Spin Coupling Effect on Geometry-Dependent X-ray Absorption of Diradicals

We theoretically investigate the influence of diradical electron spin coupling on the time-resolved X-ray absorption spectra of the photochemical ring opening of furanone. We predict geometry dependent carbon K-edge signals involving transitions from core orbitals to both singly and unoccupied molecular orbitals. The most obvious features of the ring opening come from the carbon atom directly involved in the bond breaking, through its transition to both the newly formed SOMO and the available LUMO state. In addition to this primary feature, the singlet spin coupling of four unpaired electrons that arises in the core-to-LUMO states creates additional geometry dependence in some spectral features, with both oscillator strengths and relative excitation energies varying observably as a function of the ring opening. We attribute this behavior to a spin-occupancy-induced selection rule, which occurs when singlet spin coupling is enforced in the diradical state. Notably, one of these geometry-sensitive core-to-LUMO transitions excites core electrons from a backbone carbon not involved in the bond breaking, providing a novel non-local X-ray probe of chemical dynamics arising from electron spin coupling.Comment: 52 Pages, 13 Figure

On the role of stochastic Fermi acceleration in setting the dissipation scale of turbulence in the interstellar medium

We consider the dissipation by Fermi acceleration of magnetosonic turbulence in the Reynolds Layer of the interstellar medium. The scale in the cascade at which electron acceleration via stochastic Fermi acceleration (STFA) becomes comparable to further cascade of the turbulence defines the inner scale. For any magnetic turbulent spectra equal to or shallower than Goldreich-Sridhar this turns out to be $\ge 10^{12}$cm, which is much larger than the shortest length scales observed in radio scintillation measurements. While STFA for such spectra then contradict models of scintillation which appeal directly to an extended, continuous turbulent cascade, such a separation of scales is consistent with the recent work of \citet{Boldyrev2} and \citet{Boldyrev3} suggesting that interstellar scintillation may result from the passage of radio waves through the galactic distribution of thin ionized boundary surfaces of HII regions, rather than density variations from cascading turbulence. The presence of STFA dissipation also provides a mechanism for the non-ionizing heat source observed in the Reynolds Layer of the interstellar medium \citep{Reynolds}. STFA accommodates the proper heating power, and the input energy is rapidly thermalized within the low density Reynolds layer plasma.Comment: 12 Pages, no figures. Accepted for publication in MNRA

Ultrafast X-ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron Withdrawing Groups

Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. We observe the excited state dynamics following excitation with 266 nm UV light to the $^1\pi\pi^{*}$ (S$_2$) state with element and site-specificity using a broadband soft X-ray pulse produced by high harmonic generation. These results are compared to X-ray spectra computed from orbital optimized density functional theory methods. It is found that the electron withdrawing fluorine atoms decongest the X-ray absorption spectrum by enhancing separation between features originating from different carbon atoms. This facilitates the elucidation of structural and electronic dynamics at the chromophore. The evolution of the core-to-valence resonances at the carbon K-edge reveals an ultrafast population transfer between the $^1n\pi^{*}$ (S$_1$) and $^3\pi\pi^{*}$ (T$_1$) states on a $1.6\pm0.4$ ps timescale, which is similar to the 1.5 ps timescale earlier observed for acetylacetone [J. Am. Chem. Soc. 139, 16576 (2017)]. It therefore appears that terminal fluorination has little influence on the intersystem crossing rate of the acetylacetone chromophore. In addition, the significant role of hydrogen-bond opened and twisted rotational isomers is elucidated in the excited state dynamics by comparison of the experimental transient X-ray spectra with theory

Accurate prediction of core-level spectra of radicals at density functional theory cost via square gradient minimization and recoupling of mixed configurations

State-specific orbital optimized approaches are more accurate at predicting core-level spectra than traditional linear-response protocols, but their utility had been restricted on account of the risk of `variational collapse' down to the ground state. We employ the recently developed square gradient minimization (SGM, J. Chem. Theory Comput. 16, 1699-1710, 2020) algorithm to reliably avoid variational collapse and study the effectiveness of orbital optimized density functional theory (DFT) at predicting second period element 1s core-level spectra of open-shell systems. Several density functionals (including SCAN, B3LYP and $\omega$B97X-D3) are found to predict excitation energies from the core to singly occupied levels to high accuracy ($\le 0.3$ eV RMS error), against available experimental data. Higher excited states are however more challenging by virtue of being intrinsically multiconfigurational. We thus present a CI inspired route to self-consistently recouple single determinant mixed configurations obtained from DFT, in order to obtain approximate doublet states. This recoupling scheme is used to predict the C K-edge spectra of the allyl radical, the O K-edge spectra of CO$^+$ and the N K-edge of NO$_2$ to high accuracy relative to experiment, indicating substantial promise in using this approach for computation of core-level spectra for doublet species (vs more traditional time dependent DFT, EOM-CCSD or using unrecoupled mixed configurations). We also present general guidelines for computing core-excited states from orbital optimized DFT.Comment: Added more dat

