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The ultrafast photochemical reaction mechanism, transient spectra, and transition kinetics of the human blue cone visual pigment have been recorded at room temperature. Ultrafast time-resolved absorption spectroscopy revealed the progressive formation and decay of several metastable photo-intermediates, corresponding to the Batho to Meta-II photo-intermediates previously observed with bovine rhodopsin and human green cone opsin, on the picosecond to millisecond timescales following pulsed excitation. The experimental data reveal several interesting similarities and differences between the photobleaching sequences of bovine rhodopsin, human green cone opsin, and human blue cone opsin. While Meta-II formation kinetics are comparable between bovine rhodopsin and blue cone opsin, the transition kinetics of earlier photo-intermediates and qualitative characteristics of the Meta-I to Meta-II transition are more similar for blue cone opsin and green cone opsin. Additionally, the blue cone photo-intermediate spectra exhibit a high degree of overlap with uniquely small spectral shifts. The observed variation in Meta-II formation kinetics between rod and cone visual pigments is explained based on key structural differences. [ABSTRACT FROM AUTHOR]

In this work, the main properties characterizing the photochromism of hackmanites, tugtupites, and scapolites (three aluminosilicate natural minerals) are reported and compared. These properties are the activation energy necessary to generate the color, the absorption spectrum of the colored form, and the bleaching energy characterizing the return to a color-less mineral. An innovative joined experimental and computational approach is used to give an atomistic perspective on the origin of these properties allowing to understanding the difference of color or the lower stability of the colored form of the scapolite. It appears that the stability of the colored form is due to an unusual motion of a sodium atom, made possible by the specific structure of this mineral family, to stabilize a trapped electron responsible of the coloration. This motion is larger for hackmanite and tugtupites compared to scapolite, explaining the larger stability of the trapped electron in the two first minerals compared to the last one. [ABSTRACT FROM AUTHOR]

By introducing metallic ring structural dipole resonances in the microwave regime, we have designed and realized a metamaterial absorber with hierarchical structures that can display an averaged -19.4 dB reflection loss (~99% absorption) from 3 to 40 GHz. The measured performance is independent of the polarizations of the incident wave at normal incidence, while absorption at oblique incidence remains considerably effective up to 45°. We provide a conceptual basis for our absorber design based on the capacitive-coupled electrical dipole resonances in the lateral plane, coupled to the standing wave along the incident wave direction. To realize broadband impedance matching, resistive dissipation of the metallic ring is optimally tuned by using the approach of dispersion engineering. To further extend the absorption spectrum to an ultrabroadband range, we employ a double-layer self-similar structure in conjunction with the absorption of the diffracted waves at the higher end of the frequency spectrum. The overall thickness of the final sample is 14.2 mm, only 5% over the theoretical minimum thickness dictated by the causality limit. [ABSTRACT FROM AUTHOR]

Isoprene has the highest emission into Earth's atmosphere of any nonmethane hydrocarbon. Atmospheric processing of alkenes, including isoprene, via ozonolysis leads to the formation of zwitterionic reactive intermediates, known as Criegee intermediates (CIs). Direct studies have revealed that reactions involving simple CIs can significantly impact the tropospheric oxidizing capacity, enhance particulate formation, and degrade local air quality. Methyl vinyl ketone oxide (MVK-oxide) is a four-carbon, asymmetric, resonance-stabilized CI, produced with 21 to 23% yield from isoprene ozonolysis, yet its reactivity has not been directly studied. We present direct kinetic measurements of MVK-oxide reactions with key atmospheric species using absorption spectroscopy. Direct UV-Vis absorption spectra from two independent flow cell experiments overlap with the molecular beam UV-Vis-depletion spectra reported recently [M. F. Vansco, B. Marchetti, M. I. Lester, J. Chem. Phys. 149, 44309 (2018)] but suggest different conformer distributions under jet-cooled and thermal conditions. Comparison of the experimental lifetime herein with theory indicates only the syn-conformers are observed; anti-conformers are calculated to be removed much more rapidly via unimolecular decay. We observe experimentally and predict theoretically fast reaction of syn-MVK-oxide with SO2 and formic acid, similar to smaller alkyl-substituted CIs, and by contrast, slow removal in the presence of water. We determine products through complementary multiplexed photoionization mass spectrometry, observing SO3 and identifying organic hydroperoxide formation from reaction with SO2 and formic acid, respectively. The tropospheric implications of these reactions are evaluated using a global chemistry and transport model. [ABSTRACT FROM AUTHOR]

Infrared (IR) optoacoustic spectroscopy can separate a multitude of molecules based on their absorption spectra. However, the technique is limited when measuring target molecules in aqueous solution by strong water absorption at IR wavelengths, which reduces detection sensitivity. Based on the dependence of optoacoustic signal on the temperature of the probed medium, we introduce cooled IR optoacoustic spectroscopy (CIROAS) to mute water contributions in optoacoustic spectroscopy. We showcase that spectral measurements of proteins, lipids, and glucose in the short-wavelength IR region, performed at 4 °C, lead to marked sensitivity improvements over conventional optoacoustic or IR spectroscopy. We elaborate on the dependence of optoacoustic signals on water temperature and demonstrate polarity changes in the recorded signal at temperatures below 4 °C. We further elucidate the dependence of the optoacoustic signal and the muting temperature on sample concentration and demonstrate that changes in these dependences enable quantification of the solute concentration. We discuss how CIROAS may enhance abilities for molecular sensing in the IR. [ABSTRACT FROM AUTHOR]

