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Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease
Abstract RNA ligases of the RTCB-type play an essential role in tRNA splicing, the unfolded protein response and RNA repair. RTCB is the catalytic subunit of the pentameric human tRNA ligase complex. RNA ligation by the tRNA ligase complex requires GTP-dependent activation of RTCB. This active site guanylylation reaction relies on the activation factor Archease. The mechanistic interplay between both proteins has remained unknown. Here, we report a biochemical and structural analysis of the human RTCB-Archease complex in the pre- and post-activation state. Archease reaches into the active site of RTCB and promotes the formation of a covalent RTCB-GMP intermediate through coordination of GTP and metal ions. During the activation reaction, Archease prevents futile RNA substrate binding to RTCB. Moreover, monomer structures of Archease and RTCB reveal additional states within the RNA ligation mechanism. Taken together, we present structural snapshots along the reaction cycle of the human tRNA ligase.
Assembled peptoid crystalline nanomaterials as carbonic anhydrase mimics for promoted hydration and sequestration of CO 2
Carbonic anhydrase (CA) mimics have received significant attention due to their promising applications in the enhanced hydration and sequestration of CO 2 . Herein, we report the assembly of sequence-defined peptoids into crystalline nanomaterials with controlled microenvironment of active sites as CA mimics for promoted hydration and sequestration of CO 2 . By incorporating specific ligands into self-assembling peptoids and coordinating these ligands with metal cations, we synthesize a variety of crystalline nanosheets and nanotubes as efficient CA mimics comparable to natural bovine CA. Molecular dynamics simulations reveal the critical roles of peptoid-Zn 2+ binding energy and the active site local microenvironment on the catalytic performance of these CA mimics. CO 2 precipitation results show that these CA mimics promote the hydration and sequestration of CO 2 while retaining high thermal and chemical stabilities. This study offers essential guidance for the future design of high-performance CA-mimics suitable for applications in CO 2 capture and sequestration.
Selective sorption of oxygen and nitrous oxide by an electron donor-incorporated flexible coordination network
Incorporating strong electron donor functionality into flexible coordination networks is intriguing for sorption applications due to a built-in mechanism for electron-withdrawing guests. Here we report a 2D flexible porous coordination network, [Ni 2 (4,4'-bipyridine)(VTTF) 2 ]n(1) (where H 2 VTTF = 2,2;-[1,2-bis(4-benzoic acid)-1,2ethanediylidene]bis-1,3-benzodithiole), which exhibits large structural deformation from the as-synthesized or open phase (1α) into the closed phase (1β) after guest removal, as demonstrated by X-ray and electron diffraction. Interestingly, upon exposure to electron-withdrawing species, 1β reversibly undergoes guest accommodation transitions; 1α$\supset$O 2 (90 K) and 1α$\supset$N 2 O (185 K). Moreover, the 1β phase showed exclusive O 2 sorption over other gases (N 2 , Ar, and CO) at 120 K. The phase transformations between the 1α and 1β phases under these gases were carefully investigated by in-situ X-ray diffraction, in-situ spectroscopic studies, and DFT calculations, validating that the unusual sorption was attributed to the combination of flexible frameworks and VTTF (electron-donor) that induces strong interactions with electron-withdrawing species.
Heterometal incorporation in NH2-MIL-125(Ti) and its participation in the photoinduced charge-separated excited state
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Evaluating solvothermal and mechanochemical routes towards the metal–organic framework Mg 2 ( m -dobdc)
Metal–organic frameworks bearing coordinatively unsaturated Mg(II) sites are promising materials for gas storage, chemical separations, and drug delivery due to their low molecular weights and lack of toxicity. Furthermore, there remains a limited number of such MOFs reported in the literature. Herein, we investigate the gas sorption properties of the understudied framework Mg 2 (m-dobdc) (dobdc 4– = 4,6-dioxido-1,3-benzenedicarboxylate) synthesized under both solvothermal and mechanochemical conditions. Both materials are found to be permanently porous, as confirmed by 77 K N 2 adsorption measurements. In particular, Mg 2 (m-dobdc) synthesized under mechanochemical conditions using exogenous organic base displays one of the highest capacities reported to date (6.14 mmol g –1 ) for CO 2 capture in a porous solid under simulated coal flue gas conditions (150 mbar, 40 °C). As such, mechanochemically synthesized Mg 2 (m-dobdc) represents a promising new framework for applications requiring high gas adsorption capacities in a porous solid.
