Pub Date : 2023-06-21DOI: 10.1088/2516-1075/ace0a9
Melissa Berteau-Rainville, E. Orgiu, Ingo Salzmann
Understanding the p-doping of organic semiconductors often relies on spectroscopic fingerprints of cyano vibrations, which strongly depend on the charge state of the dopant molecule following intermolecular charge transfer. Interpreting these vibrations can be difficult as a number of other factors can impact them. Here, we formalize the assumptions behind the determination of molecular charge from cyano vibrations and we use computational modeling to demonstrate key obfuscating factors in this process. We notably demonstrate that cyano vibrations do not necessarily shift linearly with the molecular charge and investigate which molecular parameters can explain that. Finally, we provide guidelines for the study of charge transfers involving new molecular dopants based on their cyano vibrations.
{"title":"On validity and limits of deducing the degree of charge transfer from shifts of cyano vibrations","authors":"Melissa Berteau-Rainville, E. Orgiu, Ingo Salzmann","doi":"10.1088/2516-1075/ace0a9","DOIUrl":"https://doi.org/10.1088/2516-1075/ace0a9","url":null,"abstract":"Understanding the p-doping of organic semiconductors often relies on spectroscopic fingerprints of cyano vibrations, which strongly depend on the charge state of the dopant molecule following intermolecular charge transfer. Interpreting these vibrations can be difficult as a number of other factors can impact them. Here, we formalize the assumptions behind the determination of molecular charge from cyano vibrations and we use computational modeling to demonstrate key obfuscating factors in this process. We notably demonstrate that cyano vibrations do not necessarily shift linearly with the molecular charge and investigate which molecular parameters can explain that. Finally, we provide guidelines for the study of charge transfers involving new molecular dopants based on their cyano vibrations.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42114063","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 : 2023-06-16DOI: 10.1088/2516-1075/acdf33
P. Gupta, Naziha Tarannam, Shani Zev, D. Major
The G- and V-type nerve agents are among the most toxic compounds known, where inhalation of a few mg could cause potential death. Over the years wild-type phosphotriesterase (PTE) has gained much attention due to its capability of detoxifying these deadly compounds. The underlying mechanism proceeds via a hydroxyl attack on the P or C centers of the organophosphate nerve agents followed by the departure of the leaving group. Two Zn2+ cations present in the active site center of PTE indirectly assist the hydrolysis. Apart from the wild-type PTE, several designer enzyme variants reportedly catalyze the hydrolysis process much more efficiently. Herein, we studied the hydrolysis of eight toxic compounds with one of the enzyme variants (PTE_27) that show higher efficiency than the wild type as reported in a recent article. We docked both the high energy intermediate state and substrate for all the eight ligands using a consensus docking scheme as implemented in the docking program EnzyDock. Additionally, we investigated the hydrolytic reaction mechanism for all eight ligands employing density functional theory in implicit chloroform solvent and found that hydrolysis for these ligands follows three different possible mechanisms. Finally, EnzyDock successfully predicted correct enantiomeric poses and also score these as low energy docked structures.
