Pub Date : 2023-01-31DOI: 10.1088/2516-1075/acb7b8
Soumyadip Ray, Debasish Koner, Padmabati Mondal
Electronic and vibrational spectroscopic studies of molecules are of crucial importance to characterizing a molecule and detecting the molecular species in different environments. In this review article, we summarized some important theoretical methods to calculate high-resolution electronic spectra and ro-vibrational states for small molecular systems with the inclusion of vibronic and ro-vibrational couplings, respectively. We have also reviewed a number of theoretical studies exploring some interesting organic chromophores like indole, isoalloxazine, transition metal trifluoride CoF3 and NiF3, and molecular ions like protonated rare gases and azido ions. These studies involve the calculation of spectroscopic features based on analytical potential energy surfaces (PESs) constructed using high-level ab initio energies. The topology of the PESs has been explored for these selected systems. The vibronic spectra and ro-vibrational states calculated using various theoretical methods and their comparison to available experimental results are reported in this review.
{"title":"High-resolution electronic and vibrational spectroscopy of small-to-medium sized molecules with ab initio potential energy surface","authors":"Soumyadip Ray, Debasish Koner, Padmabati Mondal","doi":"10.1088/2516-1075/acb7b8","DOIUrl":"https://doi.org/10.1088/2516-1075/acb7b8","url":null,"abstract":"Electronic and vibrational spectroscopic studies of molecules are of crucial importance to characterizing a molecule and detecting the molecular species in different environments. In this review article, we summarized some important theoretical methods to calculate high-resolution electronic spectra and ro-vibrational states for small molecular systems with the inclusion of vibronic and ro-vibrational couplings, respectively. We have also reviewed a number of theoretical studies exploring some interesting organic chromophores like indole, isoalloxazine, transition metal trifluoride CoF3 and NiF3, and molecular ions like protonated rare gases and azido ions. These studies involve the calculation of spectroscopic features based on analytical potential energy surfaces (PESs) constructed using high-level ab initio energies. The topology of the PESs has been explored for these selected systems. The vibronic spectra and ro-vibrational states calculated using various theoretical methods and their comparison to available experimental results are reported in this review.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43787944","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 : 2023-01-10DOI: 10.1088/2516-1075/acb1e7
Dongbo Zhao, K. Liao, Benkun Hong, Wei Li, Shuhua Li
The vibrational circular dichroism (VCD) spectra could determine the molecular chirality of condensed-phase systems, but their quantum chemistry calculations are costly. The fragment-based methods have not been applied to the VCD spectra of periodic systems yet. In this work, we have extended the generalized energy-based fragmentation (GEBF) approach to accurately and efficiently compute the VCD spectra of chiral molecular crystals under periodic boundary conditions (PBCs) and macromolecules in solutions. In this approach, the Hessian matrices, atomic polar/axial tensors of a target system, are evaluated as a linear combination of the corresponding quantities from a series of small electrostatically embedded subsystems. Comparisons of GEBF and conventional VCD spectra of two large molecules show that this approach can satisfactorily reproduce the conventional computational results. Then, we applied the PBC-GEBF method to calculate the VCD spectra of a chiral molecular crystal and two macromolecules in solutions. Our results show that the experimental VCD spectrum can be roughly reproduced in terms of both band shape and vibrational peaks. The GEBF-VCD and PBC-GEBF-VCD approaches are expected to be practical tools to investigate the chirality of molecular crystals and macromolecules in solutions.
