ChemRxiv最新文献

Binding mechanism of adenylate kinase-specific monobodies 腺苷酸激酶特异性单体的结合机制

ChemRxiv Pub Date : 2024-12-14 DOI: 10.26434/chemrxiv-2024-7591m

Takashi, Matsuo, Ibuki, Nakamura, Hiroshi, Amesaka, Satoshi, Nagao, Shigeru, Negi, Shun-ichi, Tanaka

引用次数: 0

Ligand-induced Changes in the Electrocatalytic Activity of Atomically Precise Au₂₅ Nanoclusters 配体诱导原子级精密金₂₅纳米团簇电催化活性的变化

ChemRxiv Pub Date : 2024-12-14 DOI: 10.26434/chemrxiv-2024-t9f58

Qing, Tang, Lipan, Luo, Xia, Zhou, Yuping, Chen, Fang, Sun, Likai, Wang

{"title":"Ligand-induced Changes in the Electrocatalytic Activity of Atomically Precise Au₂₅ Nanoclusters","authors":"Qing, Tang, Lipan, Luo, Xia, Zhou, Yuping, Chen, Fang, Sun, Likai, Wang","doi":"10.26434/chemrxiv-2024-t9f58","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-t9f58","url":null,"abstract":"Atomically precise gold nanoclusters have shown great promise as model elctrocatalysts in pivotal electrocatalytic processes such as hydrogen evolution reaction (HER) and carbon dioxide reduction reaction (CO2RR). Although the influence of ligands on the electronic properties of these nanoclusters are well acknowledged, the ligand effects on their electrocatalytic performances have been rarely explored. Herein, using [Au25(SR)18]- nanocluster as the prototype model, we demonstrated the importance of ligand hydrophilicity versus hydrophobicity in modulating the interface dynamics and electrocatalytic performance. Our first-principle computations revealed that Au25 protected by hydrophilic -SCH2COOH ligands dictates faster kinetics in stripping the thiolate ligand and exhibits better HER activity due to enhanced proton transfer facilitated by boosted interface hydrogen bonding. Conversely, Au25 protected by hydrophobic -SCH2CH3 ligands demonstrates enhanced CO2RR performance by minimizing water interference to stabilize the key *COOH intermediate and lower the barrier for CO formation. Experimental validation using synthesized [Au25(MPA)18]- (MPA=Mercaptopropionic acid) and [Au25(SC6H13)18]- confirms these findings, where [Au25(MPA)18]- exhibits better activity and stability in HER, while [Au25(SC6H13)18]- achieves higher Faradaic efficiency and current density in CO2RR. The mechanistic insights in this study provide valuable guidance for the rational design of surface microenvironment in efficient nanocatalysts for sustainable energy applications.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Photochemistry of Ni(II) tolyl chlorides supported by bidentate ligand frameworks 双叉配体框架支持的镍(II)甲苯基氯化物的光化学作用

ChemRxiv Pub Date : 2024-12-14 DOI: 10.26434/chemrxiv-2024-d6sj9

Liviu, Mirica, Luke, Westawker, Bailey, Bouley, Josh, Vura-Weis

{"title":"Photochemistry of Ni(II) tolyl chlorides supported by bidentate ligand frameworks","authors":"Liviu, Mirica, Luke, Westawker, Bailey, Bouley, Josh, Vura-Weis","doi":"10.26434/chemrxiv-2024-d6sj9","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-d6sj9","url":null,"abstract":"Herein, we investigate the photoactivity of four NiII tolyl chloride complexes supported by either the bulky, bidentate [2.2]pyridinophane (HN2) ligand or the traditional 2,2′-bipyridine (tBubpy) ligand. Despite a change in ligand framework, we observe comparable quantum yields for the photodegradation of all four NiII complexes but do see changes in their affinity for side reactivity and stabilization of photogenerated NiI monomeric species. Additionally, we show that tBubpyNi(tolyl)Cl compounds are not bench-stable, while also observing side reactivity that leads to C-O bond formation and C-C bond formation. By varying the location of the methyl on the tolyl group, we can further perturb the quantum yield of the compounds and the extent of their side reactivity. Time-dependent density functional theory (TDDFT) and ab initio modeling (CASSCF) reveal that a smaller HOMO/LUMO gap and a more energetically accessible tetrahedral-geometry triplet state correlates with increased quantum yields and O2 side-reactivity. By leveraging our HN2 ligand, a bidentate ligand that hinders axial interactions around the nickel center, the radical side reactivity is limited. This study of this new bidentate pyridinophane ligand highlights how photoactivity is affected by the steric environment around the Ni center, and that such photoactivity is not unique to bipyridyl-supported Ni compounds.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Chemical Investigation Approach of the Paraconiothyrium sp. FKR-0637 Fungal Strain Enables the Isolation of the New Chlorinated Chromone, Nohocumone 通过对 Paraconiothyrium sp. FKR-0637 真菌菌株进行化学研究，分离出新型氯化铬酮 Nohocumone

