Pub Date : 2022-12-01DOI: 10.1088/2516-1075/aca944
DattatrayJ. Late, S. Duhm
Dattatray J Late1,∗ and Steffen Duhm2,3,∗ 1 Centre for Nanoscience and Nanotechnology, Amity University Maharashtra, Mumbai-Pune Expressway, Bhatan, Post Somatne, Panvel, Mumbai, Maharashtra 410206, India 2 Institute of Functional Nano & Soft Materials (FUNSOM), Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People’s Republic of China 3 Jiangsu Key Laboratory of Advanced Negative Carbon Technologies, Soochow University, Suzhou 215123, People’s Republic of China ∗ Authors to whom any correspondence should be addressed.
{"title":"Theoretical and experimental insight into nano-optoelectronics","authors":"DattatrayJ. Late, S. Duhm","doi":"10.1088/2516-1075/aca944","DOIUrl":"https://doi.org/10.1088/2516-1075/aca944","url":null,"abstract":"Dattatray J Late1,∗ and Steffen Duhm2,3,∗ 1 Centre for Nanoscience and Nanotechnology, Amity University Maharashtra, Mumbai-Pune Expressway, Bhatan, Post Somatne, Panvel, Mumbai, Maharashtra 410206, India 2 Institute of Functional Nano & Soft Materials (FUNSOM), Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou 215123, People’s Republic of China 3 Jiangsu Key Laboratory of Advanced Negative Carbon Technologies, Soochow University, Suzhou 215123, People’s Republic of China ∗ Authors to whom any correspondence should be addressed.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46958622","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 : 2022-11-22DOI: 10.1088/2516-1075/aca4ff
Solomon Yamoah Effah, W. Kaushalya, M. Hix, Alice R. Walker
Synthetically modified fluorescent nucleotides (SFNs) are highly popular in a variety of experiments to explore biochemistry in molecular imaging, but the connection between their photodynamics and quenching mechanisms to their molecular structure remain relatively unstudied computationally. We combine various levels of theory, including classical force field dynamics and excited state quantum mechanic/molecular mechanic Born–Oppenheimer dynamics to characterize a set of polycyclic aromatic hydrocarbon based substituents bound to cytidine (dC) and guanine (dG) nucleobases. We specifically focus on perylene (P) bound to C5 and C6 of dC, and the naturally occurring benzo[a]pyrene diol epoxide (B[a]PDE) on dG. We find that specific angles of the connection points between them modulate mechanisms of intramolecular charge transfer, where an electron moves from P to dC and dG to B[a]PDE once an optimal angle is reached. Functionalization location and flexibility of the substituent affect access to these angles and, therefore, the amount of rapid charge transfer quenching of the fluorescence that we observe. This work demonstrates that the choice of functionalization location for SFNs changes the accessibility of charge transfer mechanisms via steric hindrance, and suggest that this feature can be applied for future tuning of fluorescence properties.