Femtosecond Symmetry Breaking and Coherent Relaxation of Methane Cations at the Carbon K-Edge

Understanding the relaxation pathways of photoexcited molecules is essential to gain atomistic level insight into photochemistry. Herein, we perform a time-resolved study of ultrafast molecular symmetry breaking via geometric relaxation (Jahn-Teller distortion) on the methane cation. Attosecond transient absorption spectroscopy with soft X-rays at the carbon K-edge reveals that the distortion occurs within $10\pm 2$ femtoseconds after few-femtosecond strong-field ionization of methane. The distortion activates coherent oscillations in the scissoring vibrational mode of the symmetry broken cation, which are detected in the X-ray signal. These oscillations are damped within $58\pm13$ femtoseconds, as vibrational coherence is lost with the energy redistributing into lower-frequency vibrational modes. This study completely reconstructs the molecular relaxation dynamics of this prototypical example and opens new avenues for exploring complex systems

Laboratory Plasma Dynamos, Astrophysical Dynamos, and Magnetic Helicity Evolution

The term ``dynamo'' means different things to the laboratory fusion plasma and astrophysical plasma communities. To alleviate the resulting confusion and to facilitate interdisciplinary progress, we pinpoint conceptual differences and similarities between laboratory plasma dynamos and astrophysical dynamos. We can divide dynamos into three types: 1. magnetically dominated helical dynamos which sustain a large scale magnetic field against resistive decay and drive the magnetic geometry toward the lowest energy state, 2. flow-driven helical dynamos which amplify or sustain large scale magnetic fields in an otherwise turbulent flow, and 3. flow-driven nonhelical dynamos which amplify fields on scales at or below the driving turbulence. We discuss how all three types occur in astrophysics whereas plasma confinement device dynamos are of the first type. Type 3 dynamos requires no magnetic or kinetic helicity of any kind. Focusing on type 1 and 2 dynamos, we show how different limits of a unified set of equations for magnetic helicity evolution reveal both types. We explicitly describe a steady-state example of a type 1 dynamo, and three examples of type 2 dynamos: (i) closed volume and time dependent; (ii) steady-state with open boundaries; (iii) time dependent with open boundaries.Comment: accepted by MNRA

Jahn-Teller Distortion and Dissociation of CCl4+_4^+ by Transient X-ray Spectroscopy Simultaneously at the Carbon K- and Chlorine L-Edge

X-ray Transient Absorption Spectroscopy (XTAS) and theoretical calculations are used to study CCl$_4^+$ prepared by 800 nm strong-field ionization. XTAS simultaneously probes atoms at the carbon K-edge (280-300 eV) and chlorine L-edge (195-220 eV). Comparison of experiment to X-ray spectra computed by orbital-optimized density functional theory (OO-DFT) indicates that after ionization, CCl$_4^+$ undergoes symmetry breaking driven by Jahn-Teller distortion away from the initial tetrahedral structure (T$_d$) in 6$\pm$2 fs. The resultant symmetry-broken covalently bonded form subsequently separates to a noncovalently bound complex between CCl$_3^+$ and Cl over 90$\pm$10 fs, which is again predicted by theory. Finally, after more than 800 fs, L-edge signals for atomic Cl are observed, indicating dissociation to free CCl$_3^+$ and Cl. The results for Jahn-Teller distortion to the symmetry-broken form of CCl$_4^+$ and formation of the Cl -- CCl$_3^+$ complex characterize previously unobserved new species along the route to dissociation

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair

Carcinogenesis and neoplastic progression are mediated by the accumulation of somatic mutations. Here we report that the local density of somatic mutations in cancer genomes is highly reduced specifically in accessible regulatory DNA defined by DNase I hypersensitive sites. This reduction is independent of any known factors influencing somatic mutation density and is observed in diverse cancer types, suggesting a general mechanism. By analyzing individual cancer genomes1, we show that the reduced local mutation density within regulatory DNA is linked to intact global genome repair machinery, with nearly complete abrogation of the hypomutation phenomenon in individual cancers that possess mutations in multiple nucleotide excision repair components. Together, our results connect chromatin structure, gene regulation and cancer-associated somatic mutation

The Human Mitochondrial Transcriptome

SummaryThe human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs, and rRNAs. Here, we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance and precisely resolve transcript processing and maturation events. We identify previously undescribed transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single-nucleotide resolution, revealing regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. This integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA and provides a resource for future studies of mitochondrial function (accessed at http://mitochondria.matticklab.com)