Triple tube heat exchangers (TTHEs) are suitable equipment for thick viscosity products, with or without particulates, with various applications in the food and pharmaceutical industries. Of less widespread use than double tube heat exchangers (DTHEs), they generally perform better when compared to the latter. However, in the case of thermal models of "TTHEs with heat loss to the surroundings" (TTHEs-HL), there is no analytical solution in which the character of the roots has been analyzed. - except for the analogous problem of a "tubular moving bed heat exchanger, indirectly heated and with heat loss to the surroundings " (MBHE-HL), but only for certain flow arrangements -. Thus, it is not certain that the known solutions are of general application. Furthermore, regarding the important design parameter for co-current flow TTHEs, the crossover point, very little is known for TTHEs-HL. Also, recently published analogies provide an opportunity to synergistically increase the knowledge of TTHEs and MBHEs, for the case of non-adiabatic external surface. Aware of these needs and opportunities, the present work starts from a known analytical solution for a MBHE-HL thermal model and, by analogy, develops a compact form of an analytical solution for TTHE-HL, suitable for co-current and counter-current flow arrangements. The character analysis of the roots - not trivial for this solution - is performed according to a methodology recently described in the literature, consisting of several mathematical techniques. Approximate expressions for crossover point and temperature equality point between streams are obtained. In the case studies, the values calculated by the analytical solution and by a numerical solution by the finite analytical method (FAM), were shown to be very close. For the flow arrangements analyzed, it was possible to conclude about the generality of the solutions, in addition, the analogies between MBHE and TTHE made it possible to advance in the understanding of the thermal operation of these equipments. For a better understanding of the underlying physics, a scale analysis was performed.
{"title":"A simple solution form for triple tube heat exchanger with non-adiabatic condition on the outer wall by analogy with moving bed heat exchanger","authors":"Natan, Padoin, Cíntia, Soares, Sávio, Bertoli, Jesús, Apolinar-Hernández","doi":"10.26434/chemrxiv-2024-f5ngq","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-f5ngq","url":null,"abstract":"Triple tube heat exchangers (TTHEs) are suitable equipment for thick viscosity products, with or without particulates, with various applications in the food and pharmaceutical industries. Of less widespread use than double tube heat exchangers (DTHEs), they generally perform better when compared to the latter. However, in the case of thermal models of \"TTHEs with heat loss to the surroundings\" (TTHEs-HL), there is no analytical solution in which the character of the roots has been analyzed. - except for the analogous problem of a \"tubular moving bed heat exchanger, indirectly heated and with heat loss to the surroundings \" (MBHE-HL), but only for certain flow arrangements -. Thus, it is not certain that the known solutions are of general application. Furthermore, regarding the important design parameter for co-current flow TTHEs, the crossover point, very little is known for TTHEs-HL. Also, recently published analogies provide an opportunity to synergistically increase the knowledge of TTHEs and MBHEs, for the case of non-adiabatic external surface. Aware of these needs and opportunities, the present work starts from a known analytical solution for a MBHE-HL thermal model and, by analogy, develops a compact form of an analytical solution for TTHE-HL, suitable for co-current and counter-current flow arrangements. The character analysis of the roots - not trivial for this solution - is performed according to a methodology recently described in the literature, consisting of several mathematical techniques. Approximate expressions for crossover point and temperature equality point between streams are obtained. In the case studies, the values calculated by the analytical solution and by a numerical solution by the finite analytical method (FAM), were shown to be very close. For the flow arrangements analyzed, it was possible to conclude about the generality of the solutions, in addition, the analogies between MBHE and TTHE made it possible to advance in the understanding of the thermal operation of these equipments. For a better understanding of the underlying physics, a scale analysis was performed.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267310","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}
A convenient, inexpensive synthesis of the previously reported and well-defined complex Ni(tmeda)(o-tol)Cl is described. This protocol enables rapid and safe access to Ni(tmeda)(o-tol)Cl, obviating the use of the hazardous reagent AlMe3 or the air-sensitive Ni(COD)2. Ni(tmeda)(o-tol) is prepared, from the commercially available and easily synthesized precursor, Ni(acac)2 at room temperature and the product can be isolated at gram scale in air via simple filtration. We expect this simple method to be attractive to chemical industry and academia given the types of solvents, reaction temperature and reagents used.
