Low-temperature Absorption Spectroscopy Research Articles

Second-Coordination-Sphere Effects Reveal Electronic Structure Differences between the Mitochondrial Amidoxime Reducing Component and Sulfite Oxidase.

A combination of X-ray absorption and low-temperature electronic absorption spectroscopies has been used to probe the geometric and electronic structures of the human mitochondrial amidoxime reducing component enzyme (hmARC1) in the oxidized Mo(VI) and reduced Mo(IV) forms. Extended X-ray absorption fine structure analysis revealed that oxidized enzyme possesses a 5-coordinate [MoO2(SCys)(PDT)]- (PDT = pyranopterin dithiolene) active site with a cysteine coordinated to Mo. A 5-coordinate geometry is retained in the reduced state, with the equatorial oxo being protonated. Low-temperature electronic absorption spectroscopy of hmARC1 reveals a spectrum for the oxidized enzyme that is significantly different from what has been reported for sulfite oxidase family enzymes. Time-dependent density functional theory computations on oxidized and reduced hmARC1, and a small molecule analogue for hmARC1ox, have been used to assist us in making detailed band assignments and developing a greater understanding of enzyme electronic structure contributions to reactivity. Our understanding of the hmARCred HOMO and the LUMO of the benzamidoxime substrate reveal a potential π-bonding interaction between these redox orbitals, with two-electron occupation of the substrate LUMO along the reaction coordinate activating the O-N bond for cleavage and promoting oxygen atom transfer to the Mo site.

Theory of 2D electronic spectroscopy of water soluble chlorophyll-binding protein (WSCP): Signatures of Chl b derivate.

We investigate how electronic excitations and subsequent dissipative dynamics in the water soluble chlorophyll-binding protein (WSCP) are connected to features in two-dimensional (2D) electronic spectra, thereby comparing results from our theoretical approach with experimental data from the literature. Our calculations rely on third-order response functions, which we derived from a second-order cumulant expansion of the dissipative dynamics involving the partial ordering prescription, assuming a fast vibrational relaxation in the potential energy surfaces of excitons. Depending on whether the WSCP complex containing a tetrameric arrangement of pigments composed of two dimers with weak excitonic coupling between them binds the chlorophyll variant Chl a or Chl b, the resulting linear absorption and circular dichroism spectra and particularly the 2D spectra exhibit substantial differences in line shapes. These differences between Chl a WSCP and Chl b WSCP cannot be explained by the slightly modified excitonic couplings within the two variants. In the case of Chl a WSCP, the assumption of equivalent dimer subunits facilitates a reproduction of substantial features from the experiment by the calculations. In contrast, for Chl b WSCP, we have to assume that the sample, in addition to Chl b dimers, contains a small but distinct fraction of chemically modified Chl b pigments. The existence of such Chl b derivates has been proposed by Pieper et al. [J. Phys. Chem. B 115, 4042 (2011)] based on low-temperature absorption and hole-burning spectroscopy. Here, we provide independent evidence.

Impurity-induced enhancement of parity-forbidden optical intracenter transitions of shallow donors in silicon

Different defects in silicon crystals cause lattice distortion that may violate selection rules for certain intracenter optical transitions of hydrogen-like donor centers. Perturbations due to large concentration of substitutional donors enhance all parity-forbidden atomic transitions, but cause large concentration broadening of the transition lines, prohibiting observation of transitions at close energies. Substitutional residual carbon atoms in silicon induce, in contrast, a weak-to-moderate broadening of donor absorption lines enabling the resolution of some parity-forbidden intracenter transitions in impurity absorption spectra at moderate donor densities. Binding energies of several series of s- and d-type states were obtained by resolving of intracenter transitions terminating in these states, by low-temperature infrared absorption spectroscopy in carbon-rich and/or heavily doped silicon crystals.

Selective C-H Bond Cleavage with a High-Spin FeIV-Oxido Complex.

Non-heme Fe monooxygenases activate C-H bonds using intermediates with high-spin FeIV-oxido centers. To mimic these sites, a new tripodal ligand [pop]3- was prepared that contains three phosphoryl amido groups that are capable of stabilizing metal centers in high oxidation states. The ligand was used to generate [FeIVpop(O)]-, a new FeIV-oxido complex with an S = 2 spin ground state. Spectroscopic measurements, which included low-temperature absorption and electron paramagnetic resonance spectroscopy, supported the assignment of a high-spin FeIV center. The complex showed reactivity with benzyl alcohol as the external substrate but not with related compounds (e.g., ethyl benzene and benzyl methyl ether), suggesting the possibility that hydrogen bonding interaction(s) between the substrate and [FeIVpop(O)]- was necessary for reactivity. These results exemplify the potential role of the secondary coordination sphere in metal-mediated processes.

