In the domain of exchange-coupled PNTM clusters, local emergent symmetries exist which can be exploited to greatly increase the sparsity of the CI eigensolutions of such systems. Sparsity of the CI secular problem is revealed by exploring the site permutation space within spin-adapted many-body bases, and highly compressed wave functions may arise by finding optimal site orderings. However, the factorial cost of searching through the permutation space remains a bottleneck for clusters with a large number of metal centers. In this work, we explore ways to reduce the factorial scaling, by combining permutation and point group symmetry arguments, and using commutation relations between cumulative partial spin and the Hamiltonian operators, [(S(n))2, H]. Certain site orderings lead to commuting operators, from which more sparse wave functions arise. Two graphical strategies will be discussed, one to rapidly evaluate the commutators of interest, and one in the form of a tree search algorithm to predict how many and which distinct site permutations are to be analyzed, eliminating redundancies in the permutation space. Particularly interesting is the case of the singlet spin states for which an additional reversal symmetry can be utilized to further reduce the distinct site permutations.
在交换耦合 PNTM 簇领域，存在着局部新兴对称性，利用这些对称性可以大大提高此类系统的 CI 特征解的稀疏性。通过探索自旋适配多体基内的位点排列空间，可以揭示 CI 世俗问题的稀疏性；通过寻找最佳位点排序，可以产生高度压缩的波函数。然而，对于具有大量金属中心的集群来说，搜索排列空间的因子成本仍然是一个瓶颈。在这项工作中，我们结合了置换和点群对称性论证，并利用累积部分自旋和哈密顿算子[(S(n))2, H]之间的换向关系，探索了减少因子缩放的方法。某些位点排序会导致换向算子，从而产生更稀疏的波函数。我们将讨论两种图形策略，一种是快速评估感兴趣的换向算子，另一种是以树形搜索算法的形式预测有多少种不同的位点排列需要分析，从而消除排列空间中的冗余。特别有趣的是单子自旋态，可以利用额外的反转对称性来进一步减少不同位点的排列。
{"title":"Permutation Symmetry in Spin Adapted Many-Body Wave Functions","authors":"Maru Song, Ali Alavi, Giovanni Li Manni","doi":"10.1039/d4fd00061g","DOIUrl":"https://doi.org/10.1039/d4fd00061g","url":null,"abstract":"In the domain of exchange-coupled PNTM clusters, local emergent symmetries exist which can be exploited to greatly increase the sparsity of the CI eigensolutions of such systems. Sparsity of the CI secular problem is revealed by exploring the site permutation space within spin-adapted many-body bases, and highly compressed wave functions may arise by finding optimal site orderings. However, the factorial cost of searching through the permutation space remains a bottleneck for clusters with a large number of metal centers. In this work, we explore ways to reduce the factorial scaling, by combining permutation and point group symmetry arguments, and using commutation relations between cumulative partial spin and the Hamiltonian operators, [(S<small><sup>(n)</sup></small>)<small><sup>2</sup></small>, H]. Certain site orderings lead to commuting operators, from which more sparse wave functions arise. Two graphical strategies will be discussed, one to rapidly evaluate the commutators of interest, and one in the form of a tree search algorithm to predict how many and which distinct site permutations are to be analyzed, eliminating redundancies in the permutation space. Particularly interesting is the case of the singlet spin states for which an additional reversal symmetry can be utilized to further reduce the distinct site permutations.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140797771","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}
Sophie Bonnassieux, Raj Pandya, Dhyllan Adan Skiba, Damien Degoulange, Dorothee Petit, Peter Seem, Russell Cowburn, Betar M Gallant, Alexis Jules Louis Grimaud
Liquid phase separation using aqueous biphasic systems (ABS) is widely used in industrial processes for the extraction, separation and purification of macromolecules. Using water as the single solvent, a wide variety of solutes have been used to induce phase separation including polymers, ionic liquids or salts. For each system - polymer-polymer, polymer-ionic liquid, polymer-salt or salt-salt - different driving forces were proposed to induce phase separation. Specifically, for polymer-salt systems, a difference in solvation structure between the polymer-rich and the salt-rich was proposed, while other reports suggested that a large change in enthalpy and entropy accompanied the phase separation. Here, we reinvestigated the PEG/K2HPO4/H2O systems using a combination of liquid-phase nuclear magnetic resonance (NMR) and high-resolution Raman spectroscopies, coupled with injection microcalorimetry. Both NMR and Raman reveal a decreased water concentration in the PEG-rich phase, with nonetheless no significant differences observed for both 1H chemical shift or OH