{"title":"A Practical, Large Scale Preparation of Ni(tmeda)(o-tol)Cl","authors":"Scott, Stewart, Morgan, John, Daven , Foster, Stephen, Moggach, George , Koutsantonis, Reto, Dorta","doi":"10.26434/chemrxiv-2024-pw0pg","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-pw0pg","url":null,"abstract":"A convenient, inexpensive synthesis of the previously reported and well-defined complex Ni(tmeda)(o-tol)Cl is described. This protocol enables rapid and safe access to Ni(tmeda)(o-tol)Cl, obviating the use of the hazardous reagent AlMe3 or the air-sensitive Ni(COD)2. Ni(tmeda)(o-tol) is prepared, from the commercially available and easily synthesized precursor, Ni(acac)2 at room temperature and the product can be isolated at gram scale in air via simple filtration. We expect this simple method to be attractive to chemical industry and academia given the types of solvents, reaction temperature and reagents used.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267376","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 era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant role of graphical processing units (GPUs), demands a fundamental shift in software development strategies. This review examines the changing landscape of hardware and software for exascale computing, highlighting the limitations of traditional algorithms and software implementations in light of the increasing use of heterogeneous architectures in high-end systems. We discuss the challenges of adapting quantum chemistry software to these new architectures, including the fragmentation of the software stack, the need for more efficient algorithms (including reduced precision versions) tailored for GPUs, and the importance of developing standardized libraries and programming models.
{"title":"Exascale Quantum Mechanical Simulations: Navigating the Shifting Sands of Hardware and Software","authors":"Ravindra, Shinde, Claudia, Filippi, Anthony, Scemama, William, Jalby","doi":"10.26434/chemrxiv-2024-qcgfd-v2","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-qcgfd-v2","url":null,"abstract":"The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant role of graphical processing units (GPUs), demands a fundamental shift in software development strategies. This review examines the changing landscape of hardware and software for exascale computing, highlighting the limitations of traditional algorithms and software implementations in light of the increasing use of heterogeneous architectures in high-end systems. We discuss the challenges of adapting quantum chemistry software to these new architectures, including the fragmentation of the software stack, the need for more efficient algorithms (including reduced precision versions) tailored for GPUs, and the importance of developing standardized libraries and programming models.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267137","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 reactivity of the phosphinoborenium cation supported by a 1,3,4,5-tetramethylimidazolin-2-ylidene ligand toward small molecules was explored. The phosphinoborenium cation exhibited dual Lewis acid–base properties due to the presence of the Lewis acidic boron center and the Lewis basic phosphido ligand connected by a covalent bond. The reaction of the title cation with CO2 led to the insertion of a CO2 molecule into the P-B bond. The obtained borenium CO2-adduct underwent hydrolysis, forming an N-heterocyclic carbene stabilized diborenium dication bearing a B-O-B functionality. The activation of N2O proceeded via the insertion of an oxygen atom into the B-P bond of the parent cation, yielding a borenium cation with a phosphinite moiety. An alternative synthetic pathway to borenium cations with a B-O-P skeleton was achieved via the activation of secondary phosphine oxides by the phosphinoborenium cation. Furthermore, borenium cations and diborenium dications with B-O-C structural motifs were obtained from the reaction of the title compound with perfluorinated tert-butyl alcohol and hydroquinone, respectively. The structure of the obtained borenium cations is discussed based on multinuclear NMR spectroscopy, X-ray diffraction, and density functional theory calculations.