Zam Is a Redox-Regulated Member of the RNB-Family Required for Optimal Photosynthesis in Cyanobacteria.

The zam gene mediating resistance to acetazolamide in cyanobacteria was discovered thirty years ago during a drug tolerance screen. We use phylogenetics to show that Zam proteins are distributed across cyanobacteria and that they form their own unique clade of the ribonuclease II/R (RNB) family. Despite being RNB family members, multiple sequence alignments reveal that Zam proteins lack conservation and exhibit extreme degeneracy in the canonical active site—raising questions about their cellular function(s). Several known phenotypes arise from the deletion of zam, including drug resistance, slower growth, and altered pigmentation. Using room-temperature and low-temperature fluorescence and absorption spectroscopy, we show that deletion of zam results in decreased phycocyanin synthesis rates, altered PSI:PSII ratios, and an increase in coupling between the phycobilisome and PSII. Conserved cysteines within Zam are identified and assayed for function using in vitro and in vivo methods. We show that these cysteines are essential for Zam function, with mutation of either residue to serine causing phenotypes identical to the deletion of Zam. Redox regulation of Zam activity based on the reversible oxidation-reduction of a disulfide bond involving these cysteine residues could provide a mechanism to integrate the ‘central dogma’ with photosynthesis in cyanobacteria.

Pigment structure in the light-harvesting protein of the siphonous green alga Codium fragile

The siphonaxanthin-siphonein-chlorophyll-a/b-binding protein (SCP), a trimeric light-harvesting complex isolated from photosystem II of the siphonous green alga Codium fragile, binds the carotenoid siphonaxanthin (Sx) and/or its ester siphonein in place of lutein, in addition to chlorophylls a/b and neoxanthin. SCP exhibits a higher content of chlorophyll b (Chl-b) than its counterpart in green plants, light-harvesting complex II (LHCII), increasing the relative absorption of blue-green light for photosynthesis. Using low temperature absorption and resonance Raman spectroscopies, we reveal the presence of two non-equivalent Sx molecules in SCP, and assign their absorption peaks at 501 and 535 nm. The red-absorbing Sx population exhibits a significant distortion that is reminiscent of lutein 2 in trimeric LHCII. Unexpected enhancement of the Raman modes of Chls-b in SCP allows an unequivocal description of seven to nine non-equivalent Chls-b, and six distinct Chl-a populations in this protein.

The primary donor of far-red photosystem II: ChlD1 or PD2?

Far-red light (FRL) Photosystem II (PSII) isolated from Chroococcidiopsis thermalis is studied using parallel analyses of low-temperature absorption, circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopies in conjunction with fluorescence measurements. This extends earlier studies (Nurnberg et al 2018 Science 360 (2018) 1210–1213). We confirm that the chlorophyll absorbing at 726 nm is the primary electron donor. At 1.8 K efficient photochemistry occurs when exciting at 726 nm and shorter wavelengths; but not at wavelengths longer than 726 nm. The 726 nm absorption peak exhibits a 21 ± 4 cm−1 electrochromic shift due to formation of the semiquinone anion, QA−. Modelling indicates that no other FRL pigment is located among the 6 central reaction center chlorins: PD1, PD2 ChlD1, ChlD2, PheoD1 and PheoD2. Two of these chlorins, ChlD1 and PD2, are located at a distance and orientation relative to QA− so as to account for the observed electrochromic shift. Previously, ChlD1 was taken as the most likely candidate for the primary donor based on spectroscopy, sequence analysis and mechanistic arguments. Here, a more detailed comparison of the spectroscopic data with exciton modelling of the electrochromic pattern indicates that PD2 is at least as likely as ChlD1 to be responsible for the 726 nm absorption. The correspondence in sign and magnitude of the CD observed at 726 nm with that predicted from modelling favors PD2 as the primary donor. The pros and cons of PD2 vs ChlD1 as the location of the FRL-primary donor are discussed.

Electronic Structure of Tetracyanonickelate(II).

Tetracyanonickelate(II) has been a poster child of ligand field theory for several decades. We have revisited the literature assignments of the absorption spectrum of [Ni(CN)4]2- and the calculated ordering of orbitals with metal d character. Using low-temperature single-crystal absorption spectroscopy and accurate ab initio and density functional quantum mechanical methods (NEVPT2-CASSCF, EOM-CCSD, TD-DFT), we find an ordering of the frontier d- and p-orbitals of xy < xz, yz < z2 < z < x2-y2 < x, y and assign the d-d bands in the absorption spectrum to 1A1g → 3B1g < 3Eg < 3A2g < 1B1g < 1Eg < 1A2g. While differing from all previous interpretations, our assignments accord with an MO model in which strong π-backbonding in the plane of the molecule stabilizes dxy more than out-of-plane bonding stabilizes dxz and dyz.

