Pub Date : 2022-08-23DOI: 10.1088/2516-1075/ac9d79
Wenhan Chen, A. James, S. Dugdale
The Fermi surface topology plays an important role in the macroscopic properties of metals. It can be particularly sensitive to electron correlation, which appears to be especially significant for the weak itinerant ferromagnet ZrZn2. Here, we look at the differences in the predicted Fermi surface sheets of this metallic compound in its paramagnetic phase for both density functional theory (DFT) and the combination of DFT with dynamical mean field theory (DFT + DMFT). The theoretical spectral functions evaluated at the Fermi level were used along with calculations of the electron–positron momentum density (also known as the two-photon momentum density) in k-space to provide insights into the origin of certain features of the Fermi surface topology. We compare this two photon momentum density to that extracted from the positron annihilation experimental data (2004 Phys. Rev. Lett. 92 107003). The DFT + DMFT densities are in better agreement with the experiment than the DFT, particularly with regard to the flat bands around the L and W high symmetry points. The experimental neck around L, which relates to a van Hove singularity, is present in DFT + DMFT but not in the DFT. We find that these flat bands, and as such the Fermi surface topology, are sensitive to the many body electron correlation description, and show that the positron annihilation technique is able to probe this. This description is significant for the observed behavior such as the Lifshiftz transition around the quantum critical point.
{"title":"Local electron correlation effects on the fermiology of the weak itinerant ferromagnet ZrZn2","authors":"Wenhan Chen, A. James, S. Dugdale","doi":"10.1088/2516-1075/ac9d79","DOIUrl":"https://doi.org/10.1088/2516-1075/ac9d79","url":null,"abstract":"The Fermi surface topology plays an important role in the macroscopic properties of metals. It can be particularly sensitive to electron correlation, which appears to be especially significant for the weak itinerant ferromagnet ZrZn2. Here, we look at the differences in the predicted Fermi surface sheets of this metallic compound in its paramagnetic phase for both density functional theory (DFT) and the combination of DFT with dynamical mean field theory (DFT + DMFT). The theoretical spectral functions evaluated at the Fermi level were used along with calculations of the electron–positron momentum density (also known as the two-photon momentum density) in k-space to provide insights into the origin of certain features of the Fermi surface topology. We compare this two photon momentum density to that extracted from the positron annihilation experimental data (2004 Phys. Rev. Lett. 92 107003). The DFT + DMFT densities are in better agreement with the experiment than the DFT, particularly with regard to the flat bands around the L and W high symmetry points. The experimental neck around L, which relates to a van Hove singularity, is present in DFT + DMFT but not in the DFT. We find that these flat bands, and as such the Fermi surface topology, are sensitive to the many body electron correlation description, and show that the positron annihilation technique is able to probe this. This description is significant for the observed behavior such as the Lifshiftz transition around the quantum critical point.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":"4 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41524165","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 : 2022-08-22DOI: 10.1088/2516-1075/acbc5e
Ignacio M. Alliati, M. Grüning
We present a Floquet scheme for the ab-initio calculation of nonlinear optical properties in extended systems. This entails a reformulation of the real-time approach based on the dynamical Berry-phase polarisation (Attaccalite and Grüning 2013 Phys. Rev. B 88 1–9) and retains the advantage of being non-perturbative in the electric field. The proposed method applies to periodically-driven Hamiltonians and makes use of this symmetry to turn a time-dependent problem into a self-consistent time-independent eigenvalue problem. We implemented this Floquet scheme at the independent particle level and compared it with the real-time approach. Our reformulation reproduces real-time-calculated 2nd and 3rd order susceptibilities for a number of bulk and two-dimensional materials, while reducing the associated computational cost by one or two orders of magnitude.