{"title":"Multistate multiscale docking study of the hydrolysis of toxic nerve agents by phosphotriesterase","authors":"P. Gupta, Naziha Tarannam, Shani Zev, D. Major","doi":"10.1088/2516-1075/acdf33","DOIUrl":"https://doi.org/10.1088/2516-1075/acdf33","url":null,"abstract":"The G- and V-type nerve agents are among the most toxic compounds known, where inhalation of a few mg could cause potential death. Over the years wild-type phosphotriesterase (PTE) has gained much attention due to its capability of detoxifying these deadly compounds. The underlying mechanism proceeds via a hydroxyl attack on the P or C centers of the organophosphate nerve agents followed by the departure of the leaving group. Two Zn2+ cations present in the active site center of PTE indirectly assist the hydrolysis. Apart from the wild-type PTE, several designer enzyme variants reportedly catalyze the hydrolysis process much more efficiently. Herein, we studied the hydrolysis of eight toxic compounds with one of the enzyme variants (PTE_27) that show higher efficiency than the wild type as reported in a recent article. We docked both the high energy intermediate state and substrate for all the eight ligands using a consensus docking scheme as implemented in the docking program EnzyDock. Additionally, we investigated the hydrolytic reaction mechanism for all eight ligands employing density functional theory in implicit chloroform solvent and found that hydrolysis for these ligands follows three different possible mechanisms. Finally, EnzyDock successfully predicted correct enantiomeric poses and also score these as low energy docked structures.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49172617","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 : 2023-06-16DOI: 10.1088/2516-1075/acdf32
S. Kera, Fumihiko Matsui, Kiyohisa Tanaka, Y. Taira, T. Araki, T. Ohigashi, H. Iwayama, M. Fujimoto, H. Matsuda, E. Salehi, M. Katoh
The synchrotron radiation facility is a large-scale public infrastructure that provides advanced light sources and is used for various academic research and application development. For 40 years, UVSOR Synchrotron Facility has been leading the field as a facility that has developed and utilized cutting-edge light source technology in the low-photon-energy regime. The next UVSOR aims to establish a center for quantum photon science research through the development of unexplored characterization technologies by advanced use of light sources and a measurement and analysis support environment. The science of molecular dynamics with spatio-temporal hierarchies for evaluating and controlling the functions of complex systems will be pioneered. The assets of UVSOR and the fundamental measurement and analysis technology of the Institute for Molecular Science will be inherited effectively and progressively. We plan to contribute to strengthening the foundation of many fundamental disciplines to create next-generation industrial applications.
{"title":"Prospects required for future light-source facilities: a case of UVSOR synchrotron facility","authors":"S. Kera, Fumihiko Matsui, Kiyohisa Tanaka, Y. Taira, T. Araki, T. Ohigashi, H. Iwayama, M. Fujimoto, H. Matsuda, E. Salehi, M. Katoh","doi":"10.1088/2516-1075/acdf32","DOIUrl":"https://doi.org/10.1088/2516-1075/acdf32","url":null,"abstract":"The synchrotron radiation facility is a large-scale public infrastructure that provides advanced light sources and is used for various academic research and application development. For 40 years, UVSOR Synchrotron Facility has been leading the field as a facility that has developed and utilized cutting-edge light source technology in the low-photon-energy regime. The next UVSOR aims to establish a center for quantum photon science research through the development of unexplored characterization technologies by advanced use of light sources and a measurement and analysis support environment. The science of molecular dynamics with spatio-temporal hierarchies for evaluating and controlling the functions of complex systems will be pioneered. The assets of UVSOR and the fundamental measurement and analysis technology of the Institute for Molecular Science will be inherited effectively and progressively. We plan to contribute to strengthening the foundation of many fundamental disciplines to create next-generation industrial applications.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45671398","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 : 2023-06-01DOI: 10.1088/2516-1075/ace015
Sallam Alagawani, V. Vasilyev, Feng Wang
Optical spectroscopy (UV–vis and fluorescence spectroscopy) is sensitive to the chemical environment and conformation of fluorophores and therefore, serves as an ideal probe for the conformation and solvent responses. Tyrosine kinase inhibitors (TKI) such as AG-1478 of epidermal growth factor receptor when containing a quinazolinamine scaffold are fluorophores. It is, however, very important to benchmark density functional theory (DFT) method against optical spectral measurements, when time-dependent DFT is applied. In this study, the performance of up to 22 DFT functionals is benchmarked with respect to the measured optical spectra of AG-1478 in dimethyl sulfoxide (DMSO) solvent. It is discovered when combined with the 6–311++G(d, p) basis set, there are top seven functionals; B3PW91, B3LYP, B3P86, PBE1PBE, APFD, HSEH1PBE, and N12SX DFT-VXC functionals are identified as the top performers. Becke’s three-parameter exchange functional (B3) tends to generate accurate optical spectra to form the best three functionals, B3LYP, B3PW91 and B3P86. Specifically, B3PW91 was recommended for studying the optical properties of 4-quinazolinamine TKIs, B3LYP was found to be excellent for absorption spectrum, while B3P86 was identified as the best for emission spectrum. Any further corrections to B3LYP, such as CAM-B3LYP, LC-B3LYP, and B3LYP-D3 result in larger errors in the optical spectra of AG-1478 in DMSO solvent. These best three (B3Vc) functionals are reliable tools for optical properties of the TKIs and therefore the design of new agents with larger Stokes shift for medical image applications. To obtain reliable optical spectra for this class of 4-quinazolinamine based TKIs, it is important to include the electron correlation energy.
