Johanna P. Carbone, Andreas Irmler, Alejandro Gallo, Tobias Schäfer, William Z. Van Benschoten, James J. Shepherd and Andreas Grüneis
{"title":"CO adsorption on Pt(111) studied by periodic coupled cluster theory","authors":"Johanna P. Carbone, Andreas Irmler, Alejandro Gallo, Tobias Schäfer, William Z. Van Benschoten, James J. Shepherd and Andreas Grüneis","doi":"10.1039/D4FD00085D","DOIUrl":"10.1039/D4FD00085D","url":null,"abstract":"<p >We present an application of periodic coupled-cluster theory to the calculation of CO adsorption energies on the Pt(111) surface for different adsorption sites. The calculations employ a range of recently developed theoretical and computational methods. In particular, we use a recently introduced coupled-cluster ansatz, denoted as CCSD(cT), to compute correlation energies of the metallic Pt surface with and without adsorbed CO molecules. The convergence of Hartree–Fock adsorption energy contributions with respect to randomly shifted <em>k</em>-meshes is discussed. Recently introduced basis set incompleteness error corrections make it possible to achieve well-converged correlation energy contributions to the adsorption energies. We show that CCSD(cT) theory predicts the correct order of adsorption energies for the considered adsorption sites. Furthermore, we find that binding of the CO molecule to the top and fcc site is dominated by Hartree–Fock and correlation energy contributions, respectively.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"254 ","pages":" 586-597"},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11339635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Magdalena Abramiuk, Carlos Acevedo-Rocha, Abdulrahman Alogaidi, Fraser Armstrong, Amulyasai Bakshi, Uwe T. Bornscheuer, Dominic J. Campopiano, Pimchai Chaiyen, Friedrich Johannes Ehinger, Sabine Flitsch, Jeremy N. Harvey, Donald Hilvert, Amanda G. Jarvis, Rhiannon E. H. Jones, Bruce R. Lichtenstein, Louis Y. P. Luk, Tara C. Lurshay, Thomas Malcomson, E. Neil G. Marsh, Neil R. McFarlane, Alexander McKenzie, Clare F. Megarity, Vicent Moliner, Adrian J. Mulholland, Ben Orton, Joelle N. Pelletier, Agata Raczyńska, Per-Olof Syrén, Sean Adeoti Thompson, Nicholas Turner, Francesca Valetti, Lu Shin Wong and Cathleen Zeymer
{"title":"Biocatalytic pathways, cascades, cells and systems: general discussion","authors":"Magdalena Abramiuk, Carlos Acevedo-Rocha, Abdulrahman Alogaidi, Fraser Armstrong, Amulyasai Bakshi, Uwe T. Bornscheuer, Dominic J. Campopiano, Pimchai Chaiyen, Friedrich Johannes Ehinger, Sabine Flitsch, Jeremy N. Harvey, Donald Hilvert, Amanda G. Jarvis, Rhiannon E. H. Jones, Bruce R. Lichtenstein, Louis Y. P. Luk, Tara C. Lurshay, Thomas Malcomson, E. Neil G. Marsh, Neil R. McFarlane, Alexander McKenzie, Clare F. Megarity, Vicent Moliner, Adrian J. Mulholland, Ben Orton, Joelle N. Pelletier, Agata Raczyńska, Per-Olof Syrén, Sean Adeoti Thompson, Nicholas Turner, Francesca Valetti, Lu Shin Wong and Cathleen Zeymer","doi":"10.1039/D4FD90023E","DOIUrl":"10.1039/D4FD90023E","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"252 ","pages":" 241-261"},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gil Alexandrowicz, Dmitri Babikov, Mark Brouard, Alexander Butler, Helen Chadwick, David W. Chandler, Michal Fárník, Jan Fingerhut, Hua Guo, Tibor Győri, Christian T. Haakansson, Dan J. Harding, Dwayne Heard, Brianna R. Heazlewood, David Heathcote, Nils Hertl, Pablo G. Jambrina, Geert-Jan Kroes, Olivia A. Krohn, Paul D. Lane, Viet Le Duc, Heather J. Lewandowski, Jérôme Loreau, Max McCrea, Kenneth G. McKendrick, Jennifer Meyer, Daniel R. Moon, Amy S. Mullin, Gilbert M. Nathanson, Daniel M. Neumark, Kang-Kuen Ni, Nitish Pal, Eva Pluhařová, Christopher Reilly, Patrick Robertson, Steven J. Sibener, Chris Sparling, Vimala Sridurai, Ajeet Srivastav, Matt Strutton, Arthur G. Suits, Joshua Wagner, Peter D. Watson, Roland Wester, Stefan Willitsch, Alec. M. Wodtke and Bum Suk Zhao