stretching vibrations. Hence, both PEG- and salt-rich phases exhibit similar water solvation properties, which is thus not the driving force for phase separation. Furthermore, NMR reveals a that PEG interacts with salt ions in the PEG-rich solution, inducing a downfield shift with increasing salt concentration. Injection microcalorimetry measurements were carried out to investigate any effect due to enthalpy change during mixing. Nevertheless, these measurements indicate very small enthalpy changes when mixing PEG- and salt-rich solutions in comparison with that previously recorded for salt-salt systems or associated with mixing of two solvents. Hence, our study discards any large change of enthalpy as the origin for phase separation of PEG/K2HPO4 systems, in addition to large difference in solvation properties.
{"title":"Revisiting the driving force inducing phase separation in PEG-phosphate aqueous biphasic systems","authors":"Sophie Bonnassieux, Raj Pandya, Dhyllan Adan Skiba, Damien Degoulange, Dorothee Petit, Peter Seem, Russell Cowburn, Betar M Gallant, Alexis Jules Louis Grimaud","doi":"10.1039/d4fd00058g","DOIUrl":"https://doi.org/10.1039/d4fd00058g","url":null,"abstract":"Liquid phase separation using aqueous biphasic systems (ABS) is widely used in industrial processes for the extraction, separation and purification of macromolecules. Using water as the single solvent, a wide variety of solutes have been used to induce phase separation including polymers, ionic liquids or salts. For each system - polymer-polymer, polymer-ionic liquid, polymer-salt or salt-salt - different driving forces were proposed to induce phase separation. Specifically, for polymer-salt systems, a difference in solvation structure between the polymer-rich and the salt-rich was proposed, while other reports suggested that a large change in enthalpy and entropy accompanied the phase separation. Here, we reinvestigated the PEG/K2HPO4/H2O systems using a combination of liquid-phase nuclear magnetic resonance (NMR) and high-resolution Raman spectroscopies, coupled with injection microcalorimetry. Both NMR and Raman reveal a decreased water concentration in the PEG-rich phase, with nonetheless no significant differences observed for both 1H chemical shift or OH stretching vibrations. Hence, both PEG- and salt-rich phases exhibit similar water solvation properties, which is thus not the driving force for phase separation. Furthermore, NMR reveals a that PEG interacts with salt ions in the PEG-rich solution, inducing a downfield shift with increasing salt concentration. Injection microcalorimetry measurements were carried out to investigate any effect due to enthalpy change during mixing. Nevertheless, these measurements indicate very small enthalpy changes when mixing PEG- and salt-rich solutions in comparison with that previously recorded for salt-salt systems or associated with mixing of two solvents. Hence, our study discards any large change of enthalpy as the origin for phase separation of PEG/K2HPO4 systems, in addition to large difference in solvation properties.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140797819","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}
Maximilian Gantz, Simon Valentin Mathis, Friederike Nintzel, Pietro Lio, Florian Hollfelder
Protein design and directed evolution have separately contributed enormously to protein engineering. Without being mutually exclusive, the former relies on computation from first principles, while the latter is a combinatorial approach based on chance. Advances in ultrahigh throughput (uHT) screening, next generation sequencing and machine learning may create alternative routes to engineered proteins, where functional information linked to specific sequences is interpreted and extrapolated in silico. In particular, the miniaturisation of functional tests in water-in-oil emulsion droplets with picoliter volumes and their rapid generation and analysis (>1 kHz) allows screening of >107-membered libraries in a day. Subsequently decoding the selected clones by short or long-read sequencing methods leads to large sequence-function datasets that may allow extrapolation from experimental directed evolution to further improved mutants beyond the observed hits. In this work, we explore experimental strategies for how to draw up ‘fitness landscapes’ in sequence space with uHT droplet microfluidics, review the current state of AI/ML in enzyme engineering and discuss how uHT datasets may be combined with AI/ML to make meaningful predictions and accelerate biocatalyst engineering.