{"title":"Computational investigations of the excited state dynamics and quenching mechanisms of polycyclic aromatic hydrocarbon DNA adducts in solution","authors":"Solomon Yamoah Effah, W. Kaushalya, M. Hix, Alice R. Walker","doi":"10.1088/2516-1075/aca4ff","DOIUrl":"https://doi.org/10.1088/2516-1075/aca4ff","url":null,"abstract":"Synthetically modified fluorescent nucleotides (SFNs) are highly popular in a variety of experiments to explore biochemistry in molecular imaging, but the connection between their photodynamics and quenching mechanisms to their molecular structure remain relatively unstudied computationally. We combine various levels of theory, including classical force field dynamics and excited state quantum mechanic/molecular mechanic Born–Oppenheimer dynamics to characterize a set of polycyclic aromatic hydrocarbon based substituents bound to cytidine (dC) and guanine (dG) nucleobases. We specifically focus on perylene (P) bound to C5 and C6 of dC, and the naturally occurring benzo[a]pyrene diol epoxide (B[a]PDE) on dG. We find that specific angles of the connection points between them modulate mechanisms of intramolecular charge transfer, where an electron moves from P to dC and dG to B[a]PDE once an optimal angle is reached. Functionalization location and flexibility of the substituent affect access to these angles and, therefore, the amount of rapid charge transfer quenching of the fluorescence that we observe. This work demonstrates that the choice of functionalization location for SFNs changes the accessibility of charge transfer mechanisms via steric hindrance, and suggest that this feature can be applied for future tuning of fluorescence properties.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49285513","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 : 2022-11-18DOI: 10.1088/2516-1075/aca458
B. R. Westbrook, Joshua P Layfield, Timothy J. Lee, R. Fortenberry
Reparameterized semi-empirical methods can reproduce gas-phase experimental vibrational frequencies to within 24 cm−1 or better for a 100-fold decrease in computational cost in the anharmonic fundamental vibrational frequencies. To achieve such accuracy and efficiency, the default parameters in the PM6 semi-empirical model are herein optimized to reproduce the experimental and high-level theoretical vibrational spectra of three small hydrocarbon molecules, C2H2, c-C3H2, and C2H4, with the hope that these same parameters will be applicable to large polycyclic aromatic hydrocarbons (PAHs). This massive cost reduction allows for the computation of explicit anharmonic frequencies and the inclusion of resonance corrections that have been shown to be essential for accurate predictions of anharmonic frequencies. Such accurate predictions are necessary to help to disentangle the heretofore unidentified infrared spectral features observed around diverse astronomical bodies and hypothesized to be caused by PAHs, especially with the upcoming influx of observational data from the James Webb Space Telescope. The optimized PM6 parameters presented herein represent a substantial step in this direction with those obtained for ethylene (C2H4) yielding a 37% reduction in the mean absolute error of the fundamental frequencies compared to the default PM6 parameters.
{"title":"Reparameterized semi-empirical methods for computing anharmonic vibrational frequencies of multiply-bonded hydrocarbons","authors":"B. R. Westbrook, Joshua P Layfield, Timothy J. Lee, R. Fortenberry","doi":"10.1088/2516-1075/aca458","DOIUrl":"https://doi.org/10.1088/2516-1075/aca458","url":null,"abstract":"Reparameterized semi-empirical methods can reproduce gas-phase experimental vibrational frequencies to within 24 cm−1 or better for a 100-fold decrease in computational cost in the anharmonic fundamental vibrational frequencies. To achieve such accuracy and efficiency, the default parameters in the PM6 semi-empirical model are herein optimized to reproduce the experimental and high-level theoretical vibrational spectra of three small hydrocarbon molecules, C2H2, c-C3H2, and C2H4, with the hope that these same parameters will be applicable to large polycyclic aromatic hydrocarbons (PAHs). This massive cost reduction allows for the computation of explicit anharmonic frequencies and the inclusion of resonance corrections that have been shown to be essential for accurate predictions of anharmonic frequencies. Such accurate predictions are necessary to help to disentangle the heretofore unidentified infrared spectral features observed around diverse astronomical bodies and hypothesized to be caused by PAHs, especially with the upcoming influx of observational data from the James Webb Space Telescope. The optimized PM6 parameters presented herein represent a substantial step in this direction with those obtained for ethylene (C2H4) yielding a 37% reduction in the mean absolute error of the fundamental frequencies compared to the default PM6 parameters.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46802091","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 : 2022-11-07DOI: 10.1088/2516-1075/ac9bb3
B. Chan, Masanari Kimura
In the present study, we have used computational quantum chemistry to explore the reduction of various types of substrates by group-13 hydrides. We use the high-level L-W1X method to obtain the energies for the constituent association and hydride transfer reactions. We find that the hydride transfer reactions are highly exothermic, while the preceding association reactions are less so. Thus, improving the thermodynamics of substrate association may improve the overall process. Among the various substrates, amine and imine show the strongest binding, while CO2 shows the weakest. Between the group-13 hydrides, alanes bind most strongly with the substrates, and they also have the most exothermic hydride transfer reactions. To facilitate CO2 binding, we have examined alanes with electron-withdrawing groups, and we indeed find CF3 groups to be effective. Drawing inspiration from the RuBisCO enzyme for CO2 fixation, we have further examined the activation of CO2 with two independent AlH(CF3)2 molecules, with the results showing an even more exothermic association. This observation may form the basis for designing an effective dialane reagent for CO2 reduction. We have also assessed a range of lower-cost computational methods for the calculation of systems in the present study. We find the DSD-PBEP86 double-hybrid DFT method to be the most suitable for the study of related medium-sized systems.