{"title":"Accurate and efficient prediction of vibrational circular dichroism spectra of condensed-phase systems with the generalized energy-based fragmentation method","authors":"Dongbo Zhao, K. Liao, Benkun Hong, Wei Li, Shuhua Li","doi":"10.1088/2516-1075/acb1e7","DOIUrl":"https://doi.org/10.1088/2516-1075/acb1e7","url":null,"abstract":"The vibrational circular dichroism (VCD) spectra could determine the molecular chirality of condensed-phase systems, but their quantum chemistry calculations are costly. The fragment-based methods have not been applied to the VCD spectra of periodic systems yet. In this work, we have extended the generalized energy-based fragmentation (GEBF) approach to accurately and efficiently compute the VCD spectra of chiral molecular crystals under periodic boundary conditions (PBCs) and macromolecules in solutions. In this approach, the Hessian matrices, atomic polar/axial tensors of a target system, are evaluated as a linear combination of the corresponding quantities from a series of small electrostatically embedded subsystems. Comparisons of GEBF and conventional VCD spectra of two large molecules show that this approach can satisfactorily reproduce the conventional computational results. Then, we applied the PBC-GEBF method to calculate the VCD spectra of a chiral molecular crystal and two macromolecules in solutions. Our results show that the experimental VCD spectrum can be roughly reproduced in terms of both band shape and vibrational peaks. The GEBF-VCD and PBC-GEBF-VCD approaches are expected to be practical tools to investigate the chirality of molecular crystals and macromolecules in solutions.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49507967","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 : 2023-01-09DOI: 10.1088/2516-1075/acd28e
Z. Hashemi, Matthias Knodt, Mário R. G. Marques, L. Leppert
Photoinduced charge-transfer excitations are key to understand the primary processes of natural photosynthesis and for designing photovoltaic and photocatalytic devices. In this paper, we use Bacteriochlorophyll dimers extracted from the light harvesting apparatus and reaction center of a photosynthetic purple bacterium as model systems to study such excitations using first-principles numerical simulation methods. We distinguish four different regimes of intermolecular coupling, ranging from very weakly coupled to strongly coupled, and identify the factors that determine the energy and character of charge-transfer excitations in each case. We also construct an artificial dimer to systematically study the effects of intermolecular distance and orientation on charge-transfer excitations, as well as the impact of molecular vibrations on these excitations. Our results provide design rules for tailoring charge-transfer excitations in Bacteriochloropylls and related photoactive molecules, and highlight the importance of including charge-transfer excitations in accurate models of the excited-state structure and dynamics of Bacteriochlorophyll aggregates.
{"title":"Mapping charge-transfer excitations in Bacteriochlorophyll dimers from first principles","authors":"Z. Hashemi, Matthias Knodt, Mário R. G. Marques, L. Leppert","doi":"10.1088/2516-1075/acd28e","DOIUrl":"https://doi.org/10.1088/2516-1075/acd28e","url":null,"abstract":"Photoinduced charge-transfer excitations are key to understand the primary processes of natural photosynthesis and for designing photovoltaic and photocatalytic devices. In this paper, we use Bacteriochlorophyll dimers extracted from the light harvesting apparatus and reaction center of a photosynthetic purple bacterium as model systems to study such excitations using first-principles numerical simulation methods. We distinguish four different regimes of intermolecular coupling, ranging from very weakly coupled to strongly coupled, and identify the factors that determine the energy and character of charge-transfer excitations in each case. We also construct an artificial dimer to systematically study the effects of intermolecular distance and orientation on charge-transfer excitations, as well as the impact of molecular vibrations on these excitations. Our results provide design rules for tailoring charge-transfer excitations in Bacteriochloropylls and related photoactive molecules, and highlight the importance of including charge-transfer excitations in accurate models of the excited-state structure and dynamics of Bacteriochlorophyll aggregates.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45145545","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 : 2023-01-06DOI: 10.1088/2516-1075/acba6f
Roberta Favata, A. Marrazzo
We present an approach for the calculation of the Z2 topological invariant in non-crystalline two-dimensional quantum spin Hall insulators. While topological invariants were originally mathematically introduced for crystalline periodic systems, and crucially hinge on tracking the evolution of occupied states through the Brillouin zone, the introduction of disorder or dynamical effects can break the translational symmetry and imply the use of larger simulation cells, where the k-point sampling is typically reduced to the single Γ-point. Here, we introduce a single-point formula for the spin Chern number that enables to adopt the supercell framework, where a single Hamiltonian diagonalisation is performed. Inspired by the work of Prodan (2009 Phys. Rev. B 80 125327), our single-point approach allows to calculate the spin Chern number even when the spin operator sˆz does not commute with the Hamiltonian, as in the presence of Rashba spin–orbit coupling. We validate our method on the Kane–Mele model, both pristine and in the presence of Anderson disorder. Finally, we investigate the disorder-driven transition from the trivial phase to the topological state known as topological Anderson insulator. Beyond disordered systems, our approach is particularly useful to investigate the role of defects, to study topological alloys and in the context of ab-initio molecular dynamics simulations at finite temperature.
