Phosphorus Kβ X-ray emission spectroscopy detects non-covalent interactions of phosphate biomolecules in situ
TL;DR: P Kβ spectra offer a detailed picture of phosphate valence electronic structure, reporting on subtle non-covalent effects, such as hydrogen bonding and ionic interactions, that are key to enzymatic catalysis.
Abstract: Phosphorus is ubiquitous in biochemistry, being found in the phosphate groups of nucleic acids and the energy-transferring system of adenine nucleotides (e.g. ATP). Kβ X-ray emission spectroscopy (XES) of phosphorus has been largely unexplored, with no previous applications to biomolecules. Here, the potential of P Kβ XES to study phosphate-containing biomolecules, including ATP and NADPH, is evaluated, as is the application of the technique to aqueous solution samples. P Kβ spectra offer a detailed picture of phosphate valence electronic structure, reporting on subtle non-covalent effects, such as hydrogen bonding and ionic interactions, that are key to enzymatic catalysis. Spectral features are interpreted using density functional theory (DFT) calculations, and potential applications to the study of biological energy conversion are highlighted.
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TL;DR: In this article , the authors review the range of hard X-ray photon-in, photon-out experiments that are presently possible, and highlight their recent applications in catalysis research, and discuss the ongoing need for conventional XAS applications, either in standalone applications or in combination with more advanced approaches.
Abstract: X-ray spectroscopy has had a significant and continually growing impact on catalysis research for nearly 50 years. In particular, the ability to obtain element selective electronic and geometric structural information via the X-ray absorption (XAS) edge and extended X-ray absorption fine structure regions, respectively, has been a major asset for catalysis research. In the last two decades, the development of dedicated synchrotron-based X-ray emission spectrometers has greatly expanded the range of possible experiments, enabling both nonresonant and resonant X-ray emission spectroscopy experiments that can provide greater selectivity and more detailed electronic and structural information. Herein, we briefly review the range of hard X-ray photon-in, photon-out experiments that are presently possible, and highlight their recent applications in catalysis research. We also discuss the ongoing need for conventional XAS applications, either in standalone applications or in combination with more advanced approaches. The open opportunities and ongoing challenges for applying these methods, and ultimately for analyzing and interpreting the data, are also discussed.
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Journal Article•
TL;DR: Pushkar et al. as discussed by the authors used X-ray emission spectroscopy (XES) to identify the oxo-bridging ligands of the Mn 4 Ca complex of photosystem II, a multisubunit membrane protein, that catalyzes the water oxidizing reaction.
Abstract: Direct Detection of Oxygen Ligation to the Mn 4 Ca Cluster of Photosystem II by X-ray Emission Spectroscopy Yulia Pushkar †,# , Xi Long †,‡ , Pieter Glatzel †,€ , Gary W. Brudvig § , G. Charles Dismukes ¶ , Terrence J. Collins $ , Vittal K. Yachandra †,* , Junko Yano †,* , Uwe Bergmann ∆,* Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, § Dept. of Chemistry, Yale Univ., New Haven, CT, ¶ Dept. of Chemistry, Princeton Univ., Princeton, NJ, $ Dept. of Chemistry, Carnegie-Mellon Univ., Pittsburgh, PA, ∆ Stanford Synchrotron Radiation Lightsource, Menlo Park, CA. RECEIVED DATE (automatically inserted by publisher); vkyachandra@lbl.gov, jyano@lbl.gov, ubergmann@slac.stanford.edu Ligands play critical roles during the catalytic reactions in metalloproteins through bond formation/breaking, protonation/deprotonation, and electron/spin delocalization. While there are well-defined element-specific spectroscopic handles, such as X-ray spectroscopy and EPR, to follow the chemistry of metal catalytic sites in a large protein matrix, directly probing particular ligand atoms like C, N, and O is challenging due to their abundance in the protein. FTIR/Raman and ligand-sensitive EPR techniques such as ENDOR and ESEEM have been applied to study metal-ligand interactions. X-ray absorption spectroscopy (XAS) can also indirectly probe the ligand environment; its element-specificity allows us to focus only on the catalytic metal site, and EXAFS and XANES provide metal-ligand distances, coordination numbers, and symmetry of ligand environments. However, the information is limited, since one cannot distinguish among ligand elements with similar atomic number (i.e. C, N. and O). As an alternative and a more direct method to probe the specific metal-ligand chemistry in the protein matrix, we investigated the application of X-ray emission spectroscopy (XES). Using this technique we have identified the oxo-bridging ligands of the Mn 4 Ca complex of photosystem II (PS II), a multisubunit membrane protein, that catalyzes the water oxidizing reaction. 1 The catalytic mechanism has been studied intensively by Mn XAS. 2 The fundamental question of this reaction, however, is how the water molecules are ligated to the Mn 4 Ca cluster and how the O-O bond formation occurs before the evolution of O 2 . 