Surface plasmon resonances of metallic nanostructures offer great opportunities to guide and manipulate light on the nanoscale. In the design of novel plasmonic devices, a central topic is to clarify the intricate relationship between the resonance spectrum and the geometry of the nanostructure. Despite many advances, the design becomes quite challenging when the desired spectrum is highly complex. Here we develop a theoretical model for surface plasmons of interacting nanoparticles to reduce the complexity of the design process significantly. Our model is developed by combining plasmon hybridization theory with transformation optics, which yields an efficient way of simultaneously controlling both global and local features of the resonance spectrum. As an application, we propose a design of metasurface whose absorption spectrum can be controlled over a large class of complex patterns through only a few geometric parameters in an intuitive way. Our approach provides fundamental tools for the effective design of plasmonic metamaterials with on-demand functionality. [ABSTRACT FROM AUTHOR]

A series of mono- and dinuclear alkynylplatinum(II) terpyridine complexes containing the hydrophilic oligo(para-phenylene ethynylene) with two 3,6,9-trioxadec-1-yloxy chains was designed and synthesized. Themononuclear alkynylplatinum(II) terpyridine complex was found to display a very strong tendency toward the formation of supramolecular structures. Interestingly, additional end-capping with another platinum(II) terpyridine moiety of various steric bulk at the terminal alkyne would lead to the formation of nanotubes or helical ribbons. These desirable nanostructures were found to be governed by the steric bulk on the platinum(II) terpyridine moieties, which modulates the directional metal-metal interactions and controls the formation of nanotubes or helical ribbons. Detailed analysis of temperature-dependent UV-visible absorption spectra of the nanostructured tubular aggregates also provided insights into the assembly mechanism and showed the role of metal-metal interactions in the cooperative supramolecular polymerization of the amphiphilic platinum(II) complexes. [ABSTRACT FROM AUTHOR]

Materials in nature are characterized by structural order over multiple length scales have evolved for maximum performance and multifunctionality, and are often produced by self-assembly processes. A striking example of this design principle is structural coloration, where interference, diffraction, and absorption effects result in vivid colors. Mimicking this emergence of complex effects from simple building blocks is a key challenge for manmade materials. Here, we show that a simple confined selfassembly process leads to a complex hierarchical geometry that displays a variety of optical effects. Colloidal crystallization in an emulsion droplet creates micron-sized superstructures, termed photonic balls. The curvature imposed by the emulsion droplet leads tofrustrated crystallization. We observe spherical colloidal crystals with ordered, crystalline layers and a disordered core. This geometry produces multiple optical effects. The ordered layers give rise to structural color from Bragg diffraction with limited angular dependence and unusual transmission due to the curved nature of the individual crystals. The disordered core contributes nonresonant scattering that induces a macroscopically whitish appearance, which we mitigate by incorporating absorbing gold nanoparticles that suppress scattering and macroscopically purify the color. With increasing size of the constituent colloidal particles, grating diffraction effects dominate, which result from order along the crystal's curved surface and induce a vivid polychromatic appearance. The control of multiple optical effects induced by the hierarchical morphology in photonic balls paves the way to use them as building blocks for complex optical assemblies-potentially as more efficient mimics of structural color as it occurs in nature. [ABSTRACT FROM AUTHOR]

Knowledge of the dynamical behavior of proteins, and in particular their conformational fluctuations, is essential to understanding the mechanisms underlying their reactions. Here, transient enhancement of the isothermal partial molar compressibility, which is directly related to the conformational fluctuation, during a chemical reaction of a blue light sensor protein from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, TII0078) was investigated in a time-resolved manner. The UV-Vis absorption spectrum of TePixD did not change with the application of high pressure. Conversely, the transient grating signal intensities representing the volume change depended significantly on the pressure. This result implies that the compressibility changes during the reaction. From the pressure dependence of the amplitude, the compressibility change of two short-lived intermediate (I1, and I2) states were determined to be +(5.6 ± 0.6) x 10-2 cm3.mol-1.MPa-1 for I1, and +(6.6 ± 0.7)x10-2 cm3.mol-1.MPa-1 for l2. This result showed that the structural fluctuation of intermediates was enhanced during the reaction. To clarify the relationship between the fluctuation and the reaction, the compressibility of multiply excited TePixD was investigated. The isothermal compressibility of l1 and l2 intermediates of TePixD showed a monotonic decrease with increasing excitation laser power, and this tendency correlated with the reactivity of the protein. This result indicates that the TePixD decamer cannot react when its structural fluctuation is small. We concluded that the enhanced compressibility is an important factor for triggering the reaction of TePixD. To our knowledge, this is the first report showing enhanced fluctuations of intermediate species during a protein reaction, supporting the importance of fluctuations. [ABSTRACT FROM AUTHOR]

Strategies for O2 activation by copper enzymes were recently expanded to include mononuclear Cu sites, with the discovery of the copper-dependent polysaccharide monooxygenases, also classified as auxiliary-activity enzymes 9-11 (AA9-11). These enzymes are finding considerable use in industrial biofuel production. Crystal structures of polysaccharide monooxygenases have emerged, but experimental studies are yet to determine the solution structure of the Cu site and how this relates to reactivity. From X-ray absorption near edge structure and extended X-ray absorption fine structure spectroscopies, we observed a change from four-coordinate Cu(ll) to three-coordinate Cu(l) of the active site in solution, where three protein-derived nitrogen ligands coordinate the Cu in both redox states, and a labile hydroxide ligand is lost upon reduction. The spectroscopic data allowed for density functional theory calculations of an enzyme active site model, where the optimized Cu(l) and (II) structures were consistent with the experimental data. The O2 reactivity of the Cu(l) site was probed by EPR and stopped-flow absorption spectroscopies, and a rapid one-electron reduction of O2 and regeneration of the resting Cu(ll) enzyme were observed. This reactivity was evaluated computationally, and by calibration to Cu-superoxide model complexes, formation of an end-on Cu-AA9-superoxide species was found to be thermodynamically favored. We discuss how this thermodynamically difficult one-electron reduction of O2 is enabled by the unique protein structure where two nitrogen ligands from His1 dictate formation of a T-shaped Cu(l) site, which provides an open coordination position for strong O2 binding with very little reorganization energy. [ABSTRACT FROM AUTHOR]