{"title":"Floquet formulation of the dynamical Berry-phase approach to nonlinear optics in extended systems","authors":"Ignacio M. Alliati, M. Grüning","doi":"10.1088/2516-1075/acbc5e","DOIUrl":"https://doi.org/10.1088/2516-1075/acbc5e","url":null,"abstract":"We present a Floquet scheme for the ab-initio calculation of nonlinear optical properties in extended systems. This entails a reformulation of the real-time approach based on the dynamical Berry-phase polarisation (Attaccalite and Grüning 2013 Phys. Rev. B 88 1–9) and retains the advantage of being non-perturbative in the electric field. The proposed method applies to periodically-driven Hamiltonians and makes use of this symmetry to turn a time-dependent problem into a self-consistent time-independent eigenvalue problem. We implemented this Floquet scheme at the independent particle level and compared it with the real-time approach. Our reformulation reproduces real-time-calculated 2nd and 3rd order susceptibilities for a number of bulk and two-dimensional materials, while reducing the associated computational cost by one or two orders of magnitude.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":"210 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41280240","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 : 2022-08-09DOI: 10.1088/2516-1075/ac884d
S. Duhm
The energy-level alignment at the ubiquitous interfaces of optoelectronic devices is decisive for their performance and almost all pertinent publications include energy-level diagrams (ELDs). However, in most of these ELDs vacuum-level alignment across the complete heterojunction is assumed, which is oversimplified. On the contrary, the functioning of virtually all optoelectronic devices relies on interface phenomena like band bending, interface dipoles or potential drops. Consequently, such oversimplified ELDs do not help to understand the working mechanism of devices and have limited meaning. In this focus article, we give best practice rules for drawing ELDs: (1) give references for all the values of an ELD. (2) Mention the methods which have been used to obtain these values. (3) Add a disclaimer about the limitations of the ELD. (4) Measure as many energy levels as possible.
{"title":"Interface energetics make devices","authors":"S. Duhm","doi":"10.1088/2516-1075/ac884d","DOIUrl":"https://doi.org/10.1088/2516-1075/ac884d","url":null,"abstract":"The energy-level alignment at the ubiquitous interfaces of optoelectronic devices is decisive for their performance and almost all pertinent publications include energy-level diagrams (ELDs). However, in most of these ELDs vacuum-level alignment across the complete heterojunction is assumed, which is oversimplified. On the contrary, the functioning of virtually all optoelectronic devices relies on interface phenomena like band bending, interface dipoles or potential drops. Consequently, such oversimplified ELDs do not help to understand the working mechanism of devices and have limited meaning. In this focus article, we give best practice rules for drawing ELDs: (1) give references for all the values of an ELD. (2) Mention the methods which have been used to obtain these values. (3) Add a disclaimer about the limitations of the ELD. (4) Measure as many energy levels as possible.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43389493","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 : 2022-08-02DOI: 10.1088/2516-1075/ac8631
Y. Ohtsubo, S. Kimura, F. Iga
The peculiar metallic electronic states proposed and observed in Kondo insulators (KIs), whose bandgap opens at low temperature derived from the Kondo effect between itinerant and localized electrons, have attracted considerable attention in this decade, because it suggests the coexistence of strong electron correlation and non-trivial topological order (TO) in such KIs, namely topological Kondo insulators (TKIs). However, experimental studies of these states have led to controversial conclusions mainly owing to the difficulty and inhomogeneity of the single crystal surfaces of the TKI candidates, samarium hexaboride (SmB6) and ytterbium dodecaboride (YbB12). In this article, we review studies focused on the surface atomic and electronic structures of TKI candidates and recent progress to form homogeneous, well-defined clean surfaces of them. Due to the homogeneous surface formation, the surface electronic states and their non-trivial TO are elucidated well in SmB6 and YbB12, by using spin- and angle-resolved photoelectron spectroscopy.