我们提出了一种计算非晶二维量子自旋霍尔绝缘体中Z2拓扑不变量的方法。虽然拓扑不变量最初是在数学上引入晶体周期系统的，并且关键取决于通过布里温区跟踪占位状态的演变，但引入无序或动态效应可能会打破平移对称性，并意味着使用更大的模拟单元，其中k点采样通常减少到单个Γ-point。在这里，我们引入了自旋陈恩数的单点公式，该公式能够采用超级单体框架，其中执行单个哈密顿对角化。受到Prodan(2009年物理学家)工作的启发。Rev. B 80 125327)，我们的单点方法允许计算自旋陈恩数，即使自旋算符s * z不与哈密顿量交换，如在Rashba自旋轨道耦合存在的情况下。我们在Kane-Mele模型上验证了我们的方法，无论是原始的还是存在安德森紊乱的。最后，我们研究了无序驱动的从平凡相到拓扑状态的转变，即拓扑安德森绝缘子。除了无序系统之外，我们的方法对于研究缺陷的作用，研究拓扑合金以及在有限温度下从头算分子动力学模拟的背景下特别有用。
{"title":"Single-point spin Chern number in a supercell framework","authors":"Roberta Favata, A. Marrazzo","doi":"10.1088/2516-1075/acba6f","DOIUrl":"https://doi.org/10.1088/2516-1075/acba6f","url":null,"abstract":"We present an approach for the calculation of the Z2 topological invariant in non-crystalline two-dimensional quantum spin Hall insulators. While topological invariants were originally mathematically introduced for crystalline periodic systems, and crucially hinge on tracking the evolution of occupied states through the Brillouin zone, the introduction of disorder or dynamical effects can break the translational symmetry and imply the use of larger simulation cells, where the k-point sampling is typically reduced to the single Γ-point. Here, we introduce a single-point formula for the spin Chern number that enables to adopt the supercell framework, where a single Hamiltonian diagonalisation is performed. Inspired by the work of Prodan (2009 Phys. Rev. B 80 125327), our single-point approach allows to calculate the spin Chern number even when the spin operator sˆz does not commute with the Hamiltonian, as in the presence of Rashba spin–orbit coupling. We validate our method on the Kane–Mele model, both pristine and in the presence of Anderson disorder. Finally, we investigate the disorder-driven transition from the trivial phase to the topological state known as topological Anderson insulator. Beyond disordered systems, our approach is particularly useful to investigate the role of defects, to study topological alloys and in the context of ab-initio molecular dynamics simulations at finite temperature.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46189083","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 : 2023-01-04DOI: 10.1088/2516-1075/acb02c
Thomas J. Summers, Nathan J. DeYonker
Human carbonic anhydrase (CA) metalloenzymes utilize a Zn2+-containing active site to catalyze the interconversion of carbon dioxide to bicarbonate. The Zn2+ ion may be replaced with other divalent transition metals, though the catalytic efficiency of the enzyme will be reduced. In this work, quantum mechanical cluster models of the active site are used to map the reaction profile for the hydration mechanism of carbon dioxide. The Lipscomb proton transfer and Lindskog rotation mechanisms were examined for the native Zn2+-enzyme along with variants where the metal was substituted with Cd2+, Ni2+, Fe2+, and Fe3+. The findings highlight the impact the metal coordination geometry has on the reaction profile. The results also suggest Fe2+, which is the functional metal for a prototypical CA of an anaerobic bacterium, might also be functional for human CA if cultured within an anaerobic environment.
{"title":"QM-cluster model study of CO2 hydration mechanisms in metal-substituted human carbonic anhydrase II","authors":"Thomas J. Summers, Nathan J. DeYonker","doi":"10.1088/2516-1075/acb02c","DOIUrl":"https://doi.org/10.1088/2516-1075/acb02c","url":null,"abstract":"Human carbonic anhydrase (CA) metalloenzymes utilize a Zn2+-containing active site to catalyze the interconversion of carbon dioxide to bicarbonate. The Zn2+ ion may be replaced with other divalent transition metals, though the catalytic efficiency of the enzyme will be reduced. In this work, quantum mechanical cluster models of the active site are used to map the reaction profile for the hydration mechanism of carbon dioxide. The Lipscomb proton transfer and Lindskog rotation mechanisms were examined for the native Zn2+-enzyme along with variants where the metal was substituted with Cd2+, Ni2+, Fe2+, and Fe3+. The findings highlight the impact the metal coordination geometry has on the reaction profile. The results also suggest Fe2+, which is the functional metal for a prototypical CA of an anaerobic bacterium, might also be functional for human CA if cultured within an anaerobic environment.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46540456","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 : 2022-12-24DOI: 10.1088/2516-1075/acc626
M. Penz, M. Csirik, A. Laestadius
For a quantum-mechanical many-electron system, given a density, the Zhao–Morrison–Parr method allows to compute the effective potential that yields precisely that density. In this work, we demonstrate how this and similar inversion procedures mathematically relate to the Moreau–Yosida regularization of density functionals on Banach spaces. It is shown that these inversion procedures can in fact be understood as a limit process as the regularization parameter approaches zero. This sheds new insight on the role of Moreau–Yosida regularization in density-functional theory and allows to systematically improve density-potential inversion. Our results apply to the Kohn–Sham setting with fractional occupation that determines an effective one-body potential that in turn reproduces an interacting density.
