Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'.

Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.

Reactive high-spin iron(IV)-oxo sites through dioxygen activation in a metal-organic framework.

In nature, nonheme iron enzymes use dioxygen to generate high-spin iron(IV)=O species for a variety of oxygenation reactions. Although synthetic chemists have long sought to mimic this reactivity, the enzyme-like activation of O2 to form high-spin iron(IV) = O species remains an unrealized goal. Here, we report a metal-organic framework featuring iron(II) sites with a local structure similar to that in α-ketoglutarate-dependent dioxygenases. The framework reacts with O2 at low temperatures to form high-spin iron(IV) = O species that are characterized using in situ diffuse reflectance infrared Fourier transform, in situ and variable-field Mössbauer, Fe Kß x-ray emission, and nuclear resonance vibrational spectroscopies. In the presence of O2, the framework is competent for catalytic oxygenation of cyclohexane and the stoichiometric conversion of ethane to ethanol.

Stabilization of a Heme-HNO Model Complex Using a Bulky Bis-Picket Fence Porphyrin and Reactivity Studies with NO.

Nitroxyl, HNO/NO-, the one-electron reduced form of NO, is suggested to take part in distinct signaling pathways in mammals and is also a key intermediate in various heme-catalyzed NOx interconversions in the nitrogen cycle. Cytochrome P450nor (Cyt P450nor) is a heme-containing enzyme that performs NO reduction to N2O in fungal denitrification. The reactive intermediate in this enzyme, termed "Intermediate I", is proposed to be an Fe-NHO/Fe-NHOH type species, but it is difficult to study its electronic structure and exact protonation state due to its instability. Here, we utilize a bulky bis-picket fence porphyrin to obtain the first stable heme-HNO model complex, [Fe(3,5-Me-BAFP)(MI)(NHO)], as a model for Intermediate I, and more generally HNO adducts of heme proteins. Due to the steric hindrance of the bis-picket fence porphyrin, [Fe(3,5-Me-BAFP)(MI)(NHO)] is stable (τ1/2 = 56 min at -30 °C), can be isolated as a solid, and is available for thorough spectroscopic characterization. In particular, we were able to solve a conundrum in the literature and provide the first full vibrational characterization of a heme-HNO complex using IR and nuclear resonance vibrational spectroscopy (NRVS). Reactivity studies of [Fe(3,5-Me-BAFP)(MI)(NHO)] with NO gas show a 91 ± 10% yield for N2O formation, demonstrating that heme-HNO complexes are catalytically competent intermediates for NO reduction to N2O in Cyt P450nor. The implications of these results for the mechanism of Cyt P450nor are further discussed.

A novel integrated time-resolved array avalanche photodiode detection system for nuclear resonant scattering measurements.

The nuclear resonant scattering (NRS) experiment requires photon-counting detectors with high time resolution, short dead time, large dynamic range, low noise, and large detection area. An 8-channel avalanche photodiode (APD) array detector system with high integrity, flexibility, and reliability has been developed to adapt to the demands of NRS experiments. The detector system mainly consists of four key parts: (i) an array-APD sensor, (ii) 8-channel integrated fast preamplifiers, (iii) the time-to-digital converter readout electronics, and (iv) a data acquisition system and EPICS support software. Remarkably, the system exhibits a time resolution of better than 500 ps and has a sufficiently low noise level, allowing for the lowest detection energy threshold of 4 keV. The performance of the new array-APD system as well as its real application in nuclear forward scattering (NFS) and nuclear resonant inelastic x-ray scattering (NRIXS) experiments was tested in two synchrotron facilities. With the new system, the NFS signal very close to the prompt electronic scattering signal can be extracted. Thanks to the customized EPICS-areaDetector-based control software, NRIXS spectra can be readily measured with time and energy information of the NRIXS signal stored in the raw data, which is promising for developing NRIXS data analysis in the time domain. The array-APD detector can be deployed for nuclear resonant scattering experiments at various synchrotron radiation facilities.

