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At least 1,477 records · Page 82

Understanding flavin electronic structure and spectra

Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy

59 BASIC BIOLOGICAL SCIENCES↗

Dry Printing Pure Copper with High Conductivity and Adhesion for Flexible Electronics

Additive manufacturing of functional devices on various rigid and flexible substrates is rising rapidly due to their design flexibility, rapid manufacturing, and lower cost. Current printing technologies are ink-based and focused on printing silver (Ag) as conductive lines due to its matured ink formulation process, low sintering temperature, ease of printing, and low oxidation rate. However, Ag is the 68th most abundant element on Earth, while copper (Cu) is the 25th, making it much cheaper (>100×) while having a comparable conductivity to Ag. Therefore, printing Cu has become technologically and economically more attractive than Ag. Nevertheless, Cu printing is still a significant challenge in ink-based printing methods due to the higher sintering temperature relative to the glass-transition temperature of most flexible substrates, the higher oxidation rate, the challenging ink formulation process, and ink stability concerns. Here, we demonstrate printing highly conductive Cu on flexible polyimide substrates using a dry printing technique. Cu nanoparticles (~3–30 nm) are generated by on-demand laser ablation of a solid Cu target inside the printer head and under argon background gas. These Cu nanoparticles are then transported through a nozzle and onto the substrate, where they are laser-sintered in real time. The argon gas plays three critical roles in laser plume condensation for nanoparticle generation, transport, and sheath gas to avoid oxidation during sintering. The sintered nanoparticles thus show high electrical conductivity and mechanical stability under static and cyclic tests. Our dry printing technique can potentially revolutionize how electronic devices and sensors are additively manufactured for earth and space applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomically dispersed zeolite-supported rhodium complex: Selective and stable catalyst for acetylene semi-hydrogenation

In this study, supported rhodium catalysts are known to be unselective for semi-hydrogenation reactions. Here, by tuning the electronic structure of supported mononuclear rhodium sites determined by the metal nuclearity and the electron-donor properties of the support, we report that atomically dispersed HY zeolite-supported rhodium with reactive acetylene ligands affords a stable ethylene selectivity > 90 % for acetylene semi-hydrogenation at 373 K and atmospheric pressure, even when ethylene is present in a large excess over acetylene. Infrared and X-ray absorption spectra and measurements of rates of the catalytic reaction complemented with calculations at the level of density functional theory show how the catalyst performance depends on the electronic structure of the rhodium, influenced by the support as a ligand that is a weak electron donor.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electron transfer in a crystalline cytochrome with four hemes

Diffusion of electrons over distances on the order of 100 μm has been observed in crystals of a small tetraheme cytochrome (STC) from Shewanella oneidensis [J. Huang et al . J. Am. Chem. Soc. 142, 10459–10467 (2020)]. Electron transfer between hemes in adjacent subunits of the crystal is slower and more strongly dependent on temperature than had been expected based on semiclassical electron-transfer theory. Here, in this work, we explore explanations for these findings by molecular-dynamics simulations of crystalline and monomeric STC. New procedures are developed for including time-dependent quantum mechanical energy differences in the gap between the energies of the reactant and product states and for evaluating fluctuations of the electronic-interaction matrix element that couples the two hemes. Rate constants for electron transfer are calculated from the time- and temperature-dependent energy gaps, coupling factors, and Franck–Condon-weighted densities of states using an expression with no freely adjustable parameters. Back reactions are considered, as are the effects of various protonation states of the carboxyl groups on the heme side chains. Interactions with water are found to dominate the fluctuations of the energy gap between the reactant and product states. The calculated rate constant for electron transfer from heme IV to heme Ib in a neighboring subunit at 300 K agrees well with the measured value. However, the calculated activation energy of the reaction in the crystal is considerably smaller than observed. We suggest two possible explanations for this discrepancy. The calculated rate constant for transfer from heme I to II within the same subunit of the crystal is about one-third that for monomeric STC in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Highly Distorted Chiral Two-Dimensional Tin Iodide Perovskites for Spin Polarized Charge Transport