The layering structure of a painting contains awealth of information about the artist's choice of materials and working methods, but currently, no 3D noninvasive method exists to replace the taking of small paint samples in the study of the stratigraphy. Here, we adapt femtosecond pump-probe imaging, previously shown in tissue, to the case of the color palette in paintings, where chromophores have much greater variety. We show that combining the contrasts of multispectral and multidelay pump-probe spectroscopy permits nondestructive 3D imaging of paintings with molecular and structural contrast, even for pigments with linear absorption spectra that are broad and relatively featureless. We show virtual crosssectioning capabilities in mockup paintings, with pigment separation and nondestructive imaging on an intact 14th century painting (The Crucifixion by Puccio Capanna). Our approach makes it possible to extract microscopic information for a broad range of applications to cultural heritage. [ABSTRACT FROM AUTHOR]

This paper describes measurements of the dynamics of hot electron cooling in photoexcited gold nanoparticles (Au NP5) with diameters of ~3.5 nm. and passivated with either a hexadecylamine or hex- adecanethiolate adlayer, using ultrafast transient absorption spectroscopy. Fits of these dynamics with temperature-dependent Mie theory reveal that both the electronic heat capacity and the electron-phonon coupling constant are larger for the thiolated NPs than for the aminated NP5, by 40% and 30%, respectively. Density functional theory calculations on ligand-functionalized Au slabs show that the increase in these quantities is due to an increased electronic density of states near the Fermi level upon ligand exchange from amines to thiolates. The lifetime of hot electrons, which have thermalized from the initial plasmon excitation, increases with increasing electronic heat capacity, but decreases with increasing electron- phonon coupling, so the effects of changing surface chemistry on these two quantities partially cancel to yield a hot electron lifetime of thiolated NP5 that is only 20% longer than that of aminated NPs. This analysis also reveals that incorporation of a temperature- dependent electron-phonon coupling constant is necessary to adequately fit the dynamics of electron cooling. [ABSTRACT FROM AUTHOR]

Most of what is known about the structure of the hydrated electron comes from mixed quantum/classical simulations, which depend on the pseudopotential that couples the quantum electron to the classical water molecules. These potentials usually are highly repulsive, producing cavity-bound hydrated electrons that break the local water H-bonding structure. However, we recently developed a more attractive potential, which produces a hydrated electron that encompasses a region of enhanced water density. Both our noncavity and the various cavity models predict similar experimental observables. In this paper, we work to distinguish between these models by studying both the temperature dependence of the optical absorption spectrum, which provides insight into the balance of the attractive and repulsive terms in the potential, and the resonance Raman spectrum, which provides a direct measure of the local H-bonding environment near the electron. We find that only our noncavity model can capture the experimental red shift of the hydrated electron's absorption spectrum with increasing temperature at constant density. Cavity models of the hydrated electron predict a solvation structure similar to that of the larger aqueous halides, leading to a Raman O-H stretching band that is blue-shifted and narrower than that of bulk water. In contrast, experiments show the hydrated electron has a broader and red-shifted O-H stretching band compared with bulk water, a feature recovered by our noncavity model. We conclude that although our noncavity model does not provide perfect quantitative agreement with experiment, the hydrated electron must have a significant degree of noncavity character. [ABSTRACT FROM AUTHOR]

We report unambiguous spectroscopic evidence of peptide bond formation at the air-water interface, yielding a possible mechan-ism providing insight into the formation of modern ribosomal pep-tide bonds, and a means for the emergence of peptides on early Earth. Protein synthesis in aqueous environments, facilitated by sequential amino acid condensation forming peptides, is a ubiqui-tous process in modern biology, and a fundamental reaction neces-sary in prebiotic chemistry. Such reactions, however, are conden-sation reactions, requiring the elimination of a water molecule for every peptide bond formed, and are thus unfavorable in aqu-eous environments both from a thermodynamic and kinetic point of view. We use the hydrophobic environment of the air-water interface as a favorable venue for peptide bond synthesis, and de-monstrate the occurrence of this chemistry with in situ techniques using Langmuir-trough methods and infrared reflection absorption spectroscopy. Leucine ethyl ester (a small amino acid ester) first partitions to the water surface, then coordinates with Cu2+ ions at the interface, and subsequently undergoes a condensation reac-tion selectively forming peptide bonds at the air-water interface [ABSTRACT FROM AUTHOR]

