In this work, the hydrodenitrogenation (HDN) of a primary amine (dodecylamine), a secondary amine (didodecylamine), and a tertiary amine (tridodecylamine) over a Pt/ZrO2 catalyst was compared in a batch reactor. The main product of the amine hydrotreating was dodecane, but significant amounts of secondary amine were also formed as an intermediate during HDN of the primary and the tertiary amine. It was found that the primary amine is the only species for which direct HDN is possible; HDN of the secondary amine thus proceeds through a primary amine intermediate and HDN of the tertiary amine involves formation of secondary amine, which decomposes to primary amine. Consequently, HDN of the tertiary and secondary amines is slower than that of the primary amine. Kinetic modeling indicated that bimolecular condensation reactions of the primary amine, as well as potentially of the primary amine and the secondary amine, have a significant effect on the HDN process. Formation of secondary amine from primary amine increases the initial conversion and nitrogen removal rate but appeared to slow down the overall rate of nitrogen removal. The results thus demonstrate how condensation reactions affect amine HDN, which has implications for catalyst design for HDN of renewable feeds containing aliphatic amines.
{"title":"Catalytic hydrodenitrogenation of primary, secondary, and tertiary C12-alkyl amines over a platinum on zirconia catalyst","authors":"Joakim, Kattelus, Leoni-Franziska, Klingelhöfer, Emma, Verkama, Jorge, Velasco, Leonhard, Iser, Marcus, Rose, Reetta, Karinen, Riikka, Puurunen","doi":"10.26434/chemrxiv-2024-z1kc3","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-z1kc3","url":null,"abstract":"In this work, the hydrodenitrogenation (HDN) of a primary amine (dodecylamine), a secondary amine (didodecylamine), and a tertiary amine (tridodecylamine) over a Pt/ZrO2 catalyst was compared in a batch reactor. The main product of the amine hydrotreating was dodecane, but significant amounts of secondary amine were also formed as an intermediate during HDN of the primary and the tertiary amine. It was found that the primary amine is the only species for which direct HDN is possible; HDN of the secondary amine thus proceeds through a primary amine intermediate and HDN of the tertiary amine involves formation of secondary amine, which decomposes to primary amine. Consequently, HDN of the tertiary and secondary amines is slower than that of the primary amine. Kinetic modeling indicated that bimolecular condensation reactions of the primary amine, as well as potentially of the primary amine and the secondary amine, have a significant effect on the HDN process. Formation of secondary amine from primary amine increases the initial conversion and nitrogen removal rate but appeared to slow down the overall rate of nitrogen removal. The results thus demonstrate how condensation reactions affect amine HDN, which has implications for catalyst design for HDN of renewable feeds containing aliphatic amines.","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":"142214940","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-kl8mp
Suzanne, Blum, Pia, Lopez
Fluorescence lifetime imaging microscopy (FLIM) is an emerging tool to characterize ongoing chemical reactions in synthetic chemistry and catalysis. Initially applied to biological systems, FLIM now reveals spatially resolved chemical reaction species and system-wide physiochemical changes that accompany ongoing reactions. FLIM combines the advantage of environmental sensitivity with high signal sensitivity (as sensitive as single molecules) and has the key ability to operate under synthetic conditions (e.g., high concentrations of reagents, in organic solvents, under ambient temperature and pressure, in opaque mixtures, and in multiphasic systems). Chemical reactions inherently induce changes in the reaction medium, neighboring compounds, surface compositions, and/or the bonding structure of the compounds involved, resulting in environmental changes. The FLIM methods recently developed harness and interpret these changes in ways that lead to characterizing compounds and enhancing mechanistic understanding. Here, current advantages and limitations of FLIM method are considered, common factors influencing fluorescence lifetime in chemical systems are discussed in a tutorial format, and seven research case studies are strategically analyzed—chosen to highlight how FLIM provided complementary information to understand chemical reaction mechanisms, intermediates, product distributions, partitioning, roles of reagents, and catalyst behaviors. These data and insights obtained from FLIM assist the rational design and optimization of synthetic and catalytic methods.