{"title":"Density-potential inversion from Moreau–Yosida regularization","authors":"M. Penz, M. Csirik, A. Laestadius","doi":"10.1088/2516-1075/acc626","DOIUrl":"https://doi.org/10.1088/2516-1075/acc626","url":null,"abstract":"For a quantum-mechanical many-electron system, given a density, the Zhao–Morrison–Parr method allows to compute the effective potential that yields precisely that density. In this work, we demonstrate how this and similar inversion procedures mathematically relate to the Moreau–Yosida regularization of density functionals on Banach spaces. It is shown that these inversion procedures can in fact be understood as a limit process as the regularization parameter approaches zero. This sheds new insight on the role of Moreau–Yosida regularization in density-functional theory and allows to systematically improve density-potential inversion. Our results apply to the Kohn–Sham setting with fractional occupation that determines an effective one-body potential that in turn reproduces an interacting density.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43089674","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 : 2022-12-13DOI: 10.1088/2516-1075/acab47
Zhicheng Jiang, Jiayu Liu, Zhengtai Liu, D. Shen
The MnBi2Te4 family compounds have drawn enormous attention in recent years due to their potential to realize the high-temperature quantum anomalous Hall effect. As one of the most direct techniques to probe electronic structure, angle-resolved photoemission spectroscopy (ARPES) has been widely applied to investigate the interplay between the magnetism and non-trivial topological band structure of MnBi2Te4 family materials. Here, we briefly review some of latest progress in ARPES study of MnBi2Te 4⋅ (Bi2Te3) (n = 0, 1, 2, 3) and analogous MnSb2Te 4⋅ (Sb2Te3)2 (n = 1, 2) series of materials. Aside from the direct observation of the non-trivial topological band structure, ARPES results reveal that their surface band gap can be well modulated by both temperature and Bi2Te3 interpolation. In addition, although ARPES results of the topological surface states are still under hot debate, the extensive experimental results have provided an opportunity to shed light on the complex interactions in intrinsic magnetic topological insulator.
{"title":"A review of angle-resolved photoemission spectroscopy study on topological magnetic material family of MnBi2Te4","authors":"Zhicheng Jiang, Jiayu Liu, Zhengtai Liu, D. Shen","doi":"10.1088/2516-1075/acab47","DOIUrl":"https://doi.org/10.1088/2516-1075/acab47","url":null,"abstract":"The MnBi2Te4 family compounds have drawn enormous attention in recent years due to their potential to realize the high-temperature quantum anomalous Hall effect. As one of the most direct techniques to probe electronic structure, angle-resolved photoemission spectroscopy (ARPES) has been widely applied to investigate the interplay between the magnetism and non-trivial topological band structure of MnBi2Te4 family materials. Here, we briefly review some of latest progress in ARPES study of MnBi2Te 4⋅ (Bi2Te3) (n = 0, 1, 2, 3) and analogous MnSb2Te 4⋅ (Sb2Te3)2 (n = 1, 2) series of materials. Aside from the direct observation of the non-trivial topological band structure, ARPES results reveal that their surface band gap can be well modulated by both temperature and Bi2Te3 interpolation. In addition, although ARPES results of the topological surface states are still under hot debate, the extensive experimental results have provided an opportunity to shed light on the complex interactions in intrinsic magnetic topological insulator.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42589032","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 : 2022-12-09DOI: 10.1088/2516-1075/acaa7a
Mateus M. Quintano, A. A. A. Delgado, Renaldo T. Moura Jr., M. Freindorf, E. Kraka
Two-dimensional infrared spectroscopy has reported highly delocalized in-plane base vibrations in the fingerprint region of nucleotide monophosphates, suggesting the involvement of base pair C=O and C=C ring bonds and considerable interaction between C=O bond stretches. The high delocalization results in congested vibrational spectra, which complicates the assignment of the peaks. This congestion also extends to Watson–Crick base pairs. We applied in this work the characterization of normal mode procedure, a special feature of our local mode analysis, and could for the first time identify the C=O and C=C bonds being engaged in base pair coupling and quantify their contribution to each of the delocalized fingerprint vibration. In addition, a detailed and quantitative description of the hydrogen bonds involved in the Watson–Crick base pairs was provided. Based on the results of this study, we developed a new protocol to elucidate on the assignment of bands in the vibrational spectra of nucleic acids by probing the vibrational space for specific interactions between functional groups prior to and upon base pairing. This protocol will aid to fill the gap between deoxyribonucleic acid structural information and vibrational spectroscopy experiments by facilitating the interpretation of spectra on a quantitative basis.