{"title":"On synergy between ultrahigh throughput screening and machine learning in biocatalyst engineering","authors":"Maximilian Gantz, Simon Valentin Mathis, Friederike Nintzel, Pietro Lio, Florian Hollfelder","doi":"10.1039/d4fd00065j","DOIUrl":"https://doi.org/10.1039/d4fd00065j","url":null,"abstract":"Protein design and directed evolution have separately contributed enormously to protein engineering. Without being mutually exclusive, the former relies on computation from first principles, while the latter is a combinatorial approach based on chance. Advances in ultrahigh throughput (uHT) screening, next generation sequencing and machine learning may create alternative routes to engineered proteins, where functional information linked to specific sequences is interpreted and extrapolated in silico. In particular, the miniaturisation of functional tests in water-in-oil emulsion droplets with picoliter volumes and their rapid generation and analysis (>1 kHz) allows screening of >107-membered libraries in a day. Subsequently decoding the selected clones by short or long-read sequencing methods leads to large sequence-function datasets that may allow extrapolation from experimental directed evolution to further improved mutants beyond the observed hits. In this work, we explore experimental strategies for how to draw up ‘fitness landscapes’ in sequence space with uHT droplet microfluidics, review the current state of AI/ML in enzyme engineering and discuss how uHT datasets may be combined with AI/ML to make meaningful predictions and accelerate biocatalyst engineering.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140797837","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}
Fabrizio Casilli, Miquel Canyelles-Niño, Gerard Roelfes, Lur Alonso-Cotchico
Artificial enzymes are valuable biocatalysts able to perform new-to-nature transformations with the precision and (enantio-)selectivity of natural enzymes. Although being highly engineered biocatalysts, they often cannot reach catalytic rates akin those of their natural counterparts, slowing down their application in real-world industrial processes. Typically, their designs only optimise the chemistry inside the active site, while overlooking the role of protein dynamics on catalysis. In this work, we show how the catalytic performance of an already engineered artificial enzyme can be further improved by modulating its long-range network of interactions. To this aim, we subjected a specialised artificial enzyme based on the Lactococcal multidrug resistance regulator (LmrR) to an innovative algorithm that quickly inspects the whole protein sequence space for protein dynamics hotspots. From an initial predicted selection of 73 variants, two variants with mutations distant more than 11 Å showed increased catalytic activity towards the new-to-nature hydrazone formation reaction. Their recombination displayed a 60% higher turnover number and 14 ℃ higher thermostability. Microsecond time scale molecular dynamics simulations evidenced a shift in the distribution of productive enzyme conformations, which are the result of a cascade of interactions initiated by the introduced mutations.