Fumarate an d nitrate reduction (FNR) regulatory proteins are O2-sensing bacterial transcription factors that control the switch between aerobic and anaerobic metabolism. Under anaerobic conditions [4Fe-4S]2+-FNR exists as a DNA-binding homodimer. In response to elevated oxygen levels, the [4Fe-4S]2+ cluster undergoes a rapid conversion to a [2Fe-2S]2+ cluster, resulting in a dimer-to-monomer transition and loss of site-specific DNA binding. In this work, resonance Raman and UV-visible absorption/CD spectroscopies and MS were used to characterize the interconversion between [4Fe-4S]2+ and [2Fe-2S]2+ clusters In Escheríchía coli FNR. Selective 34S labeling of the bridging sulfides in the [4Fe-4S]2+ cluster-bound form of FNR facilitated identification of resonantly enhanced Cys32S-34S stretching modes in the resonance Raman spectrum of the O2-exposed [2Fe-2S]2+ duster-bound form of FNR. This result indicates O2-induced oxidation and retention of bridging sulfides in the form of [2Fe-2S]2+ duster-bound cysteine persulfides. MS also demonstrates that multiple cysteine persulfides are formed on O2 exposure of [4Fe-4S]2+-FNR. The [4Fe-4S]2+ cluster in FNR can also be regenerated from the cysteine persulfide-coordinated [2Fe-2S]2+ cluster by anaerobic incubation with DTT and Fe2+ ion in the absence of exogenous sulfide. Resonance Raman data indicate that this type of cluster conversion involving sulfide oxidation is not unique to FNR, because it also occurs in O2-exposed forms of O2-sensitive [4Fe-4S] clusters in radical S-adeno-sylmethionine enzymes. The results provide fresh insight into the molecular mechanism of O2 sensing by FNR and iron-sulfur cluster conversion reactions in general, and suggest unique mechanisms for the assembly or repair of biological [4Fe-4S] clusters. [ABSTRACT FROM AUTHOR]

This paper addresses the origin of the decrease in the external elec-trical bias required for water photoelectrolysis with hematite photoanodes, observed following surface treatments of such elec-trodes. We consider two alternative surface modifications: a cobalt oxo/hydroxo-based (CoOx) overlayer, reported previously to func-tion as an efficient water oxidation electrocatalyst, and a Ga203 overlayer, reported to passivate hematite surface states. Transient absorption studies of these composite electrodes under applied bias showed that the cathodic shift of the photocurrent onset observed after each of the surface modifications is accompanied by a similar cathodic shift of the appearance of long-lived hematite photoholes, due to a retardation of electron/hole recombination. The origin of the slower electron/hole recombination is assigned primarily to enhanced electron depletion in the Fe203 for a given applied bias. [ABSTRACT FROM AUTHOR]

In conventional spectroscopy, transitions between electronic levels are governed by the electric dipole selection rule because electric quadrupole, magnetic dipole, and coupled electric dipole-magnetic dipole transitions are forbidden in a far field. We demonstrated that by using nanostructured electromagnetic fields, the selection rules of absorption spectroscopy could be fundamentally manipulated. We also show that forbidden transitions between discrete quantum levels in a semiconductor nanorod structure are allowed within the near-field of a noble metal nanoparticle. Atomistic simulations analyzed by an effective mass model reveal the breakdown of the dipolar selection rules where quadrupole and octupole transitions are allowed. Our demonstration could be generalized to the use of nanostructured near-fields for enhancing light-matter interactions that are typically weak or forbidden. [ABSTRACT FROM AUTHOR]

Bleomycin (BLM) is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate, prior to DNA cleavage is a low spin FeIII peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4' hydrogen atom of the deoxyribose sugar unit Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure spectroscopy and density functional theory (DFT) calculations are applied to define the natures of FeIIIBLM and ABLM as (BLM)FeIII_ OH and (BLM)FeIII(η¹-OOH) species, respectively. The NRVS spectra of FeIIIBLM and ABLM are strikingly different because in ABLM the öFe-O--O bending mode mixes with, and energetically splits, the doubly degenerate, intense O-Fe-Nax transaxial bends. DFT calculations of the reaction of ABLM with DNA. based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways. [ABSTRACT FROM AUTHOR]

The use of nanoscale x-ray probes overcomes several key limitations in the study of materials up to multir iegabar (>200) pressures, namely, the spatial resolution of measurements of multiple samples, stress gradients, and crystal domains in micron to submicron size samples in diamond-anvil cells. Mixtures of Fe, Pt, and W were studied up to 282 GPa with 250-600 nm size synchrotron x-ray absorption and diffraction probes. The probes readily resolve signals from individual materials, between sample and gasket, and peak pressures, in contrast to the 5-jim-sized x-ray beams that are now becoming routine. The use of nanoscale x-ray beams also enables single-crystal x-ray diffraction studies in nominally polycrystalline samples at ultrahigh pressures, as demonstrated in measurements of (Mg,Fe)SiO3 postperovskite. These capabilities have potential for driving a push toward higher maximum pressures and further miniaturization of high-pressure devices, in the process advancing studies at extreme conditions. [ABSTRACT FROM AUTHOR]

Green algae such as Chiamydomonas reinhardtii synthesize an [FeFe] hydrogenase that is highly active in hydrogen evolution. However, the extreme sensitivity of [FeFe] hydrogenases to oxygen presents a major challenge for exploiting these organisms to achieve sustainable photosynthetic hydrogen production. In this study, the mechanism of oxygen inactivation of the [FeFe] hydrogenase CrHydAl from C. reinhardtii has been investigated. X-ray absorption spectroscopy shows that reaction with oxygen results in destruction of the [4Fe-4SJ domain of the active site H-cluster while leaving the di-iron domain (2FeH) essentially intact. By protein film electrochemistry we were able to determine the order of events leading up to this destruction. Carbon monoxide, a competitive inhibitor of CrHydAl which binds to an Fe atom of the 2FeH domain and is otherwise not known to attack FeS clusters in proteins, reacts nearly two orders of magnitude faster than oxygen and protects the enzyme against oxygen damage. These results therefore show that destruction of the [4Fe-4S] cluster is initiated by binding and reduction of oxygen at the di-iron domain-a key step that is blocked by carbon monoxide. The relatively slow attack by oxygen compared to carbon monoxide suggests that a very high level of discrimination can be achieved by subtle factors such as electronic effects (specific orbital overlap requirements) and steric constraints at the active site. [ABSTRACT FROM AUTHOR]

