184 research outputs found

    Probing aqueous ions with non-local Auger relaxation

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    Non-local analogues of Auger decay are increasingly recognized as important relaxation processes in the condensed phase. Here, we explore non-local autoionization, specifically Intermolecular Coulombic Decay (ICD), of a series of aqueous-phase isoelectronic cations following 1s core-level ionization. In particular, we focus on Na+, Mg2+, and Al3+ ions. We unambiguously identify the ICD contribution to the K-edge Auger spectrum. The different strength of the ion-water interactions is manifested by varying intensities of the respective signals: the ICD signal intensity is greatest for the Al3+ case, weaker for Mg2+, and absent for weakly-solvent-bound Na+. With the assistance of ab initio calculations and molecular dynamics simulations, we provide a microscopic understanding of the non-local decay processes. We assign the ICD signals to decay processes ending in two-hole states, delocalized between the central ion and neighbouring water. Importantly, these processes are shown to be highly selective with respect to the promoted water solvent ionization channels. Furthermore, using a core-hole-clock analysis, the associated ICD timescales are estimated to be around 76 fs for Mg2+ and 34 fs for Al3+. Building on these results, we argue that Auger and ICD spectroscopy represents a unique tool for the exploration of intra- and inter-molecular structure in the liquid phase, simultaneously providing both structural and electronic information

    Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse

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    Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed

    Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

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    Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 angstrom resolution and determine its serial femtosecond crystallography structure to 3.5 angstrom resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure

    Актуальність впровадження систем газового обліку в сучасних умовах

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    Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p

    Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

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    Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution
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