CSSQ: a ChIP-seq signal quantifier pipeline.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has revolutionized the studies of epigenomes and the massive increase in ChIP-seq datasets calls for robust and user-friendly computational tools for quantitative ChIP-seq. Quantitative ChIP-seq comparisons have been challenging due to noisiness and variations inherent to ChIP-seq and epigenomes. By employing innovative statistical approaches specially catered to ChIP-seq data distribution and sophisticated simulations along with extensive benchmarking studies, we developed and validated CSSQ as a nimble statistical analysis pipeline capable of differential binding analysis across ChIP-seq datasets with high confidence and sensitivity and low false discovery rate with any defined regions. CSSQ models ChIP-seq data as a finite mixture of Gaussians faithfully that reflects ChIP-seq data distribution. By a combination of Anscombe transformation, k-means clustering, estimated maximum normalization, CSSQ minimizes noise and bias from experimental variations. Further, CSSQ utilizes a non-parametric approach and incorporates comparisons under the null hypothesis by unaudited column permutation to perform robust statistical tests to account for fewer replicates of ChIP-seq datasets. In sum, we present CSSQ as a powerful statistical computational pipeline tailored for ChIP-seq data quantitation and a timely addition to the tool kits of differential binding analysis to decipher epigenomes.

Spin polarization assisted facile C-H activation by an S = 1 iron(iv)-bisimido complex: a comprehensive spectroscopic and theoretical investigation.

High valent iron terminal imido species (Fe[double bond, length as m-dash]NR) have been shown to be key reactive intermediates in C-H functionalization. However, the detailed structure-reactivity relationship in Fe[double bond, length as m-dash]NR species derived from studies of structurally well-characterized high-valent Fe[double bond, length as m-dash]NR complexes are still scarce, and the impact of imido N-substituents (electron-donating vs. electron-withdrawing) on their electronic structures and reactivities has not been thoroughly explored. In this study, we report spectroscopic and computational studies on a rare S = 1 iron(iv)-bisimido complex featuring trifluoromethyl groups on the imido N-substituents, [(IPr)Fe(NC(CF3)2Ph)2] (2), and two closely related S = 0 congeners bearing alkyl and aryl substituents, [(IPr)Fe(NC(CMe3)2Ph)2] (3) and [(IPr)Fe(NDipp)2] (1), respectively. Compared with 1 and 3, 2 exhibits a decreased Fe[double bond, length as m-dash]NR bond covalency due to the electron-withdrawing and the steric effect of the N-substituents, which further leads to a pseudo doubly degenerate ground electronic structure and spin polarization induced ß spin density on the imido nitrogens. This unique electronic structure, which differs from those of the well-studied Fe(iv)-oxido complexes and many previously reported Fe(iv)-imido complexes, provides both kinetic and thermodynamic advantages for facile C-H activation, compared to the S = 0 counterparts.

Europium-151 and iron-57 nuclear resonant vibrational spectroscopy of naturally abundant KEu(III)Fe(II)(CN)6 and Eu(III)Fe(III)(CN)6 complexes.

We have performed and analyzed the first combined 151Eu and 57Fe nuclear resonant vibrational spectroscopy (NRVS) for naturally abundant KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] complexes. Comparison of the observed 151Eu vs.57Fe NRVS spectroscopic features confirms that Eu(III) in both KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] occupies a position outside the [Fe(CN)6] core and coordinates to the N atoms of the CN- ions, whereas Fe(III) or Fe(II) occupies the site inside the [Fe(CN)6]4- core and coordinates to the C atoms of the CN- ions. In addition to the spectroscopic interest, the results from this study provide invaluable insights for the design and evaluation of the nanoparticles of such complexes as potential cellular contrast agents for their use in magnetic resonance imaging. The combined 151Eu and 57Fe NRVS measurements are also among the first few explorations of bi-isotopic NRVS experiments.

rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles.

