The worldwide spread of antibiotic resistance is considered to be one of the major health threats to society. While developing new antibiotics is primordial, there is also a high need for next-generation analytical methods for surveying the physiological state of live bacteria in heterogeneous populations and their response to environmental stress. Here we report a single-cell high-throughput method for monitoring bacterial stress and environmental adaptation based on ratiometric flow cytometry. We used a combination of a sensitive fluorescent molecular tool, the red solvatochromic antimicrobial peptide UNR-1 with defined cellular localization in Gram-positive and Gram-negative bacteria, with a robust protocol of calculating generalized polarization (GP) of fluorescence adapted to flow cytometry. Our methodology enabled rapid detection of perturbations in the bacterial cell envelope caused by heat shock, transfer to a nutrient-poor medium, fixation, and exposure to antibiotics.
{"title":"Single-Cell Analysis of Perturbations in the Bacterial Cell Envelope Enabled by Monitoring Generalized Polarization of a Nile Red-Based Solvatochromic Peptide UNR-1","authors":"Julie, Karpenko, Lucille, Weiss, Dominique, Bonnet, Dmytro, Dziuba","doi":"10.26434/chemrxiv-2024-t8x5w","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-t8x5w","url":null,"abstract":"The worldwide spread of antibiotic resistance is considered to be one of the major health threats to society. While developing new antibiotics is primordial, there is also a high need for next-generation analytical methods for surveying the physiological state of live bacteria in heterogeneous populations and their response to environmental stress. Here we report a single-cell high-throughput method for monitoring bacterial stress and environmental adaptation based on ratiometric flow cytometry. We used a combination of a sensitive fluorescent molecular tool, the red solvatochromic antimicrobial peptide UNR-1 with defined cellular localization in Gram-positive and Gram-negative bacteria, with a robust protocol of calculating generalized polarization (GP) of fluorescence adapted to flow cytometry. Our methodology enabled rapid detection of perturbations in the bacterial cell envelope caused by heat shock, transfer to a nutrient-poor medium, fixation, and exposure to antibiotics.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214935","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}
The reverse water-gas shift reaction (RWGS) is a key technology of the chemical industry, central to the emerging circular carbon economy. Pt-based catalysts have previously been shown to effectively promote the RWGS, especially when modified by promoter elements. However, their active state is still poorly understood. Here, we show that the intimate incorporation of an iron promoter into metal-oxide supported Pt-based nanoparticles can increase their activity and selectivity for the low temperature reverse water-gas shift (LT-RWGS) substantially and drastically outperform unpromoted Pt-based materials. Specifically, the study explores the promotional effect of iron in Pt-Fe bimetallic systems supported on silica (PtxFey@SiO2) prepared by surface organometallic chemistry (SOMC). The most active catalyst (Pt1Fe1@SiO2) shows high selectivity (>99% CO) towards CO at a formation rate of 0.192 molCO h-1 gcat-1, which is significantly higher than that of monometallic Pt@SiO2 (96% sel. and 0.022 molCO h-1 gcat-1). In-situ diffuse reflectance FT-IR spectroscopy (DRIFTS) and X-ray absorption spectroscopy (XAS) indicate a dynamic process at the catalyst surface under reaction conditions, revealing distinct reaction pathways for the monometallic Pt@SiO2 and bimetallic PtxFey@SiO2 systems.