{"title":"Fluorescence Lifetime Imaging Microscopy (FLIM) as a Tool to Understand Chemical Reactions and Catalysis","authors":"Suzanne, Blum, Pia, Lopez","doi":"10.26434/chemrxiv-2024-kl8mp","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-kl8mp","url":null,"abstract":"Fluorescence lifetime imaging microscopy (FLIM) is an emerging tool to characterize ongoing chemical reactions in synthetic chemistry and catalysis. Initially applied to biological systems, FLIM now reveals spatially resolved chemical reaction species and system-wide physiochemical changes that accompany ongoing reactions. FLIM combines the advantage of environmental sensitivity with high signal sensitivity (as sensitive as single molecules) and has the key ability to operate under synthetic conditions (e.g., high concentrations of reagents, in organic solvents, under ambient temperature and pressure, in opaque mixtures, and in multiphasic systems). Chemical reactions inherently induce changes in the reaction medium, neighboring compounds, surface compositions, and/or the bonding structure of the compounds involved, resulting in environmental changes. The FLIM methods recently developed harness and interpret these changes in ways that lead to characterizing compounds and enhancing mechanistic understanding. Here, current advantages and limitations of FLIM method are considered, common factors influencing fluorescence lifetime in chemical systems are discussed in a tutorial format, and seven research case studies are strategically analyzed—chosen to highlight how FLIM provided complementary information to understand chemical reaction mechanisms, intermediates, product distributions, partitioning, roles of reagents, and catalyst behaviors. These data and insights obtained from FLIM assist the rational design and optimization of synthetic and catalytic methods.","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":"142214977","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-ncqtl
Henrik, Pedersen, Nathan, O'Brien
Molecules featuring a metal centre in a positive valance surrounded by 1,3-dialkyltrianzenide ligands, Mx+(R–N=N–N–R’)x, were shown to have both high thermal stability and volatility, making them interesting as precursors in chemical vapour deposition (CVD) and atomic layer deposition (ALD). Several metals in groups 11-14 and lanthanoids form stable triazenides. So far, the In and Ga triazenides have proven to be excellent precursors for InN, In2O3, GaN and InGaN. We believe that we have only begun to explore the potential of triazenides as CVD and ALD precursors and hope to inspire further research with this perspective.
{"title":"Triazenide based metal precursors for vapour deposition","authors":"Henrik, Pedersen, Nathan, O'Brien","doi":"10.26434/chemrxiv-2024-ncqtl","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-ncqtl","url":null,"abstract":"Molecules featuring a metal centre in a positive valance surrounded by 1,3-dialkyltrianzenide ligands, Mx+(R–N=N–N–R’)x, were shown to have both high thermal stability and volatility, making them interesting as precursors in chemical vapour deposition (CVD) and atomic layer deposition (ALD). Several metals in groups 11-14 and lanthanoids form stable triazenides. So far, the In and Ga triazenides have proven to be excellent precursors for InN, In2O3, GaN and InGaN. We believe that we have only begun to explore the potential of triazenides as CVD and ALD precursors and hope to inspire further research with this perspective.","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":"142214932","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-hf343
Sandip, Murarka, Prahallad, Meher, M. Siva, Prasad, Karan Ramdas, Thombare
There is a scarcity of general strategies for the site-selective α-Csp3-H arylation of glycine derivatives to synthesize non-proteinogenic α-arylglycines that occur frequently in commercial drugs and bioactive molecules. We disclose a copper-photoredox catalyzed site-selective α-Csp3-H arylation of glycine derivatives using diaryliodonium reagents (DAIRs) as aryl transfer agents. This strategy harnesses the underexplored ability of copper catalysts to generate aryl radicals from DAIRs under sustainable conditions. The method applies to the glycine-selective C-H arylation of peptides with electronically and structurally diverse DAIRs. Moreover, we demonstrate that the photoinduced copper-catalyzed single electron transfer (SET) strategy can be coupled with the halogen atom transfer (XAT) process in the presence of alkyl iodides to accomplish site-selective α-Csp3-H alkylation of glycines and peptides. In this synergistic SET/XAT approach, phenyl radicals generated from diphenyl iodonium triflate mediate the XAT process to generate alkyl radicals from alkyl iodides. Both these methods operate under mild and sustainable conditions and exhibit broad scope with appreciable functional group tolerance. Overall, the presented divergent toolbox strategies facilitate access to various alkylated and arylated glycines and peptides and enable bioconjugation between peptides and drug molecules.