{"title":"Scattering in extreme environments: general discussion","authors":"Gil Alexandrowicz, Dmitri Babikov, Mark Brouard, Alexander Butler, Helen Chadwick, David W. Chandler, Michal Fárník, Jan Fingerhut, Hua Guo, Tibor Győri, Christian T. Haakansson, Dan J. Harding, Dwayne Heard, Brianna R. Heazlewood, David Heathcote, Nils Hertl, Pablo G. Jambrina, Geert-Jan Kroes, Olivia A. Krohn, Paul D. Lane, Viet Le Duc, Heather J. Lewandowski, Jérôme Loreau, Max McCrea, Kenneth G. McKendrick, Jennifer Meyer, Daniel R. Moon, Amy S. Mullin, Gilbert M. Nathanson, Daniel M. Neumark, Kang-Kuen Ni, Nitish Pal, Eva Pluhařová, Christopher Reilly, Patrick Robertson, Steven J. Sibener, Chris Sparling, Vimala Sridurai, Ajeet Srivastav, Matt Strutton, Arthur G. Suits, Joshua Wagner, Peter D. Watson, Roland Wester, Stefan Willitsch, Alec. M. Wodtke and Bum Suk Zhao","doi":"10.1039/D4FD90018A","DOIUrl":"10.1039/D4FD90018A","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"251 ","pages":" 171-204"},"PeriodicalIF":3.4,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Daniel J. Auerbach, Dmitri Babikov, Alexander Butler, David W. Chandler, Jan Fingerhut, Hua Guo, Dan J. Harding, David Heathcote, Nils Hertl, Bin Jiang, Geert-Jan Kroes, Paul D. Lane, Jérôme Loreau, Stuart R. Mackenzie, Kenneth G. McKendrick, Daniel R. Moon, Gilbert M. Nathanson, Daniel M. Neumark, Rahul Pandey, George C. Schatz, Steven J. Sibener, Ajeet Srivastav, Claire Vallance, Robert A. B. van Bree, Joshua Wagner, Gilbert C. Walker, Peter D. Watson, Stefan Willitsch, Alec M. Wodtke and Bum Suk Zhao
{"title":"Scattering at condensed-phase surfaces: general discussion","authors":"Daniel J. Auerbach, Dmitri Babikov, Alexander Butler, David W. Chandler, Jan Fingerhut, Hua Guo, Dan J. Harding, David Heathcote, Nils Hertl, Bin Jiang, Geert-Jan Kroes, Paul D. Lane, Jérôme Loreau, Stuart R. Mackenzie, Kenneth G. McKendrick, Daniel R. Moon, Gilbert M. Nathanson, Daniel M. Neumark, Rahul Pandey, George C. Schatz, Steven J. Sibener, Ajeet Srivastav, Claire Vallance, Robert A. B. van Bree, Joshua Wagner, Gilbert C. Walker, Peter D. Watson, Stefan Willitsch, Alec M. Wodtke and Bum Suk Zhao","doi":"10.1039/D4FD90020K","DOIUrl":"10.1039/D4FD90020K","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"251 ","pages":" 471-508"},"PeriodicalIF":3.4,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F. Javier Aoiz, Nadia Balucani, Astrid Bergeat, Alexander Butler, David W. Chandler, Gábor Czakó, Tibor Győri, Dwayne E. Heard, David Heathcote, Brianna R. Heazlewood, Nils Hertl, Pablo G. Jambrina, Ralf I. Kaiser, Olivia A. Krohn, Viet Le Duc, Jérôme Loreau, Stuart R. Mackenzie, Kenneth G. McKendrick, Jennifer Meyer, Gilbert M. Nathanson, Daniel M. Neumark, Rahul Pandey, Christopher Reilly, Patrick Robertson, George C. Schatz, Steven J. Sibener, Arthur G. Suits, Peter D. Watson, Roland Wester, Stefan Willitsch, Alec M. Wodtke and Bum Suk Zhao
{"title":"Scattering of larger molecules – part 2: general discussion","authors":"F. Javier Aoiz, Nadia Balucani, Astrid Bergeat, Alexander Butler, David W. Chandler, Gábor Czakó, Tibor Győri, Dwayne E. Heard, David Heathcote, Brianna R. Heazlewood, Nils Hertl, Pablo G. Jambrina, Ralf I. Kaiser, Olivia A. Krohn, Viet Le Duc, Jérôme Loreau, Stuart R. Mackenzie, Kenneth G. McKendrick, Jennifer Meyer, Gilbert M. Nathanson, Daniel M. Neumark, Rahul Pandey, Christopher Reilly, Patrick Robertson, George C. Schatz, Steven J. Sibener, Arthur G. Suits, Peter D. Watson, Roland Wester, Stefan Willitsch, Alec M. Wodtke and Bum Suk Zhao","doi":"10.1039/D4FD90021A","DOIUrl":"10.1039/D4FD90021A","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"251 ","pages":" 622-665"},"PeriodicalIF":3.4,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141905063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dmitri Babikov, Nadia Balucani, Astrid Bergeat, Mark Brouard, David W. Chandler, Matthew L. Costen, Michal Fárník, Hua Guo, Tibor Győri, Dwayne Heard, David Heathcote, Nils Hertl, Pablo G. Jambrina, Nathanael M. Kidwell, O. A. Krohn, Viet Le Duc, Jérôme Loreau, Stuart R. Mackenzie, Max McCrea, Kenneth G. McKendrick, Jennifer Meyer, Daniel R. Moon, Amy S. Mullin, Gilbert S. Nathanson, Daniel M. Neumark, Kang-Kuen Ni, Martin J. Paterson, Eva Pluhařová, Patrick Robertson, Christopher Reilly, George C. Schatz, Chris Sparling, Arthur G. Suits, Peter D. Watson, Roland Wester, Stefan Willitsch and Alec M. Wodtke