{"title":"Decoding the Promotional Effect of Iron in Bimetallic Pt-Fe-Nanoparticles for the Low Temperature Reverse Water-Gas Shift Reaction","authors":"Colin, Hansen, Wei, Zhou, Enzo, Brack, Yuhao, Wang, Chunliang, Wang, James, Paterson, Jamie, Southouse, Christophe, Copéret","doi":"10.26434/chemrxiv-2024-hzlgd-v2","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-hzlgd-v2","url":null,"abstract":"The reverse water-gas shift reaction (RWGS) is a key technology of the chemical industry, central to the emerging circular carbon economy. Pt-based catalysts have previously been shown to effectively promote the RWGS, especially when modified by promoter elements. However, their active state is still poorly understood. Here, we show that the intimate incorporation of an iron promoter into metal-oxide supported Pt-based nanoparticles can increase their activity and selectivity for the low temperature reverse water-gas shift (LT-RWGS) substantially and drastically outperform unpromoted Pt-based materials. Specifically, the study explores the promotional effect of iron in Pt-Fe bimetallic systems supported on silica (PtxFey@SiO2) prepared by surface organometallic chemistry (SOMC). The most active catalyst (Pt1Fe1@SiO2) shows high selectivity (>99% CO) towards CO at a formation rate of 0.192 molCO h-1 gcat-1, which is significantly higher than that of monometallic Pt@SiO2 (96% sel. and 0.022 molCO h-1 gcat-1). In-situ diffuse reflectance FT-IR spectroscopy (DRIFTS) and X-ray absorption spectroscopy (XAS) indicate a dynamic process at the catalyst surface under reaction conditions, revealing distinct reaction pathways for the monometallic Pt@SiO2 and bimetallic PtxFey@SiO2 systems.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226959","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}
The proton coupled electron transfer reactivity of an octahedral Ta(V) aniline complex ligated by an acridane-derived redox active NNN pincer ligand is reported. Reversible association of aniline to a Ta(V) dichloride leads to significant coordination induced bond weakening of aniline’s N–H bonds allowing for two-fold hydrogen atom abstraction yielding a terminal imido complex accompanied by two-electron oxidation of the NNN pincer ligand under retention of the metal oxidation state. The bond dissociation free energies of the amine and a transient radical amido complex are estimated via stoichiometric reactions with hydrogen atom abstractor and donor reagents complemented by DFT calculations.
{"title":"Two-fold proton coupled electron transfer of a Ta(V) aniline complex mediated by a redox active NNN pincer ligand","authors":"Josh, Abbenseth, Sotirios, Pavlidis, Jasmin, Alasadi, Amanda, Opis-Basilio","doi":"10.26434/chemrxiv-2024-5rjl7","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-5rjl7","url":null,"abstract":"The proton coupled electron transfer reactivity of an octahedral Ta(V) aniline complex ligated by an acridane-derived redox active NNN pincer ligand is reported. Reversible association of aniline to a Ta(V) dichloride leads to significant coordination induced bond weakening of aniline’s N–H bonds allowing for two-fold hydrogen atom abstraction yielding a terminal imido complex accompanied by two-electron oxidation of the NNN pincer ligand under retention of the metal oxidation state. The bond dissociation free energies of the amine and a transient radical amido complex are estimated via stoichiometric reactions with hydrogen atom abstractor and donor reagents complemented by DFT calculations.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214974","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}
Pub Date : 2024-09-13DOI: 10.26434/chemrxiv-2024-kh8dv
Huy Vu Duc, Nguyen, Angus C. L. A. , Crampton, Daniel F, Schmidt, Tim, Huber
Nanofibrillated cellulose (NFC) has applications in many sectors, but economical production of large volumes with a minimized ecological footprint remains challenging. In this study, we have developed a new design to upgrade the Masuko Supermasscolloider from a traditional batch mode to continuous circulation. This upgrade includes a pump-controlled circulating system, an in-line viscosimeter for real-time measurement of cellulose suspension viscosity, and a power meter to monitor and evaluate the energy consumption of both the pump and the grinder throughout the process. These modifications address the limitations of scaling up NFC production, offering a more efficient and effective approach. We investigated the production of NFC from cellulose feedstock derived from miscanthus biomass under various conditions, including different initial cellulose concentrations (1 wt%, 1.5 wt% and 2 wt%) and processing volumes (15L and 25 L) at different grinding time (from 15 minutes to 120 minutes, with 15 minutes intervals). A systematic study on the effect of these processing conditions on the size distribution of NFC particles was conducted using an analytical centrifuge (Lumisizer). A prevalence of particles with equivalent hydrodynamic diameters between ~250 nm and ~300 nm was observed regardless of the processing conditions. Notably, in the context of large-scale NFC production, our approach demonstrated a 70% reduction in specific energy consumption by either increasing the processing volume from 15 L to 25 L and increasing the initial cellulose concentration from 1 wt% to 2 wt%. Additionally, we explored the application of produced NFC as nanofillers in nanocomposite packaging materials. Specifically, NFC particles processed at different grinding times were incorporated into a glycerol-plasticized carboxymethyl cellulose (CMC) matrix to form bio-nanocomposite films. We have found that particles obtained with longer grinding time did not lead to increased mechanical performance. This simplifies the NFC production process by reducing the need for prolonged grinding, thereby saving time and energy while maintaining the desired properties of the nanocomposite samples.