{"title":"Copper-Photoredox-Catalyzed Divergent Strategy for the Site-selective Arylation and Alkylation of Glycines and peptides","authors":"Sandip, Murarka, Prahallad, Meher, M. Siva, Prasad, Karan Ramdas, Thombare","doi":"10.26434/chemrxiv-2024-hf343","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-hf343","url":null,"abstract":"There is a scarcity of general strategies for the site-selective α-Csp3-H arylation of glycine derivatives to synthesize non-proteinogenic α-arylglycines that occur frequently in commercial drugs and bioactive molecules. We disclose a copper-photoredox catalyzed site-selective α-Csp3-H arylation of glycine derivatives using diaryliodonium reagents (DAIRs) as aryl transfer agents. This strategy harnesses the underexplored ability of copper catalysts to generate aryl radicals from DAIRs under sustainable conditions. The method applies to the glycine-selective C-H arylation of peptides with electronically and structurally diverse DAIRs. Moreover, we demonstrate that the photoinduced copper-catalyzed single electron transfer (SET) strategy can be coupled with the halogen atom transfer (XAT) process in the presence of alkyl iodides to accomplish site-selective α-Csp3-H alkylation of glycines and peptides. In this synergistic SET/XAT approach, phenyl radicals generated from diphenyl iodonium triflate mediate the XAT process to generate alkyl radicals from alkyl iodides. Both these methods operate under mild and sustainable conditions and exhibit broad scope with appreciable functional group tolerance. Overall, the presented divergent toolbox strategies facilitate access to various alkylated and arylated glycines and peptides and enable bioconjugation between peptides and drug molecules.","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":"142214942","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-cjnmw
Shuchen, Wang, Anna , Constantinou, Guanglei , Zhang, Yihuai , Zhang, Mohammad Javad , Shojaei, Bo , Zhou, Davey, Jones, Tiina, Roose, Martin, Blunt, Theoni, Georgiou, Iain , Dunlop
The current need to develop alternative agricultures that preserve soil health with a reduced contribution to climate change, has led to a growth of interest in understanding natural processes within soil. This creates a demand for 3D imaging techniques that dynamically image soil processes such as fluid and nutrient transport with high resolution. Microscale X-ray computed tomography (X-CT) delivers high-contrast and high-resolution (down to ~1 m) imaging of soil mineral phases. However it does not readily distinguish low-density aqueous and organic phases, nor image water transport. Here we have developed polymer-templated gold nanoparticles as a contrast agent to label the aqueous phase in soil, with gold selected for low toxicity. Nanoparticles are generated by templated synthesis within pre-assembled block copolymer micelles, poly(2-(dimethylamino)ethyl methacrylate)-block-poly[poly(ethylene glycol) methyl ether methacrylate)], poly(DEAEMA-b-PEGMA), to intrinsically exhibit a stabilizing PEG-bottlebrush corona. Block copolymers are generated by group transfer polymerization (GTP). Overall, this process generates gold nanoparticles at high concentrations and in large volumes for soil imaging. The nanoparticles show exceptional colloidal stability (to at least 4M ionic strength), and are stable in the challenging soil environment, showing no adsorption to the soil mineral phase. X-CT imaging within soil distinguished aqueous phase labelled with the nanoparticle contrast agent from unlabelled aqueous phase, at ~ 5 mg/ml Au. In a transport experiment, we determined the effective bulk diffusion constant of the nanoparticle system in water to be 1.1 0.3 10-10 m2s-1. Intriguingly, this is greater than the single particle diffusion constant in dilute solution, suggesting a role for crowding effects. Taken together, these results demonstrate this nanoparticle system as an effective and practical contrast agent for imaging flow and transport processes in living soil.