{"title":"Computation-guided engineering of distal mutations in an artificial enzyme","authors":"Fabrizio Casilli, Miquel Canyelles-Niño, Gerard Roelfes, Lur Alonso-Cotchico","doi":"10.1039/d4fd00069b","DOIUrl":"https://doi.org/10.1039/d4fd00069b","url":null,"abstract":"Artificial enzymes are valuable biocatalysts able to perform new-to-nature transformations with the precision and (enantio-)selectivity of natural enzymes. Although being highly engineered biocatalysts, they often cannot reach catalytic rates akin those of their natural counterparts, slowing down their application in real-world industrial processes. Typically, their designs only optimise the chemistry inside the active site, while overlooking the role of protein dynamics on catalysis. In this work, we show how the catalytic performance of an already engineered artificial enzyme can be further improved by modulating its long-range network of interactions. To this aim, we subjected a specialised artificial enzyme based on the Lactococcal multidrug resistance regulator (LmrR) to an innovative algorithm that quickly inspects the whole protein sequence space for protein dynamics hotspots. From an initial predicted selection of 73 variants, two variants with mutations distant more than 11 Å showed increased catalytic activity towards the new-to-nature hydrazone formation reaction. Their recombination displayed a 60% higher turnover number and 14 ℃ higher thermostability. Microsecond time scale molecular dynamics simulations evidenced a shift in the distribution of productive enzyme conformations, which are the result of a cascade of interactions initiated by the introduced mutations.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140634192","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}
Hannah Wood, Hannah M Burnett, Robert Dryfe, Paola Carbone
It has recently been demonstrated that aqueous lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and lithium chloride (LiCl) solutions can form stable liquid-liquid biphasic systems when both elec- trolyte phases have sufficiently high concentrations. In this work, we combine molecular dynamics simulations and experimental analysis to investigate what drives the formation of the interface and how the interfacial molecular structure correlates with its thermodynamic stability. We observe that at the liquid-vapour interface, TFSI− anions exhibit surfactant-like properties, leading to a reduction in surface tension and an increase in interfacial thickness. On the contrary, the interfacial stability of the LiTFSI-LiCl biphasic systems increases with the concentration of both salts, as evidenced by the increasing surface tension and decreasing interfacial thickness. The opposing effects that the ionic concentration has on the thermodynamic stability of the different interfaces are linked to the anions’ interfacial adsorption/desorption, which in turn affects the number and strength of water-water hy- drogen bonds, the interfacial molecular structure and the diffusion of cations across the interface. Finally, calculations and experiments indicate that the liquid-liquid separation is driven primarily by the concentration of LiCl, and is the result of a ’salting out’ effect.
{"title":"Stability and Structure of the Aqueous LiTFSI-LiCl Interface","authors":"Hannah Wood, Hannah M Burnett, Robert Dryfe, Paola Carbone","doi":"10.1039/d4fd00026a","DOIUrl":"https://doi.org/10.1039/d4fd00026a","url":null,"abstract":"It has recently been demonstrated that aqueous lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and lithium chloride (LiCl) solutions can form stable liquid-liquid biphasic systems when both elec- trolyte phases have sufficiently high concentrations. In this work, we combine molecular dynamics simulations and experimental analysis to investigate what drives the formation of the interface and how the interfacial molecular structure correlates with its thermodynamic stability. We observe that at the liquid-vapour interface, TFSI− anions exhibit surfactant-like properties, leading to a reduction in surface tension and an increase in interfacial thickness. On the contrary, the interfacial stability of the LiTFSI-LiCl biphasic systems increases with the concentration of both salts, as evidenced by the increasing surface tension and decreasing interfacial thickness. The opposing effects that the ionic concentration has on the thermodynamic stability of the different interfaces are linked to the anions’ interfacial adsorption/desorption, which in turn affects the number and strength of water-water hy- drogen bonds, the interfacial molecular structure and the diffusion of cations across the interface. Finally, calculations and experiments indicate that the liquid-liquid separation is driven primarily by the concentration of LiCl, and is the result of a ’salting out’ effect.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140626828","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}
Lithium (Li) metal negative electrodes have enticed a wide attention for high-energy-density batteries. However, its low Coulombic efficiency (CE) due to parasitic electrolyte reduction has been an alarming concern. Concentrated electrolytes are one of the promising concepts that can stabilize the Li metal/electrolyte interface, thus increasing the CE; however, its mechanism has been still controversial. In this work, we used LiN(SO2F)2 (LiFSI) and weakly solvating 1,2-diethoxyethane (DEE) as a model electrolyte to study how its liquid structure changes upon increasing salt concentration and how it is linked to the Li plating/stripping CE. Based on previous works, we focused on Li electrode potential (ELi with reference to the redox of ferrocene) and solid electrolyte interphase (SEI) formation. Although the ELi shows a different trend in DEE as compared to conventional 1,2-dimethoxyethane (DME), which is accounted for by different ion-pairing states of Li+ and FSI-, the ELi-CE plots are overlapped for both electrolytes, suggesting that the ELi is one of the dominant factors of the CE. On the other hand, the extensive ion pairing results in the upward shift of FSI- reduction potential, as demonstrated both experimentally and theoretically, which promotes FSI--derived inorganic SEI. Both ELi and SEI contribute to increasing the Li plating/stripping CE.