3-5 This implies that it is necessary to follow the chemistry of the oxygen ligands in order to understand the mechanism. XES which is a complementary method to XAS, has the potential to directly probe ligation modes. 6 Among the several emission lines, Kβ 1,3 and Kβ′ lines originate from the metal 3p to 1s transition, and they have been used as an indicator of the charge and spin states on Mn in the OEC (Figure 1). 7,8 The higher energy region corresponds to valence to core transitions just below the Fermi level, and can be divided into the Kβ′′ and the Kβ 2,5 emission (Fig.1 left scheme). Kβ 2,5 emission is predominantly from ligand 2p (metal 4p) to metal 1s, and the Kβ′′ emission is assigned to a ligand 2s to metal 1s, and are referred to as crossover transitions. 9-11 Therefore, only direct ligands to the metal of interest are probed with Kβ ,2,5 /Kβ′′ emission; i.e. other C, N, and O atoms in the protein media do not contribute to the spectra. In this report, we focus on the Kβ′′ spectral region to characterize metal-ligand interactions, in particular contributions from ligated oxygens. The energy of the Kβ′′ transition is dependent on the difference between the metal 1s and ligand 2s binding energies, which is dependent on the environment of the Present addresses: # Dept. of Physics, Purdue Univ., West Lafayette, IN 47904; ‡ Dept. of Chemistry, Univ. of California, Santa Cruz, CA 95064; ESRF, BP 220, 38043 Grenoble Cedex, France. Figure 1. (A) Energy diagram of Mn Kβ transitions in MnO. The Kβ′′ and Kβ 2,5 transitions are from valence molecular orbitals, Kβ′′ is O 2s to Mn 1s ‘cross-over’ transition. (B) Logarithmic plot of MnO Kβ spectrum. The O-Mn cross-over Kβ′′ transition is highlighted. ligand due to orbital hybridization. Therefore the Kβ′′ energy is affected by the charge density on the metal, the ligand protonation state, and changes in the coordination environment. The Kβ′′ intensity is influenced by the spatial overlap between the wavefunction that describes the Mn 1s orbital and the molecular orbitals on the ligands. The Kβ′′ intensity is affected by the metal to ligand distance, and the number of ligands per metal ion. Shorter distances (e.g. from higher bond order or deprotonation) result in increased Kβ′′ intensity with an approximate exponential dependence. 9 On the other hand, a spread of the molecular wavefunction over next-nearest neighbor atoms will decrease the Kβ′′ spectral intensity. Therefore contribution from single atom ligands such as oxo-bridges, or terminal oxo ligands bonded to Mn is predominant (see below). These combination of factors makes the Kβ′′ spectrum a powerful tool for detection and characterization of oxo-bridges in the Mn 4 Ca cluster of PS II. However, because of the weak intensity of the Kβ′′ spectrum obtaining such spectra from biological samples as dilute as PS II (800µM Mn) has been difficult. For O ligation in a typical model compound, the signal is ~10 3 times weaker than that of Kα and there is an additional large background from both the Kβ 1,3 and the Kβ 2,5 spectral features (Fig. 1). Furthermore the work is challenging because of the high sensitivity of the Mn 4 Ca cluster to radiation damage. 12 This study of PS II became possible by using a new high resolution spectrometer equipped with 8-14 analyzer crystals collecting a large solid angle (Suppl. Info.). Fig. 2 shows the Kβ′′ spectrum of a sample of PS II in the S 1 state compared with a series of Mn oxide spectra. Each spectrum is normalized by the Kβ 1,3 peak intensity which is proportional to the number of Mn atoms in the system. The 1 st moment energy of
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4 citations
TL;DR: In this paper , a full-cylindrical x-ray spectrometer based on flexible pyrolitic graphite mosaic crystals is proposed for high-energy resolution core-level spectroscopy at synchrotron radiation sources or free-electron lasers.
Abstract: High-energy resolution core-level spectroscopies, including a group of different techniques to obtain element-specific information of the electronic structure around an absorption site, have become powerful tools for studying the chemical state, local geometric structure, and the nature of chemical bonding. High-resolution x-ray absorption and x-ray emission spectroscopies are well-established experimental techniques but have always been limited by the number of emitted photons and the limited acceptance of solid angles, as well as requiring high energy stability and repeatability for the whole experimental setup. A full-cylindrical x-ray spectrometer based on flexible HAPG (highly annealed pyrolitic graphite) mosaic crystals is an effective solution for the above issues. However, large-area HAPG remains expensive and is often not easy to access. Here, we present an alternative approach by using segmented single crystals (Si and Ge) with different orientations instead of the HAPG as a dispersive element. The proposed method drastically improved the energy resolution up to 0.2-2 eV in the range of 2-10 keV. High-pressure x-ray emission and resonant x-ray emission spectra are presented to demonstrate the capabilities of the instrument. The new design is particularly suitable for high-resolution spectroscopy applications at fourth-generation synchrotron radiation sources or free-electron lasers.