The ribosomal core is universally conserved across the tree of life. However, eukaryotic ribosomes contain diverse rRNA expansion segments (ESs) on their surfaces. Sites of ES insertions are predicted from sites of insertion of micro-ESs in archaea. Expansion segment 7 (ES7) is one of the most diverse regions of the ribosome, emanating from a short stem loop and ranging to over 750 nucleotides in mammals. We present secondary and full-atom 3D structures of ES7 from species spanning eukaryotic diversity. Our results are based on experimental 3D structures, the accretion model of ribosomal evolution, phylogenetic relationships, multiple sequence alignments, RNA folding algorithms and 3D modeling by RNAComposer. ES7 contains a distinct motif, the 'ES7 Signature Fold', which is generally invariant in 2D topology and 3D structure in all eukaryotic ribosomes. We establish a model in which ES7 developed over evolution through a series of elementary and recursive growth events. The data are sufficient to support an atomic-level accretion path for rRNA growth. The non-monophyletic distribution of some ES7 features across the phylogeny suggests acquisition via convergent processes. And finally, illustrating the power of our approach, we constructed the 2D and 3D structure of the entire LSU rRNA of Mus musculus.

What Is the Right Level of Activation of a High-Spin {FeNO}7 Complex to Enable Direct N-N Coupling? Mechanistic Insight into Flavodiiron NO Reductases.

Flavodiiron nitric oxide reductases (FNORs), found in pathogenic bacteria, are capable of reducing nitric oxide (NO) to nitrous oxide (N2O) to detoxify NO released by the human immune system. Previously, we reported the first FNOR model system that mediates direct NO reduction (Dong, H. T.; J. Am. Chem. Soc. 2018, 140, 13429-13440), but no intermediate of the reaction could be characterized. Here, we present a new set of model complexes that, depending on the ligand substitution, can either mediate direct NO reduction or stabilize a highly activated high-spin (hs) {FeNO}7 complex, the first intermediate of the reaction. The precursors, [{FeII(MPA-(RPhO)2)}2] (1, R = H and 2, R = tBu, Me), were prepared first and fully characterized. Complex 1 (without steric protection) directly reduces NO to N2O almost quantitatively, which constitutes only the second example of this reaction in model systems. Contrarily, the reaction of sterically protected 2 with NO forms the stable mononitrosyl complex 3, which shows one of the lowest N-O stretching frequencies (1689 cm-1) observed so far for a mononuclear hs-{FeNO}7 complex. This study confirms that an N-O stretch ≤1700 cm-1 represents the appropriate level of activation of the FeNO unit to enable direct NO reduction. The higher activation level of these hs-{FeNO}7 complexes required for NO reduction compared to those formed in FNORs emphasizes the importance of hydrogen bonding residues in the active sites of FNORs to activate the bound NO ligands for direct N-N coupling and N2O formation. The implications of these results for FNORs are further discussed.

High-throughput nuclear resonance time domain interferometry using annular slits.

Nuclear resonance time domain interferometry (NR-TDI) is used to study the slow dynamics of liquids (that do not require Mössbauer isotopes) at atomic and molecular length scales. Here the TDI method of using a stationary two-line magnetized 57Fe foil as a source and a stationary single-line stainless steel foil analyzer is employed. The new technique of adding an annular slit in front of a single silicon avalanche photodiode detector enables a wide range of momentum transfers (1 to 100 nm-1 by varying the distance between the annular slits and sample) with a high count rate of up to 160 Hz with a Δq resolution of ±1.7 nm-1 at q = 14 nm-1. The sensitivity of this method in determining relaxation times is quantified and discussed. The Kohlrausch-Williams-Watts (KWW) model was used to extract relaxation times for glycerol. These relaxation times give insight into the dynamics of the electron density fluctuations of glycerol as a function of temperature and momentum transfers.

Distortion of the [FeNO]2 Core in Flavodiiron Nitric Oxide Reductase Models Inhibits N-N Bond Formation and Promotes Formation of Unusual Dinitrosyl Iron Complexes: Implications for Catalysis and Reactivity.

