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X-ray and electron scattering from free gas-phase molecules is examined using the independent atom model (IAM) andab initioelectronic structure calculations. The IAM describes the effect of the molecular geometry on the scattering, but does not account for the redistribution of valence electrons due to, for instance, chemical bonding. By examining the total,i.e.energy-integrated, scattering from three molecules, fluoroform (CHF₃), 1,3-cyclohexadiene (C₆H₈) and naphthalene (C₁₀H₈), the effect of electron redistribution is found to predominantly reside at small-to-medium values of the momentum transfer (q≤ 8 Å⁻¹) in the scattering signal, with a maximum percent difference contribution at 2 ≤q≤ 3 Å⁻¹. A procedure to determine the molecular geometry from the large-qscattering is demonstrated, making it possible to more clearly identify the deviation of the scattering from the IAM approximation at small and intermediateqand to provide a measure of the effect of valence electronic structure on the scattering signal. 

Disulfide bonds are ubiquitous molecular motifs that influence the tertiary structure and biological functions of many proteins. Yet, it is well known that the disulfide bond is photolabile when exposed to ultraviolet C (UVC) radiation. The deep-UV–induced S─S bond fragmentation kinetics on very fast timescales are especially pivotal to fully understand the photostability and photodamage repair mechanisms in proteins. In 1,2-dithiane, the smallest saturated cyclic molecule that mimics biologically active species with S─S bonds, we investigate the photochemistry upon 200-nm excitation by femtosecond time-resolved x-ray scattering in the gas phase using an x-ray free electron laser. In the femtosecond time domain, we find a very fast reaction that generates molecular fragments with one and two sulfur atoms. On picosecond and nanosecond timescales, a complex network of reactions unfolds that, ultimately, completes the sulfur dissociation from the parent molecule. 

Abstract Advances in x-ray free electron lasers have made ultrafast scattering a powerful method for investigating molecular reaction kinetics and dynamics. Accurate measurement of the ground-state, static scattering signals of the reacting molecules is pivotal for these pump-probe x-ray scattering experiments as they are the cornerstone for interpreting the observed structural dynamics. This article presents a data calibration procedure, designed for gas-phase x-ray scattering experiments conducted at the Linac Coherent Light Source x-ray Free-Electron Laser at SLAC National Accelerator Laboratory, that makes it possible to derive a quantitative dependence of the scattering signal on the scattering vector. A self-calibration algorithm that optimizes the detector position without reference to a computed pattern is introduced. Angle-of-scattering corrections that account for several small experimental non-idealities are reported. Their implementation leads to near quantitative agreement with theoretical scattering patterns calculated withab-initiomethods as illustrated for two x-ray photon energies and several molecular test systems. 

Abstract The light-induced ultrafast switching between molecular isomers norbornadiene and quadricyclane can reversibly store and release a substantial amount of chemical energy. Prior work observed signatures of ultrafast molecular dynamics in both isomers upon ultraviolet excitation but could not follow the electronic relaxation all the way back to the ground state experimentally. Here we study the electronic relaxation of quadricyclane after exciting in the ultraviolet (201 nanometres) using time-resolved gas-phase extreme ultraviolet photoelectron spectroscopy combined with non-adiabatic molecular dynamics simulations. We identify two competing pathways by which electronically excited quadricyclane molecules relax to the electronic ground state. The fast pathway (<100 femtoseconds) is distinguished by effective coupling to valence electronic states, while the slow pathway involves initial motions across Rydberg states and takes several hundred femtoseconds. Both pathways facilitate interconversion between the two isomers, albeit on different timescales, and we predict that the branching ratio of norbornadiene/quadricyclane products immediately after returning to the electronic ground state is approximately 3:2. 

Abstract Data encoded in molecules offers opportunities for secret messaging and extreme information density. Here, we explore how the same chemical and physical dimensions used to encode molecular information can expose molecular messages to detection and manipulation. To address these vulnerabilities, we write data using an object’s pre-existing surface chemistry in ways that are indistinguishable from the original substrate. While it is simple to embed chemical information onto common objects (covers) using routine steganographic permutation, chemically embedded covers are found to be resistant to detection by sophisticated analytical tools. Using Turbo codes for efficient digital error correction, we demonstrate recovery of secret keys hidden in the pre-existing chemistry of American one dollar bills. These demonstrations highlight ways to improve security in other molecular domains, and show how the chemical fingerprints of common objects can be harnessed for data storage and communication. 

Measuring the attosecond movement of electrons in molecules is challenging due to the high temporal and spatial resolutions required. X-ray scattering-based methods are promising, but many questions remain concerning the sensitivity of the scattering signals to changes in density, as well as the means of reconstructing the dynamics from these signals. In this paper, we present simulations of stationary core-holes and electron dynamics following inner-shell ionization of the oxazole molecule. Using a combination of time-dependent density functional theory simulations along with X-ray scattering theory, we demonstrate that the sudden core-hole ionization produces a significant change in the X-ray scattering response and how the electron currents across the molecule should manifest as measurable modulations to the time dependent X-ray scattering signal. This suggests that X-ray scattering is a viable probe for measuring electronic processes at time scales faster than nuclear motion. 

We present a comprehensive investigation of a recently introduced method to determine transient structures of molecules in excited electronic states with sub-ångstrom resolution from time-resolved gas-phase scattering signals. The method, which is examined using time-resolved X-ray scattering data measured on the molecule N -methylmorpholine (NMM) at the Linac Coherent Light Source (LCLS), compares the experimentally measured scattering patterns against the simulated patterns corresponding to a large pool of molecular structures to determine the full set of structural parameters. In addition, we examine the influence of vibrational state distributions and find the effect negligible within the current experimental detection limits, despite that the molecules have a comparatively high internal vibrational energy. The excited state structures determined using three structure pools generated using three different computational methods are in good agreement, demonstrating that the procedure is largely independent of the computational chemistry method employed as long as the pool is sufficiently expansive in the vicinity of the sought structure and dense enough to yield good matches to the experimental patterns.