ChemRxiv Pub Date : 2024-12-14 DOI: 10.26434/chemrxiv-2024-ks826-v2

Akihiro, Sugawara, Haruki, Azami, Yoshihiro, Watanabe, Takahito, Ouchi, Mika, Watabe, Hiroki, Kojima, Yui, Hirano, Saki, Owada, Toshiyuki, Tokiwa, Mayuka, Higo, Kenichi, Nonaka, Toshiaki, Teruya, Hideaki, Hanaki, Masato, Iwatsuki

{"title":"A Chemical Investigation Approach of the Paraconiothyrium sp. FKR-0637 Fungal Strain Enables the Isolation of the New Chlorinated Chromone, Nohocumone","authors":"Akihiro, Sugawara, Haruki, Azami, Yoshihiro, Watanabe, Takahito, Ouchi, Mika, Watabe, Hiroki, Kojima, Yui, Hirano, Saki, Owada, Toshiyuki, Tokiwa, Mayuka, Higo, Kenichi, Nonaka, Toshiaki, Teruya, Hideaki, Hanaki, Masato, Iwatsuki","doi":"10.26434/chemrxiv-2024-ks826-v2","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-ks826-v2","url":null,"abstract":"The discovery of novel natural products (NPs) from diverse microorganisms is essential for advancing drug discovery. In this study, a chemical approach was employed for NP exploration using the genus Paraconiothyrium sp. isolated from the root soil of Ficus microcarpa on Noho Island, Okinawa. Consequently, we isolated five compounds, including a new chromone, nohocumone (1), as well as four known compounds, known chromone (2), 10-norparvulenone (3), sclerotinin A (4), and calbistrin A (5), from the culture broth of Paraconiothyrium sp. FKR-0637. The planar structure of 1 were elucidated using 1D and 2D NMR analyses, HR-ESI-MS, and chemical derivatization. Chlorinated chromone 1 is a novel compound that was not previously isolated from Paraconiothyrium sp. These results contribute to expanding the structural diversity and collection of NPs that can be obtained from the culture broths of Paraconiothyrium sp.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"44 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing Activation Energy Predictions under Data Constraints Using Graph Neural Networks

ChemRxiv Pub Date : 2024-12-13 DOI: 10.26434/chemrxiv-2024-78w36-v2

Han-Chung, Chang, Yi-Pei, Li, Ming-Hsuan, Tsai

{"title":"Enhancing Activation Energy Predictions under Data Constraints Using Graph Neural Networks","authors":"Han-Chung, Chang, Yi-Pei, Li, Ming-Hsuan, Tsai","doi":"10.26434/chemrxiv-2024-78w36-v2","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-78w36-v2","url":null,"abstract":"Accurately predicting activation energies is crucial for understanding chemical reactions and modeling complex reaction systems. However, the high computational cost of quantum chemistry methods often limits the feasibility of large-scale studies, leading to a scarcity of high-quality activation energy data. In this work, we explore and compare three innovative approaches—transfer learning, delta learning, and feature engineering—to enhance the accuracy of activation energy predictions using graph neural networks, specifically focusing on methods that incorporate low-cost, low-level computational data. Using the Chemprop model, we systematically evaluated how these methods leverage data from semiempirical quantum mechanical (SQM) calculations to improve predictions. Delta learning, which adjusts low-level SQM activation energies to align with high-level CCSD(T)-F12a targets, emerged as the most effective method, achieving high accuracy with substantially reduced high-level data requirements. Notably, delta learning trained with just 20%–30% of high-level data matched or exceeded the performance of other methods trained with full datasets, making it advantageous in data-scarce scenarios. However, its reliance on transition state searches imposes significant computational demands during model application. Transfer learning, which pretrains models on large datasets of low-level data, provided mixed results, particularly when there was a mismatch in the reaction distributions between the training and target datasets. Feature engineering, which involves adding computed molecular properties as input features, showed modest gains, particularly when incorporating thermodynamic properties. Our study highlights the trade-offs between accuracy and computational demand in selecting the best approach for enhancing activation energy predictions. These insights provide valuable guidelines for researchers aiming to apply machine learning in chemical reaction engineering, helping to balance accuracy with resource constraints.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhanced Sampling with Sub-optimal Collective Variables: Reconciling Accuracy and Convergence Speed 次优集合变量的增强采样：兼顾精度与收敛速度