Flavodiiron nitric oxide reductases (FNORs) carry out the reduction of nitric oxide (NO) to nitrous oxide (N2O), allowing infectious pathogens to mitigate toxic levels of NO generated in the human immune response. We previously reported the model complex [Fe2(BPMP)(OPr)(NO)2](OTf)2 (1, OPr- = propionate) that contains two coplanar NO ligands and that is capable of quantitative NO reduction to N2O [White et al. J. Am. Chem. Soc. 2018, 140, 2562-2574]. Here we investigate, for the first time, how a distortion of the active site affects the ability of the diiron core to mediate N2O formation. For this purpose, we prepared several analogues of 1 that contain two monodentate ligands in place of the bridging carboxylate, [Fe2(BPMP)(X)2(NO)2]3+/1+ (2-X; X = triflate, 1-methylimidazole, or methanol). Structural data of 2-X show that without the bridging carboxylate, the diiron core expands, leading to elongated (O)N-N(O) distances (from 2.80 Å in 1 to 3.00-3.96 Å in 2-X) and distorted (O)N-Fe-Fe-N(O) dihedral angles (from coplanarity (5.9°) in 1 to 52.9-85.1° in 2-X). Whereas 1 produces quantitative amounts of N2O upon one-electron reduction, N2O production is substantially impeded in 2-X, to an initial 5-10% N2O yield. The main products after reduction are unprecedented hs-FeII/{Fe(NO)2}9/10 dinitrosyl iron complexes (DNICs). Even though mononuclear DNICs are stable and do not show N-N coupling (since it is a spin-forbidden process), the hs-FeII/{Fe(NO)2}9/10 DNICs obtained from 2-X show unexpected reactivity and produce up to quantitative N2O yields after 2 h. The implications of these results for the active site structure of FNORs are discussed.

Exploring the Limits of Dative Boratrane Bonding: Iron as a Strong Lewis Base in Low-Valent Non-Heme Iron-Nitrosyl Complexes.

We previously reported the synthesis and preliminary characterization of a unique series of low-spin (ls) {FeNO}8-10 complexes supported by an ambiphilic trisphosphineborane ligand, [Fe(TPB)(NO)]+/0/-. Herein, we use advanced spectroscopic techniques and density functional theory (DFT) calculations to extract detailed information as to how the bonding changes across the redox series. We find that, in spite of the highly reduced nature of these complexes, they feature an NO+ ligand throughout with strong Fe-NO π-backbonding and essentially closed-shell electronic structures of their FeNO units. This is enabled by an Fe-B interaction that is present throughout the series. In particular, the most reduced [Fe(TPB)(NO)]- complex, an example of a ls-{FeNO}10 species, features a true reverse dative Fe → B bond where the Fe center acts as a strong Lewis-base. Hence, this complex is in fact electronically similar to the ls-{FeNO}8 system, with two additional electrons "stored" on site in an Fe-B single bond. The outlier in this series is the ls-{FeNO}9 complex, due to spin polarization (quantified by pulse EPR spectroscopy), which weakens the Fe-NO bond. These data are further contextualized by comparison with a related N2 complex, [Fe(TPB)(N2)]-, which is a key intermediate in Fe(TPB)-catalyzed N2 fixation. Our present study finds that the Fe → B interaction is key for storing the electrons needed to achieve a highly reduced state in these systems, and highlights the pitfalls associated with using geometric parameters to try to evaluate reverse dative interactions, a finding with broader implications to the study of transition metal complexes with boratrane and related ligands.

Operando NRIXS and XAFS Investigation of Segregation Phenomena in Fe-Cu and Fe-Ag Nanoparticle Catalysts during CO2 Electroreduction.