Tuning antenna function through hydrogen bonds to chlorophyll a

We describe a molecular mechanism tuning the functional properties of chlorophyll a (Chl-a) molecules in photosynthetic antenna proteins. Light-harvesting complexes from photosystem II in higher plants – specifically LHCII purified with α- or β-dodecyl-maltoside, along with CP29 – were probed by low-temperature absorption and resonance Raman spectroscopies. We show that hydrogen bonding to the conjugated keto carbonyl group of protein-bound Chl-a tunes the energy of its Soret and Qy absorption transitions, inducing red-shifts that are proportional to the strength of the hydrogen bond involved. Chls-a with non-H-bonded keto C131 groups exhibit the blue-most absorption bands, while both transitions are progressively red-shifted with increasing hydrogen-bonding strength – by up 382 & 605 cm−1 in the Qy and Soret band, respectively. These hydrogen bonds thus tune the site energy of Chl-a in light-harvesting proteins, determining (at least in part) the cascade of energy transfer events in these complexes.

Crystal growth, low-temperature spectroscopy and multi-watt laser operation of Yb:Ca3NbGa3Si2O14

We report on the crystal growth, structure, room- and low-temperature (6K) absorption and emission spectroscopy of a 3at% Yb3+-doped trigonal ordered langasite-type silicate crystal, Ca3NbGa3Si2O14 (Yb: CNGS). The Rietveld refinement data are presented. Absorption, stimulated-emission and gain cross-sections are determined for the Yb3+ ion in CNGS for π and σ polarizations. The maximum stimulated emission cross-section amounts to σSE = 0.97 × 10−20cm−2 at 1014nm (σ-polarization). The Stark splitting of the Yb3+ multiplets is resolved. Microchip laser operation is obtained with both a-cut and c-cut 3at% Yb: CNGS samples under end-pumping at 976nm by a Volume Bragg Grating-stabilized diode laser. For the latter cut, the maximum output power reaches 7.61W at 1048–1060nm with a slope efficiency of 59%. By varying the output coupling, multi-watt emission over a 50nm-broad spectral range is achieved.

The deep red state of photosystem II in Cyanidioschyzon merolae

We identified and characterised the deep red state (DRS), an optically-absorbing charge transfer state of PSII, which lies at lower energy than P680, in the red algae Cyanidioschyzon merolae by means of low temperature absorption and magnetic circular dichroism spectroscopies. The photoactive DRS has been previously studied in PSII of the higher plant Spinacia oleracea, and in the cyanobacterium Thermosynechococcus vulcanus. We found the DRS in PSII of C. merolae has similar spectral properties. Treatment of PSII with dithionite leads to reduction of cytochrome (cyt) b559 and the PsbV-based cyt c550 as well as the disassembly of the oxygen-evolving complex. Whereas the overall visible absorption spectrum of PSII was little affected, the DRS absorption in the reduced sample was no longer seen. This bleaching of the DRS is discussed in terms of a corresponding lack of a DRS feature in D1D2/cyt b559 reaction centre preparations of PSII.

Spectroscopic identification of active sites for the oxygen evolution reaction on iron-cobalt oxides

The emergence of disordered metal oxides as electrocatalysts for the oxygen evolution reaction and reports of amorphization of crystalline materials during electrocatalysis reveal a need for robust structural models for this class of materials. Here we apply a combination of low-temperature X-ray absorption spectroscopy and time-resolved in situ X-ray absorption spectroelectrochemistry to analyze the structure and electrochemical properties of a series of disordered iron-cobalt oxides. We identify a composition-dependent distribution of di-μ-oxo bridged cobalt–cobalt, di-μ-oxo bridged cobalt–iron and corner-sharing cobalt structural motifs in the composition series. Comparison of the structural model with (spectro)electrochemical data reveals relationships across the composition series that enable unprecedented assignment of voltammetric redox processes to specific structural motifs. We confirm that oxygen evolution occurs at two distinct reaction sites, di-μ-oxo bridged cobalt–cobalt and di-μ-oxo bridged iron–cobalt sites, and identify direct and indirect modes-of-action for iron ions in the mixed-metal compositions.