{"title":"A nanoparticle contrast agent enables dynamic microscale X-ray computed tomography imaging of the soil aqueous phase","authors":"Shuchen, Wang, Anna , Constantinou, Guanglei , Zhang, Yihuai , Zhang, Mohammad Javad , Shojaei, Bo , Zhou, Davey, Jones, Tiina, Roose, Martin, Blunt, Theoni, Georgiou, Iain , Dunlop","doi":"10.26434/chemrxiv-2024-cjnmw","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-cjnmw","url":null,"abstract":"The current need to develop alternative agricultures that preserve soil health with a reduced contribution to climate change, has led to a growth of interest in understanding natural processes within soil. This creates a demand for 3D imaging techniques that dynamically image soil processes such as fluid and nutrient transport with high resolution. Microscale X-ray computed tomography (X-CT) delivers high-contrast and high-resolution (down to ~1 m) imaging of soil mineral phases. However it does not readily distinguish low-density aqueous and organic phases, nor image water transport. Here we have developed polymer-templated gold nanoparticles as a contrast agent to label the aqueous phase in soil, with gold selected for low toxicity. Nanoparticles are generated by templated synthesis within pre-assembled block copolymer micelles, poly(2-(dimethylamino)ethyl methacrylate)-block-poly[poly(ethylene glycol) methyl ether methacrylate)], poly(DEAEMA-b-PEGMA), to intrinsically exhibit a stabilizing PEG-bottlebrush corona. Block copolymers are generated by group transfer polymerization (GTP). Overall, this process generates gold nanoparticles at high concentrations and in large volumes for soil imaging. The nanoparticles show exceptional colloidal stability (to at least 4M ionic strength), and are stable in the challenging soil environment, showing no adsorption to the soil mineral phase. X-CT imaging within soil distinguished aqueous phase labelled with the nanoparticle contrast agent from unlabelled aqueous phase, at ~ 5 mg/ml Au. In a transport experiment, we determined the effective bulk diffusion constant of the nanoparticle system in water to be 1.1 0.3 10-10 m2s-1. Intriguingly, this is greater than the single particle diffusion constant in dilute solution, suggesting a role for crowding effects. Taken together, these results demonstrate this nanoparticle system as an effective and practical contrast agent for imaging flow and transport processes in living soil.","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":"142214939","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}
Membrane-based technologies are widely used in oily wastewater treatment. This study selects two superhydrophilic ultrafiltration (UF) membranes (denoted M1 and M2) for oil-in-water emulsion separation and evaluates the environmental impact of membrane fabrication using life cycle assessment (LCA). Although the two membranes have similar separation performance, M1 exhibits ~40% lower environmental impacts than M2 in almost every category owing to its fewer modification steps, lower electricity use, and less solvent consumption. Electricity consumption, reactive-copolymer synthesis, and toxic-solvent use are identified as environmental hotspots in membrane fabrication. A sensitivity analysis of different energy sources reveals that coal-based electricity has the greatest environmental impact, while photovoltaic energy reduces the impact by up to 71%. Considering solvents, dimethylformamide (DMF) shows a slightly lower environmental impact than N-methyl-2-pyrrolidone (NMP).
{"title":"Fabrication of superhydrophilic membranes for oil-water separation: A life cycle assessment study","authors":"Junjie, Shen, Dixit V, Bhalani, Qian, Zhang, Yi, Yang, Suresh Kumar, Jewrajka","doi":"10.26434/chemrxiv-2024-c9w7l","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-c9w7l","url":null,"abstract":"Membrane-based technologies are widely used in oily wastewater treatment. This study selects two superhydrophilic ultrafiltration (UF) membranes (denoted M1 and M2) for oil-in-water emulsion separation and evaluates the environmental impact of membrane fabrication using life cycle assessment (LCA). Although the two membranes have similar separation performance, M1 exhibits ~40% lower environmental impacts than M2 in almost every category owing to its fewer modification steps, lower electricity use, and less solvent consumption. Electricity consumption, reactive-copolymer synthesis, and toxic-solvent use are identified as environmental hotspots in membrane fabrication. A sensitivity analysis of different energy sources reveals that coal-based electricity has the greatest environmental impact, while photovoltaic energy reduces the impact by up to 71%. Considering solvents, dimethylformamide (DMF) shows a slightly lower environmental impact than N-methyl-2-pyrrolidone (NMP).","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":"142214741","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 : 2024-09-12DOI: 10.26434/chemrxiv-2024-jnbgl
Christian, Ehinger, Christophe, Copéret
Supported catalysts are central to industrial catalytic processes. While traditional synthesis methods often yield poorly defined materials, thus complicating structural elucidation, Surface Organometallic Chemistry (SOMC) offers a solution, producing well-defined structures. Recent advances in SOMC precursor development have shown that amidinate-based precursors are a privileged class of precursors to generate supported metallic nanoparticles. In that context, this study investigates the grafting mechanism of a prototypical amidinate precursor, Ir(COD)(DIA) (1-Ir), onto SiO2. Unique to amidinate complexes, grafting is shown to occur without ligand release, creating a reversible covalent bond. Using tris(tert-butoxy)silanol as a molecular analogue for a silanol group on SiO2, the structure of the grafted species is elucidated by single X-Ray diffraction, and comparison of IR spectroscopy, and X-Ray absorption spectroscopy (XAS) data. The reversibility of the reaction with O-H groups is demonstrated using variable-temperature NMR spectroscopy, IR spectroscopy, and is supported by DFT calculations. Notably, we show that a partial degrafting is also possible at elevated temperatures under vacuum.