{"title":"Activation of small molecules by ambiphilic NHC-stabilized phosphinoborenium cation: formation of boreniums with B-O-C, B-O-B, and B-O-P structural motifs","authors":"Rafał, Grubba, Tomasz, Wojnowski, Anna, Ordyszewska, Hanna, Halenka, Iwona, Anusiewicz, Jarosław, Chojnacki, Kinga, Kaniewska-Laskowska","doi":"10.26434/chemrxiv-2024-qwnb2","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-qwnb2","url":null,"abstract":"The reactivity of the phosphinoborenium cation supported by a 1,3,4,5-tetramethylimidazolin-2-ylidene ligand toward small molecules was explored. The phosphinoborenium cation exhibited dual Lewis acid–base properties due to the presence of the Lewis acidic boron center and the Lewis basic phosphido ligand connected by a covalent bond. The reaction of the title cation with CO2 led to the insertion of a CO2 molecule into the P-B bond. The obtained borenium CO2-adduct underwent hydrolysis, forming an N-heterocyclic carbene stabilized diborenium dication bearing a B-O-B functionality. The activation of N2O proceeded via the insertion of an oxygen atom into the B-P bond of the parent cation, yielding a borenium cation with a phosphinite moiety. An alternative synthetic pathway to borenium cations with a B-O-P skeleton was achieved via the activation of secondary phosphine oxides by the phosphinoborenium cation. Furthermore, borenium cations and diborenium dications with B-O-C structural motifs were obtained from the reaction of the title compound with perfluorinated tert-butyl alcohol and hydroquinone, respectively. The structure of the obtained borenium cations is discussed based on multinuclear NMR spectroscopy, X-ray diffraction, and density functional theory calculations.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267249","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 : 2024-09-19DOI: 10.26434/chemrxiv-2024-q6b3g
Lichang, Wang, Junpeng, Zhuang
Encouraged by the superior performance of the D-A-A-D dimer in generating Wannier excitons, we developed a new motif to construct A-D-D-A type organic small molecules. The donor moieties consist of 4,4’-dimethyl-4”-((4-amino)styryl)-triphenylamine, while the acceptor is an s-triazine derivative. DFT studies, using two detection techniques, confirmed that a pair of Wannier exictons is generated in one of the newly designed compounds studied here. Based on the analysis of molecular orbitals and the UV-Vis spectrum, A-D-D-A-2 has been identified as the Wannier molecule. Although A-D-D-A-1 is not confirmed as a Wannier molecule based on the molecular orbital inspection, it may still generate Wannier excitons; however further studies with new techniques are needed to confirm this. A brief discussion of the double excitation in A-D-D-A-2 is also provided. The motif used in the formation of Wannier molecules of A-D-D-A type dimers, i.e. A-D-D-A-2, is the same motif as in the other high performing organic small molecules. This suggests that these high-performance organic molecules may already generate Wannier excitons, which could be the primary reason for their exceptional performance as photosensitizers in solar cells.