Operando nuclear resonant inelastic X-ray scattering (NRIXS) and X-ray absorption fine-structure spectroscopy (XAFS) measurements were used to gain insight into the structure and surface composition of FeCu and FeAg nanoparticles (NPs) during the electrochemical CO2 reduction (CO2 RR) and to extract correlations with their catalytic activity and selectivity. The formation of a core-shell structure during CO2 RR for FeAg NPs was inferred from the analysis of the operando NRIXS data (phonon density of states, PDOS) and XAFS measurements. Electrochemical analysis of the FeAg NPs revealed a faradaic selectivity of 36 % for CO in 0.1 M KHCO3 at -1.1 V vs. RHE, similar to that of pure Ag NPs. In contrast, a predominant selectivity towards H2 evolution is obtained in the case of the FeCu NPs, analogous to the results obtained for pure Fe NPs, although small Cu NPs have also been shown to favor H2 production.

Effects of Noncovalent Interactions on High-Spin Fe(IV)-Oxido Complexes.

High-valent nonheme FeIV-oxido species are key intermediates in biological oxidation, and their properties are proposed to be influenced by the unique microenvironments present in protein active sites. Microenvironments are regulated by noncovalent interactions, such as hydrogen bonds (H-bonds) and electrostatic interactions; however, there is little quantitative information about how these interactions affect crucial properties of high valent metal-oxido complexes. To address this knowledge gap, we introduced a series of FeIV-oxido complexes that have the same S = 2 spin ground state as those found in nature and then systematically probed the effects of noncovalent interactions on their electronic, structural, and vibrational properties. The key design feature that provides access to these complexes is the new tripodal ligand [poat]3-, which contains phosphinic amido groups. An important structural aspect of [FeIVpoat(O)]- is the inclusion of an auxiliary site capable of binding a Lewis acid (LAII); we used this unique feature to further modulate the electrostatic environment around the Fe-oxido unit. Experimentally, studies confirmed that H-bonds and LAII s can interact directly with the oxido ligand in FeIV-oxido complexes, which weakens the Fe═O bond and has an impact on the electronic structure. We found that relatively large vibrational changes in the Fe-oxido unit correlate with small structural changes that could be difficult to measure, especially within a protein active site. Our work demonstrates the important role of noncovalent interactions on the properties of metal complexes, and that these interactions need to be considered when developing effective oxidants.

The influence of phonon softening on the superconducting critical temperature of Sn nanostructures.

The increase in superconducting transition temperature (TC) of Sn nanostructures in comparison to bulk, was studied. Changes in the phonon density of states (PDOS) of the weakly coupled superconductor Sn were analyzed and correlated with the increase in TC measured by magnetometry. The PDOS of all nanostructured samples shows a slightly increased number of low-energy phonon modes and a strong decrease in the number of high-energy phonon modes in comparison to the bulk Sn PDOS. The phonon densities of states, which were determined previously using nuclear resonant inelastic X-ray scattering, were used to calculate the superconducting transition temperature using the Allen-Dynes-McMillan (ADMM) formalism. Both the calculated as well as the experimentally determined values of TC show an increase compared to the bulk superconducting transition temperature. The good agreement between these values indicates that phonon softening has a major influence on the superconducting transition temperature of Sn nanostructures. The influence of electron confinement effects appears to be minor in these systems.

Exploring the Vibrational Side of Spin-Phonon Coupling in Single-Molecule Magnets via 161 Dy Nuclear Resonance Vibrational Spectroscopy.

Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) using the Mössbauer isotope 161 Dy has been employed for the first time to study the vibrational properties of a single-molecule magnet (SMM) incorporating DyIII , namely [Dy(Cy3 PO)2 (H2 O)5 ]Br3 ⋅2 (Cy3 PO)⋅2 H2 O ⋅2 EtOH. The experimental partial phonon density of states (pDOS), which includes all vibrational modes involving a displacement of the DyIII ion, was reproduced by means of simulations using density functional theory (DFT), enabling the assignment of all intramolecular vibrational modes. This study proves that 161 Dy NRVS is a powerful experimental tool with significant potential to help to clarify the role of phonons in SMMs.