{"title":"Recent progress in clean-surface formation of topological Kondo insulators and topological surface states observed there","authors":"Y. Ohtsubo, S. Kimura, F. Iga","doi":"10.1088/2516-1075/ac8631","DOIUrl":"https://doi.org/10.1088/2516-1075/ac8631","url":null,"abstract":"The peculiar metallic electronic states proposed and observed in Kondo insulators (KIs), whose bandgap opens at low temperature derived from the Kondo effect between itinerant and localized electrons, have attracted considerable attention in this decade, because it suggests the coexistence of strong electron correlation and non-trivial topological order (TO) in such KIs, namely topological Kondo insulators (TKIs). However, experimental studies of these states have led to controversial conclusions mainly owing to the difficulty and inhomogeneity of the single crystal surfaces of the TKI candidates, samarium hexaboride (SmB6) and ytterbium dodecaboride (YbB12). In this article, we review studies focused on the surface atomic and electronic structures of TKI candidates and recent progress to form homogeneous, well-defined clean surfaces of them. Due to the homogeneous surface formation, the surface electronic states and their non-trivial TO are elucidated well in SmB6 and YbB12, by using spin- and angle-resolved photoelectron spectroscopy.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44666568","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 : 2022-07-29DOI: 10.1088/2516-1075/ac858c
Owen Moulding, T. Muramatsu, C. Sayers, E. da Como, S. Friedemann
TiSe2 undergoes charge density wave (CDW) order which can be suppressed under pressure. We use high-resolution electrical resistivity and magnetoresistance measurements to trace the CDW to the highest pressures of any transport study so far. Comparison with previous work shows that the CDW is very sensitive to pressure conditions resulting in a reduced critical pressure in the presence of non-hydrostaticity. Our analysis indicates that in perfect pressure conditions the intrinsic critical pressure might be as high as 5.6 GPa. At the same time, we observe signatures of enhanced scattering linked to the critical pressure, P CDW. The sensitivity of P CDW to non-hydrostaticity and the enhanced scattering linked to it raises questions of how the superconductivity induced in TiSe2 under pressure is related to the CDW order.
{"title":"Suppression of charge-density-wave order in TiSe2 studied with high-pressure magnetoresistance","authors":"Owen Moulding, T. Muramatsu, C. Sayers, E. da Como, S. Friedemann","doi":"10.1088/2516-1075/ac858c","DOIUrl":"https://doi.org/10.1088/2516-1075/ac858c","url":null,"abstract":"TiSe2 undergoes charge density wave (CDW) order which can be suppressed under pressure. We use high-resolution electrical resistivity and magnetoresistance measurements to trace the CDW to the highest pressures of any transport study so far. Comparison with previous work shows that the CDW is very sensitive to pressure conditions resulting in a reduced critical pressure in the presence of non-hydrostaticity. Our analysis indicates that in perfect pressure conditions the intrinsic critical pressure might be as high as 5.6 GPa. At the same time, we observe signatures of enhanced scattering linked to the critical pressure, P CDW. The sensitivity of P CDW to non-hydrostaticity and the enhanced scattering linked to it raises questions of how the superconductivity induced in TiSe2 under pressure is related to the CDW order.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42454496","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 : 2022-07-25DOI: 10.1088/2516-1075/acbff8
M. Alaei, H. Karimi
In this study, we use Hubbard-corrected density functional theory (DFT+U) to derive spin model Hamiltonians consisting of Heisenberg exchange interactions up to the fourth nearest neighbors and bi-quadratic interactions. We map the DFT+U results of several magnetic configurations to the Heisenberg spin model Hamiltonian to estimate Heisenberg exchanges. We demonstrate that the number of magnetic configurations should be at least twice the number of exchange parameters to estimate exchange parameters correctly. To calculate biquadratic interaction, we propose specific non-collinear magnetic configurations that do not change the energy of the Heisenberg spin model. We use classical Monte Carlo (MC) simulations to evaluate DFT+U results. We obtain the temperature dependence of magnetic susceptibility and specific heat to determine the Curie–Weiss and Néel temperatures. The MC simulations reveal that although the biquadratic interaction can not change the Néel temperature, it modifies the order parameter. We indicate that for a fair comparison between classical MC simulations and experiments, we need to consider the quantum effect by applying (S+1)/S correction in classical MC simulations.