Structural chemistry of penta- and hexanitrato thorium($\tiny{IV}$) complexes isolated using N–H donors
In this study, a series of fifteen tetravalent thorium phases were prepared. The compounds were isolated from acidic aqueous nitrate solutions using protonated nitrogen heterocycles of varying hydrogen-bond donation strength. Structural analysis via single crystal X-ray diffraction showed that the structures are built from pentanitrato, [Th(NO 3 ) 5 (H 2 O) 2 ] 1- , and hexanitrato, [Th(NO 3 ) 6 ] 2- , molecular units, with the latter being far more prevalent in the solid state. The vibrational properties of the compounds were examined using Raman and IR spectroscopy; the spectra are dominated by stretches characteristic of nitrate and the organic ions. The relative energetics of nitrate complexation was examined using electronic structure theory. These results confirmed that there are clear thermodynamic sinks for the penta- and hexanitrato structural units that were observed experimentally. Additionally, electrostatic surface potentials (ESPs) were calculated in an effort to better understand the counterion stabilization of the complexes. The ESP surfaces showed that the position of the water and nitrate molecules and the coordination geometry of the metal complex had a clear effect on the polarizability of the two structural motifs. Despite limited speciation of the Th–nitrate structural units, the compounds exhibit rich supramolecular chemistry resulting from hydrogen bonding of the Th complexes with the organic N–H donors and π–π stacking interactions from the protonated N-heterocycles.
Aberration-corrected STEM imaging of 2D materials: Artifacts and practical applications of threefold astigmatism
High-resolution scanning transmission electron microscopy (HR-STEM) with spherical aberration correction enables researchers to peer into two-dimensional (2D) materials and correlate the material properties with those of single atoms. The maximum intensity of corrected electron beam is confined in the area having sub-angstrom size. Meanwhile, the residual threefold astigmatism of the electron probe implies a triangular shape distribution of the intensity, whereas its tails overlap and thus interact with several atomic species simultaneously. The result is the resonant modulation of contrast that interferes the determination of phase transition of 2D materials. Here, we theoretically reveal and experimentally determine the origin of resonant modulation of contrast and its unintended impact on violating the power-law dependence of contrast on coordination modes between transition metal and chalcogenide atoms. The finding illuminates the correlation between atomic contrast, spatially inequivalent chalcogenide orientation, and residual threefold astigmatism on determining the atomic structure of emerging 2D materials.
Understanding Proton Movement in [Fe-Fe] Hydrogenases
Nature uses specialized metalloenzymes to carry out small molecule activation reactions, including CO 2 fixation, O 2 activation, and proton reduction, with unparalleled efficiency, rates, and selectivity. The latter reactions are performed by hydrogenases, protein metallo-complexes that interconverts H 2 to protons and electrons (H 2 oxidation) and the reverse reaction (H 2 production) with incredibly low energy input and amazingly fast kinetics. Reproducing both the activity and efficiency of metalloenzymes in sustainable anthropogenic systems remains one of the “holy grails” of inorganic chemistry. However, identifying the precise molecular components responsible for these desirable properties has been challenging in the natural metalloenzymes, hindering efforts to develop analogous processes in synthetic compounds. Considering the inherent complexity of a metalloenzyme and the many interactions, both strong and weak, that contribute to the function of an enzyme, we have elected to model natural metalloenzymes on a biochemical platform. Towards this end, we have a developed structural, functional, and mechanistic mimic of the [Ni-Fe] hydrogenases within a robust protein scaffold, rubredoxin, to understand the influence of the secondary coordination environment on the metal center. This involved preparing a series of three rubredoxin constructs containing a single point mutation at Val positions and making the NMR chemical shift assignments for the paramagnetic (nickel-substituted) and non-paramagnetic (zinc-substituted) form. These physical studies were complemented with in silico molecular dynamic studies on proteins with [Fe-S] clusters to engineer new proton channels to test in vitro . To assist our search for new natural metalloprotein scaffolds within the vast number of sequenced genomes, we created a neural network-based program to identify proteins with specific metal-binding sites. These computational and physical studies with metalloenzymes provide direct insight into the fundamental chemical principles driving the natural systems and offer design principles for developing catalysts that utilize analogous principles.