{"title":"Evaluating ultra-fine friction grinding for the continuous production of nanofibrillated cellulose","authors":"Huy Vu Duc, Nguyen, Angus C. L. A. , Crampton, Daniel F, Schmidt, Tim, Huber","doi":"10.26434/chemrxiv-2024-kh8dv","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-kh8dv","url":null,"abstract":"Nanofibrillated cellulose (NFC) has applications in many sectors, but economical production of large volumes with a minimized ecological footprint remains challenging. In this study, we have developed a new design to upgrade the Masuko Supermasscolloider from a traditional batch mode to continuous circulation. This upgrade includes a pump-controlled circulating system, an in-line viscosimeter for real-time measurement of cellulose suspension viscosity, and a power meter to monitor and evaluate the energy consumption of both the pump and the grinder throughout the process. These modifications address the limitations of scaling up NFC production, offering a more efficient and effective approach. We investigated the production of NFC from cellulose feedstock derived from miscanthus biomass under various conditions, including different initial cellulose concentrations (1 wt%, 1.5 wt% and 2 wt%) and processing volumes (15L and 25 L) at different grinding time (from 15 minutes to 120 minutes, with 15 minutes intervals). A systematic study on the effect of these processing conditions on the size distribution of NFC particles was conducted using an analytical centrifuge (Lumisizer). A prevalence of particles with equivalent hydrodynamic diameters between ~250 nm and ~300 nm was observed regardless of the processing conditions. Notably, in the context of large-scale NFC production, our approach demonstrated a 70% reduction in specific energy consumption by either increasing the processing volume from 15 L to 25 L and increasing the initial cellulose concentration from 1 wt% to 2 wt%. Additionally, we explored the application of produced NFC as nanofillers in nanocomposite packaging materials. Specifically, NFC particles processed at different grinding times were incorporated into a glycerol-plasticized carboxymethyl cellulose (CMC) matrix to form bio-nanocomposite films. We have found that particles obtained with longer grinding time did not lead to increased mechanical performance. This simplifies the NFC production process by reducing the need for prolonged grinding, thereby saving time and energy while maintaining the desired properties of the nanocomposite samples.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214976","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}
Pub Date : 2024-09-13DOI: 10.26434/chemrxiv-2024-9l6jc-v3
Georg K. H., Madsen, Ralf, Wanzenböck, Esther, Heid, Michele, Riva, Giada, Franceschi, Alexander M., Imre, Jesús, Carrete, Ulrike, Diebold
The investigation of inhomogeneous surfaces, where various local structures co-exist, is crucial for understanding interfaces of technological interest, yet it presents significant challenges. Here, we study the atomic configurations of the (2 × m) Ti-rich surfaces at (110)-oriented SrTiO3 by bringing together scanning tunneling microscopy and transferable neural-network force fields combined with evolutionary exploration. We leverage an active learning methodology to iteratively extend the training data as needed for different configurations. Training on only small well-known reconstructions, we are able to extrapolate to the complicated and diverse overlayers encountered in different regions of the heterogeneous SrTiO3(110)-(2×m) surface. Our machine-learning-backed approach generates several new candidate structures, in good agreement with experiment and verified using density functional theory. The approach could be extended to other complex metal oxides featuring large coexisting surface reconstructions.