{"title":"Optical spectra of EGFR inhibitor AG-1478 for benchmarking DFT functionals","authors":"Sallam Alagawani, V. Vasilyev, Feng Wang","doi":"10.1088/2516-1075/ace015","DOIUrl":"https://doi.org/10.1088/2516-1075/ace015","url":null,"abstract":"Optical spectroscopy (UV–vis and fluorescence spectroscopy) is sensitive to the chemical environment and conformation of fluorophores and therefore, serves as an ideal probe for the conformation and solvent responses. Tyrosine kinase inhibitors (TKI) such as AG-1478 of epidermal growth factor receptor when containing a quinazolinamine scaffold are fluorophores. It is, however, very important to benchmark density functional theory (DFT) method against optical spectral measurements, when time-dependent DFT is applied. In this study, the performance of up to 22 DFT functionals is benchmarked with respect to the measured optical spectra of AG-1478 in dimethyl sulfoxide (DMSO) solvent. It is discovered when combined with the 6–311++G(d, p) basis set, there are top seven functionals; B3PW91, B3LYP, B3P86, PBE1PBE, APFD, HSEH1PBE, and N12SX DFT-VXC functionals are identified as the top performers. Becke’s three-parameter exchange functional (B3) tends to generate accurate optical spectra to form the best three functionals, B3LYP, B3PW91 and B3P86. Specifically, B3PW91 was recommended for studying the optical properties of 4-quinazolinamine TKIs, B3LYP was found to be excellent for absorption spectrum, while B3P86 was identified as the best for emission spectrum. Any further corrections to B3LYP, such as CAM-B3LYP, LC-B3LYP, and B3LYP-D3 result in larger errors in the optical spectra of AG-1478 in DMSO solvent. These best three (B3Vc) functionals are reliable tools for optical properties of the TKIs and therefore the design of new agents with larger Stokes shift for medical image applications. To obtain reliable optical spectra for this class of 4-quinazolinamine based TKIs, it is important to include the electron correlation energy.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48120164","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 : 2023-06-01DOI: 10.1088/2516-1075/acdbf5
Nikita V Natalin, E. Kundelev, I. Rukhlenko, N. Tepliakov
Even when fabricated under ideal conditions twisted bilayer graphene (TBG) inevitably contains various defects which may significantly affect its physical properties. Here we comprehensively analyze the impact of typical point defects, represented by adsorbed hydrogen atoms, on the electronic and optical properties of TBG. It is shown using self-consistent tight-binding Hamiltonians that such point defects make TBG ferromagnetic, and that its ground state comprises a pair of nearly dispersionless spin-polarized energy bands around the Fermi level. Transitions to and from these bands strongly modify the infrared absorption of TBG and result in a sharp low-energy peak in its spectrum. It is also revealed that the adsorption of hydrogen atoms suppresses the circular dichroism of TBG due to the weakening of the electronic coupling between the graphene layers. Our findings will guide future experimental studies on the optical properties of TBG in realistic, impurity-rich environments.