锂（Li）金属负极在高能量密度电池领域受到广泛关注。然而，寄生电解质还原导致的低库仑效率（CE）一直是一个令人担忧的问题。浓缩电解质是很有前景的概念之一，它可以稳定锂金属/电解质界面，从而提高库仑效率；然而，其机理仍存在争议。在这项工作中，我们使用 LiN(SO2F)2 (LiFSI) 和弱溶解的 1,2- 二乙氧基乙烷 (DEE) 作为模型电解质，研究其液体结构在盐浓度增加时如何变化，以及如何与锂镀层/剥离 CE 联系起来。在以往工作的基础上，我们重点研究了锂电极电位（ELi，参考二茂铁的氧化还原）和固态电解质相间（SEI）的形成。虽然与传统的 1,2-二甲氧基乙烷（DME）相比，ELi 在 DEE 中显示出不同的趋势，这是由于 Li+ 和 FSI- 的离子配对状态不同造成的，但两种电解质的 ELi-CE 图都是重叠的，这表明 ELi 是 CE 的主要因素之一。另一方面，正如实验和理论所证明的那样，广泛的离子配对会导致 FSI- 还原电位上移，从而促进 FSI 衍生出无机 SEI。ELi 和 SEI 都有助于提高锂镀层/剥离 CE。
{"title":"Stabilization of lithium metal in concentrated electrolytes: effects of electrode potential and solid electrolyte interphase formation","authors":"Anusha Pradhan, Shoma Nishimura, Yasuyuki Kondo, Tomoaki Kaneko, Yu Katayama, Keitaro Sodeyama, Yuki Yamada","doi":"10.1039/d4fd00038b","DOIUrl":"https://doi.org/10.1039/d4fd00038b","url":null,"abstract":"Lithium (Li) metal negative electrodes have enticed a wide attention for high-energy-density batteries. However, its low Coulombic efficiency (CE) due to parasitic electrolyte reduction has been an alarming concern. Concentrated electrolytes are one of the promising concepts that can stabilize the Li metal/electrolyte interface, thus increasing the CE; however, its mechanism has been still controversial. In this work, we used LiN(SO<small><sub>2</sub></small>F)<small><sub>2</sub></small> (LiFSI) and weakly solvating 1,2-diethoxyethane (DEE) as a model electrolyte to study how its liquid structure changes upon increasing salt concentration and how it is linked to the Li plating/stripping CE. Based on previous works, we focused on Li electrode potential (<em>E</em><small><sub>Li</sub></small> with reference to the redox of ferrocene) and solid electrolyte interphase (SEI) formation. Although the <em>E</em><small><sub>Li</sub></small> shows a different trend in DEE as compared to conventional 1,2-dimethoxyethane (DME), which is accounted for by different ion-pairing states of Li<small><sup>+</sup></small> and FSI<small><sup>-</sup></small>, the <em>E</em><small><sub>Li</sub></small>-CE plots are overlapped for both electrolytes, suggesting that the <em>E</em><small><sub>Li</sub></small> is one of the dominant factors of the CE. On the other hand, the extensive ion pairing results in the upward shift of FSI<small><sup>-</sup></small> reduction potential, as demonstrated both experimentally and theoretically, which promotes FSI<small><sup>-</sup></small>-derived inorganic SEI. Both <em>E</em><small><sub>Li</sub></small> and SEI contribute to increasing the Li plating/stripping CE.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140576841","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}
Erika Magnusson, Aaron Fitzpatrick, Stefan Knecht, Martin Rahm, Werner Dobrautz
The near-term utility of quantum computers is hindered by hardware constraints in the form of noise. One path to achieving noise resilience in hybrid quantum algorithms is to decrease the required circuit depth -- the number of applied gates -- to solve a given problem. This work demonstrates how to reduce circuit depth by combining the transcorrelated (TC) approach with adaptive quantum ansätze and their implementations in the context of variational quantum imaginary time evolution (AVQITE). The combined TC-AVQITE method is used to calculate ground state energies across the potential energy surfaces of H$_4$, LiH, and H$_2$O. In particular, H$_4$ is a notoriously difficult case where unitary coupled cluster theory, including singles and doubles excitations, fails to provide accurate results. Adding TC yields energies close to the complete basis set (CBS) limit while reducing the number of necessary operators -- and thus circuit depth -- in the adaptive ansätze. The reduced circuit depth furthermore makes our algorithm more noise-resilient and accelerates convergence. Our study demonstrates that combining the TC method with adaptive ansätze yields compact, noise-resilient, and easy-to-optimize quantum circuits that yield accurate quantum chemistry results close to the CBS limit.