{"title":"A Motif for Generating Coherently Degenerate States in A-D-D-A Type Organic Small Molecules","authors":"Lichang, Wang, Junpeng, Zhuang","doi":"10.26434/chemrxiv-2024-q6b3g","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-q6b3g","url":null,"abstract":"Encouraged by the superior performance of the D-A-A-D dimer in generating Wannier excitons, we developed a new motif to construct A-D-D-A type organic small molecules. The donor moieties consist of 4,4’-dimethyl-4”-((4-amino)styryl)-triphenylamine, while the acceptor is an s-triazine derivative. DFT studies, using two detection techniques, confirmed that a pair of Wannier exictons is generated in one of the newly designed compounds studied here. Based on the analysis of molecular orbitals and the UV-Vis spectrum, A-D-D-A-2 has been identified as the Wannier molecule. Although A-D-D-A-1 is not confirmed as a Wannier molecule based on the molecular orbital inspection, it may still generate Wannier excitons; however further studies with new techniques are needed to confirm this. A brief discussion of the double excitation in A-D-D-A-2 is also provided. The motif used in the formation of Wannier molecules of A-D-D-A type dimers, i.e. A-D-D-A-2, is the same motif as in the other high performing organic small molecules. This suggests that these high-performance organic molecules may already generate Wannier excitons, which could be the primary reason for their exceptional performance as photosensitizers in solar cells.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267375","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}
Here we report an efficient and practical protocol for the generation of halo radicals (Br and Cl) using inexpensive and readily available NXS/TBHP reagent system at rt. The halo radicals were further utilized for the site-selective C-H bromination and chlorination of the unexplored benzo-core of quinoxalinones. This protocol offers excellent regioselectivity towards C7 position of benzo-core over readily functionalized C3 position in hetero-core of quinoxalinones under mild reaction conditions. Notably, this transformation showed good functional group compatibility and a wide substrate scope. Further, selective synthesis of gem-dihaloketones from alkynes has been accomplished using the same reagent system.
{"title":"Metal-free generation of halogen radicals using NXS/TBHP: Application in site-selective halogenation of quinoxalin-2(1H)-ones and synthesis of gem-dihaloketones","authors":"Navin, Yadav, Jarugu Narasimha, Moorthy, Ajay Kumar, Sahoo, Debarghya, Sarkar","doi":"10.26434/chemrxiv-2024-jqq3t","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-jqq3t","url":null,"abstract":"Here we report an efficient and practical protocol for the generation of halo radicals (Br and Cl) using inexpensive and readily available NXS/TBHP reagent system at rt. The halo radicals were further utilized for the site-selective C-H bromination and chlorination of the unexplored benzo-core of quinoxalinones. This protocol offers excellent regioselectivity towards C7 position of benzo-core over readily functionalized C3 position in hetero-core of quinoxalinones under mild reaction conditions. Notably, this transformation showed good functional group compatibility and a wide substrate scope. Further, selective synthesis of gem-dihaloketones from alkynes has been accomplished using the same reagent system.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267250","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 : 2024-09-19DOI: 10.26434/chemrxiv-2024-zzs16
Lei, Sun, Xiya, Du
Lanthanide-based spin qubits are intriguing candidates for high-fidelity quantum memories owing to their spin-optical interfaces. Metal−organic frameworks (MOFs) offer promising solid-state platforms to host lanthanide ions because their bottom-up synthesis enables rational optimization of both spin coherence and luminescence. Here, we incorporated Nd3+ and Gd3+ into a La3+-based MOF with various doping levels and examined their qubit performance including the spin relaxation time (T1) and phase memory time (Tm). Both Nd3+ and Gd3+ behave as spin qubits with T1 exceeding 1 ms and Tm approaching 2 μs at 3.2 K under low doping levels. Variable-temperature spin dynamic studies unveiled spin relaxation and decoherence mechanisms, highlighting critical roles of spin-phonon coupling and spin-spin dipolar coupling. Accordingly, reducing the spin concentration, spin-orbit coupling strength, and ground spin state improves the qubit performance of lanthanide-based MOFs. These optimization strategies serve as guidelines for future development of solid-state lanthanide qubits targeting quantum information technologies.