{"title":"A deep investigation of NiO and MnO through the first principle calculations and Monte Carlo simulations","authors":"M. Alaei, H. Karimi","doi":"10.1088/2516-1075/acbff8","DOIUrl":"https://doi.org/10.1088/2516-1075/acbff8","url":null,"abstract":"In this study, we use Hubbard-corrected density functional theory (DFT+U) to derive spin model Hamiltonians consisting of Heisenberg exchange interactions up to the fourth nearest neighbors and bi-quadratic interactions. We map the DFT+U results of several magnetic configurations to the Heisenberg spin model Hamiltonian to estimate Heisenberg exchanges. We demonstrate that the number of magnetic configurations should be at least twice the number of exchange parameters to estimate exchange parameters correctly. To calculate biquadratic interaction, we propose specific non-collinear magnetic configurations that do not change the energy of the Heisenberg spin model. We use classical Monte Carlo (MC) simulations to evaluate DFT+U results. We obtain the temperature dependence of magnetic susceptibility and specific heat to determine the Curie–Weiss and Néel temperatures. The MC simulations reveal that although the biquadratic interaction can not change the Néel temperature, it modifies the order parameter. We indicate that for a fair comparison between classical MC simulations and experiments, we need to consider the quantum effect by applying (S+1)/S correction in classical MC simulations.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42139748","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 : 2022-06-23DOI: 10.1088/2516-1075/ac7bca
Liqin Xue Toro, S. Kiriakidi, A. Thapper, S. Ott, M. Lundberg
Cobalt polypyridyl complexes efficiently catalyze hydrogen evolution in aqueous media and exhibit high stability under reducing conditions. Their stability and activity can be tuned through electronic and steric considerations, but the rationalization of these effects requires detailed mechanistic understanding. As an example, tetradentate ligands with two non-permanently occupied coordination sites show higher activity with these sites in cis compared to trans configuration. Here reaction mechanisms of the Co-polypyridyl complex [CoII(bpma)Cl2] (bpma = bipyridinylmethyl-pyridinylmethyl-methyl-amine) have been studied using hybrid density-functional theory. This complex has two exchangeable cis sites, and provides a flexible ligand environment with both pyridyl and amine coordination. Two main pathways with low barriers are found. One pathway, which includes both open sites, is hydrogen evolution from a CoII-H intermediate with a water ligand as the proton donor. In the second pathway H–H bond formation occurs between the hydride and the protonated bpma ligand, with one open site acting as a spectator. The two pathways have similar barriers at higher pH, while the latter becomes more dominant at lower pH. The calculations consider a large number of interconnected variables; protonation sites, isomers, spin multiplicities, and the identities of the open binding sites, as well as their combinations, thus exploring many simultaneous dimensions within each pathway. The results highlight the effects of having two open cis-coordination sites and how their relative binding affinities change during the reaction pathway. They also illustrate why CoII-H intermediates are more active than CoIII-H ones, and why pyridyl protonation gives lower reaction barriers than amine protonation.
{"title":"Two routes to hydrogen evolution for a Co-polypyridyl complex with two open sites","authors":"Liqin Xue Toro, S. Kiriakidi, A. Thapper, S. Ott, M. Lundberg","doi":"10.1088/2516-1075/ac7bca","DOIUrl":"https://doi.org/10.1088/2516-1075/ac7bca","url":null,"abstract":"Cobalt polypyridyl complexes efficiently catalyze hydrogen evolution in aqueous media and exhibit high stability under reducing conditions. Their stability and activity can be tuned through electronic and steric considerations, but the rationalization of these effects requires detailed mechanistic understanding. As an example, tetradentate ligands with two non-permanently occupied coordination sites show higher activity with these sites in cis compared to trans configuration. Here reaction mechanisms of the Co-polypyridyl complex [CoII(bpma)Cl2] (bpma = bipyridinylmethyl-pyridinylmethyl-methyl-amine) have been studied using hybrid density-functional theory. This complex has two exchangeable cis sites, and provides a flexible ligand environment with both pyridyl and amine coordination. Two main pathways with low barriers are found. One pathway, which includes both open sites, is hydrogen evolution from a CoII-H intermediate with a water ligand as the proton donor. In the second pathway H–H bond formation occurs between the hydride and the protonated bpma ligand, with one open site acting as a spectator. The two pathways have similar barriers at higher pH, while the latter becomes more dominant at lower pH. The calculations consider a large number of interconnected variables; protonation sites, isomers, spin multiplicities, and the identities of the open binding sites, as well as their combinations, thus exploring many simultaneous dimensions within each pathway. The results highlight the effects of having two open cis-coordination sites and how their relative binding affinities change during the reaction pathway. They also illustrate why CoII-H intermediates are more active than CoIII-H ones, and why pyridyl protonation gives lower reaction barriers than amine protonation.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44177003","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 : 2022-06-20DOI: 10.1088/2516-1075/ac89c3