{"title":"Towards Efficient Quantum Computing for Quantum Chemistry: Reducing Circuit Complexity with Transcorrelated and Adaptive Ansatz Techniques","authors":"Erika Magnusson, Aaron Fitzpatrick, Stefan Knecht, Martin Rahm, Werner Dobrautz","doi":"10.1039/d4fd00039k","DOIUrl":"https://doi.org/10.1039/d4fd00039k","url":null,"abstract":"The near-term utility of quantum computers is hindered by hardware constraints in the form of noise. One path to achieving noise resilience in hybrid quantum algorithms is to decrease the required circuit depth -- the number of applied gates -- to solve a given problem. This work demonstrates how to reduce circuit depth by combining the transcorrelated (TC) approach with adaptive quantum ansätze and their implementations in the context of variational quantum imaginary time evolution (AVQITE). The combined TC-AVQITE method is used to calculate ground state energies across the potential energy surfaces of H$_4$, LiH, and H$_2$O. In particular, H$_4$ is a notoriously difficult case where unitary coupled cluster theory, including singles and doubles excitations, fails to provide accurate results. Adding TC yields energies close to the complete basis set (CBS) limit while reducing the number of necessary operators -- and thus circuit depth -- in the adaptive ansätze. The reduced circuit depth furthermore makes our algorithm more noise-resilient and accelerates convergence. Our study demonstrates that combining the TC method with adaptive ansätze yields compact, noise-resilient, and easy-to-optimize quantum circuits that yield accurate quantum chemistry results close to the CBS limit.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140576716","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}
Pattarawan Intasian, Chalermroj Sutthaphirom, Oliver Bodeit, Duangthip Trisrivirat, Ninlapan Kimprasoot, Juthamas Jaroensuk, Barbara Bakker, Edda Klipp, Pimchai Chaiyen
A scarcity of cofactors, necessary metabolites or substrates for in vivo enzymatic reactions are among the major barriers of product synthesis in metabolically engineered cells. This work compares our recently developed cofactor boosting strategy, which uses xylose reductase (XR) and lactose to increase the intracellular levels of reduced or oxidized nicotinamide adenine dinucleotide (phosphate) NAD(P)H, adenosine triphosphate (ATP) and acetyl coenzymeA (acetyl-CoA) with other previously reported methods. We demonstrated that the XR/lactose approach enhances levels of sugar alcohols and sugar phosphates which leads to elevated levels of crucial cofactors required by specific metabolic pathways. The patterns of cofactor enhancement are not uniform and depend upon the specific pathway components that are overexpressed. We term this model the “user-pool” model. Here, we investigated metabolite alteration in the fatty alcohol producing system in the presence of XR/lactose within an early time frame (5 mins after the bioconversion started). All metabolite data were analyzed using untargeted metabolomics. We found that the XR/lactose system could improve fatty alcohol production as early as 5 mins after the bioconversion started. The enhancement of key cofactors and intermediates such as hexitol, NAD(P)H, ATP, 3-phosphoglycerate, acetyl-CoA, 6-phosphogluconate (6-PG) and glutathione was consistent with those previously reported on a longer time scale (after 1 hr). However, measurements performed at the early time reported here showed detectable differences in metabolite enhancement patterns such as those of ATP, NADPH, acetyl-CoA and glutathione. These data can serve as a basis for future analysis of metabolic flux alteration by the XR/lactose system. Comparative analysis of the cofactor enhancement by XR and other methods suggests that the XR/lactose can serve as a simple tool to increase levels of various cofactors for microbial cell factories.