Programmable Catalyst Structures via Adsorbate-Induced Adatom Assembly
The electronic structure and geometric configuration of oxide-supported metal ions are important coordination properties that can be related to catalytic activity and stability. Herein, we interrogate the coordination environment of mononuclear Pd ions supported on ceria using CO adsorption, infrared vibrational spectroscopy, and DFT modeling. We observed the 15 h continuous co-evolution of a palladium- (2167 cm -1 ) and cerium-carbonyl (2177 cm -1 ) complex by monitoring the $\nu$(CO) infrared region. The slow CO adsorption kinetics were caused by the reactive ligand exchange between an oxygen atom of the support and the CO adsorbate to yield an oxygen vacancy and adsorbed CO 2 . We hypothesize that the co-evolved cerium-carbonyl complex was formed upon CO adsorption at or adjacent to this oxygen vacancy. Our hypothesis was experimentally supported by a dramatic attenuation of the cerium carbonyl signal upon pre-adsorption of water through an apparent competitive adsorption mechanism. The attenuation was also accompanied by a 6 cm -1 redshift of the palladium carbonyl band (2161 cm -1 ) attributed to hydrogen bonding between the carbonyl and a nearby hydroxyl. Characteristic n(CO) stretch frequencies catalogued through CO adsorption onto single crystal ceria by Wöll et al.1 led us to index the cerium carbonyl to the {100} nanofacet of the polycrystalline ceria support. It follows from the observed co-evolution of the two carbonyl complexes that Pd was also adsorbed at the {100} nanofacet. Redeployment of a previously developed DFT model by Ivanova-Shor et al.2 featuring square-planar coordination of Pd2+ at the {100} nanofacet (O 4 Pd) of a Ce 21 O 42 nanoparticle model qualitatively reproduced several experimental observations.
Homocoupling Reactions of Azoles and Their Applications in Coordination Chemistry
Pyrazole, a member of the structural class of azoles, exhibits molecular properties of interest in pharmaceuticals and materials chemistry, owing to the two adjacent nitrogen atoms in the five-membered ring system. The weakly basic nitrogen atoms of deprotonated pyrazoles have been applied in coordination chemistry, particularly to access coordination polymers and metal-organic frameworks, and homocoupling reactions can in principle provide facile access to bipyrazole ligands. In this context, we summarize recent advances in homocoupling reactions of pyrazoles and other types of azoles (imidazoles, triazoles and tetrazoles) to highlight the utility of homocoupling reactions in synthesizing symmetric bi-heteroaryl systems compared with traditional synthesis. Metal-free reactions and transition-metal catalyzed homocoupling reactions are discussed with reaction mechanisms in detail.
Leveraging Intramolecular π-Stacking to Access an Exceptionally Long-Lived 3 MC Excited State in an Fe(II) Carbene Complex
The ability to manipulate excited-state decay cascades using molecular structure is essential to the application of abundant-metal photosensitizers and chromophores. Ligand design has yielded some spectacular results elongating charge-transfer excited state lifetimes of Fe(II) coordination complexes, but triplet metal-centered ( 3 MC) excited states - recently demonstrated to be critical to the photoactivity of isoelectronic Co(III) polypyridyls - have to date remained elusive, with temporally isolable examples limited to the picosecond regime. Here, with this report, we show how strong-field donors and intramolecular π-stacking can conspire to stabilize a long-lived 3 MC excited state for a remarkable 4.1 ± 0.3 ns in fluid solution at ambient temperature. Analysis of variable-temperature time-resolved absorption data using theoretical models ranging from Arrhenius to semiclassical Marcus theory, combined with computational modeling and X-ray crystallography, reveal a Jahn−Teller stabilized excited state with a high activation barrier for ground-state recovery. The net result is a chromophore with a 3 MC excited-state lifetime that is orders of magnitude longer than anything yet observed for an Fe(II) complex.
A Panoramic View of MXenes via an Atomic Coordination‐Based Design Strategy
Two‐dimensional (2D) transition metal carbides and nitrides, known as MXenes, possess unique physical and chemical properties, enabling diverse applications in fields ranging from energy storage to communication, catalysis, sensing, healthcare, and beyond. Despite extensive research and notable advancements, a fundamental understanding of MXenes’ phase diversity and its connection to their hierarchical precursors, including the intermediate MAX phases and the ancestral bulk phases, remains limited. Here, in this study, it is hypothesized that the atomic coordination environments adopted by transition metal and nonmetallic atoms in their three‐dimensional (3D) bulk precursors may persist in 2D MXenes to govern their phase diversity. Using high‐throughput modeling based on first‐principles density functional theory, a wide range of MXene phases is unveiled and comprehensively evaluate their relative stabilities across a large chemical space. The key to the approach lies in considering various atomic coordination environments drawn from four types of ancestral bulk phases. Through this comprehensive structural library of MXenes, general guiding principles are uncovered, such as a close alignment between the phase stability of MXenes and that of their 3D precursors. These findings introduce a new design strategy in which the atomic coordination environments in bulk phases can serve as reliable predictors for accessing the diverse structural landscape of MXenes.
Metal–Organic Frameworks with Low‐Valent Metal Nodes
Abstract Metal–organic frameworks (MOFs) are crystalline, 2‐ and 3‐dimensional coordination polymers formed by bonding interactions between metals and multitopic organic ligands. These are typically formed using hard Lewis basic organic ligands with high oxidation state metal ions. The use of low‐valent metals as structural elements in MOFs is far less common, despite the widespread use of such metals for catalysis, luminescence, and other applications. This Minireview focuses on recent advances in the field of low‐valent MOFs and offers a perspective on the future development of these materials.