{"title":"High-level quantum chemistry exploration of reduction by group-13 hydrides: insights into the rational design of bio-mimic CO2 reduction","authors":"B. Chan, Masanari Kimura","doi":"10.1088/2516-1075/ac9bb3","DOIUrl":"https://doi.org/10.1088/2516-1075/ac9bb3","url":null,"abstract":"In the present study, we have used computational quantum chemistry to explore the reduction of various types of substrates by group-13 hydrides. We use the high-level L-W1X method to obtain the energies for the constituent association and hydride transfer reactions. We find that the hydride transfer reactions are highly exothermic, while the preceding association reactions are less so. Thus, improving the thermodynamics of substrate association may improve the overall process. Among the various substrates, amine and imine show the strongest binding, while CO2 shows the weakest. Between the group-13 hydrides, alanes bind most strongly with the substrates, and they also have the most exothermic hydride transfer reactions. To facilitate CO2 binding, we have examined alanes with electron-withdrawing groups, and we indeed find CF3 groups to be effective. Drawing inspiration from the RuBisCO enzyme for CO2 fixation, we have further examined the activation of CO2 with two independent AlH(CF3)2 molecules, with the results showing an even more exothermic association. This observation may form the basis for designing an effective dialane reagent for CO2 reduction. We have also assessed a range of lower-cost computational methods for the calculation of systems in the present study. We find the DSD-PBEP86 double-hybrid DFT method to be the most suitable for the study of related medium-sized systems.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43944538","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 : 2022-11-03DOI: 10.1088/2516-1075/ac9ffb
T. Schultz
Photoelectron spectroscopy is a powerful surface analysis technique that can differentiate different bonding environments and directly determine the absolute work function of a sample. Despite its ever-easier accessibility—or perhaps precisely because of it—some common mistakes or bad habits are often found in the literature when it comes to the evaluation or presentation of photoelectron spectroscopy data. Here we address some of these issues and give suggestions for best practice, i.e., a proper presentation of the secondary electron cut-off used for work function determination, correct binding energy referencing and some tips for appropriate peak fitting, as well as valuable literature references to more detailed tutorials. Finally, we present a concise step-by-step guide on how to conduct a complete x-ray photoelectron spectroscopy analysis of an unknown sample.
{"title":"A unified secondary electron cut-off presentation and common mistakes in photoelectron spectroscopy","authors":"T. Schultz","doi":"10.1088/2516-1075/ac9ffb","DOIUrl":"https://doi.org/10.1088/2516-1075/ac9ffb","url":null,"abstract":"Photoelectron spectroscopy is a powerful surface analysis technique that can differentiate different bonding environments and directly determine the absolute work function of a sample. Despite its ever-easier accessibility—or perhaps precisely because of it—some common mistakes or bad habits are often found in the literature when it comes to the evaluation or presentation of photoelectron spectroscopy data. Here we address some of these issues and give suggestions for best practice, i.e., a proper presentation of the secondary electron cut-off used for work function determination, correct binding energy referencing and some tips for appropriate peak fitting, as well as valuable literature references to more detailed tutorials. Finally, we present a concise step-by-step guide on how to conduct a complete x-ray photoelectron spectroscopy analysis of an unknown sample.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47256255","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 : 2022-10-11DOI: 10.1088/2516-1075/ac9942
J. Sancho‐García, É. Brémond, Á. Pérez‐Jiménez, Ilaria Ciofini, C. Adamo
The development of universal and accurate approximations for electronic structure calculations lies at the central core of (past and modern) research in theoretical and computational chemistry. For that purpose, any reliable method needs to treat in a balanced way exchange and correlation effects arising from the intricate structure of matter at the nanoscopic level. Following this principle, we have developed a set of non-empirical (double-hybrid) density functional expressions, minimizing the parameterization and also widely applicable even for systems of considerable size, while being accurate enough to compete with wavefunction methods or even matching experimental information. The underlying expressions are now implemented in many available codes worldwide, then allowing the access to the whole set of key properties needed for addressing chemical structure, reactivity, and bonding, at all nanostructured levels and/or states of matter. Additionally, the recent extension to excited states through a time-dependent (linear-response) formalism also allows one to deal with photochemistry, photophysical, and related properties. Therefore, this family of methods can now be successfully applied to organic, inorganic, or biomolecular compounds, or any other complex system, within an affordable computational effort.