支撑催化剂是工业催化过程的核心。传统的合成方法通常会产生定义不清的材料，从而使结构阐释变得复杂，而表面有机金属化学（SOMC）提供了一种解决方案，可以产生定义明确的结构。SOMC 前体开发的最新进展表明，基于脒基的前体是生成支撑金属纳米颗粒的一类理想前体。在此背景下，本研究探讨了脒基前驱体 Ir(COD)(DIA) (1-Ir) 与二氧化硅的接枝机理。与脒基配合物不同的是，接枝发生时不会释放配体，从而形成可逆的共价键。利用三（叔丁氧基）硅烷醇作为二氧化硅上硅烷醇基团的分子类似物，通过单 X 射线衍射以及红外光谱和 X 射线吸收光谱 (XAS) 数据的比较，阐明了接枝物种的结构。利用变温核磁共振光谱和红外光谱证明了与 O-H 基团反应的可逆性，并得到了 DFT 计算的支持。值得注意的是，我们发现在真空条件下，部分脱嫁接反应也可以在高温下进行。
{"title":"Reversible Grafting in Surface Organometallic Chemistry with a Late Transition-Metal Amidinate Precursor","authors":"Christian, Ehinger, Christophe, Copéret","doi":"10.26434/chemrxiv-2024-jnbgl","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-jnbgl","url":null,"abstract":"Supported catalysts are central to industrial catalytic processes. While traditional synthesis methods often yield poorly defined materials, thus complicating structural elucidation, Surface Organometallic Chemistry (SOMC) offers a solution, producing well-defined structures. Recent advances in SOMC precursor development have shown that amidinate-based precursors are a privileged class of precursors to generate supported metallic nanoparticles. In that context, this study investigates the grafting mechanism of a prototypical amidinate precursor, Ir(COD)(DIA) (1-Ir), onto SiO2. Unique to amidinate complexes, grafting is shown to occur without ligand release, creating a reversible covalent bond. Using tris(tert-butoxy)silanol as a molecular analogue for a silanol group on SiO2, the structure of the grafted species is elucidated by single X-Ray diffraction, and comparison of IR spectroscopy, and X-Ray absorption spectroscopy (XAS) data. The reversibility of the reaction with O-H groups is demonstrated using variable-temperature NMR spectroscopy, IR spectroscopy, and is supported by DFT calculations. Notably, we show that a partial degrafting is also possible at elevated temperatures under vacuum.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214748","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}
Alkane monooxygenase (AlkB) is the dominant enzyme that catalyzes the oxidation of liquid alkanes in the environment. Two recent structural models derived from cryo-electron microscopy (cryo-EM) data make visible numerous attributes of the enzyme that had previously been the source of speculation. The structure of the diiron active site is unusual: a histidine-rich center that binds two iron ions without a bridging ligand. This finding makes it difficult to understand how the iron ions coordinate oxidation state changes to achieve the high-valent conditions presumed necessary to activate strong C-H bonds. To ensure that potential photoreduction and radiation damage are not responsible for the absence of a bridging ligand in the resting state cryo-EM structures, spectroscopic methods are needed. We present the results of extended x-ray absorption fine structure (EXAFS) experiments collected under conditions where photodamage was avoided. Careful data analysis reveals an active site structure consistent with the cryo-EM structures in which the two iron ions are ligated by nine histidines and are separated by at least 5 Å. The EXAFS data were used to inform structural models for molecular dynamics (MD) simulations. The MD simulations corroborate EXAFS observations that neither of the two key carboxylate-containing residues (E281 and D190) are likely candidates for metal ion bridging. To further explore the role of these carboxylate residues, we used mutagenesis experiments, spectroscopy, and additional MD simulations to understand the role of these residues. A variant in which a carboxylate containing residue (E281) was changed to a methyl residue (E281A) showed little change in pre-edge features, consistent with the observation that it is not essential for activity and hence unlikely to serve as a bridging ligand at any point in the catalytic cycle. D190 variants had substantially diminished activity, suggesting an important role in catalysis not yet fully understood.