Distributions of sulfur isotopes in geological samples would provide a record of atmospheric composition if the mechanism producing the isotope effects could be described quantitatively. We determined the UV absorption spectra of 32SO2, 33SO2, and 34SO3 and use them to interpret the geological record. The calculated isotopic fractionation factors for SO2 photolysis give mass independent distributions that are highly sensitive to the atmospheric concentrations of O3, O3, CO2. H2O, CS2, NH3, N2O, H2S, OCS, and SO2 itself. Various UV-shielding scenarios are considered and we conclude that the negative Δ33S observed in the Archean sulfate deposits can only be explained by OCS shielding. Of relevant Archean gases, OCS has the unique ability to prevent SO2 photolysis by sunlight at λ >202 nm. Scenarios run using a photochemical box model show that ppm levels of OCS will accumulate in a CO-rich, reducing Archean atmosphere. The radiative forcing, due to this level of OCS, is able to resolve the faint young sun paradox. Further, the decline of atmospheric OCS may have caused the late Archean glaciation. [ABSTRACT FROM AUTHOR]

This paper presents a computational model for color coding that provides a functional explanation of how humans perceive colors in a homogeneous color space. Beginning with known properties of human cone photoreceptors. the model estimates the locations of the reflectance spectra of Munsell color chips in perceptual color space as represented in the CIE L*a*b* color system. The fit between the two structures is within the limits of expected measurement error. Estimates of the structure of perceptual color space for color anomalous dichromats missing one of the normal cone photoreceptors correspond closely to results from the Farnsworth-Munsell color test. An unanticipated outcome of the model provides a functional explanation of why additive lights are always red, green, and blue and provide maximum gamut for color monitors and color television even though they do not correspond to human cone absorption spectra. [ABSTRACT FROM AUTHOR]

The cofactor composition and electron-transfer kinetics of the reaction center (RC) from a magnesium chelatase (bchD) mutant of Rhodobactersphaeroides were characterized. In this RC, the special pair (P) and accessory (B) bacteriochlorophyll (BChI)-binding sites contain Zn-BChl rather than BChI a. Spectroscopic measurements reveal that Zn-BChI also occupies the H sites that are normally occupied by bacteriopheophytin in wild type, and at least 1 of these Zn-BChI molecules is involved in electron transfer in intact Zn-RC5 with an efficiency of >95% of the wild-type RC. The absorption spectrum of this Zn-containing RC in the near-infrared region associated with P and B is shifted from 865 to 855 nm and from 802 to 794 nm respectively, compared with wild type. The bands of P and B in the visible region are centered at 600 nm, similar to those of wild type, whereas the H-cofactors have a band at 560 nm, which is a spectral signature of monomeric Zn-BChI in organic solvent. The Zn-BChI H-cofactor spectral differences compared with the P and B positions in the visible region are proposed to be due to a difference in the 5th ligand coordinating the Zn. We suggest that this coordination is a key feature of protein-cofactor interactions, which significantly contributes to the redox midpoint potential of H and the formation of the charge-separated state, and provides a unifying explanation for the properties of the primary acceptor in photosystems I (PS1) and II (PS2). [ABSTRACT FROM AUTHOR]

Ultrafast transient absorption spectroscopy of wild-type bacterio-rhodopsin (WT bR) and 2 tryptophan mutants (W86F and W182F) is performed with visible light excitation (pump) and UV probe. The aim is to investigate the photoinduced change in the charge distribution with 50-fs time resolution by probing the effects on the tryptophan absorption bands. A systematic, quantitative comparison of the transient absorption of the 3 samples is carried out. The main result is the absence in the W86F mutant of a transient induced absorption band observed at ≈300-310 nm in WT bR and W182F. A simple model describing the dipolar interaction of the retinal moiety with the 2 tryptophan residues of interest allows us to reproduce the dominant features of the transient signals observed in the 3 samples at ultrashort pump-probe delays. In particular, we show that Trp86 undergoes a significant Stark shift induced by the transient retinal dipole moment. The corresponding transient signal can be isolated by direct subtraction of experimental data obtained for WI bR and W86F. It shows an instantaneous rise, followed by a decay over ≈500 fs corresponding to the isomerization time. Interestingly, it does not decay back to zero, thus revealing a change in the local electrostatic environment that remains long after isomerization, in the K intermediate state of the protein cycle. The comparison of WT bR and W86F also leads to a revised interpretation of the overall transient UV absorption of bR. [ABSTRACT FROM AUTHOR]

The formation of substitutional alloys has been restricted to elements with similar atomic radii and electronegativity. Using high-pressure at 298 K, we synthesized a face-centered cubic disordered alloy of highly dissimilar elements (large Ce and small Al atoms) by compressing the Ce3Al intermetallic compound >15 GPa or the Ce3AI metallic glass >25 GPa. Synchrotron X-ray diffraction, Ce L3-edge absorption spectroscopy, and ab initio calculations revealed that the pressure-induced Kondo volume collapse and 4f electron delocalization of Ce reduced the differences between Ce and Al and brought them within the Hume-Rothery (HR) limit for substitutional alloying. The alloy re- mained after complete release of pressure, which was also accompanied by the transformation of Ce back to its ambient 4f electron localized state and reversal of the Kondo volume collapse, resulting in a non-HR alloy at ambient conditions. [ABSTRACT FROM AUTHOR]