{"title":"Non-empirical double-hybrid density functionals as reliable tools for electronic structure calculations","authors":"J. Sancho‐García, É. Brémond, Á. Pérez‐Jiménez, Ilaria Ciofini, C. Adamo","doi":"10.1088/2516-1075/ac9942","DOIUrl":"https://doi.org/10.1088/2516-1075/ac9942","url":null,"abstract":"The development of universal and accurate approximations for electronic structure calculations lies at the central core of (past and modern) research in theoretical and computational chemistry. For that purpose, any reliable method needs to treat in a balanced way exchange and correlation effects arising from the intricate structure of matter at the nanoscopic level. Following this principle, we have developed a set of non-empirical (double-hybrid) density functional expressions, minimizing the parameterization and also widely applicable even for systems of considerable size, while being accurate enough to compete with wavefunction methods or even matching experimental information. The underlying expressions are now implemented in many available codes worldwide, then allowing the access to the whole set of key properties needed for addressing chemical structure, reactivity, and bonding, at all nanostructured levels and/or states of matter. Additionally, the recent extension to excited states through a time-dependent (linear-response) formalism also allows one to deal with photochemistry, photophysical, and related properties. Therefore, this family of methods can now be successfully applied to organic, inorganic, or biomolecular compounds, or any other complex system, within an affordable computational effort.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43617399","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 : 2022-09-30DOI: 10.1088/2516-1075/ac96b8
M. J. Rodríguez, Carlos Ramírez
We propose a divide-and-conquer algorithm to find recursively the scattering matrix of general tight-binding structures. The scattering matrix allows a direct calculation of transport properties in mesoscopic systems by using the Landauer formula. The method is exact, and by analyzing the performance of the algorithm in square, triangular and honeycomb lattices, we show a significant improvement in comparison to other state-of-the-art recursive and non-recursive methods. We utilize this algorithm to compute the conductance of a rotated graphene nanoribbon side-contact junction, revealing that for electrons with energies smaller than −2.7 eV the transmission function depends negligibly on the angle of the junction, whereas for electrons with energies greater than −2.7 eV, there exists a set of angles for the system that increase its conductance independently of the energy of the particles.
{"title":"A divide-and-conquer method to improve performance in quantum transport calculations: conductance in rotated graphene nanoribbons side-contact junctions","authors":"M. J. Rodríguez, Carlos Ramírez","doi":"10.1088/2516-1075/ac96b8","DOIUrl":"https://doi.org/10.1088/2516-1075/ac96b8","url":null,"abstract":"We propose a divide-and-conquer algorithm to find recursively the scattering matrix of general tight-binding structures. The scattering matrix allows a direct calculation of transport properties in mesoscopic systems by using the Landauer formula. The method is exact, and by analyzing the performance of the algorithm in square, triangular and honeycomb lattices, we show a significant improvement in comparison to other state-of-the-art recursive and non-recursive methods. We utilize this algorithm to compute the conductance of a rotated graphene nanoribbon side-contact junction, revealing that for electrons with energies smaller than −2.7 eV the transmission function depends negligibly on the angle of the junction, whereas for electrons with energies greater than −2.7 eV, there exists a set of angles for the system that increase its conductance independently of the energy of the particles.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44678491","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 : 2022-09-23DOI: 10.1088/2516-1075/ac94ac
Z. Varga, Yinan Shu, Jiaxin Ning, D. Truhlar
Dissociation and energy transfer in high-energy collisions of O2 play important roles in simulating thermal energy content and heat flux in flows around hypersonic vehicles. Furthermore, atomic oxygen reactions on the vehicle surface are an important contributor to heat shield erosion. Molecular dynamics modeling is needed to better understand the relevant rate processes. Because it is necessary to model the gas flows in high-temperature shock waves, electronically excited states of O2 and O can be populated, and molecular dynamics simulations should include collisions of electronically excited species and electronically nonadiabatic collisions. This requires potential energy surfaces and state couplings for many energetically accessible electronic states. Here we report a systematic strategy to calculate such surfaces and couplings. We have applied this method to the fourteen lowest-energy potential energy surfaces in the 3 A′ manifold of O3, and we report a neural-network fit to diabatic potential energy matrix (DPEM). We illustrate the use of the resulting DPEM by carrying out semiclassical dynamics calculations of cross sections for excitation of O2 in 3 A′ collisions with O at two collision energies; these dynamics calculations are carried out by the curvature-driven coherent switching with decay of mixing method.