S. Mankovsky, H. Ebert
While the ground state of magnetic materials is in general well described on the basis of spin density functional theory (SDFT), the theoretical description of finite-temperature and non-equilibrium properties require an extension beyond the standard SDFT. Time-dependent SDFT (TD-SDFT), which give for example access to dynamical properties are computationally very demanding and can currently be hardly applied to complex solids. Here we focus on the alternative approach based on the combination of a parameterized phenomenological spin Hamiltonian and SDFT-based electronic structure calculations, giving access to the dynamical and finite-temperature properties for example via spin-dynamics simulations using the Landau–Lifshitz–Gilbert (LLG) equation or Monte Carlo simulations. We present an overview on the various methods to calculate the parameters of the various phenomenological Hamiltonians with an emphasis on the KKR Green function method as one of the most flexible band structure methods giving access to practically all relevant parameters. Concerning these, it is crucial to account for the spin–orbit coupling (SOC) by performing relativistic SDFT-based calculations as it plays a key role for magnetic anisotropy and chiral exchange interactions represented by the DMI parameters in the spin Hamiltonian. This concerns also the Gilbert damping parameters characterizing magnetization dissipation in the LLG equation, chiral multispin interaction parameters of the extended Heisenberg Hamiltonian, as well as spin–lattice interaction parameters describing the interplay of spin and lattice dynamics processes, for which an efficient computational scheme has been developed recently by the present authors.
{"title":"First-principles calculation of the parameters used by atomistic magnetic simulations","authors":"S. Mankovsky, H. Ebert","doi":"10.1088/2516-1075/ac89c3","DOIUrl":"https://doi.org/10.1088/2516-1075/ac89c3","url":null,"abstract":"While the ground state of magnetic materials is in general well described on the basis of spin density functional theory (SDFT), the theoretical description of finite-temperature and non-equilibrium properties require an extension beyond the standard SDFT. Time-dependent SDFT (TD-SDFT), which give for example access to dynamical properties are computationally very demanding and can currently be hardly applied to complex solids. Here we focus on the alternative approach based on the combination of a parameterized phenomenological spin Hamiltonian and SDFT-based electronic structure calculations, giving access to the dynamical and finite-temperature properties for example via spin-dynamics simulations using the Landau–Lifshitz–Gilbert (LLG) equation or Monte Carlo simulations. We present an overview on the various methods to calculate the parameters of the various phenomenological Hamiltonians with an emphasis on the KKR Green function method as one of the most flexible band structure methods giving access to practically all relevant parameters. Concerning these, it is crucial to account for the spin–orbit coupling (SOC) by performing relativistic SDFT-based calculations as it plays a key role for magnetic anisotropy and chiral exchange interactions represented by the DMI parameters in the spin Hamiltonian. This concerns also the Gilbert damping parameters characterizing magnetization dissipation in the LLG equation, chiral multispin interaction parameters of the extended Heisenberg Hamiltonian, as well as spin–lattice interaction parameters describing the interplay of spin and lattice dynamics processes, for which an efficient computational scheme has been developed recently by the present authors.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47548529","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 : 2022-06-16DOI: 10.1088/2516-1075/ac7993
Zilin Song, Peng-Chu Tao
Pathogen resistance to carbapenem antibiotics compromises effective treatments of superbug infections. One major source of carbapenem resistance is the bacterial production of carbapenemases which effectively hydrolyze carbapenem drugs. In this computational study, the deacylation reaction of imipenem (IPM) by GES-5 carbapenemases (GES) is modeled to unravel the mechanistic factors that facilitate carbapenem resistance. Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations are applied to sample the GES/IPM deacylation barriers on the minimum energy pathways (MEPs). In light of the recent emergence of graph-based deep-learning techniques, we construct graph representations of the GES/IPM active site. An edge-conditioned graph convolutional neural network (ECGCNN) is trained on the acyl-enzyme conformational graphs to learn the underlying correlations between the GES/IPM conformations and the deacylation barriers. A perturbative approach is proposed to interpret the latent representations from the graph-learning (GL) model and extract essential mechanistic understanding with atomistic detail. In general, our study combining QM/MM MEPs calculations and GL models explains mechanistic landscapes underlying the IPM resistance driven by GES carbapenemases. We also demonstrate that GL methods could effectively assist the post-analysis of QM/MM calculations whose data span high dimensionality and large sample-size.
