionization resulted in elongation of the O*=C bond length. The TI method facilitated the assignment of experimental spectra to different atoms or tautomers, where the atom-specific vibronic profiles of all 6 molecules exhibited similarity, with the 0-2 transitions dominating. TD enabled a more comprehensive exploration of the temperature effect, and the tautomeric effect of hypoxanthine by incorporating the Boltzmann population ratios of tautomers. We observed significant temperature dependence in the vibronic features present in these spectra.

physics.chem-ph↗

arXiv2023

Franck-Condon Simulation of Vibrationally-Resolved X-ray Spectra for Diatomic Systems: Validation of Harmonic Approximation and Density Functional Theory

Under the Franck-Condon approximation, we systematically validated the performance of density functional theory (DFT) and the effects of anharmonicity in simulating C/N/O K-edge vibrationally-resolved X-ray spectra of common diatomic molecules. To get ``transparent'' validations, vibronic fine structures of only the lowest 1s excited or ionized state in the X-ray absorption (XAS) or photoelectron (XPS) spectra were investigated. All 6 systems (N$_2$, N$_2^+$; NO, NO$^+$; CO, CO$^+$) were studied within the harmonic oscillator (HO) approximation using DFT with four functionals (BLYP, BP86, B3LYP, M06-2X) for 10 XAS and 4 XPS spectra, and excellent agreement between theoretical and experimental spectra was found in most systems, except O1s XAS of NO, CO, and NO$^+$. We analyzed and established a connection between their complex vibronic structures (many weak oscillating features within a broad peak) and the significant geometrical changes induced by the O1s hole. The three spectra were well reproduced with anharmonic (AH) calculations by using quantum wavepacket dynamics based on potential energy curves (PECs) generated by DFT methods or multiconfigurational levels, highlighting sensitivity to the anharmonic effect and the PEC quality. In other examples of XAS (CO$^+$, C1s and O1s; NO, N1s) corresponding to smaller structural changes, HO and AH approaches lead to similar fine structures, which are dominated by 0-0 and 0-1 transitions. This study highlights the use of DFT with selected functionals for such diatomic calculations due to its easy execution and generally reliable accuracy. Functional dependence in diatomic systems is generally more pronounced than in polyatomic ones. We found that BLYP, BP86, and B3LYP functionals consistently exhibited high accuracy in predicting spectral profiles, bond lengths, and vibrational frequencies, which slightly outperformed M06-2X.

physics.chem-ph↗

arXiv2023

Vibronic fine structure in the nitrogen 1s photoelectron spectra from Franck-Condon simulations. III. Rules for amine/imine N atoms in small N-heterocycles

Vibronic coupling plays a crucial role in X-ray photoelectron spectra (XPS) of molecules. In a series of three papers, we present a comprehensive exploration of the N-heterocycles family, known for their diverse structures, to summarize the general rules of vibronic coupling in high-resolution vibrationally-resolved XPS spectra at the N1s edge. Building upon our previous studies on six-membered monocyclic azines [Phys. Rev. A 106, 022811 (2022)] and fused bicyclic compounds indoles with five and six members [Phys. Rev. A 108, 022816 (2023)], in this study, we focus on investigating a series of 12 five-membered N-heterocycles using Franck-Condon simulations, incorporating Duschinsky rotation effects and density functional theory. Our calculations reveal distinct spectral characteristics of amine and imine within these 12 systems in binding energies, spectral characteristics, structural changes, vibrational coupling strengths, and effects of hydrogenation. Furthermore, we expand our analysis to encompass all 35 N-heterocycles discussed in the three papers and consolidate these findings into the general rules. we find that 1s ionization in amine nitrogen induces more substantial geometrical changes, resulting in larger vibronic coupling strength compared to imine nitrogens. The spectra of imine nitrogens exhibit two distinct characteristic peaks originating from the 0-0 and 0-1 transitions, whereas the spectra of amine nitrogens are characterized by a broad peak with numerous weak fingerprints due to significant mixing of various 0-$n$ transitions. We observe that amine (imine) nitrogens generally cause a negative (positive) change in zero-point vibrational energy. This study provides valuable insights into vibronic coupling in N-heterocycles, shedding light on the distinguishing features and behavior of amine and imine nitrogens in vibrationally-resolved XPS spectra.

physics.chem-ph↗

arXiv2023

Vibronic fine structure in the nitrogen 1s photoelectron spectra from Franck-Condon simulations II: Indoles

The vibronic coupling effect in nitrogen 1s X-ray photoelectron spectra (XPS) was systematically studied for a family of 17 bicyclic indole molecules by combining Franck-Condon simulations (including the Duschinsky rotation effect) and density functional theory. The simulated vibrationally-resolved spectra of 4 molecules agree well with available experiments. Reliable predictions for this family further allowed us to summarize rules for spectral evolution in response to three types of common structural changes (side chain substitution, CH$\leftrightarrow$N replacement, and isomerization). Interestingly, vibronic properties of amine and imine nitrogen are clearly separated: they show negative and positive $Δ$ZPE (zero-point vibration energy of the core-ionized with respect to the ground state), respectively, indicating flatter and steeper PESs induced by the N 1s ionization; amine N's show stronger mode mixing effects than imine N's; the 1s ionizations on two types of nitrogens led to distinct changes in local bond lengths and angles. The rules are useful for a basic understanding of vibronic coupling in this family, and the precise spectra are useful for future reference and data mining studies.

physics.chem-ph↗