The cytochrome P450 enzyme CYP119. its compound II derivative. and its nitrosyl complex were studied by iron K-edge x-ray absorption spectroscopy. The compound II derivative was prepared by reaction of the resting enzyme with peroxynitrite and had a lifetime of ≈1O s at 23°C. The CYP119 nitrosyl complex was prepared by reaction of the enzyme with nitrogen monoxide gas or with a nitrosyl donor and was stable at 23°C for hours. Samples of CYP119 and its derivatives were studied by x-ray absorption spectroscopy at temperatures below 140 (K) at the Advanced Photon Source of Argonne National Laboratory. The x-ray absorption near-edge structure spectra displayed shifts in edge and pre-edge energies consistent with increasing effective positive charge on iron in the series native CYP119 < CYP119 nitrosyl complex < CVP1 19 compound II derivative. Extended x-ray absorption fine structure spectra were simulated with good fits fork = 12 A-i for native CYP1 19 and k = 13 Å[sup-1] for both the nitrosyl complex and the compound II derivative. The important structural features for the compound II derivative were an iron-oxygen bond length of 1.82 Å and an iron-sulfur bond length of 2.24 A, both of which indicate an iron-oxygen single bond in a ferryl-hydroxide, Fe[supIV]OH, moiety. [ABSTRACT FROM AUTHOR]

Brown algae of the Laminariales (kelps) are the strongest accumulators of iodine among living organisms. They represent a major pump in the global biogeochemical cycle of iodine and, in particular, the major source of iodocarbons in the coastal atmosphere. Nevertheless, the chemical state and biological significance of accumulated iodine have remained unknown to this date. Using x-ray absorption spectroscopy, we show that the accumulated form is iodide, which readily scavenges a variety of reactive oxygen species (ROS). We propose here that its biological role is that of an inorganic antioxidant, the first to be described in a living system. Upon oxidative stress, iodide is effluxed. On the thallus surface and in the apoplast, iodide detoxifies both aqueous oxidants and ozone, the latter resulting in the release of high levels of molecular iodine and the consequent formation of hygroscopic iodine oxides leading to particles, which are precursors to cloud condensation nuclei. In a complementary set of experiments using a heterologous system, iodide was found to effectively scavenge ROS in human blood cells. [ABSTRACT FROM AUTHOR]

We describe an approach for characterizing selective binding between oppositely charged ionic functional groups under biologically relevant conditions. Relative shifts in K-shell x-ray absorption spectra of aqueous cations and carboxylate anions indicate the corresponding binding strengths via perturbations of carbonyl antibonding orbitals. XAS spectra measured for aqueous formate and acetate solutions containing lithium, sodium, and potassium cations reveal monotonically stronger binding of the lighter metals, supporting recent results from simulations and other experiments. The carbon K-edge spectra of the acetate carbonyl feature centered near 290 eV clearly indicate a preferential interaction of sodium versus potassium, which was less apparent with formate. These results are in accord with the Law of Matching Water Affinities, relating relative hydration strengths of ions to their respective tendencies to form contact ion pairs. Density functional theory calculations of K-shell spectra support the experimental findings. [ABSTRACT FROM AUTHOR]

Magnetosomes are magnetite nanoparticles formed by biomineralization within magnetotactic bacteria. Although there have been numerous genetic and proteomic studies of the magnetosome-formation process, there have been only limited and inconclusive studies of mineral-phase evolution during the formation process. and no real-time studies of such processes have yet been performed. Thus, suggested formation mechanisms still need substantiating with data. Here we report the examination of the magnetosome material throughout the formation process in a real-time in viva study of Magnetospirillum gryphiswaldense, strain MSR-1. Transmission EM and x-ray absorption spectroscopy studies reveal that full-sized magnetosomes are seen 15 min after formation is initiated. These immature magnetosomes contain a surface layer of the nonmagnetic iron oxide-phase hematite. Mature magnetite is found after another 15 min, concurrent with a dramatic increase in magnetization. This rapid formation result is contrary to previously reported studies and discounts the previously proposed slow, multistep formation mechanisms. Thus, we conclude that the biomineralization of magnetite occurs rapidly in magnetotactic bacteria on a similar time scale to high-temperature chemical precipitation reactions, and we suggest that this finding is caused by a biological catalysis of the process. [ABSTRACT FROM AUTHOR]

MitoNEET is a protein of unknown function present in the mitochondrial membrane that was recently shown to bind specifically the antidiabetic drug pioglizatone. Here, we report the crystal structure of the soluble domain (residues 32-108) of human mitoNEET at 1.8-Å resolution. The structure reveals an intertwined homodimer, and each subunit was observed to bind a [2Fe-2S] cluster. The [2Fe-2S] ligation pattern of three cysteines and one histidine differs from the known pattern of four cysteines in most cases or two cysteines and two histidines as observed in Rieske proteins. The [2Fe-2S] cluster is packed in a modular structure formed by 17 consecutive residues. The cluster-binding motif is conserved in at least seven distinct groups of proteins from bacteria, archaea, and eukaryotes, which show a consensus sequence of (hb)-C-X1-C-X2-(S/T)·X3-P-(hb)-C-D-X2-H, where hb represents a hydrophobic residue; we term this a CCCH-type [2Fe-2S] binding motif. The nine conserved residues in the motif contribute to iron ligation and structure stabilization. UV-visible absorption spectra indicated that mitoNEET can exist in oxidized and reduced states. Our study suggests an electron transfer function for mitoNEET and for other proteins containing the CCCH motif. [ABSTRACT FROM AUTHOR]