Frederick Yi-Tung Cho (1939–2011)

We present here a Tribute to Frederick Yi-Tung Cho (1939-2011), an innovative and ingenious biophysicist and an entrepreneur. He was one of the 4 earliest PhD students [see: Cederstrand (1965)-Carl Nelson Cederstrand; coadvisor: Eugene Rabinowitch; Papageorgiou (1968)-George C. Papageorgiou (coauthor of this paper); and Munday (1968)-John C. Munday Jr. (also a coauthor of this paper)] of one of us (Govindjee) in Biophysics at the University of Illinois at Urbana-Champaign (UIUC) during the late 1960s (1963-1968). Fred was best known, in the photosynthesis circle for his pioneering work on low temperature (down to liquid helium temperature, 4K) absorption and fluorescence spectroscopy of photosynthetic systems; he showed temperature independence of excitation energy transfer from (i) chlorophyll (Chl) b to Chl a and (ii) from Chl a 670 to Chl a 678; and temperature dependence of energy transfer from the phycobilins to Chl a and from Chl a 678 to its suggested trap. After doing research in biophysics of photosynthesis, Fred shifted to do research in solid-state physics/engineering in the Government Electronics Division (Group) of the Motorola Company, Scottsdale, Arizona, from where he published research papers in that area and had several patents granted. We focus mainly on his days at the UIUC in context of the laboratory in which he worked. We also list some of his papers and most of his patents in engineering physics. His friends and colleagues have correctly described him as an innovator and an ingenious scientist of the highest order. On the personal side, he was a very easy-going and amiable individual.

Characterization and Subsequent Reactivity of an Fe-Peroxo Porphyrin Generated by Electrochemical Reductive Activation of O2.

Reductive activation of O2 is achieved by using the [FeIII(F20TPP)Cl] (F20TPP = 5,10,15,20-tetrakis(pentafluorophenyl) porphyrinate) porphyrin through electrochemical reduction of the [FeIII(F20TPP)(O2•-)] superoxo complex. Formation of the [FeIII(F20TPP)(OO)]- peroxo species is monitored by using low-temperature electronic absorption spectroscopy, electron paramagnetic resonance, and cyclic voltammetry. Its subsequent protonation to yield the [FeIII(F20TPP)(OOH)] hydroperoxo intermediate is probed using low-temperature electronic absorption spectroscopy and electron paramagnetic resonance.

Electrically active light-element complexes in silicon crystals grown by cast method

Electrically active light-element complexes called thermal donors and shallow thermal donors in silicon crystals grown by the cast method were studied by low-temperature far-infrared absorption spectroscopy. The relationship between these complexes and either crystal defects or light-element impurities was investigated by comparing different types of silicon crystals, that is, conventional cast-grown multicrystalline Si, seed-cast monolike-Si, and Czochralski-grown Si. The dependence of thermal and the shallow thermal donors on the light-element impurity concentration and their annealing behaviors were examined to compare the crystals. It was found that crystal defects such as dislocations and grain boundaries did not affect the formation of thermal or shallow thermal donors. The formation of these complexes was dominantly affected by the concentration of light-element impurities, O and C, independent of the existence of crystal defects.

Spectroscopic and Computational Studies of Nitrile Hydratase: Insights into Geometric and Electronic Structure and the Mechanism of Amide Synthesis.

Nitrile hydratases (NHases) are mononuclear nonheme enzymes that catalyze the hydration of nitriles to amides. NHase is unusual in that it utilizes a low-spin (LS) FeIII center and a unique ligand set comprised of two deprotonated backbone amides, cysteine-based sulfenic acid (RSO(H)) and sulfinic acid (RSO2-), and an unmodified cysteine trans to an exogenous ligand site. Electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD) and low-temperature absorption (LT-Abs) spectroscopies are used to determine the geometric and electronic structures of butyrate-bound (NHaseBA) and active (NHaseAq) NHase. These data calibrate DFT models, which are then extended to explore the mechanism of nitrile hydration by NHase. In particular, the nitrile is activated by coordination to the LS FeIII and the sulfenate group is found to be deprotonated and a significantly better nucleophile than water that can attack the coordinated nitrile to form a cyclic species. Attack at the sulfenate S atom of the cyclic species is favorable and leads to a lower kinetic barrier than attack by water on coordinated, uncyclized nitrile, while attack at the C of the cyclic species is unfavorable. The roles of the unique ligand set and low-spin nature of the NHase active site in function are also explored. It is found that the oxidized thiolate ligands are crucial to maintaining the LS state, which is important in the binding and activation of nitrile susbtrates. The dominant role of the backbone amidate ligands appears to be as a chelate in keeping the sulfenate properly oriented for nucleophilic attack on the coordinated substrate.