{"title":"Diabatic potential energy surfaces and semiclassical multi-state dynamics for fourteen coupled 3 A′ states of O3","authors":"Z. Varga, Yinan Shu, Jiaxin Ning, D. Truhlar","doi":"10.1088/2516-1075/ac94ac","DOIUrl":"https://doi.org/10.1088/2516-1075/ac94ac","url":null,"abstract":"Dissociation and energy transfer in high-energy collisions of O2 play important roles in simulating thermal energy content and heat flux in flows around hypersonic vehicles. Furthermore, atomic oxygen reactions on the vehicle surface are an important contributor to heat shield erosion. Molecular dynamics modeling is needed to better understand the relevant rate processes. Because it is necessary to model the gas flows in high-temperature shock waves, electronically excited states of O2 and O can be populated, and molecular dynamics simulations should include collisions of electronically excited species and electronically nonadiabatic collisions. This requires potential energy surfaces and state couplings for many energetically accessible electronic states. Here we report a systematic strategy to calculate such surfaces and couplings. We have applied this method to the fourteen lowest-energy potential energy surfaces in the 3 A′ manifold of O3, and we report a neural-network fit to diabatic potential energy matrix (DPEM). We illustrate the use of the resulting DPEM by carrying out semiclassical dynamics calculations of cross sections for excitation of O2 in 3 A′ collisions with O at two collision energies; these dynamics calculations are carried out by the curvature-driven coherent switching with decay of mixing method.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41999778","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 : 2022-09-02DOI: 10.1088/2516-1075/ac8f03
Sruthil lal S B, Murali D, M. Posselt, A. A. Sasikala Devi, A. Sharan
The influence of non-interacting Kohn–Sham Hamiltonian on the non-self consistent GW(G 0 W 0) quasiparticle gap and Bethe–Salpeter-equation (BSE) optical spectra of anatase TiO2 is systematically evaluated. G 0 W 0 and BSE calculations are carried out starting with HSE06 (Heyd–Scuseria–Ernzerhof) type functionals containing 20%, 25% and 30% exact Hartree–Fock exchange. The results are also compared against G 0 W 0 + BSE calculations starting from semi-local (PBE) functionals. Our results indicate that the G 0 W 0 and BSE calculations of anatase TiO2 depend critically on the mean-field starting point, wherein its dependence is mainly introduced through the dielectric screening evaluated at the intermediate G 0 W 0. We find that the band dispersion, density of states, and consequently the oscillator strengths of optical excitation and spatial localization of excitons are insensitive to the starting points while the quasiparticle gap, optical gap and exciton binding energies are strongly affected. G 0 W 0 quasiparticle gap of anatase TiO2 computed over hybrid functional starting points is typically overestimated compared to measured values. However, by varying the amount of exact exchange, the dielectric screening can be tuned, and thus the quasiparticle gap. Exciton binding energy is shown to increase in proportion to the increase of the amount of exact exchange. A simple extrapolation of the calculated data leads to the exact match with the recently measured value with 13% of the exact exchange. Systematic analysis of G 0 W 0 + BSE calculation starting from screened hybrid functionals provided in this study forms a reference for all such future calculations of pristine anatase TiO2 and its derivatives.