We have determined the crystal structure of the chloroperoxidase (CPO) hydroperoxo reaction intermediate (CPO compound O) at 1.75-Å resolution. The intermediate was generated through controlled photoreduction of the CPO oxygen complex during x-ray data collection, which was monitored by recording of the crystal absorption spectra. Initially, the peroxo-anion species was formed and then protonated to yield compound 0. Quantum chemical calculations indicate that the peroxo-anion species is not stable and collapses instantaneously to compound 0. Compound 0 is present in the ferric low-spin doublet ground state and is characterized by a long O—O bond length of 1.5 Å and a Fe—O bond distance of 1.8 Å, which is also observed in the crystal structure. [ABSTRACT FROM AUTHOR]

Electronic structure calculations on a conjugated polymer chain by Hartree—Fock and density functional theory show a sequence of self-localized states, which stand in contrast to the single self-localized soliton state described by the Su-Schrieffer-Heeger model Hamiltonian. An extended Hubbard model, which treats electron-electron interactions up to second neighbors, is constructed to demonstrate that the additional states arise from a strong band-bending effect due to the presence of localized electric fields of charged solitons. We suggest the optical response of these electronic states may be associated with the near-edge oscillations observed in photo-induced absorption spectra. Our calculations indicate further that in the presence of counterions, the additional localized states continue to exist. Implications regarding soliton mobility and high-resolution ion sensing are briefly discussed. [ABSTRACT FROM AUTHOR]

It has been suggested, based on x-ray absorption spectroscopy (XAS) experiments on liquid water [Wernet, Ph., et al. (2004) Science 304, 995-999], that a condensed-phase water molecule's asymmetric electron density results in only two hydrogen bonds per water molecule on average. The larger implication of the XAS interpretation is that the conventional view of liquid water being a tetrahedrally coordinated random network is now replaced by a structural organization that instead strongly favors hydrogen- bonded water chains or large rings embedded in a weakly hydrogen-bonded disordered network. This work reports that the asymmetry of the hydrogen density exhibited in the XAS experiments agrees with reported x-ray scattering structure factors and intensities for Q > 6.5 Å-1. However, the assumption that the asymmetry in the hydrogen electron density does not fluctuate and is persistent in all local molecular liquid water environments is inconsistent with longer-ranged tetrahedral network signatures present in experimental x-ray scattering intensity and structure factor data for Q < 6.5 Å-1. [ABSTRACT FROM AUTHOR]

Absorption spectra of the purified cytochrome b6f complex from Chlamydomonas reinhardtii were monitored as a function of the redox potential. Four spectral and redox components were identified: in addition to heme f and the two b hemes, the fourth component must be the new heme ci (also denoted x) recently discovered in the crystallographic structures. This heme is covalently attached to the protein, but has no amino acid axial ligand. It is located in the plastoquinone-reducing site Qi in the immediate vicinity of a b hems. Each heme titrated as a one-electron Nernst curve, with midpoint potentials at pH 7.0 of -130 mV and -35 mV (hemes b), +100 my (heme ci, and +355 my (heme /). The reduced minus oxidized spectrum of heme ci consists of a broad absorption increase centered ≈425 nm. Its potential has a dependence of -60 mV/pH unit, implying that the reduced form binds one proton in the pH 6-9 range. The Qi site inhibitor 2-n-nonyl-4-hydroxyquinoline N-oxide, a semiquinone analogue, induces a shift of this potential by about -225 mV. The spectrum of ci matches the absorption changes previously observed in vivo for an unknown redox center denoted "G." The data are discussed with respect to the effect of the membrane potential on the electron transfer equilibrium between 6 and heme bH found in earlier experiments. [ABSTRACT FROM AUTHOR]

X-ray absorption spectroscopy was used to measure the damage caused by exposure to x-rays to the Mn4Ca active site in single crystals of photosystem II as a function of dose and energy of x-rays, temperature, and time. These studies reveal that the conditions used for structure determination by x-ray crystallography cause serious damage specifically to the metal-site structure. The x-ray absorption spectra show that the structure changes from one that is characteristic of a high-valent Mn4(III2,IV2) oxo-bridged Mn4Ca cluster to that of Mn(II) in aqueous solution. This damage to the metal site occurs at a dose that is more than one order of magnitude lower than the dose that results in loss of diffractivity and is commonly considered safe for protein crystallography. These results establish quantitative x-ray dose parameters that are applicable to redox-active metalloproteins. This case study shows that a careful evaluation of the structural intactness of the active site(s) by spectroscopic techniques can validate structures derived from crystallography and that it can be a valuable complementary method before structure–function correlations of metalloproteins can be made on the basis of high-resolution x-ray crystal structures. [ABSTRACT FROM AUTHOR]