{"title":"Enhancement of essential cofactors for in vivo biocatalysis","authors":"Pattarawan Intasian, Chalermroj Sutthaphirom, Oliver Bodeit, Duangthip Trisrivirat, Ninlapan Kimprasoot, Juthamas Jaroensuk, Barbara Bakker, Edda Klipp, Pimchai Chaiyen","doi":"10.1039/d4fd00013g","DOIUrl":"https://doi.org/10.1039/d4fd00013g","url":null,"abstract":"A scarcity of cofactors, necessary metabolites or substrates for in vivo enzymatic reactions are among the major barriers of product synthesis in metabolically engineered cells. This work compares our recently developed cofactor boosting strategy, which uses xylose reductase (XR) and lactose to increase the intracellular levels of reduced or oxidized nicotinamide adenine dinucleotide (phosphate) NAD(P)H, adenosine triphosphate (ATP) and acetyl coenzymeA (acetyl-CoA) with other previously reported methods. We demonstrated that the XR/lactose approach enhances levels of sugar alcohols and sugar phosphates which leads to elevated levels of crucial cofactors required by specific metabolic pathways. The patterns of cofactor enhancement are not uniform and depend upon the specific pathway components that are overexpressed. We term this model the “user-pool” model. Here, we investigated metabolite alteration in the fatty alcohol producing system in the presence of XR/lactose within an early time frame (5 mins after the bioconversion started). All metabolite data were analyzed using untargeted metabolomics. We found that the XR/lactose system could improve fatty alcohol production as early as 5 mins after the bioconversion started. The enhancement of key cofactors and intermediates such as hexitol, NAD(P)H, ATP, 3-phosphoglycerate, acetyl-CoA, 6-phosphogluconate (6-PG) and glutathione was consistent with those previously reported on a longer time scale (after 1 hr). However, measurements performed at the early time reported here showed detectable differences in metabolite enhancement patterns such as those of ATP, NADPH, acetyl-CoA and glutathione. These data can serve as a basis for future analysis of metabolic flux alteration by the XR/lactose system. Comparative analysis of the cofactor enhancement by XR and other methods suggests that the XR/lactose can serve as a simple tool to increase levels of various cofactors for microbial cell factories.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140576715","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}
Hyunsoo Park, Anthony Onwuli, Keith Butler, Aron Walsh
The combination of elements from the Periodic Table defines a vast chemical space. Only a small fraction of these combinations yields materials that occur naturally or are accessible synthetically. Here, we enumerate binary, ternary, and quaternary element and species combinations to produce an extensive library of over 10^10 stoichiometric inorganic compositions. The unique combinations are vectorised using compositional embedding vectors drawn from a variety of published machine-learning models. Dimensionality reduction techniques are employed to present a two-dimensional representation of inorganic crystal-chemical space, which is labelled according to whether they pass standard chemical filters and if they appear in known materials databases.
