Phenopacket-tools: Building and validating GA4GH Phenopackets.

The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers. Phenopacket-tools can be used to validate the syntax and semantics of phenopackets as well as to assess adherence to additional user-defined requirements. The documentation includes examples showing how to use the Java library and the command-line tool to create and validate phenopackets. We demonstrate how to create, convert, and validate phenopackets using the library or the command-line application. Source code, API documentation, comprehensive user guide and a tutorial can be found at https://github.com/phenopackets/phenopacket-tools. The library can be installed from the public Maven Central artifact repository and the application is available as a standalone archive. The phenopacket-tools library helps developers implement and standardize the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications.

RING NMR dynamics: software for analysis of multiple NMR relaxation experiments.

Molecular motions are fundamental to the existence of life, and NMR spectroscopy remains one of the most useful and powerful methods to measure their rates and molecular characteristics. Multiple experimental methods are available for measuring the NMR relaxation properties and these can require different methods for extracting model parameters. We present here a new software application, RING NMR Dynamics, that is designed to support analysis of multiple relaxation types. The initial release of RING NMR Dynamics supports the analysis of exponential decay experiments such as T1 and T2, as well as CEST and R2 and R1ρ relaxation dispersion. The software runs on multiple operating systems in both a command line mode and a user-friendly GUI that allows visualizing and simulating relaxation data. Interaction with another program, NMRFx Analyst, allows drilling down from the derived relaxation parameters to the raw spectral data.

How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II.

First principle calculations of extended X-ray absorption fine structure (EXAFS) data have seen widespread use in bioinorganic chemistry, perhaps most notably for modeling the Mn4Ca site in the oxygen evolving complex (OEC) of photosystem II (PSII). The logic implied by the calculations rests on the assumption that it is possible to a priori predict an accurate EXAFS spectrum provided that the underlying geometric structure is correct. The present study investigates the extent to which this is possible using state of the art EXAFS theory. The FEFF program is used to evaluate the ability of a multiple scattering-based approach to directly calculate the EXAFS spectrum of crystallographically defined model complexes. The results of these parameter free predictions are compared with the more traditional approach of fitting FEFF calculated spectra to experimental data. A series of seven crystallographically characterized Mn monomers and dimers is used as a test set. The largest deviations between the FEFF calculated EXAFS spectra and the experimental EXAFS spectra arise from the amplitudes. The amplitude errors result from a combination of errors in calculated S0(2) and Debye-Waller values as well as uncertainties in background subtraction. Additional errors may be attributed to structural parameters, particularly in cases where reliable high-resolution crystal structures are not available. Based on these investigations, the strengths and weaknesses of using first-principle EXAFS calculations as a predictive tool are discussed. We demonstrate that a range of DFT optimized structures of the OEC may all be considered consistent with experimental EXAFS data and that caution must be exercised when using EXAFS data to obtain topological arrangements of complex clusters.

Imaging Shock Waves in Diamond with Both High Temporal and Spatial Resolution at an XFEL.

The advent of hard x-ray free-electron lasers (XFELs) has opened up a variety of scientific opportunities in areas as diverse as atomic physics, plasma physics, nonlinear optics in the x-ray range, and protein crystallography. In this article, we access a new field of science by measuring quantitatively the local bulk properties and dynamics of matter under extreme conditions, in this case by using the short XFEL pulse to image an elastic compression wave in diamond. The elastic wave was initiated by an intense optical laser pulse and was imaged at different delay times after the optical pump pulse using magnified x-ray phase-contrast imaging. The temporal evolution of the shock wave can be monitored, yielding detailed information on shock dynamics, such as the shock velocity, the shock front width, and the local compression of the material. The method provides a quantitative perspective on the state of matter in extreme conditions.

The protonation states of oxo-bridged Mn(IV) dimers resolved by experimental and computational Mn K pre-edge X-ray absorption spectroscopy.