Incorporating chiral organic molecules into organic/inorganic hybrid 2D-layered metal-halide perovskites results in a novel family of chiral hybrid semiconductors with unique spin-dependent properties. The embedded chiral organic moieties induce a chiroptical response from the inorganic metal-halide sublattice. However, the structural interplay between the chiral organic molecules and the inorganic sublattice, as well as their synergic effect on the resulting electronic band structure need to be explored in a broader material scope. Here we present three new layered tin iodide perovskites templated by chiral ( R/S -)methylbenzylammonium ( R/S -MBA), i.e. ( R-/S -MBA) 2 SnI 4 , and their racemic phase ( rac -MBA) 2 SnI 4 . These MBA 2 SnI 4 compounds exhibit the largest level of octahedral bond distortion compared to any other reported layered tin iodide perovskite. The incorporation of chiral MBA cations leads to circularly polarized absorption from the inorganic Sn–I sublattice, displaying chiroptical activity in the 300–500 nm wavelength range. The bandgap and chiroptical activity are modulated by alloying Sn with Pb, in the series of (MBA) 2 Pb 1-x Sn x I 4 . Finally, we show that vertical charge transport through oriented ( R-/S -MBA) 2 SnI 4 thin films is highly spin-dependent, arising from a chiral-induced spin selectivity (CISS) effect. We demonstrate a spin-polarization in the current-voltage characteristics as high as 94%. Our work shows the tremendous potential of these chiral hybrid semiconductors for controlling both spin and charge degrees of freedom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Super-Resolution Airy Disk Microscopy of Individual Color Centers in Diamond

Super-resolution imaging techniques enable nanoscale microscopy in fields such as physics, biology, and chemistry. However, many super-resolution techniques require specialized optical components, such as a helical-phase mask. In this work, we present a novel technique, super-resolution Airy disk microscopy, that can be used in a standard confocal microscope without any specialized optics. We demonstrate this technique, in combination with ground state depletion, to image and control nitrogen-vacancy (NV) centers in bulk diamond below the diffraction limit. A greater than 14-fold improvement in resolution compared to the diffraction limit is achieved, corresponding to a spatial resolution of 16.9(8) nm for a 1.3 NA microscope with 589 nm light. We make use of our enhanced spatial resolution to control the spins states of individual NV centers separated from each other by less than the diffraction limit, including pairs sharing the same orientation that are indistinguishable with a conventional electron spin resonance measurement.

36 MATERIALS SCIENCE↗

Prediction of correlation energies using variational subspace valence bond

In the variational subspace valence bond (VSVB) [G. D. Fletcher, J. Chem. Phys. 142, 134112 (2015)] method, the electronic orbitals comprising the wave function correspond to chemically meaningful objects, such as bonds, lone pairs, atomic cores, and so on. Selected regions of a molecule (for example, a single chemical bond, as opposed to all the bonds) can be modeled with different levels of basis set and possible methods for modeling correlation from the other regions. The interactions between the components of a molecule (say, a bond and a neighboring orbital) can then be studied in detail for their impact on a chemical phenomenon while avoiding the expense of necessarily applying the higher levels and methods to the entire molecule. Here, this work presents the theoretical basis for modeling correlation effects between specific electron pairs by incorporating terms in the inter-electronic coordinates (“r 12 ”) into VSVB. The approach is validated with calculations on small systems using single-reference wave functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deciphering Photochemical Reaction Pathways of Aqueous Tetrachloroauric Acid by X-ray Transient Absorption Spectroscopy

Photolysis reaction pathways of [Au(III)Cl 4 ] - in aqueous solution have been investigated by time-resolved X-ray absorption spectroscopy. Ultraviolet excitation directly breaks the Au-Cl bond in [Au(III)Cl 4 ] - to form [Au(II)Cl 3 ] - that becomes highly reactive within 79 ps. Disproportionation of [Au(II)Cl 3 ] - generates [Au(I)Cl 2 ] - , which is stable for ≤ 10 mu s. In contrast, intense near-infrared lasers photolyze water to generate hydrated electrons, which then reduce [Au(III)Cl 4 ] - to [Au(II)Cl 3 ] - at 5 ns. Hydrated electrons further induce a chain reaction from [Au(II)Cl 3 ] - to [Au(0)Cl] - by successively removing one Cl - . The zero-valency Au anions quickly polymerize and condense to form Au nanoparticles, which become the dominating product after 400 s. Here our results reveal that the condensation of zero-valency Au starts with dimerization of gold clusters coordinated with chloride ions rather than direct condensation of pristine Au atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Influence of cellular redox reactions on the structure and function of light harvesting and photosystems