1 citations
Dissertation•
01 Jan 2015
TL;DR: Striking differences in the energetics of the natural reaction and the reactions in pieces provide a deeper insight into the contribution of enzyme–phosphodianion interactions to the reaction coordinate.
Abstract: Several mechanistically unrelated enzymes utilize the binding energy of their substrate’s nonreacting phosphoryl group to accelerate catalysis. Evidence for the involvement of the phosphodianion in transition state formation has come from reactions of the substrate in pieces, in which reaction of a truncated substrate lacking its phosphorylmethyl group is activated by inorganic phosphite. What has remained unknown until now is how the phosphodianion group influences the reaction energetics at different points along the reaction coordinate. 1-Deoxy-d-xylulose-5-phosphate (DXP) reductoisomerase (DXR), which catalyzes the isomerization of DXP to 2-C-methyl-d-erythrose 4-phosphate (MEsP) and subsequent NADPH-dependent reduction, presents a unique opportunity to address this concern. Previously, we have reported the effect of covalently linked phosphate on the energetics of DXP turnover. Through the use of chemically synthesized MEsP and its phosphate-truncated analogue, 2-C-methyl-d-glyceraldehyde, the current study revealed a loss of 6.1 kcal/mol of kinetic barrier stabilization upon truncation, of which 4.4 kcal/mol was regained in the presence of phosphite dianion. The activating effect of phosphite was accompanied by apparent tightening of its interactions within the active site at the intermediate stage of the reaction, suggesting a role of the phosphodianion in disfavoring intermediate release and in modulation of the on-enzyme isomerization equilibrium. The results of kinetic isotope effect and structural studies indicate rate limitation by physical steps when the covalent linkage is severed. These striking differences in the energetics of the natural reaction and the reactions in pieces provide a deeper insight into the contribution of enzyme–phosphodianion interactions to the reaction coordinate.
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TL;DR: This work reports a gradient-corrected exchange-energy functional, containing only one parameter, that fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
Abstract: Current gradient-corrected density-functional approximations for the exchange energies of atomic and molecular systems fail to reproduce the correct 1/r asymptotic behavior of the exchange-energy density. Here we report a gradient-corrected exchange-energy functional with the proper asymptotic limit. Our functional, containing only one parameter, fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
45,683 citations
TL;DR: A large set of more than 300 molecules representing all elements-except lanthanides-in their common oxidation states was used to assess the quality of the bases all across the periodic table, and recommendations are given which type of basis set is used best for a certain level of theory and a desired quality of results.
Abstract: Gaussian basis sets of quadruple zeta valence quality for Rb-Rn are presented, as well as bases of split valence and triple zeta valence quality for H-Rn. The latter were obtained by (partly) modifying bases developed previously. A large set of more than 300 molecules representing (nearly) all elements-except lanthanides-in their common oxidation states was used to assess the quality of the bases all across the periodic table. Quantities investigated were atomization energies, dipole moments and structure parameters for Hartree-Fock, density functional theory and correlated methods, for which we had chosen Moller-Plesset perturbation theory as an example. Finally recommendations are given which type of basis set is used best for a certain level of theory and a desired quality of results.
17,964 citations
TL;DR: An overview of the current possibilities of ORCA is provided and its efficiency is documents.
Abstract: ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many-body perturbation and coupled cluster theories, and multireference and semiempirical methods). It is designed with the aim of generality, extendibility, efficiency, and user friendliness. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. ORCA uses standard Gaussian basis functions and is fully parallelized. The article provides an overview of its current possibilities and documents its efficiency. © 2011 John Wiley & Sons, Ltd.
8,821 citations
TL;DR: The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology.
Abstract: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net
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5,816 citations
TL;DR: Results from Diffraction Experiments 1351 and results from Spectroscopic Measurements 1354 4.3.1.
Abstract: 4. Structure of Ionic Hydration Shells 1351 4.1. Results from Diffraction Experiments 1351 4.1.1. X-ray Diffraction 1351 4.1.2. Neutron Diffraction 1351 4.2. Results from Computer Simulations 1352 4.3. Results from Spectroscopic Measurements 1354 4.3.1. Vibrational Spectroscopic Measurements 1354 4.3.2. EXAFS Spectroscopy 1354 4.3.3. NMR Relaxation Studies 1355 4.3.4. Dielectric Relaxation Studies 1355 4.4. Summary of the Structure of Ionic Hydration Shells 1355
1,445 citations