{"title":"Graph-learning guided mechanistic insights into imipenem hydrolysis in GES carbapenemases","authors":"Zilin Song, Peng-Chu Tao","doi":"10.1088/2516-1075/ac7993","DOIUrl":"https://doi.org/10.1088/2516-1075/ac7993","url":null,"abstract":"Pathogen resistance to carbapenem antibiotics compromises effective treatments of superbug infections. One major source of carbapenem resistance is the bacterial production of carbapenemases which effectively hydrolyze carbapenem drugs. In this computational study, the deacylation reaction of imipenem (IPM) by GES-5 carbapenemases (GES) is modeled to unravel the mechanistic factors that facilitate carbapenem resistance. Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations are applied to sample the GES/IPM deacylation barriers on the minimum energy pathways (MEPs). In light of the recent emergence of graph-based deep-learning techniques, we construct graph representations of the GES/IPM active site. An edge-conditioned graph convolutional neural network (ECGCNN) is trained on the acyl-enzyme conformational graphs to learn the underlying correlations between the GES/IPM conformations and the deacylation barriers. A perturbative approach is proposed to interpret the latent representations from the graph-learning (GL) model and extract essential mechanistic understanding with atomistic detail. In general, our study combining QM/MM MEPs calculations and GL models explains mechanistic landscapes underlying the IPM resistance driven by GES carbapenemases. We also demonstrate that GL methods could effectively assist the post-analysis of QM/MM calculations whose data span high dimensionality and large sample-size.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47754594","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 : 2022-06-14DOI: 10.1088/2516-1075/ac78b4
J. Kas, F. Vila, T. Tan, J. Rehr
Many interesting properties of functional materials, such as dynamic response and thermodynamic behavior, depend on their excited state properties. These functional properties are often related to excitations in the system, such as phonons and plasmons, which lead to inelastic losses, lifetime, and other dynamic effects. The excitations are pure many-body correlation effects that are missing from independent particle theories. They are revealed in x-ray spectra such as photoemission and absorption, where they show up as satellites beyond the quasi-particle approximation. Our main focus in this work is the use of Green’s function methods to describe these effects. In particular, we discuss how the cumulant Green’s function provides a unified treatment of such dynamic correlation effects in many contexts. Besides a robust theoretical framework, these methods also yield widely applicable tools for practical calculations of many functional properties of materials. This methodology is illustrated with a number of applications ranging from optical and x-ray spectra to thermodynamic properties, and dynamic response. Some recent extensions for more correlated systems are also briefly discussed.
{"title":"Green’s function methods for excited states and x-ray spectra of functional materials","authors":"J. Kas, F. Vila, T. Tan, J. Rehr","doi":"10.1088/2516-1075/ac78b4","DOIUrl":"https://doi.org/10.1088/2516-1075/ac78b4","url":null,"abstract":"Many interesting properties of functional materials, such as dynamic response and thermodynamic behavior, depend on their excited state properties. These functional properties are often related to excitations in the system, such as phonons and plasmons, which lead to inelastic losses, lifetime, and other dynamic effects. The excitations are pure many-body correlation effects that are missing from independent particle theories. They are revealed in x-ray spectra such as photoemission and absorption, where they show up as satellites beyond the quasi-particle approximation. Our main focus in this work is the use of Green’s function methods to describe these effects. In particular, we discuss how the cumulant Green’s function provides a unified treatment of such dynamic correlation effects in many contexts. Besides a robust theoretical framework, these methods also yield widely applicable tools for practical calculations of many functional properties of materials. This methodology is illustrated with a number of applications ranging from optical and x-ray spectra to thermodynamic properties, and dynamic response. Some recent extensions for more correlated systems are also briefly discussed.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42244675","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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