{"title":"Exploring Inhomogeneous Surfaces: Evolutionary Exploration of Ti-rich SrTiO3(110) Surface Reconstructions via Active Learning","authors":"Georg K. H., Madsen, Ralf, Wanzenböck, Esther, Heid, Michele, Riva, Giada, Franceschi, Alexander M., Imre, Jesús, Carrete, Ulrike, Diebold","doi":"10.26434/chemrxiv-2024-9l6jc-v3","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-9l6jc-v3","url":null,"abstract":"The investigation of inhomogeneous surfaces, where various local structures co-exist, is crucial for understanding interfaces of technological interest, yet it presents significant challenges. Here, we study the atomic configurations of the (2 × m) Ti-rich surfaces at (110)-oriented SrTiO3 by bringing together scanning tunneling microscopy and transferable neural-network force fields combined with evolutionary exploration. We leverage an active learning methodology to iteratively extend the training data as needed for different configurations. Training on only small well-known reconstructions, we are able to extrapolate to the complicated and diverse overlayers encountered in different regions of the heterogeneous SrTiO3(110)-(2×m) surface. Our machine-learning-backed approach generates several new candidate structures, in good agreement with experiment and verified using density functional theory. The approach could be extended to other complex metal oxides featuring large coexisting surface reconstructions.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214990","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}
Pub Date : 2024-09-13DOI: 10.26434/chemrxiv-2024-ld2k6
Michael, Webb, Shengli, Jiang
The architectural, compositional, and chemical complexities of polymers are fundamentally important to their properties; however, these same factors obfuscate effective predictions. Machine learning offers a promising approach for predicting polymer properties, but model transferability remains a major challenge, particularly when data is insufficient due to high acquisition costs and practical limitations. We explore the integration of polymer physics theory with machine learning architectures to enhance the predictive capabilities of polymer properties. Using a dataset of 18,450 polymers with diverse architectures, molecular weights, compositions, and chemical patterns, we focus on transferability tasks for predicting moments of the distribution of squared radius of gyration. Our tandem model, GC-GNN, which combines a graph neural network with a fittable model based on ideal Gaussian chain theory, surpasses both standalone polymer-physics and graph neural network models in predictive accuracy and transferability. We also demonstrate that predictive transferability varies with polymer architecture due to deviations from the ideal Gaussian chain assumption. This study highlights the potential of combining polymer physics with data-driven models to improve predictive transferability across diverse conditions and also pathways for improvement.
{"title":"Physics-Guided Neural Networks for Transferable Prediction of Polymer Properties","authors":"Michael, Webb, Shengli, Jiang","doi":"10.26434/chemrxiv-2024-ld2k6","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-ld2k6","url":null,"abstract":"The architectural, compositional, and chemical complexities of polymers are fundamentally important to their properties; however, these same factors obfuscate effective predictions. Machine learning offers a promising approach for predicting polymer properties, but model transferability remains a major challenge, particularly when data is insufficient due to high acquisition costs and practical limitations. We explore the integration of polymer physics theory with machine learning architectures to enhance the predictive capabilities of polymer properties. Using a dataset of 18,450 polymers with diverse architectures, molecular weights, compositions, and chemical patterns, we focus on transferability tasks for predicting moments of the distribution of squared radius of gyration. Our tandem model, GC-GNN, which combines a graph neural network with a fittable model based on ideal Gaussian chain theory, surpasses both standalone polymer-physics and graph neural network models in predictive accuracy and transferability. We also demonstrate that predictive transferability varies with polymer architecture due to deviations from the ideal Gaussian chain assumption. This study highlights the potential of combining polymer physics with data-driven models to improve predictive transferability across diverse conditions and also pathways for improvement.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214979","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}
Pub Date : 2024-09-13DOI: 10.26434/chemrxiv-2024-zgxwt
Samir, MESSAOUDI, Sokna , Bazzi, Ameni , Hadj Mohamed, Dmytro , Ryzhakov, Juba , Ghouilem, Mehdi A. , Beniddir, Vincent , Gandon