Lattice distortion and its role in the magnetic behavior of the Mn-doped ZnO system

Puzzling magnetic data on the Zn1−xMnxO system such as a small magnetization values or a large negative values of the Curie–Weiss temperature have been obtained in many experimental investigations. Here we report element-specific structural and magnetic investigations on a high-quality Zn0.95Mn0.05O nanocrystalline sample. Combining low-temperature x-ray absorption spectroscopy and theoretical simulations, we show that the formation of substitutional spin-antiparallel pairs induces a large local distortion involving a contraction of the Mn–Mn distance and a reduced Mn–O–Mn bond angle. The first-principles calculation considering hole-doping reveals that such a distortion can result in a localized hole around a dopant atom, generating a ferrimagnetic ordering with a magnetization of 0.45 μB/Mn. This result may give a new insight for a better understanding of the reported magnetic data.

Spectroscopic Study of the CP43′ Complex and the PSI–CP43′ Supercomplex of the Cyanobacterium Synechocystis PCC 6803

The PSI-CP43' supercomplex of the cyanobacterium Synechocystis PCC 6803, grown under iron-starvation conditions, consists of a trimeric core Photosystem I (PSI) complex and an outer ring of 18 CP43' light-harvesting complexes. We have investigated the electronic structure and excitation energy transfer (EET) pathways within the CP43' (also known as the isiA gene product) ring using low-temperature absorption, fluorescence, fluorescence excitation, and hole-burning (HB) spectroscopies. Analysis of the absorption spectra of PSI, CP43', and PSI-CP43' complexes suggests that there are 13 chlorophylls (Chls) per CP43' monomer, i.e., a number that was observed in the CP43 complex of Photosystem II (PSII) (Umena, Y. et al. Nature 2011, 473, 55-60). This is in contrast with the recent modeling studies of Zhang et al. (Biochim. Biophys. Acta 2010, 1797, 457-465), which suggested that IsiA likely contains 15 Chls. Modeling studies of various optical spectra of the CP43' ring using the uncorrelated EET model (Zazubovich, V.; Jankowiak, R. J. Lumin. 2007, 127, 245-250) suggest that CP43' monomers (in analogy to the CP43 complexes of the PSII core) also possess two quasi-degenerate low-energy states, A' and B'. The site distribution functions of states A' and B' maxima/full width at half-maximum (fwhm) are at 684 nm/180 cm(-1) and 683 nm/80 cm(-1), respectively. Our analysis shows that pigments mostly contributing to the lowest-energy A' and B' states must be located on the side of the CP43' complex facing the PSI core, a finding that contradicts the model of Zhang et al. but is in agreement with the model suggested by Nield et al. (Biochemistry2003, 42, 3180-3188). We demonstrate that the A'-A' and B'-B' EET between different monomers is possible, though with a slower rate than intramonomer A'-B' and/or B'-A' energy transfer.

Optical spectroscopy of Yb3+ centers in BaMgF4 ferroelectric crystal

We report on the optical characterization of Yb3+ doped BaMgF4 nonlinear fluoride crystal grown by the Czochralski technique. Low temperature absorption spectroscopy reveals that Yb3+ incorporates into the matrix at four well differentiated centers. High resolution site selective experiments have been performed to determine the energy level schemes associated with the major Yb3+ centers detected in the system. The fluorescence decay times recorded at 10 K under selective excitation are analyzed for each Yb3+ center. The spectroscopic behavior of the codoped Yb3+:Na+:BaMgF4 system has been also investigated. Codoping with Na+ eliminates two Yb3+ centers present in the singly doped Yb3+:BaMgF4 crystal. The charge compensation mechanisms and site location for Yb3+ in the fluoride matrix are discussed.

Using spectroscopic tools to probe porphyrin deformation and porphyrin-protein interactions

The reactivity and functionality of heme proteins are to a significant extent determined by the conformation of their functional heme groups and by the interaction of axial ligands with their protein environment. This review focuses on experimental methods and theoretical concepts for elucidating symmetry lowering perturbations of the heme induced by the protein environment of the heme pocket. First, we discuss a variety of methods which can be used to probe the electric field at the heme, including spectral hole burning as well as low temperature absorption and room temperature circular dichroism spectroscopy. Second, we show how heme deformations can be described as superposition of deformations along normal coordinates, thereby using the irreducible representations of the D4h point group as a classification tool. Finally, resonance Raman spectroscopy is introduced as a tool to probe the deformations of metalloprophyrins in solution and in protein matrices by measuring and comparing intensities and depolarization properties rather than wavenumber positions.