{"title":"Local mode analysis of characteristic vibrational coupling in nucleobases and Watson–Crick base pairs of DNA","authors":"Mateus M. Quintano, A. A. A. Delgado, Renaldo T. Moura Jr., M. Freindorf, E. Kraka","doi":"10.1088/2516-1075/acaa7a","DOIUrl":"https://doi.org/10.1088/2516-1075/acaa7a","url":null,"abstract":"Two-dimensional infrared spectroscopy has reported highly delocalized in-plane base vibrations in the fingerprint region of nucleotide monophosphates, suggesting the involvement of base pair C=O and C=C ring bonds and considerable interaction between C=O bond stretches. The high delocalization results in congested vibrational spectra, which complicates the assignment of the peaks. This congestion also extends to Watson–Crick base pairs. We applied in this work the characterization of normal mode procedure, a special feature of our local mode analysis, and could for the first time identify the C=O and C=C bonds being engaged in base pair coupling and quantify their contribution to each of the delocalized fingerprint vibration. In addition, a detailed and quantitative description of the hydrogen bonds involved in the Watson–Crick base pairs was provided. Based on the results of this study, we developed a new protocol to elucidate on the assignment of bands in the vibrational spectra of nucleic acids by probing the vibrational space for specific interactions between functional groups prior to and upon base pairing. This protocol will aid to fill the gap between deoxyribonucleic acid structural information and vibrational spectroscopy experiments by facilitating the interpretation of spectra on a quantitative basis.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46123245","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 : 2022-12-06DOI: 10.1088/2516-1075/aca945
Juan Cruz Palermo, Jonathan A Córdova, J. Semelak, L. Capece, S. Bari, D. Estrin
The role of inorganic sulfur species in biological systems has gained considerable interest since the recognition of sulfanes, particularly dihydrogen sulfide or sulfane, H2S, disulfane, HSSH, trisulfane, HSSSH, and their conjugate bases, as endogenous species and mediators of signaling functions in different tissues. The one-electron oxidation of H2S/HS− has been assigned as the onset of signaling processes or oxidative detoxification mechanisms. These varied sulfur containing inorganic species are, together with organic counterparts, reunited as reactive sulfur species (RSS). In order to shed light on this rich and still not completely explored chemistry, we have performed electronic structure calculations at different levels of theory, to provide estimations and the molecular basis of the pKa values of the polysulfides HSSH and HSSSH and of the radical HS•. In addition, we also reported the characterization of selected inorganic RSS including both radical and non-radical species with different protonation states with the intention of assisting the interpretation of chemical/biochemical experiments involving these species.
{"title":"Computational evaluation of relevant species in inorganic sulfur biochemistry","authors":"Juan Cruz Palermo, Jonathan A Córdova, J. Semelak, L. Capece, S. Bari, D. Estrin","doi":"10.1088/2516-1075/aca945","DOIUrl":"https://doi.org/10.1088/2516-1075/aca945","url":null,"abstract":"The role of inorganic sulfur species in biological systems has gained considerable interest since the recognition of sulfanes, particularly dihydrogen sulfide or sulfane, H2S, disulfane, HSSH, trisulfane, HSSSH, and their conjugate bases, as endogenous species and mediators of signaling functions in different tissues. The one-electron oxidation of H2S/HS− has been assigned as the onset of signaling processes or oxidative detoxification mechanisms. These varied sulfur containing inorganic species are, together with organic counterparts, reunited as reactive sulfur species (RSS). In order to shed light on this rich and still not completely explored chemistry, we have performed electronic structure calculations at different levels of theory, to provide estimations and the molecular basis of the pKa values of the polysulfides HSSH and HSSSH and of the radical HS•. In addition, we also reported the characterization of selected inorganic RSS including both radical and non-radical species with different protonation states with the intention of assisting the interpretation of chemical/biochemical experiments involving these species.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41953770","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 : 2022-12-02DOI: 10.1088/2516-1075/aca859
Karan Ahmadzadeh, Xin Li, Ž. Rinkevičius, P. Norman
For general exchange–correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only ∼25% (one-photon off-resonance regions) and ∼50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules.
{"title":"Efficient Kohn–Sham density-functional theory implementation of isotropic spectroscopic observables associated with quadratic response functions","authors":"Karan Ahmadzadeh, Xin Li, Ž. Rinkevičius, P. Norman","doi":"10.1088/2516-1075/aca859","DOIUrl":"https://doi.org/10.1088/2516-1075/aca859","url":null,"abstract":"For general exchange–correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only ∼25% (one-photon off-resonance regions) and ∼50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45391268","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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