Photosynthesis enables the conversion of one of the most abundant and free forms of energy, sunlight, into chemical bonds through the utilization of highly tailored protein complexes. These enzymes work in unison to absorb, convert, and transform light into high-energy electrons which are used for various functions important to metabolism and cellular protection. Over the last ∼50 years, photosynthetic organisms, such as cyanobacteria, have been adapted and engineered to produce valuable compounds like hydrogen and ethylene, among others. Often this is performed by removing native and/or adding in exogenous energy utilization pathways so that light energy is re-directed towards the synthesis of desired compounds. However, the interplay between primary light capture, conversion reactions, and the downstream electron utilization sinks is not fully understood. Further complicating these strategies are the plethora of compensatory mechanisms that facilitate steady electron flow and the maintenance of photosynthesis under dynamic conditions. This manifests as structural and functional plasticity of the photosynthetic machinery, often seen in modulations of oligomeric compositions or changes in protein-protein interactions and coupling with redox enzymes. Understanding these mechanisms is crucial to biotechnology applications because re-engineering electron utilization sinks has profoundly different effects on the light capture and conversion reactions of photosynthesis. Optimization requires a molecular-level understanding of the functional interrelationships between electron sinks and photosynthetic components that influence photosynthetic efficiencies to realize potential improvements in product yields. Here, we aim to highlight how perturbation of reductive reactions is revealing the functional plasticity in key components of the photosynthetic energy transduction pathway.

59 BASIC BIOLOGICAL SCIENCES↗

Complex Organics from Laboratory Simulated Interstellar Ices

Many of the volatiles in interstellar dense clouds exist in ices surrounding dust grains. The low temperatures of these ices (T < 50 K) preclude most chemical reactions, but photolysis can drive reactions that produce a suite of new species, many of which are complex organics. We study the UV and proton radiation processing of interstellar ice analogs to explore links between interstellar chemistry, the organics in comets and meteorites, and the origin of life on Earth. The high D/H ratios in some interstellar species, and the knowledge that many of the organics in primitive meteorites are D-enriched, suggest that such links are plausible. Once identified, these species may serve as markers of interstellar heritage of cometary dust and meteorites. Of particular interest are our findings that UV photolysis of interstellar ice analogs produce molecules of importance in current living organisms, including quinones, amphiphiles, and amino acids. Quinones are essential in vital metabolic roles such as electron transport. Studies show that quinones should be made wherever polycyclic aromatic hydrocarbons are photolyzed in interstellar ices. In the case of anthracene-containing ices, we have observed the production of 9-anthrone and 9,10 anthraquinone, both of which have been observed in the Murchison meteorite. Amphiphiles are also made when mixed molecular ices are photolyzed. These amphiphiles self-assemble into fluorescent vesicles when placed in liquid water, as do Murchison extracts. Both have the ability to trap an ionic dye. Photolysis of plausible ices can also produce alanine, serine, and glycine as well as a number of small alcohols and amines. Flash heating of the room temperature residue generated by such experiments generates mass spectral distributions similar to those of IDPs. The detection of high D/H ratios in some interstellar molecular species, and the knowledge that many of the organics, such as hydroxy and amino acids, in primitive meteorites are D-enriched provides evidence for a connection between intact organic material in the interstellar medium and in meteorites. Thus, some of the oxidized aromatics, amphiphiles, amino acids, hydroxy acids, and other compounds found in meteorites may have had an interstellar ancestry and not solely a product of parent body aqueous alteration. Such compounds should also be targeted for searches of organics in cometary dust.

Dworkin, J. P.↗

Structure Activity Relationships for Second‐Coordination Sphere Functional Group Dependent CO 2 Reduction by Manganese Bipyridyl Electrocatalysts

Abstract A series of twelve second coordination sphere (SCS) functionalized manganese tricarbonyl bipyridyl complexes are investigated for their electrocatalytic CO 2 reduction properties in acetonitrile. A qualitative and quantitative assessment of the SCS functional groups is discussed with respect to the catalysts’ thermodynamic and kinetic efficiencies, and their product selectivities. In probing a broad scope of functional groups, it is clear that only the aprotic ortho‐arylester SCS is capable of promoting the highly desired low‐overpotential proton‐transfer electron‐transfer (PT‐ET) pathway for selective CO production. The ortho‐phenolic analogues cause an increase in overpotential with a product selectivity favoring H 2 evolution, consistent with a high‐overpotential pathway via the anionic [Mn−H] − intermediate. Alternative aprotic Lewis base functional groups such as trifluoromethyl, morpholine and acetamide are shown to also be capable of intermediate manganese hydride generation. The tertiary amine substituent, 2‐morpholinophenyl, exhibits a desirable product distribution characteristic of syn‐gas (CO : H 2 =30 : 48) with an impressive turnover frequency, while the secondary amine group, 2‐acetamidophenyl, induces a notable shift in selectivity with a faradaic yield of 55 % for the formate (HCO 2 − ) product. In addition to their catalytic properties, cyclic voltammetry and infrared spectroelectrochemistry (IR‐SEC) studies are presented to probe pre‐catalyst electronic properties and the two‐electron reduction activation pathway.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photoelectron Spectroscopic and ab Initio Computational Studies of the Anion, HThO –