ChemRxiv Pub Date : 2024-12-13 DOI: 10.26434/chemrxiv-2024-mfpcn-v2

Dhiman, Ray, Valerio, Rizzi

引用次数: 0

Chaotropic or Hydrophobic Effect: Distinct binding signatures of nano-ions to a non-ionic polymer 混沌效应或疏水效应：纳米离子与非离子聚合物的独特结合特征

ChemRxiv Pub Date : 2024-12-13 DOI: 10.26434/chemrxiv-2024-hkjpk

Max, Hohenschutz, Carlos Gonzalez, Lopez, Jasmin, Simons, Hannes, Luhmann, Martin, Dulle

{"title":"Chaotropic or Hydrophobic Effect: Distinct binding signatures of nano-ions to a non-ionic polymer","authors":"Max, Hohenschutz, Carlos Gonzalez, Lopez, Jasmin, Simons, Hannes, Luhmann, Martin, Dulle","doi":"10.26434/chemrxiv-2024-hkjpk","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-hkjpk","url":null,"abstract":"The nanometric ions (nano-ions) SiW12O404- (SiW) and B(C6H5)4- (BPh4) are considered as a superchaotropic and a hydro-phobic ion, respectively, in extension to the chaotropic side of the Hofmeister series. A distinction between chaotropic, superchaotropic and hydrophobic ions, however, has not been presented so far. Herein, we show by measurement of the viscosity B-coefficient of SiW (and other nano-ions) and of ion binding to the non-ionic polymer hydroxypropylcellulose (HPC), how chaotropic, superchaotropic and hydrophobic ions can be unambiguously distinguished. The viscosity B-coefficient of the superchaotropic SiW is positive as for hydrophobic ions, and distinct from classical chaotropic ions with a negative B-coefficient. In HPC-solution, BPh4 and SiW bind to the polymer, dramatically increasing the viscosity and the cloud point. Heating induces characteristically distinct responses for the two nano-ions: The viscosity rises for BPh4 and decreases for SiW. These effects are related to nano-ion induced aggregation and electric charging of HPC, which, upon heating, become stronger for BPh4 and weaker for SiW as shown by Small Angle X-ray and Neutron Scattering. 1H-Nuclear Magnetic Resonance and Isothermal Titration Calorimetry showed that the structural effects are linked to binding thermodynamics. Upon heating, the binding constant decreases for SiW and increases for BPh4 arising respectively from an enthalpically favorable, exothermic, chaotropic driving force or an enthalpically unfavorable, endothermic, hydropho-bic driving force. Combining the viscosity B-coefficient and sign of the binding enthalpy enables distinguishing cha-otropic, superchaotropic and hydrophobic ions. Importantly, superchaotropic binding can be stronger or weaker than hydrophobic binding depending on the temperature. Ion hydration and binding are demonstrated as powerful tools to tune polymer solution properties.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"100 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Relaxation optimized heteronuclear experiments for extending the size limit of RNA nuclear magnetic resonance