{"title":"Optimizing spin qubit performance of lanthanide-based metal−organic frameworks","authors":"Lei, Sun, Xiya, Du","doi":"10.26434/chemrxiv-2024-zzs16","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-zzs16","url":null,"abstract":"Lanthanide-based spin qubits are intriguing candidates for high-fidelity quantum memories owing to their spin-optical interfaces. Metal−organic frameworks (MOFs) offer promising solid-state platforms to host lanthanide ions because their bottom-up synthesis enables rational optimization of both spin coherence and luminescence. Here, we incorporated Nd3+ and Gd3+ into a La3+-based MOF with various doping levels and examined their qubit performance including the spin relaxation time (T1) and phase memory time (Tm). Both Nd3+ and Gd3+ behave as spin qubits with T1 exceeding 1 ms and Tm approaching 2 μs at 3.2 K under low doping levels. Variable-temperature spin dynamic studies unveiled spin relaxation and decoherence mechanisms, highlighting critical roles of spin-phonon coupling and spin-spin dipolar coupling. Accordingly, reducing the spin concentration, spin-orbit coupling strength, and ground spin state improves the qubit performance of lanthanide-based MOFs. These optimization strategies serve as guidelines for future development of solid-state lanthanide qubits targeting quantum information technologies.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267246","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 : 2024-09-19DOI: 10.26434/chemrxiv-2024-78n0x
Shannon, Stahl, Luana , Cardinale, Gregory L., Beutner, Christopher Y., Bemis, Daniel J., Weix
Sacrificial anodes composed of inexpensive metals such as Zn, Fe and Mg are widely used to support electrochemical nickel-catalyzed cross-electrophile coupling (XEC) reactions, in addition to other reductive electrochemical transformations. Such anodes are appealing because they provide a stable counter-electrode potential and typically avoid interference with the reductive chemistry. The present study outlines development of an electrochemical Ni-catalyzed XEC reaction that streamlines access to a key pharmaceutical intermediate. Metal ions derived from sacrificial anode oxidation, however, directly contribute to homocoupling and proto-dehalogenation side products that are commonly formed in chemical and electrochemical Ni-catalyzed XEC reactions. Use of a divided cell limits interference by the anode-derived metal ions and supports high product yield with negligible side product formation, introducing a strategy to overcome one of the main limitations of Ni-catalyzed XEC.
{"title":"Non-Innocent Role of Sacrificial Anodes in Electrochemical Nickel-Catalyzed C(sp2)-C(sp3) Cross-Electrophile Coupling","authors":"Shannon, Stahl, Luana , Cardinale, Gregory L., Beutner, Christopher Y., Bemis, Daniel J., Weix","doi":"10.26434/chemrxiv-2024-78n0x","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-78n0x","url":null,"abstract":"Sacrificial anodes composed of inexpensive metals such as Zn, Fe and Mg are widely used to support electrochemical nickel-catalyzed cross-electrophile coupling (XEC) reactions, in addition to other reductive electrochemical transformations. Such anodes are appealing because they provide a stable counter-electrode potential and typically avoid interference with the reductive chemistry. The present study outlines development of an electrochemical Ni-catalyzed XEC reaction that streamlines access to a key pharmaceutical intermediate. Metal ions derived from sacrificial anode oxidation, however, directly contribute to homocoupling and proto-dehalogenation side products that are commonly formed in chemical and electrochemical Ni-catalyzed XEC reactions. Use of a divided cell limits interference by the anode-derived metal ions and supports high product yield with negligible side product formation, introducing a strategy to overcome one of the main limitations of Ni-catalyzed XEC.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267242","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 : 2024-09-19DOI: 10.26434/chemrxiv-2024-cw1tt
Zisheng, Zhang, Winston, Gee, Robert H., Lavroff, Anastassia N., Alexandrova
Restructuring of surfaces and interfaces underlie the activation and/or deactivation of a wide spectrum of heterogeneous catalysts and functional materials. The statistical ensemble representation can provide unique atomistic insights into this fluxional and metastable realm, but constructing the ensemble is very challenging, especially for the systems with off-stoichiometric reconstruction and varying coverage of mixed adsorbates. Here we report GOCIA, a general-purpose global optimizer for exploring the chemical space of these systems. It features the grand canonical genetic algorithm (GCGA), which bases the target function on the grand potential and evolves across the compositional space, as well as many useful functionalities and implementation details. GOCIA has been applied to various systems in catalysis, from cluster to surfaces, and from thermal to electro-catalysis.