Here we report a macrocyclization route towards the synthesis of glycophane peptides by a selective C-H arylation of the anomeric bond. This approach demonstrates the power of Pd-catalysis C-H activation to access unfamiliar cyclic peptides
{"title":"Diastereoselective Anomeric C(sp3)-H Cyclization Towards the Design of New Generations of Cyclophane-Braced Glycopeptides","authors":"Samir, MESSAOUDI, Sokna , Bazzi, Ameni , Hadj Mohamed, Dmytro , Ryzhakov, Juba , Ghouilem, Mehdi A. , Beniddir, Vincent , Gandon","doi":"10.26434/chemrxiv-2024-zgxwt","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-zgxwt","url":null,"abstract":"Here we report a macrocyclization route towards the\u0000synthesis of glycophane peptides by a selective C-H arylation of the anomeric bond. This approach demonstrates the power of Pd-catalysis\u0000C-H activation to access unfamiliar cyclic peptides","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214978","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}
Pub Date : 2024-09-13DOI: 10.26434/chemrxiv-2024-xsnqj
MANJEET, BHATIA
Flavones exhibit a range of pharmacological and diverse biological activities, making them valuable candidates for drug development and complementary medicine. In this study, inclusive investigations of the chemical reactivity, kinetic stability, and biological activity of the flavone molecule are performed using B3LYP/6-311++G(d, p) density functional theory (DFT). The proton affinity (PA), ionisation energy (IE), and electron affinity (EA) along with global reactivity parameters such as chemical potential (µ), chemical hardness (η), softness (σ), electrophilic index (ω), and electronegativity (χ) of flavone molecule are computed. A comparative study with different DFT/correlation functional such as wB97XD, M062X, and MP2 shows that the adopted DFT method is reliable and computationally economical. Benchmark calculations using B3LYP, CAM- B3LYP, PBE0, M06-2X, LC-wHPBE, and wB97XD on the excited electronic states and absorption spectra indicate that CAM-B3LYP, M06-2X, and wB97XD are the most effective for predicting the absorption spectra of Flavone.
{"title":"Exploring Flavone Reactivity: A Quantum Mechanical Study and TDDFT Benchmark on UV-Vis Spectroscopy","authors":"MANJEET, BHATIA","doi":"10.26434/chemrxiv-2024-xsnqj","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-xsnqj","url":null,"abstract":"Flavones exhibit a range of pharmacological and diverse biological activities, making them valuable candidates for drug development and complementary medicine. In this study, inclusive investigations of the chemical reactivity, kinetic stability, and biological activity of the flavone molecule are performed using B3LYP/6-311++G(d, p) density functional theory (DFT). The proton affinity (PA), ionisation energy (IE), and electron affinity (EA) along with global reactivity parameters such as chemical potential (µ), chemical hardness (η), softness (σ), electrophilic index (ω), and electronegativity (χ) of flavone molecule are computed. A comparative study with different DFT/correlation functional such as wB97XD, M062X, and MP2 shows that the adopted DFT method is reliable and computationally economical. Benchmark calculations using B3LYP, CAM- B3LYP, PBE0, M06-2X, LC-wHPBE, and wB97XD on the excited electronic states and absorption spectra indicate that CAM-B3LYP, M06-2X, and wB97XD are the most effective for predicting the absorption spectra of Flavone.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214975","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}
Pub Date : 2024-09-13DOI: 10.26434/chemrxiv-2024-hpbl9
Takayuki, Nakamuro, Yosi, Kratish, Yiqi, Liu, Jiaqi, Li, Anusheela, Das, Leighton, O. Jones, Amol, Agarwal, Qing, Ma, Michael, J. Bedzyk, George, C. Schatz, Eiichi, Nakamura, Tobin, J. Marks
Heterogeneous catalysts dominate the chemical industry but typically feature diverse, incompletely defined active sites. Thus, describing structure-activity relationships, unlike homogeneous catalysts, remains challenging. In contrast, molecularly defined single-site heterogeneous catalysts (SSHCs), using appropriate tools, are poised to address these challenges and provide new avenues for catalysis research and development. The present study explores eco-friendly H2 production mediated by discrete MO2 sites supported on carbon nanohorns (CNHs) and active for alcohol dehydrogenation. While informative, detailed ensemble EXAFS/XANES, XPS, kinetic measurements, and DFT analysis alone cannot provide a full molecular picture of the reaction pathway. Here, using single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM), we identify four key catalytic intermediates anchored to the CNHs and uncover a new reaction pathway involving alkoxide/hemiacetal equilibration and acetal oligomerization. These intermediates are identified solely by theory and SMART-EM, and this advance highlights the potential of SMART-EM to establish and verify mechanistic hypotheses in catalysis.