In nature, the protonation of oxo bridges is a commonly encountered mechanism for fine-tuning chemical properties and reaction pathways. Often, however, the protonation states are difficult to establish experimentally. This is of particular importance in the oxygen evolving complex of photosystem II, where identification of the bridging oxo protonation states is one of the essential requirements toward unraveling the mechanism. In order to establish a combined experimental and theoretical protocol for the determination of protonation states, we have systematically investigated a series of Mn model complexes by Mn K pre-edge X-ray absorption spectroscopy. An ideal test case for selective bis-µ-oxo-bridge protonation in a Mn dimer is represented by the system [Mn(IV)2(salpn)2(µ-OHn)2](n+). Although the three species [Mn(IV)2(salpn)2(µ-O)2], [Mn(IV)2(salpn)2(µ-O)(µ-OH)](+) and [Mn(IV)2(salpn)2(µ-OH)2](2+) differ only in the protonation of the oxo bridges, they exhibit distinct differences in the pre-edge region while maintaining the same edge energy. The experimental spectra are correlated in detail to theoretically calculated spectra. A time-dependent density functional theory approach for calculating the pre-edge spectra of molecules with multiple metal centers is presented, using both high spin (HS) and broken symmetry (BS) electronic structure solutions. The most intense pre-edge transitions correspond to an excitation of the Mn 1s core electrons into the unoccupied orbitals of local e(g) character (d(z)(2) and d(xy) based in the chosen coordinate system). The lowest energy experimental feature is dominated by excitations of 1s-α electrons, and the second observed feature is primarily attributed to 1s-ß electron excitations. The observed energetic separation is due to spin polarization effects in spin-unrestricted density functional theory and models final state multiplet effects. The effects of spin polarization on the calculated Mn K pre-edge spectra, in both the HS and BS solutions, are discussed in terms of the strength of the antiferromagnetic coupling and associated changes in the covalency of Mn-O bonds. The information presented in this paper is complemented with the X-ray emission spectra of the same compounds published in an accompanying paper. Taken together, the two studies provide the foundation for a better understanding of the X-ray spectroscopic data of the oxygen evolving complex (OEC) in photosystem II.

Experimental and computational X-ray emission spectroscopy as a direct probe of protonation states in oxo-bridged Mn(IV) dimers relevant to redox-active metalloproteins.

The protonation state of oxo bridges in nature is of profound importance for a variety of enzymes, including the Mn4CaO5 cluster of photosystem II and the Mn2O2 cluster in Mn catalase. A set of dinuclear bis-µ-oxo-bridged Mn(IV) complexes in different protonation states was studied by Kß emission spectroscopy to form the foundation for unraveling the protonation states in the native complex. The valence-to-core regions (valence-to-core XES) of the spectra show significant changes in intensity and peak position upon protonation. DFT calculations were performed to simulate the valence-to-core XES spectra and to assign the spectral features to specific transitions. The Kß(2,5) peaks arise primarily from the ligand 2p to Mn 1s transitions, with a characteristic low energy shoulder appearing upon oxo-bridge protonation. The satellite Kß" peak provides a more direct signature of the protonation state change, since the transitions originating from the 2s orbitals of protonated and unprotonated µ-oxo bridges dominate this spectral region. The energies of the Kß" features differ by ~3 eV and thus are well resolved in the experimental spectra. Additionally, our work explores the chemical resolution limits of the method, namely, whether a mixed (µ-O)(µ-OH2) motif can be distinguished from a symmetric (µ-OH)2 one. The results reported here highlight the sensitivity of Kß valence-to-core XES to single protonation state changes of bridging ligands, and form the basis for further studies of oxo-bridged polymetallic complexes and metalloenzyme active sites. In a complementary paper, the results from X-ray absorption spectroscopy of the same Mn(IV) dimer series are discussed.

Manganese K-edge X-ray absorption spectroscopy as a probe of the metal-ligand interactions in coordination compounds.

A series of manganese coordination compounds has been investigated by X-ray absorption spectroscopy (XAS). The K-pre-edge spectra are interpreted with the aid of time-dependent density functional theory (TD-DFT). This method was calibrated for the prediction of manganese K-pre-edges with different functionals. Moreover the nature of all observed features could be identified and classified according to the corresponding set of acceptor orbitals, either 1s to 3d transitions or metal-to-ligand charge transfer (MLCT) bands. The observable MLCT bands are further divided into features that correspond to transitions into empty π* orbitals of π-donor ligands and those of π-acceptor ligands. The ability to computationally reproduce the observed features at the correct relative transition energy is strongly dependent on the nature of the transition. A detailed analysis of the electronic structure of a series of Mn coordination compounds reveals that the different classes of observable transitions provide added insight into metal-ligand bonding interactions.

Manganese Kß X-ray emission spectroscopy as a probe of metal-ligand interactions.

A systematic series of high-spin mononuclear Mn(II), Mn(III), and Mn(IV) complexes has been investigated by manganese Kß X-ray emission spectroscopy (XES). The factors contributing to the Kß main line and the valence to core region are discussed. The Kß main lines are dominated by 3p-3d exchange correlation (spin state) effects, shifting to lower energy upon oxidation of Mn(II) to Mn(III) due to the decrease in spin state from S = 5/2 to S = 2, whereas the valence to core region shows greater sensitivity to the chemical environment surrounding the Mn center. A density functional theory (DFT) approach has been used to calculate the valence to core spectra and assess the contributions to the energies and intensities. The valence spectra are dominated by manganese np to 1s electric dipole-allowed transitions and are particularly sensitive to spin state and ligand identity (reflected primarily in the transition energies) as well as oxidation state and metal-ligand bond lengths (reflected primarily in the transition intensities). The ability to use these methods to distinguish different ligand contributions within a heteroleptic coordination sphere is highlighted. The similarities and differences between the current Mn XES study and previous studies of Fe XES investigations are discussed. These findings serve as an important calibration for future applications to manganese active sites in biological and chemical catalysis.