Publications by authors named "Yuta Hori"
Enantioenrichment of amino acids is essential during the early chemical evolution leading to the origin of life. However, the detailed molecular mechanisms remain unsolved. Dimerization of enantiomers is the first molecular process in the nucleation of deposition and crystallization, which are both essential for enantioenrichment.
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- - Sampling reference data is essential for building accurate machine learning potentials (MLPs) in molecular dynamics simulations, as poor data coverage can lead to unphysical results.
- - This study introduces a radial distribution function (RDF)-based sampling method that captures unusual molecular structures during MLP-MD simulations by analyzing the shapes of RDFs, enhancing the reference data for better accuracy.
- - By applying this method to a water molecule cluster, researchers found that the resulting MLP-MD simulations displayed realistic behavior, comparable to advanced ab initio simulations, proving the RDF-based sampling's effectiveness in bridging molecular clusters to bulk systems.
Hydrogen-bonded organic frameworks (HOFs) are porous organic materials constructed hydrogen bonds. HOFs have solubility in specific high-polar organic solvents. Therefore, HOFs can be returned to their components and can be reconstructed, which indicates their high recyclability.
View Article and Find Full Text PDFWe propose using cocrystals as effective polarization matrices for triplet dynamic nuclear polarization (DNP) at room temperature. The polarization source can be uniformly doped into cocrystals formed through acid-acid, amide-amide, and acid-amide synthons. The dense-packing crystal structures, facilitated by multiple hydrogen bonding and π-π interactions, result in extended relaxation times, enabling efficient polarization diffusion within the crystals.
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- This study explores how reversible proton shifting (IPS) occurs alongside spin transitions (ST) in a new iron (Fe) complex connected to a carboxylic acid through hydrogen bonds.
- Researchers confirmed this dynamic behavior using advanced techniques like X-ray diffraction, neutron crystallography, and infrared spectroscopy.
- The findings provide insights into fundamental chemical processes and could help in designing new materials with adjustable properties for applications in optoelectronics and information storage.
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- This study explores the properties of mechanochromic luminescent supramolecular fibers made from amphiphilic molecules, specifically a dumbbell-shaped compound based on 9,10-bis(phenylethynyl)anthracene.
- The fibers can become water-soluble through grinding, which transforms them into micelles where excimer formation leads to a significant change in fluorescence.
- The research reveals that fibers with and without tetraethylene glycol (TEG) substituents behave differently in water and have potential applications as mechanosensors for detecting mesoscale forces.
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- A new learning model combines machine learning and reaction network techniques to predict products and reaction pathways in organic chemistry.
- It was trained on 50 fundamental organic reactions and achieved a 68.6% top-5 accuracy when predicting outcomes for 35 test reactions.
- The model also identified key intermediate structures and established basic reaction rules, such as the Markovnikov rule, to enhance understanding of organic reactions.
[NiFe]-hydrogenase from Miyazaki F is an O-sensitive enzyme that is inactivated in the presence of O but the oxidized enzyme can recover its catalytic activity by reacting with H under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å.
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- The study highlights the significance of multiple proton transfer (PT) in chemistry and material science, particularly its control through external stimuli like temperature and light.
- Researchers created a new iron(II) complex with a tridentate ligand that enables PT-coupled spin transitions, allowing for the manipulation of proton positions.
- Findings indicate that using short hydrogen bonds in molecular design is a potential strategy for achieving controlled multiple PT in crystalline materials.
Article Synopsis
- HPPD (4-hydroxyphenylpyruvate dioxygenase) is a key herbicide target, with its sensitivity to the herbicide mesotrione influenced by the dynamic behavior of its C-terminal α-helix (H11).
- The study used molecular dynamics simulations to analyze the conformational changes in H11, revealing that HPPD prefers different forms of H11 depending on whether it is bound to mesotrione or not.
- Additionally, the research identified important amino acid residues that affect H11's flexibility, indicating that inhibitor sensitivity is linked to these conformational changes and how they impact protein interactions.
Understanding the catalytic mechanism of highly active two-dimensional electrocatalysts is crucial to their rational design. Herein, we reveal the element dependence of the reactivity of two-dimensional metal dichalcogenide sheets for electrocatalytic CO reduction. We found that tin(IV) disulfide (SnS) and molybdenum(IV) disulfide (MoS) sheets exhibited Faradaic efficiencies of 63.
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- * The study focuses on dimeric molecular interactions of alanine (Ala) and Iva in solution as a preliminary step in crystal nucleation, using a precise first-principles approach.
- * The findings reveal that the dimeric interaction of Iva shows a stronger chirality dependence compared to Ala, offering insights into the enantioselectivity of amino acids in solution.
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- Aldehydes and carboxylic acids are effective catalysts for racemizing amino acids, but the exact mechanisms are not fully understood.
- The study focuses on aspartic acid racemization, utilizing salicylaldehyde and acetic acid, employing computational methods to analyze the reaction pathways.
- Findings reveal that the dehydration step presents the highest energy barrier in the process, while the presence of water significantly lowers the energy required for this step, facilitating racemization.
Article Synopsis
- - The study explores the use of single-crystal neutron diffraction (SCND) to investigate proton-transfer processes in crystalline compounds, highlighting its growing importance in understanding unique protonation states.
- - Researchers developed an iron(II) complex to study proton tautomerism, which involves different protonation states before and after proton transfer, a phenomenon not previously observed with SCND.
- - Using various analytical techniques, including X-ray crystallography, infrared spectroscopy, and density functional theory, they confirmed the successful observation of proton tautomerism via variable-temperature SCND measurements for the first time.