The synergetic combination of anion photoelectron spectroscopy and high-level relativistic coupled-cluster calculations was employed to study the anion, HThO-. The atomic connectivity of this anion was found to be HThO- and not ThOH-. Vibrational and electronic energy spacings in the HThO- photoelectron spectrum were measured and calculated, with good agreement between them being found. Computations yielded electronic energies and equilibrium structures as well as enabling orbital analyses. The adiabatic electron affinity of HThO was determined to be 1.297 ± 0.035 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Introducing the embedded random phase approximation: H 2 dissociative adsorption on Cu(111) as an exemplar

The random phase approximation (RPA) as a means of treating electron correlation recently has been shown to outperform standard density functional theory (DFT) approximations in a variety of cases. However, the computational cost of the RPA is substantially more than DFT, especially when aiming to study extended surfaces. Properly accounting for sufficient surface ensemble size, Brillouin zone sampling, and vacuum separation of periodic images in standard periodic-planewave-based DFT code raises the cost to achieve converged results. Here, we show that sub-system embedding schemes enable use of the RPA for modeling heterogeneous reactions at reduced computational cost. Further, we explore two different embedded RPA (emb-RPA) approaches, periodic emb-RPA and cluster emb-RPA. We use the (experimentally and theoretically) well-studied H 2 dissociative adsorption on Cu(111) as our exemplar, and first perform full periodic RPA calculations as a benchmark. The full RPA results match well the semi-empirical barrier fit to experimental observables and others derived from high-level computations, e.g., from recent embedded n-electron valence second order perturbation theory [Zhao et al., J. Chem. Theory Comput. 16(11), 7078–7088 (2020)] and quantum Monte Carlo [Doblhoff-Dier et al., J. Chem. Theory Comput. 13(7), 3208–3219 (2017)] simulations. Among the two emb-RPA approaches tested, the cluster emb-RPA accurately reproduces the energy profile (maximum error of 50 meV along the reaction pathway) while reducing the computational cost by approximately two orders of magnitude. We therefore expect that the embedded cluster approach will enable wider RPA implementation in heterogeneous catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metabolic Redox Coupling Controls Methane Production in Permafrost‐Affected Peatlands Through Organic Matter Quality‐Dependent Energy Allocation

ABSTRACT Permafrost thaw represents one of Earth's largest climate feedback risks, potentially releasing vast carbon (C) stores as greenhouse gases (GHG). However, our ability to predict emissions remains limited by poor understanding of how changing organic matter (OM) composition affects microbial carbon processing. We test a metabolism‐centered redox framework, which views microbial processes as coupled oxidative‐reductive reactions, to mechanistically explain how organic matter metabolite quality controls greenhouse gas production in permafrost‐affected peatland ecosystems. Rather than relying solely on geochemical redox measurements, our approach examines how microbes balance electron flow through metabolic pathways. Using active layer peat (9–19 cm) from contrasting environments (bog and fen), we employed multi‐omics approaches, including metabolomics, metagenomics, and metatranscriptomics, to link OM chemistry to microbial function. Our results reveal distinct dissolved organic matter metabolite composition, with fen systems enriched in compounds with higher substrate quality (low molecular weight (MW) sugars with high H:C ratios and low aromaticity) and bog systems dominated by compounds with lower substrate quality (high MW phenols with lower H:C ratios and higher aromaticity). In fen samples, these sugar‐like compounds correlated with higher oxidative metabolism and methanogenesis, supported by increased glycolysis gene expression. Initially, electrons from increased oxidative metabolism were balanced through nitrate and sulfate reduction, but as these electron acceptors were depleted, methanogenesis increased to maintain redox balance. Fen samples showed rapid degradation of both high‐ and low‐substrate‐quality compounds, suggesting sufficient energy for efficient C cycling. Conversely, bog samples exhibited more polyphenolic compounds, lower glycolysis activity, and higher stress‐related gene expression, suggesting energy was diverted towards cell maintenance under acidic conditions rather than C processing. This approach suggests that predicting greenhouse gas emissions requires an understanding of how organic matter quality shapes microbial energy allocation strategies, providing a mechanistic framework for improving emission predictions from permafrost‐affected peatlands and similar ecosystems.

Biodiversity & Conservation↗