{"title":"No Bridge Between Us: Two Distant Iron Ions Comprise the Active Site of Alkane Monooxygenase (AlkB)","authors":"Clorice, Reinhardt, Juliet, Lee, Noga, Rafalin, Naomi, Miller, August, Jaunzarins Roberts, Lily, Kunczynski, Tierani, Green, Heather, Kulik, Christopher, Pollock, Rachel, Narehood Austin, Lauren, Hendricks","doi":"10.26434/chemrxiv-2024-301wv","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-301wv","url":null,"abstract":"Alkane monooxygenase (AlkB) is the dominant enzyme that catalyzes the oxidation of liquid alkanes in the environment. Two recent structural models derived from cryo-electron microscopy (cryo-EM) data make visible numerous attributes of the enzyme that had previously been the source of speculation. The structure of the diiron active site is unusual: a histidine-rich center that binds two iron ions without a bridging ligand. This finding makes it difficult to understand how the iron ions coordinate oxidation state changes to achieve the high-valent conditions presumed necessary to activate strong C-H bonds. To ensure that potential photoreduction and radiation damage are not responsible for the absence of a bridging ligand in the resting state cryo-EM structures, spectroscopic methods are needed. We present the results of extended x-ray absorption fine structure (EXAFS) experiments collected under conditions where photodamage was avoided. Careful data analysis reveals an active site structure consistent with the cryo-EM structures in which the two iron ions are ligated by nine histidines and are separated by at least 5 Å. The EXAFS data were used to inform structural models for molecular dynamics (MD) simulations. The MD simulations corroborate EXAFS observations that neither of the two key carboxylate-containing residues (E281 and D190) are likely candidates for metal ion bridging. To further explore the role of these carboxylate residues, we used mutagenesis experiments, spectroscopy, and additional MD simulations to understand the role of these residues. A variant in which a carboxylate containing residue (E281) was changed to a methyl residue (E281A) showed little change in pre-edge features, consistent with the observation that it is not essential for activity and hence unlikely to serve as a bridging ligand at any point in the catalytic cycle. D190 variants had substantially diminished activity, suggesting an important role in catalysis not yet fully understood.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214785","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}
Dialkylamido compounds, such as tris-dimethylamido aluminum (TDMAA, Al(NMe2)3) and tetrakis-dimethylamido titanium (TDMAT, Ti(NMe2)4) are interesting precursors for depositing nitrides using atomic layer deposition (ALD) due to their high volatility and reactivity at low temperatures. In this study, we explored surface chemistry using mass spectrometry and discovered that the surface mechanisms involved β-hydride elimination and ligand decomposition, as well as transamination and hydrogenation reactions which facilitate ligand exchange. This is mainly based on the -N(Me)2 and HN(Me)2 detected during both TDMAA and NH3 pulses, and CH4 signals detected during the NH3 pulse stage. The expected reductive elimination of the two dimethylamido ligands, via a direct nitrogen-nitrogen coupling reaction was not observed, suggesting that it is less thermodynamically favorable compared to reduction by NH3. Arrhenius analysis between 150 and 300 °C found activation energies (Ea) = 27-30 kJmol-1 and pre-exponential factors (A) = 3-5 s-1 suggesting for the reaction between TDMAA and NH₃.