The synthetic cubane-type iron-sulfur clusters [Fe₄S₄(SR)₄]z form a four-member electron transfer series (z = 3-, 2-, 1-, and 0), all members of which except that with z = 0 have been isolated and characterized They serve as accurate analogues of protein-bound [Fe₄S₄(SR)₄]z redox centers, which, in terms of core oxidation states, exhibit the redox couples [Fe₄S₄]3+/2+ and [Fe₄S₄]2+/1+ . Clusters with the all-ferrous core [Fe₄S₄]0 have never been isolated because of their oxidative sensitivity. Recent work on the Fe protein of Azotobacter vinelandii nitrogenase has demonstrated the formation of the all-ferrous state upon reaction with a strong reductant. Treatment of the cyanide cluster [Fe₄S₄(CN)₄]3- with K[Ph₁CO] in acetonitrile/tetrahydrofuran affords the all-ferrous cluster [Fe₄S₄(CN)₄]4- , isolated as the Bu₄N+ salt. The x-ray structure demonstrates retention of a cubane-type structure with idealized D2d symmetry The Mössbauer spectrum unambiguously demonstrates the [Fe₄S₄]0 oxidation state. Bond distances, core volumes, 57Fe isomer shifts, and visible absorption spectra make evident the high degree of structural and electronic similarity with the fully reduced Fe protein. The attribute of cyanide ligation causes positive [Fe₄S₄]2+/1+ and [Fe₄S₄]1+/0 redox potential shifts, facilitating the initial isolation of an analogue of the [Fe₄S₄]0 protein site. [ABSTRACT FROM AUTHOR]

Sco1 and Cox17 are accessory proteins required for the correct assembly of eukaryotic cytochrome c oxidase. At variance with Sco1, Cox17 orthologs are found only in eukaryotes. We browsed bacterial genomes to search proteins functionally equivalent to Cox17, and we identified a class of proteins of unknown function displaying a conserved gene neighborhood to bacterial Scol genes, all sharing a potential metal binding motif H(M)X10MX21HXM. Two members of this group, DR1885 from Deinococcus rad!odurans and CC3502 from Caulobacter crescentus, were expressed, and their interaction with copper was investigated. The solution structure and extended x-ray absorption fine structure data on the former protein reveal that the protein binds copper(I) through a histidine and three Mets in a cupredoxin-like fold. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria. On the basis of our results, a possible pathway for copper delivery to the CuA center in bacteria is proposed. [ABSTRACT FROM AUTHOR]

Broad-spectrum analysis of DNA and KNA samples is of increasing importance in the growing field of biotechnology. We show that nanopore measurements may be used to assess the purity, phos phorylation state, and chemical integrity of nucleic acid preparations. In contrast with gel electrophoresis and mass spectrometry, an unprecedented dynamic range of DNA sizes and concentrations can be evaluated in a single data acquisition process that spans minutes. Because the molecule information is quantized and digitally recorded with single-molecule resolution, the sensitivity of the system can be adjusted in real time to detect trace amounts of a particular DNA species. [ABSTRACT FROM AUTHOR]

We demonstrate vibrational climbing in the CO stretch of carboxyhemoglobin pumped by midinfrared chirped ultrashort pulses. By use of spectrally resolved pump-probe measurements, we directly observed the induced absorption lines caused by excited vibrational populations up to v = 6. In some cases, we also observed stimulated emission, providing direct evidence of vibrational population inversion. This study provides important spectroscopic parameters on the CO stretch in the strong-field regime, such as transition frequencies and dephasing times up to the v = 6 to v = 7 vibrational transition. We measured equally spaced vibrational transitions, in agreement with the energy levels of a Morse potential up to v = 6. It is interesting that the integral of the differential absorption spectra was observed to deviate far from zero, in contrast to what one would expect from a simple one-dimensional Morse model assuming a linear dependence of dipole moment with bond length. [ABSTRACT FROM AUTHOR]

In vitro selection was used to investigate whether nucleic acid enzymes are capable of catalyzing photochemical reactions. The reaction chosen was photoreactivation of thymine cyclobutane dimers in DNA by using serotonin as cofactor and light of wave- lengths longer than the absorption spectrum of DNA. Curiously, the dominant single-stranded DNA sequence selected, UV1A, was found to repair its internal thymine dimer substrate efficiently even in the absence of serotonin or any other cofactor. UV1C, a 42-nucleotide fragment of UV1A, repaired the thymine dimer substrate in trans (K[subcat]/K[subuncat] = 2.5 × 10[sup4]), showing optimal activity with 305 nm light and thus resembling naturally occurring photolyase enzymes. Mechanistic investigation of UV1C indicated that its catalytic role likely exceeded the mere positioning of the substrate in a conformation favorable for photoreactivation. A higher-order structure, likely a quadruplex, formed by specific guanine bases within the deoxyribozyme, was implicated as serving as a light-harvesting antenna, with photoreactivation of the thymine dimer proceeding possibly via electron donation from an excited guanine base. In a primordial "RNA world," self-replicating nucleic acid populations may have been vulnerable to deactivation via UV light-mediated pyrimidine dimer formation. Photolyase nucleic acid enzymes such as the one described here could thus have played a role in preserving the integrity of such an RNA world. [ABSTRACT FROM AUTHOR]

Investigates the anomalous scattering properties of uranium at M absorption edges. Measurement of the fluorescence absorption spectrum from a UF[sub 4]-coated mylar film; Use of multiwavelength anomalous diffraction (MAD) for the evaluation of macromolecular crystallography; Determination of MAD structure.

The article focuses on the research which demonstrates how the 2D electronic-vibrational (2DEV) spectroscopy correlates electronic transition frequencies in photo-excitation event with infrared transitions detected by probe. It states that the 2D spectroscopy correlates absorption spectrum and enable line-broadening time scales to be distinguished by different line shapes. It mentions that the 2D line carry information about correlations between evolution of electronic and nuclear states.