Orbital energy mismatch engenders high-spin ground states in heterobimetallic complexes.

The spin state in heterobimetallic complexes heavily influences both reactivity and magnetism. Exerting control over spin states in main group-based heterobimetallics requires a different approach as the orbital interactions can differ substantially from that of classic coordination complexes. By deliberately engendering an energetic mismatch within the two metals in a bimetallic complex we can mimic the electronic structure of lanthanides. Towards this end, we report a new family of complexes, [Ph,MeTpMSnPh3] where M = Mn (3), Fe (4), Co (5), Ni (6), Zn (7), featuring unsupported bonding between a transition metal and Sn which represent an unusual high spin electronic structure. Analysis of the frontier orbitals reveal the desired orbital mismatch with Sn 5s/5p primarily interacting with 4s/4p M orbitals yielding localized, non-bonding d orbitals. This approach offers a mechanism to design and control spin states in bimetallic complexes.

Ultra-High-Frequency Reprogramming of Individual Long-Term Hematopoietic Stem Cells Yields Low Somatic Variant Induced Pluripotent Stem Cells.

Efficiency of reprogramming of human cells into induced pluripotent stem cells (iPSCs) has remained low. We report that individual adult human CD49f+ long-term hematopoietic stem cells (LT-HSCs) can be reprogrammed into iPSCs at close to 50% efficiency using Sendai virus transduction. This exquisite sensitivity to reprogramming is specific to LT-HSCs, since it progressively decreases in committed progenitors. LT-HSC reprogramming can follow multiple paths and is most efficient when transduction is performed after the cells have exited G0. Sequencing of 75 paired skin fibroblasts/LT-HSC samples collected from nine individuals revealed that LT-HSCs contain a lower load of somatic single-nucleotide variants (SNVs) and indels than skin fibroblasts and accumulate about 12 SNVs/year. Mutation analysis revealed that LT-HSCs and fibroblasts have very different somatic mutation signatures and that somatic mutations in iPSCs generally exist prior to reprogramming. LT-HSCs may become the preferred cell source for the production of clinical-grade iPSCs.

Stable Ferrous Mononitroxyl {FeNO}8 Complex with a Hindered Hydrotris(pyrazolyl)borate Coligand: Structure, Spectroscopic Characterization, and Reactivity Toward NO and O2.

The iron(II)-nitroxyl complex [Fe(NO)(L3)] (1) (with L3- = a hindered hydrotris(pyrazolyl)borate ligand), a high-spin (hs)-{FeNO}8 complex in the Enemark-Feltham notation, is surprisingly stable and is the first of its kind that could be structurally characterized. We further studied this compound using a variety of spectroscopic methods. These results indicate a hs iron(II) center with a bound 3NO- ligand where the spins are antiferromagnetic coupled ( St = 1). Vibrational data show that this complex has a very strong Fe-NO bond. DFT calculations support this result and link it to very strong π-donation from the 3NO- ligand to the iron(II) center. Furthermore, a very unusual equilibrium between the hs-{FeNO}8 complex and a dinitrosyl iron complex (DNIC) of {Fe(NO)2}9 type is observed. The O2 reactivity of the complex is finally reported.

Size-Dependent Lattice Dynamics of Atomically Precise Cadmium Selenide Quantum Dots.

Material properties depend sensitively on the atomic arrangements and atomic bonding, but these are notoriously difficult to measure in nanosized atomic clusters due to the small size of the objects and the challenge of obtaining bulk samples of identical clusters. Here, we have combined the recent ability to make gram quantities of identical semiconductor quantum-dot nanoparticles with the ability to measure lattice dynamics on small sample quantities of hydrogenated materials using high energy resolution inelastic x-ray scattering, to measure the size dependence of the phonon density of states in CdSe quantum dots. The fact that we have atomically precise structural models for these nanoparticles allows the calculation of the phonon density of states using density functional theory, providing both experimental and theoretical confirmations of the important role that the inertia of the surface capping species plays on determining the lattice dynamics.