{"title":"A Mass Spectrometrical Surface Chemistry Study of Aluminum Nitride ALD from Tris-Dimethylamido Aluminum and Ammonia","authors":"Henrik, Pedersen, Pamburayi, Mpofu, Houyem, Hafdi, Jonas, Lauridsen, Oscar, Alm, Tommy, Larsson","doi":"10.26434/chemrxiv-2024-f4c4k","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-f4c4k","url":null,"abstract":"Dialkylamido compounds, such as tris-dimethylamido aluminum (TDMAA, Al(NMe2)3) and tetrakis-dimethylamido titanium (TDMAT, Ti(NMe2)4) are interesting precursors for depositing nitrides using atomic layer deposition (ALD) due to their high volatility and reactivity at low temperatures. In this study, we explored surface chemistry using mass spectrometry and discovered that the surface mechanisms involved β-hydride elimination and ligand decomposition, as well as transamination and hydrogenation reactions which facilitate ligand exchange. This is mainly based on the -N(Me)2 and HN(Me)2 detected during both TDMAA and NH3 pulses, and CH4 signals detected during the NH3 pulse stage. The expected reductive elimination of the two dimethylamido ligands, via a direct nitrogen-nitrogen coupling reaction was not observed, suggesting that it is less thermodynamically favorable compared to reduction by NH3. Arrhenius analysis between 150 and 300 °C found activation energies (Ea) = 27-30 kJmol-1 and pre-exponential factors (A) = 3-5 s-1 suggesting for the reaction between TDMAA and NH₃.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214746","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 : 2024-09-12DOI: 10.26434/chemrxiv-2024-9m6nj
Andrés, Rodríguez-Camargo, Maxwell W., Terban, Martina, Paetsch, Elio A., Rico, Radhika, Hirpara, Viola, Duppel, Igor, Moudrakovski, Martin, Etter, Néstor, Guijarro, Robert E., Dinnebier, Liang, Yao, Bettina V., Lotsch
Covalent organic frameworks (COFs) have been extensively developed as photosensitizers for photocatalytic energy conversion over the past decade. However, current COF photocatalysts have yet to demonstrate the capability to harvest near-infrared (NIR) light (above 760 nm), which constitutes approximately 53% of the solar spectrum, for fuel or chemical conversion. In this work, we introduce a novel post-synthetic functionalization strategy for COFs by incorporating a palladacycle directly into the COF backbone, extending the light absorption of an azobenzene-based COF into the NIR region. This approach enables homogeneous, atomically-distributed Pd functionalization with a high loading amount of 12 wt% and without noticeable formation of Pd nanoparticles. The cyclopalladated COF, TpAzo-CPd, was utilized as a catalyst for photocatalytic hydrogen peroxide production under 810 nm illumination. This study represents the first implementation of COFs for NIR photocatalysis and opens the door to Pd-single-site COF catalysts for a wide range of organic transformations.
{"title":"Cyclopalladation of a Covalent Organic Framework for Near-Infrared Light-Driven Photocatalytic Hydrogen Peroxide Production","authors":"Andrés, Rodríguez-Camargo, Maxwell W., Terban, Martina, Paetsch, Elio A., Rico, Radhika, Hirpara, Viola, Duppel, Igor, Moudrakovski, Martin, Etter, Néstor, Guijarro, Robert E., Dinnebier, Liang, Yao, Bettina V., Lotsch","doi":"10.26434/chemrxiv-2024-9m6nj","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-9m6nj","url":null,"abstract":"Covalent organic frameworks (COFs) have been extensively developed as photosensitizers for photocatalytic energy conversion over the past decade. However, current COF photocatalysts have yet to demonstrate the capability to harvest near-infrared (NIR) light (above 760 nm), which constitutes approximately 53% of the solar spectrum, for fuel or chemical conversion. In this work, we introduce a novel post-synthetic functionalization strategy for COFs by incorporating a palladacycle directly into the COF backbone, extending the light absorption of an azobenzene-based COF into the NIR region. This approach enables homogeneous, atomically-distributed Pd functionalization with a high loading amount of 12 wt% and without noticeable formation of Pd nanoparticles. The cyclopalladated COF, TpAzo-CPd, was utilized as a catalyst for photocatalytic hydrogen peroxide production under 810 nm illumination. This study represents the first implementation of COFs for NIR photocatalysis and opens the door to Pd-single-site COF catalysts for a wide range of organic transformations.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214747","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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