{"title":"Mapping inorganic crystal chemical space","authors":"Hyunsoo Park, Anthony Onwuli, Keith Butler, Aron Walsh","doi":"10.1039/d4fd00063c","DOIUrl":"https://doi.org/10.1039/d4fd00063c","url":null,"abstract":"The combination of elements from the Periodic Table defines a vast chemical space. Only a small fraction of these combinations yields materials that occur naturally or are accessible synthetically. Here, we enumerate binary, ternary, and quaternary element and species combinations to produce an extensive library of over 10^10 stoichiometric inorganic compositions. The unique combinations are vectorised using compositional embedding vectors drawn from a variety of published machine-learning models. Dimensionality reduction techniques are employed to present a two-dimensional representation of inorganic crystal-chemical space, which is labelled according to whether they pass standard chemical filters and if they appear in known materials databases.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140576864","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}
Strong/static electronic correlation mediates the emergence of remarkable phases of matter, and underlies the exceptional reactivity properties in transition metal-based catalysts. Modeling strongly correlated molecules and solids calls for multi-reference Ansätze, which explicitly capture the competition of energy scales characteristic of such systems. With the efficient computational screening of correlated solids in mind, the ghost Gutzwiller (gGut) Ansatz has been recently developed. This is a variational Ansatz which can be formulated as a self-consistent embedding approach, describing the system within a non-interacting, quasiparticle model, yet providing with accurate spectra in both low and high energy regimes. Crucially, small fragments of the system are identified as responsible for the strong correlation, and are therefore enhanced by adding a set of auxiliary orbitals, the ghosts. These capture many-body correlations through one-body fluctuations and subsequent out-projection when computing physical observables. gGut has been shown to accurately describe multi-orbital lattice models at modest computational cost. In this work, we extend the gGut framework to strongly correlated molecules, for which it holds special promise. Indeed, despite the asymmetric embedding treatment, the quasiparticle Hamiltonian effectively describes all major sources of correlation in the molecule: strong correlation through the ghosts in the fragment, and dynamical correlation through the quasiparticle description of its environment. To adapt the gGut Ansatz for molecules, we address the fact that, unlike in the lattice model previously considered, electronic interactions in molecules are not local. Hence, we explore a hierarchy of approximations of increasing accuracy capturing interactions between fragments and environment, and within the environment, and discuss how these affect the embedding description of correlations in the whole molecule. We will compare the accuracy of the gGut model with established methods to capture strong correlation within active space formulations, and assess the realistic use of this novel approximation to the theoretical description of correlated molecular clusters.
{"title":"Quantum Embedding for Molecules with Auxiliary Particles - The Ghost Gutzwiller Ansatz","authors":"Carlos Mejuto-Zaera","doi":"10.1039/d4fd00053f","DOIUrl":"https://doi.org/10.1039/d4fd00053f","url":null,"abstract":"Strong/static electronic correlation mediates the emergence of remarkable phases of matter, and underlies the exceptional reactivity properties in transition metal-based catalysts. Modeling strongly correlated molecules and solids calls for multi-reference Ansätze, which explicitly capture the competition of energy scales characteristic of such systems. With the efficient computational screening of correlated solids in mind, the ghost Gutzwiller (gGut) Ansatz has been recently developed. This is a variational Ansatz which can be formulated as a self-consistent embedding approach, describing the system within a non-interacting, quasiparticle model, yet providing with accurate spectra in both low and high energy regimes. Crucially, small fragments of the system are identified as responsible for the strong correlation, and are therefore enhanced by adding a set of auxiliary orbitals, the ghosts. These capture many-body correlations through one-body fluctuations and subsequent out-projection when computing physical observables. gGut has been shown to accurately describe multi-orbital lattice models at modest computational cost. In this work, we extend the gGut framework to strongly correlated molecules, for which it holds special promise. Indeed, despite the asymmetric embedding treatment, the quasiparticle Hamiltonian effectively describes all major sources of correlation in the molecule: strong correlation through the ghosts in the fragment, and dynamical correlation through the quasiparticle description of its environment. To adapt the gGut Ansatz for molecules, we address the fact that, unlike in the lattice model previously considered, electronic interactions in molecules are not local. Hence, we explore a hierarchy of approximations of increasing accuracy capturing interactions between fragments and environment, and within the environment, and discuss how these affect the embedding description of correlations in the whole molecule. We will compare the accuracy of the gGut model with established methods to capture strong correlation within active space formulations, and assess the realistic use of this novel approximation to the theoretical description of correlated molecular clusters.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140577127","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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