Metal–Organic Frameworks with Low–Valent Metal Nodes
Metal–organic frameworks (MOFs) are crystalline, 2- and 3-dimensional coordination polymers formed by bonding interactions between metals and multitopic organic ligands. These are typically formed using hard Lewis basic organic ligands with high oxidation state metal ions. The use of low-valent metals as structural elements in MOFs is far less common, despite the widespread use of such metals for catalysis, luminescence, and other applications. Furthermore, this Minireview focuses on recent advances in the field of low-valent MOFs and offers a perspective on the future development of these materials.
Presynthetic Redox Gated Metal-to-Insulator Transition and Photothermoelectric Properties in Nickel Tetrathiafulvalene-Tetrathiolate Coordination Polymers
Photothermoelectric (PTE) materials are promising candidates for solar energy harvesting and photodetection applications, especially for near-infrared (NIR) wavelengths. Although the processability and tunability of organic materials are highly advantageous, examples of organic PTE materials are comparatively rare and their PTE performance is typically limited by poor photothermal (PT) conversion. Here, we report the use of redox-active Sn complexes of tetrathiafulvalene-tetrathiolate (TTFtt) as transmetalating agents for the synthesis of presynthetically redox tuned NiTTFtt materials. Unlike the neutral material NiTTFtt, which exhibits n-type glassy-metallic conductivity, the reduced materials Li 1.2 Ni 0.4 [NiTTFtt] and [Li(THF) 1.5 ] 1.2 Ni 0.4 [NiTTFtt] (THF = tetrahydrofuran) display physical characteristics more consistent with p-type semiconductors. The broad spectral absorption and electrically conducting nature of these TTFtt-based materials enable highly efficient NIR-thermal conversion and good PTE performance. Furthermore, in contrast to conventional PTE composites, these NiTTFtt coordination polymers are notable as single-component PTE materials. As a result, the presynthetically tuned metal-to-insulator transition in these NiTTFtt systems directly modulates their PT and PTE properties.
Atomically Dispersed Single Ni Site Catalysts for Nitrogen Reduction toward Electrochemical Ammonia Synthesis Using N 2 and H 2 O
Ammonia (NH 3 ) electrosynthesis gains significant attention as NH 3 is essentially important for fertilizer production and fuel utilization. However, electrochemical nitrogen reduction reaction (NRR) remains a great challenge because of low activity and poor selectivity. Herein, a new class of atomically dispersed Ni site electrocatalyst is reported, which exhibits the optimal NH 3 yield of 115 µg cm -2 h -1 at –0.8 V versus reversible hydrogen electrode (RHE) under neutral conditions. High faradic efficiency of 21 ± 1.9% is achieved at -0.2 V versus RHE under alkaline conditions, although the ammonia yield is lower. The Ni sites are stabilized with nitrogen, which is verified by advanced X-ray absorption spectroscopy and electron microscopy. Density functional theory calculations provide insightful understanding on the possible structure of active sites, relevant reaction pathways, and confirm that the Ni-N 3 sites are responsible for the experimentally observed activity and selectivity. Extensive controls strongly suggest that the atomically dispersed NiN 3 site-rich catalyst provides more intrinsically active sites than those in N-doped carbon, instead of possible environmental contamination. Overall, this work further indicates that single-metal site catalysts with optimal nitrogen coordination is very promising for NRR and indeed improves the scaling relationship of transition metals.
Lewis acid-assisted reduction of nitrite to nitric and nitrous oxides via the elusive nitrite radical dianion
Reduction of nitrite anions (NO 2 - ) to nitric oxide (NO), nitrous oxide (N 2 O) and ultimately dinitrogen (N 2 ) takes place in a variety of environments, including in the soil as part of the biogeochemical nitrogen cycle and in acidified nuclear waste. Nitrite reduction typically takes place within the coordination sphere of a redox-active transition metal. In this report we show that Lewis acid coordination can substantially modify the reduction potential of this polyoxoanion to allow for its reduction under non-aqueous conditions (-0.74 V versus NHE). Detailed characterization confirms the formation of the borane-capped radical nitrite dianion (NO 2 2- ), which features a N(II) oxidation state. Protonation of the nitrite dianion results in the facile loss of nitric oxide (NO), whereas its reaction with NO results in disproportionation to nitrous oxide (N 2 O) and nitrite (NO 2 - ). This system connects three redox levels in the global nitrogen cycle and provides fundamental insights into the conversion of NO 2 - to NO.