ChemRxiv Pub Date : 2024-12-13 DOI: 10.26434/chemrxiv-2024-qs8d7-v2

Jan, Marchant, Aarsh, Shah, Heer, Patel, Arjun, Kanjarpane, Michael, Summers

{"title":"Relaxation optimized heteronuclear experiments for extending the size limit of RNA nuclear magnetic resonance","authors":"Jan, Marchant, Aarsh, Shah, Heer, Patel, Arjun, Kanjarpane, Michael, Summers","doi":"10.26434/chemrxiv-2024-qs8d7-v2","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-qs8d7-v2","url":null,"abstract":"The application of NMR to large RNAs has been limited by the inability to perform heteronuclear correlation experiments essential for resolving overlapping 1H NMR signals, determining inter-proton distance restraints and inter-helical orientations for structure calcula-tions, and evaluating conformational dynamics. Approaches exploiting 1H-13C correlations that are routinely applied to proteins and small RNAs of ~60 nucleotides or fewer are impractical for larger RNAs due to rapid dipolar relaxation of protons by their attached car-bons. Here we report a 2H-enhanced, 1H-15N correlation approach that enables atom-specific NMR characterization of much larger RNAs. Purine H8 transverse relaxation rates are reduced ~20-fold with ribose perdeuteration, enabling efficient magnetization transfer via two-bond 1H-15N couplings. We focus on H8-N9 correlation spectra which benefit from favorable N9 chemical shift anisotropy. Chemical shift assignment is enabled by retention of protons at the C1′ position, which allow measurement of two-bond H1′-N9 and through-space H1′-H8 correlations with only a minor effect on H8 relaxation. The approach is demonstrated for the 232 nucleotide HIV-1 Rev response element, where chemical shift assignments, 15N-edited nuclear Overhauser effects, and 1H-15N residual dipolar couplings are readily obtained from sensitive, high-resolution spectra. Heteronuclear correlated NMR methods that have been essential for the study of proteins can now be extended to RNAs of at least 78 kDa.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Photocatalytic Chlorine Production from Iron Chlorides in Atmospheric Aerosols: Strategies for Quantifying Methane and Tropospheric Ozone Control 大气气溶胶中铁氯化物的光催化氯生产：甲烷量化和对流层臭氧控制策略

ChemRxiv Pub Date : 2024-12-13 DOI: 10.26434/chemrxiv-2024-4s0dn

Marie Kathrine, Mikkelsen, Maarten, van Herpen, Luisa, Pennacchio, Chloe, Brashear, Alfonzo, Saiz-Lopez, Thomas, Rockmann, Matthew, Johnson

{"title":"Photocatalytic Chlorine Production from Iron Chlorides in Atmospheric Aerosols: Strategies for Quantifying Methane and Tropospheric Ozone Control","authors":"Marie Kathrine, Mikkelsen, Maarten, van Herpen, Luisa, Pennacchio, Chloe, Brashear, Alfonzo, Saiz-Lopez, Thomas, Rockmann, Matthew, Johnson","doi":"10.26434/chemrxiv-2024-4s0dn","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-4s0dn","url":null,"abstract":"It was recently discovered that chlorine is produced photocatalytically from mineral dust sea spray aerosols, impacting methane and tropospheric ozone, and an evaluation was made of the climate and environmental impact of a chlorine-based intervention to draw\u0000down methane. The generation of chlorine by the iron chlorides Fe(III)Cl(3−n)n will also occur due to iron present in shipping plumes. To study efficiency and environmental implications, there is a need for additional information about the behavior of the process under a range of atmospheric conditions. Here we use box modeling to evaluate whether it is possible to experimentally observe this mechanism in a ship’s plume, or in a plume of pure iron dust, emitted for example from a tower. Detection limits for Cl, Cl2, HOCl, ClO, ClNO3, ClNO2, CO, C2H6, δ13C(CO) and CH2O are determined based on values from the literature. We find that the most promising and low-cost experimental indicators of Cl0 production are the concentration of photoactive iron and the CO:ethane ratio, and Cl2 is a useful indicator if cost is not a limitation. For ships with high NOx emissions, ClNO2 and ClNO3 could also potentially be used, and for towers emitting Fe without NOx the concentration of HOCl and ClO could be used. δ13C(CO) is a very direct method to detect methane removal, but only gives a clear signal for high iron emissions.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Presumptive Tests for Xylazine – A Computer Vision Approach 甲氧苄啶的推定检验--计算机视觉方法

ChemRxiv Pub Date : 2024-12-13 DOI: 10.26434/chemrxiv-2024-487ch-v2

Marc, Reid, Hui Yun, Chang, Kristin, Donnachie, Timothy J.D., McCabe, Felicity, Carlysle-Davies, Kristin, Ceniccola-Campos, Henry, Barrington

引用次数: 0