{"title":"Modified HSE06 functional applied to anatase TiO2: influence of exchange fraction on the quasiparticle electronic structure and optical response","authors":"Sruthil lal S B, Murali D, M. Posselt, A. A. Sasikala Devi, A. Sharan","doi":"10.1088/2516-1075/ac8f03","DOIUrl":"https://doi.org/10.1088/2516-1075/ac8f03","url":null,"abstract":"The influence of non-interacting Kohn–Sham Hamiltonian on the non-self consistent GW(G 0 W 0) quasiparticle gap and Bethe–Salpeter-equation (BSE) optical spectra of anatase TiO2 is systematically evaluated. G 0 W 0 and BSE calculations are carried out starting with HSE06 (Heyd–Scuseria–Ernzerhof) type functionals containing 20%, 25% and 30% exact Hartree–Fock exchange. The results are also compared against G 0 W 0 + BSE calculations starting from semi-local (PBE) functionals. Our results indicate that the G 0 W 0 and BSE calculations of anatase TiO2 depend critically on the mean-field starting point, wherein its dependence is mainly introduced through the dielectric screening evaluated at the intermediate G 0 W 0. We find that the band dispersion, density of states, and consequently the oscillator strengths of optical excitation and spatial localization of excitons are insensitive to the starting points while the quasiparticle gap, optical gap and exciton binding energies are strongly affected. G 0 W 0 quasiparticle gap of anatase TiO2 computed over hybrid functional starting points is typically overestimated compared to measured values. However, by varying the amount of exact exchange, the dielectric screening can be tuned, and thus the quasiparticle gap. Exciton binding energy is shown to increase in proportion to the increase of the amount of exact exchange. A simple extrapolation of the calculated data leads to the exact match with the recently measured value with 13% of the exact exchange. Systematic analysis of G 0 W 0 + BSE calculation starting from screened hybrid functionals provided in this study forms a reference for all such future calculations of pristine anatase TiO2 and its derivatives.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41920611","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 : 2022-08-24DOI: 10.1088/2516-1075/ac8c73
A. Steeves, H. Kulik
An understanding of protein stability requires capturing dynamic rearrangements and coupled properties over long lengthscales. Nevertheless, the extent of coupling in these systems has typically only been studied for classical degrees of freedom. To understand the potential benefit of extending such analysis to the coupling of electronic structure properties, we have carried out extensive semi-empirical quantum mechanical molecular dynamics of two Trp-cage variants. Small differences in the sequence of the two peptides lead to differences in their thermal stability that are revealed through electronic structure coupling analysis. In comparison, we find limited evidence that geometric coupling can distinguish the behavior of the two peptides. We show that Asp1 in the more stable variant shows significantly enhanced coupling to both sequence-adjacent and more sequence-distant residues. Non-nearest-neighbor couplings are stronger in the more stable variant, indicating a network of residues that help stabilize the protein. Our study highlights the complementary benefit of charge coupling analysis to interpret protein structure-function relationships.
{"title":"Insights into the stability of engineered mini-proteins from their dynamic electronic properties","authors":"A. Steeves, H. Kulik","doi":"10.1088/2516-1075/ac8c73","DOIUrl":"https://doi.org/10.1088/2516-1075/ac8c73","url":null,"abstract":"An understanding of protein stability requires capturing dynamic rearrangements and coupled properties over long lengthscales. Nevertheless, the extent of coupling in these systems has typically only been studied for classical degrees of freedom. To understand the potential benefit of extending such analysis to the coupling of electronic structure properties, we have carried out extensive semi-empirical quantum mechanical molecular dynamics of two Trp-cage variants. Small differences in the sequence of the two peptides lead to differences in their thermal stability that are revealed through electronic structure coupling analysis. In comparison, we find limited evidence that geometric coupling can distinguish the behavior of the two peptides. We show that Asp1 in the more stable variant shows significantly enhanced coupling to both sequence-adjacent and more sequence-distant residues. Non-nearest-neighbor couplings are stronger in the more stable variant, indicating a network of residues that help stabilize the protein. Our study highlights the complementary benefit of charge coupling analysis to interpret protein structure-function relationships.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48928174","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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