{"title":"Scattering of larger molecules – part 1: general discussion","authors":"Dmitri Babikov, Nadia Balucani, Astrid Bergeat, Mark Brouard, David W. Chandler, Matthew L. Costen, Michal Fárník, Hua Guo, Tibor Győri, Dwayne Heard, David Heathcote, Nils Hertl, Pablo G. Jambrina, Nathanael M. Kidwell, O. A. Krohn, Viet Le Duc, Jérôme Loreau, Stuart R. Mackenzie, Max McCrea, Kenneth G. McKendrick, Jennifer Meyer, Daniel R. Moon, Amy S. Mullin, Gilbert S. Nathanson, Daniel M. Neumark, Kang-Kuen Ni, Martin J. Paterson, Eva Pluhařová, Patrick Robertson, Christopher Reilly, George C. Schatz, Chris Sparling, Arthur G. Suits, Peter D. Watson, Roland Wester, Stefan Willitsch and Alec M. Wodtke","doi":"10.1039/D4FD90019G","DOIUrl":"10.1039/D4FD90019G","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"251 ","pages":" 313-341"},"PeriodicalIF":3.4,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Restoring translational symmetry in periodic all-orbital dynamical mean-field theory simulations","authors":"Jiachen Li and Tianyu Zhu","doi":"10.1039/D4FD00068D","DOIUrl":"10.1039/D4FD00068D","url":null,"abstract":"<p >Dynamical mean-field theory (DMFT) and its cluster extensions provide an efficient Green’s function formalism to simulate spectral properties of periodic systems at the quantum many-body level. However, traditional cluster DMFT breaks translational invariance in solid-state materials, and the best strategy to capture non-local correlation effects within cluster DMFT remains elusive. In this work, we investigate the use of overlapping atom-centered impurity fragments in recently-developed <em>ab initio</em> all-orbital DMFT, where all local orbitals within the impurity are treated with high-level quantum chemistry impurity solvers. We demonstrate how the translational symmetry of the lattice self-energy can be restored by designing symmetry-adapted embedding problems, which results in an improved description of spectral functions in two-dimensional boron nitride monolayers and graphene at the levels of many-body perturbation theory (GW) and coupled-cluster theory. Furthermore, we study the convergence of self-energy and density of states as the embedding size is systematically expanded in one-shot and self-consistent DMFT calculations.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"254 ","pages":" 641-652"},"PeriodicalIF":3.4,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/fd/d4fd00068d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141791345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Tiled unitary product states for strongly correlated Hamiltonians","authors":"Hugh G. A. Burton","doi":"10.1039/D4FD00064A","DOIUrl":"10.1039/D4FD00064A","url":null,"abstract":"<p >Approximating the electronic wave function for strongly correlated systems remains a major theoretical challenge. Emerging quantum computers can enable new types of wave-function ansatz to be considered, with the potential to overcome the exponential memory storage for strong correlation. I have recently introduced the tiled Unitary Product States (tUPS) ansatz, which successfully combines the preservation of particle-number and spin symmetry with shallow quantum circuits and local qubit connectivity [H. G. A. Burton, <em>Phys. Rev. Res.</em>, 2024, <strong>6</strong>, 023300]. In this contribution, I investigate the accuracy of this tUPS hierarchy for strongly-correlated Hamiltonians. I consider the picket-fence pairing Hamiltonian and the two-dimensional Hubbard lattice, which collectively describe a range of strong correlation mechanisms found in molecules. Numerical results demonstrate that highly accurate energies can be achieved with a compact approximation for both weak and strong correlation in the Hubbard model, and the repulsive pairing regime. These data provide valuable insights into the applicability of the tUPS hierarchy for strong electron correlation.