{"title":"GOCIA: grand canonical Global Optimizer for Clusters, Interfaces, and Adsorbates","authors":"Zisheng, Zhang, Winston, Gee, Robert H., Lavroff, Anastassia N., Alexandrova","doi":"10.26434/chemrxiv-2024-cw1tt","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-cw1tt","url":null,"abstract":"Restructuring of surfaces and interfaces underlie the activation and/or deactivation of a wide spectrum of heterogeneous catalysts and functional materials. The statistical ensemble representation can provide unique atomistic insights into this fluxional and metastable realm, but constructing the ensemble is very challenging, especially for the systems with off-stoichiometric reconstruction and varying coverage of mixed adsorbates. Here we report GOCIA, a general-purpose global optimizer for exploring the chemical space of these systems. It features the grand canonical genetic algorithm (GCGA), which bases the target function on the grand potential and evolves across the compositional space, as well as many useful functionalities and implementation details. GOCIA has been applied to various systems in catalysis, from cluster to surfaces, and from thermal to electro-catalysis.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267370","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 : 2024-09-19DOI: 10.26434/chemrxiv-2024-t3bp9
Robin S., Bon, Aidan V., Johnson, Sebastian Alin, Porav, Kasia L. R., Hammond, Anokhi, Shah, Joshua L., Wort, Yue, Ma, Hassane, El Mkami, Christopher M., Pask, Stephen P., Muench, Andrew J., Wilson, Christos, Pliotas
Electron paramagnetic resonance (EPR) spectroscopy is a powerful technique for the study of proteins in solution and under native conditions. Paramagnetic spin centres are usually introduced by site-directed spin labelling (SDSL) of engineered cysteine residues. However, for many (membrane) protein classes, cysteine engineering is not possible without affecting their structural and functional integrity. Here, we report the development of xanthine-based aminoxyl spin probes that allow non-covalent spin labelling of human TRPC5 ion channels. The compounds retained high potency as TRPC5 modulators and allowed assessment of ligand interaction and inter-ligand distances by continuous wave EPR (CW EPR) and double electron-electron resonance (DEER) spectroscopy. The results from EPR experiments were supported by high-resolution cryo-electron microscopy (cryoEM) structures of the TRPC5:spin probe complexes. This work shows that non-covalent, ligand-based spin labelling can be used for EPR studies of large, cysteine-rich membrane proteins and their complexes.
{"title":"Non-covalent spin labelling of TRPC5 ion channels enables EPR studies of protein-ligand interactions","authors":"Robin S., Bon, Aidan V., Johnson, Sebastian Alin, Porav, Kasia L. R., Hammond, Anokhi, Shah, Joshua L., Wort, Yue, Ma, Hassane, El Mkami, Christopher M., Pask, Stephen P., Muench, Andrew J., Wilson, Christos, Pliotas","doi":"10.26434/chemrxiv-2024-t3bp9","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-t3bp9","url":null,"abstract":"Electron paramagnetic resonance (EPR) spectroscopy is a powerful technique for the study of proteins in solution and under native conditions. Paramagnetic spin centres are usually introduced by site-directed spin labelling (SDSL) of engineered cysteine residues. However, for many (membrane) protein classes, cysteine engineering is not possible without affecting their structural and functional integrity. Here, we report the development of xanthine-based aminoxyl spin probes that allow non-covalent spin labelling of human TRPC5 ion channels. The compounds retained high potency as TRPC5 modulators and allowed assessment of ligand interaction and inter-ligand distances by continuous wave EPR (CW EPR) and double electron-electron resonance (DEER) spectroscopy. The results from EPR experiments were supported by high-resolution cryo-electron microscopy (cryoEM) structures of the TRPC5:spin probe complexes. This work shows that non-covalent, ligand-based spin labelling can be used for EPR studies of large, cysteine-rich membrane proteins and their complexes.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267238","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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