{"title":"Atomic-Resolution Cinematography of Catalytic Intermediates over a Single-Site Heterogeneous Catalyst","authors":"Takayuki, Nakamuro, Yosi, Kratish, Yiqi, Liu, Jiaqi, Li, Anusheela, Das, Leighton, O. Jones, Amol, Agarwal, Qing, Ma, Michael, J. Bedzyk, George, C. Schatz, Eiichi, Nakamura, Tobin, J. Marks","doi":"10.26434/chemrxiv-2024-hpbl9","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-hpbl9","url":null,"abstract":"Heterogeneous catalysts dominate the chemical industry but typically feature diverse, incompletely defined active sites. Thus, describing structure-activity relationships, unlike homogeneous catalysts, remains challenging. In contrast, molecularly defined single-site heterogeneous catalysts (SSHCs), using appropriate tools, are poised to address these challenges and provide new avenues for catalysis research and development. The present study explores eco-friendly H2 production mediated by discrete MO2 sites supported on carbon nanohorns (CNHs) and active for alcohol dehydrogenation. While informative, detailed ensemble EXAFS/XANES, XPS, kinetic measurements, and DFT analysis alone cannot provide a full molecular picture of the reaction pathway. Here, using single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM), we identify four key catalytic intermediates anchored to the CNHs and uncover a new reaction pathway involving alkoxide/hemiacetal equilibration and acetal oligomerization. These intermediates are identified solely by theory and SMART-EM, and this advance highlights the potential of SMART-EM to establish and verify mechanistic hypotheses in catalysis.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214983","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}
Relativistic pseudopotentials and basis sets are the workhorse for modeling heavy elements of lanthanides and actinides. The norm-conserving Goedecker, Teter, and Hutter (GTH) pseudopotential is advantageous for modeling lanthanides and actinides compounds and condensed systems because of its transferability and accuracy. In this work, we develop a set of well-benchmarked GTH-type 5f-in-core pseudopotentials with scalar-relativistic effects, together with associated Gaussian basis sets for the most commonly encountered trivalent and tetravalent actinides (An(III), An(IV); An = Pa-Lr). The 5f-in-core GTH pseudopotentials are constructed by placing 5f-subconfiguration 5fn open shells of An(III) and 5fn-1 of An(IV) (n = 2-14) into the atomic core in the core-valence separation. The different performances of 5f-in-core GTH pseudopotentials for trivalent and tetravalent actinides are further analyzed from the chemical bonding features of actinides. The formalism of 5f-in-core GTH pseudopotentials circumvent the computational difficulty arising from 5fx open valence shell. The optimized 5f-in-core GTH PPs and Gaussian basis sets can be used to accelerate the costly first-principles modeling of structure-complicated actinide compounds and condensed-phase actinide systems.
{"title":"Norm-conserving 5f-in-core Pseudopotentials and Gaussian Basis Sets Optimized for Tri- and Tetra-Valent Actinides (An = Pa-Lr)","authors":"Jian-Biao , Liu, Jun-Bo , Lu, Yang-Yang , Zhang, Jun, Li","doi":"10.26434/chemrxiv-2024-m59d9","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-m59d9","url":null,"abstract":"Relativistic pseudopotentials and basis sets are the workhorse for modeling heavy elements of lanthanides and actinides. The norm-conserving Goedecker, Teter, and Hutter (GTH) pseudopotential is advantageous for modeling lanthanides and actinides compounds and condensed systems because of its transferability and accuracy. In this work, we develop a set of well-benchmarked GTH-type 5f-in-core pseudopotentials with scalar-relativistic effects, together with associated Gaussian basis sets for the most commonly encountered trivalent and tetravalent actinides (An(III), An(IV); An = Pa-Lr). The 5f-in-core GTH pseudopotentials are constructed by placing 5f-subconfiguration 5fn open shells of An(III) and 5fn-1 of An(IV) (n = 2-14) into the atomic core in the core-valence separation. The different performances of 5f-in-core GTH pseudopotentials for trivalent and tetravalent actinides are further analyzed from the chemical bonding features of actinides. The formalism of 5f-in-core GTH pseudopotentials circumvent the computational difficulty arising from 5fx open valence shell. The optimized 5f-in-core GTH PPs and Gaussian basis sets can be used to accelerate the costly first-principles modeling of structure-complicated actinide compounds and condensed-phase actinide systems.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226960","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}
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