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"254 ","pages":" 157-169"},"PeriodicalIF":3.4,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/fd/d4fd00064a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Spiers Memorial Lecture: Engineering biocatalysts","authors":"Donald Hilvert","doi":"10.1039/D4FD00139G","DOIUrl":"10.1039/D4FD00139G","url":null,"abstract":"<p >Enzymes are being engineered to catalyze chemical reactions for many practical applications in chemistry and biotechnology. The approaches used are surveyed in this short review, emphasizing methods for accessing reactivities not expressed by native protein scaffolds. The successful generation of completely <em>de novo</em> enzymes that rival the rates and selectivities of their natural counterparts highlights the potential role that designer enzymes may play in the coming years in research, industry, and medicine. Some challenges that need to be addressed to realize this ambitious dream are considered together with possible solutions.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"252 ","pages":" 9-28"},"PeriodicalIF":3.4,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/fd/d4fd00139g?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141750535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Douglas J. Fansher, Jonathan N. Besna and Joelle N. Pelletier
{"title":"Indigo production identifies hotspots in cytochrome P450 BM3 for diversifying aromatic hydroxylation†","authors":"Douglas J. Fansher, Jonathan N. Besna and Joelle N. Pelletier","doi":"10.1039/D4FD00017J","DOIUrl":"10.1039/D4FD00017J","url":null,"abstract":"<p >Evolution of P450 BM3 is a topic of extensive research, but screening the various substrate/reaction combinations remains a time-consuming process. Indigo production has the potential to serve as a simple high-throughput method for reaction screening, as bacterial colonies expressing indigo (+) variants can be visually identified <em>via</em> their blue phenotype. Indigo (+) single variants, indigo (−) single variants and a combinatorial library, containing mutations that enable the blue phenotype, were screened for their ability to hydroxylate a panel of 12 aromatic compounds using the 4-aminoantipyrine colorimetric assay. Recombination of indigo (+) single variants to create a multiple-variant library is a particularly useful strategy, as all top performing P450 BM3 variants with high hydroxylation activity were either indigo (+) single variants or contained multiple substitutions. Furthermore, active variants, as determined using the 4-AAP assay, were further characterized and several variants were identified that gave more than 90% conversion with 1,3-dichlorobenzene and predominantly formed 2,6-dichlorophenol; other variants showed significant substrate selectivity. This supports the hypothesis that substitution at positions that enable the indigo (+) phenotype, or hotspot residues, is a general mechanism for increasing aromatic hydroxylation activity. Overall, this research demonstrates that indigo (+) single variants, identified <em>via</em> colorimetric colony-based screening, may be recombined to generate a multiply-substituted variant library containing many variants with high aromatic hydroxylation activity. The combination of colony-based screening and other screening assays greatly accelerates enzyme engineering, as readily-identified indigo (+) single variants can be recombined to create a library of active multiple variants without extensive screening of single variants.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"252 ","pages":" 29-51"},"PeriodicalIF":3.4,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141588953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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