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- Researchers synthesized guinoidal molecules using diyrrolyldiketone complexes with pyrrole units connected by a partially conjugated system, which acted as a singlet spin coupler.
- The introduction of a benzo unit stabilized a closed-shell tautomer conformation, allowing the molecules to show near-infrared absorption, particularly in deprotonated forms.
- The study highlighted cation-dependent diradical properties and demonstrated that the singlet diradical is more stable than the triplet diradical through VT NMR, ESR, and theoretical analyses.
Article Synopsis
- - The high-potential iron-sulfur protein (HiPIP) plays a key role in photosynthesis by transporting electrons, featuring a [4Fe-4S] cluster at its active site.
- - Research focused on the geometrical and electronic structures of this cluster in reduced HiPIP using density functional theory (DFT) to understand how environmental factors influence its function.
- - Findings revealed that the unique properties of the [4Fe-4S] cluster were stabilized by surrounding amino acids, which impacted its stability and the formation of certain bonds between iron atoms based on their distances.
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- The text discusses how ultraviolet circularly polarized light (UV-CPL) could preferentially create or destroy a specific enantiomer, possibly explaining the origin of homochirality in extraterrestrial environments.
- It focuses on the photoabsorption properties of propylene oxide (-CHO) in the Lyman-α region and shows that -CHO can be formed from certain chemical reactions involving carbon and oxygen.
- The study's calculations indicate that both -CHO and its intermediate can absorb UV-CPL, suggesting that their breakdown upon light exposure could lead to a chiral symmetry break, further supporting the idea of UV-CPL as a driving force in chiral molecule formation.
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- Enantiomeric excesses of l-amino acids found in meteorites spark debate about their molecular mechanisms and prebiotic origins.
- Researchers examined the stability of alanine and its chiral precursors using the minimum energy principle, suggesting more stable isomers are more abundant in the interstellar medium.
- A new isomer search algorithm revealed that 2-aminopropanenitrile is the most stable isomer, indicating its key role in forming common enantiomeric excesses in α-amino acids.
Article Synopsis
- - The study investigates the proton conduction mechanisms in anhydrous organic crystalline materials with imidazolium hydrogen succinate (Im-Suc), which are promising for solid electrolytes in fuel cells due to their high proton conductivity above 100 °C.
- - Quantum chemical calculations were employed to analyze changes in hydrogen bonding and molecular rotation, helping to characterize the local structures essential for effective proton conduction.
- - Findings indicate that proton transfer between imidazole and succinic acid is a key rate-limiting step in proton transport, revealing that proton conduction operates through a combination of proton transfer and molecular motion in a Grotthuss-type mechanism.
A proton-electron coupling system, exhibiting unique bistability or multistability of the protonated state, is an attractive target for developing new switchable materials based on proton dynamics. Herein, we present an iron(II) hydrazone crystalline compound, which displays the stepwise transition and bistability of proton transfer at the crystal level. These phenomena are realized through the coupling with spin transition.
View Article and Find Full Text PDFMonitoring method for transgene expression in target tissue by blood sampling.
Biotechnol Rep (Amst)
December 2019
Article Synopsis
- A new method was created to track transgene expression in tissues by sampling blood, using plasmid DNA (pDNA) with firefly luciferase as a reporter gene and a secretable luciferase as a monitor gene in mice.* -
- The study found strong correlations between the levels of the reporter and monitor genes in the treated muscle and their levels in the plasma, regardless of the method used to administer the pDNA.* -
- This technique was named 'Therapeutic transgene monitoring (TTM)', drawing parallels to the established concept of 'Therapeutic drug monitoring (TDM)'.*
Article Synopsis
- Formic acid (HCOOH) is an effective material for hydrogen storage due to its high hydrogen capacity by weight and volume.
- While dehydrogenation (producing hydrogen and carbon) is thermodynamically favorable, dehydration (leading to water and carbon monoxide) is the dominant decomposition pathway for HCOOH.
- The study utilizes graph theory to analyze chemical reaction networks and identifies the oxidation number of carbon and betweenness centrality as key factors affecting dehydrogenation, highlighting the challenges that favor the dehydration pathway.
Formation of an active oxygen species at the dicopper site of pMMO is studied by using density functional theory (DFT) calculations. The role of the amino acid residues of tyrosine (Tyr374) and glutamate (Glu35) located in the second coordination sphere of the dicopper site is discussed in detail. The phenolic proton of the tyrosine residue is transferred to the CuO core in a two-step manner via the glutamate residue, and an electron is directly transferred to the CuO core.
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- The research introduces a new type of compound that couples proton and electron transfer, aiming to create novel functionalities in materials.
- The study presents the first example of a proton-transfer-coupled spin-transition (PCST) behavior in an Fe(II) complex, where proton transfer occurs between pyridine and hydrazone ligands under light irradiation.
- This proton transfer happens extremely quickly (in just 50 picoseconds) at low temperatures, and the trapped states can be switched using light, suggesting potential applications in advanced molecular devices.
While hydrogenase and photosystem II enzymes are known to oxidize H and HO, respectively, a recently reported iridium aqua complex [Ir(η-CMe){bpy(COOH)}(HO)] is able to oxidize both of the molecules and generate energies as in the fuel and solar cells ( Ogo ChemCatChem 2017 , 9 , 4024 - 4028 ). To understand the mechanism behind such an interesting bifunctional catalyst, in the present study, we perform density functional theory (DFT) calculations on the dual catalytic cycle of H and HO oxidations by the iridium aqua complex. In the H oxidation, we found that the H-H bond is easily cleaved in a heterolytic fashion, and the resultant iridium hydride complex is significantly stabilized by the presence of HO molecules, due to dihydrogen bond.
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