{"title":"Optical properties of twisted bilayer graphene with magnetic defects","authors":"Nikita V Natalin, E. Kundelev, I. Rukhlenko, N. Tepliakov","doi":"10.1088/2516-1075/acdbf5","DOIUrl":"https://doi.org/10.1088/2516-1075/acdbf5","url":null,"abstract":"Even when fabricated under ideal conditions twisted bilayer graphene (TBG) inevitably contains various defects which may significantly affect its physical properties. Here we comprehensively analyze the impact of typical point defects, represented by adsorbed hydrogen atoms, on the electronic and optical properties of TBG. It is shown using self-consistent tight-binding Hamiltonians that such point defects make TBG ferromagnetic, and that its ground state comprises a pair of nearly dispersionless spin-polarized energy bands around the Fermi level. Transitions to and from these bands strongly modify the infrared absorption of TBG and result in a sharp low-energy peak in its spectrum. It is also revealed that the adsorption of hydrogen atoms suppresses the circular dichroism of TBG due to the weakening of the electronic coupling between the graphene layers. Our findings will guide future experimental studies on the optical properties of TBG in realistic, impurity-rich environments.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43817652","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 : 2023-05-20DOI: 10.1088/2516-1075/acf2d3
Sangchul Oh, S. Kais
How fast a state of a system converges to a stationary state is one of the fundamental questions in science. Some Markov chains and random walks on finite groups are known to exhibit the non-asymptotic convergence to a stationary distribution, called the cutoff phenomenon. Here, we examine how quickly a random quantum circuit could transform a quantum state to a Haar-measure random quantum state. We find that random quantum states, as stationary states of random walks on a unitary group, are invariant under the quantum Fourier transform (QFT). Thus the entropic uncertainty of random quantum states has balanced Shannon entropies for the computational basis and the QFT basis. By calculating the Shannon entropy for random quantum states and the Wasserstein distances for the eigenvalues of random quantum circuits, we show that the cutoff phenomenon occurs for the random quantum circuit. It is also demonstrated that the Dyson-Brownian motion for the eigenvalues of a random unitary matrix as a continuous random walk exhibits the cutoff phenomenon. The results here imply that random quantum states could be generated with shallow random circuits.
{"title":"Cutoff phenomenon and entropic uncertainty for random quantum circuits","authors":"Sangchul Oh, S. Kais","doi":"10.1088/2516-1075/acf2d3","DOIUrl":"https://doi.org/10.1088/2516-1075/acf2d3","url":null,"abstract":"How fast a state of a system converges to a stationary state is one of the fundamental questions in science. Some Markov chains and random walks on finite groups are known to exhibit the non-asymptotic convergence to a stationary distribution, called the cutoff phenomenon. Here, we examine how quickly a random quantum circuit could transform a quantum state to a Haar-measure random quantum state. We find that random quantum states, as stationary states of random walks on a unitary group, are invariant under the quantum Fourier transform (QFT). Thus the entropic uncertainty of random quantum states has balanced Shannon entropies for the computational basis and the QFT basis. By calculating the Shannon entropy for random quantum states and the Wasserstein distances for the eigenvalues of random quantum circuits, we show that the cutoff phenomenon occurs for the random quantum circuit. It is also demonstrated that the Dyson-Brownian motion for the eigenvalues of a random unitary matrix as a continuous random walk exhibits the cutoff phenomenon. The results here imply that random quantum states could be generated with shallow random circuits.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43229088","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 : 2023-05-04DOI: 10.1088/2516-1075/acd28d
A. James, D. Billington, S. Dugdale
Delafossite PdCrO2 is an intriguing material which displays nearly-free electron and Mott insulating behaviour in different layers. Both angle-resolved photoemission spectroscopy (ARPES) and Compton scattering measurements have established a hexagonal Fermi surface in the material’s paramagnetic phase. However, the Compton experiment detected an additional structure in the projected occupancy which was originally interpreted as an additional Fermi surface feature not seen by ARPES. Here, we revisit this interpretation of the Compton data. State-of-the-art density functional theory (DFT) with dynamical mean field theory (DMFT), the so-called DFT+DMFT method, predicts the Mott insulating state along with a single hexagonal Fermi surface in excellent agreement with ARPES and Compton. However, DFT+DMFT fails to predict the intensity of the additional spectral weight feature observed in the Compton data. We infer that this discrepancy may arise from the DFT+DMFT not being able to correctly predict certain features in the shape and dispersion of the unoccupied quasiparticle band near the Fermi level. Therefore, a theoretical description beyond our DFT+DMFT model is needed to incorporate vital electron interactions, such as inter-layer electron coupling interactions which for PdCrO2 gives rise to the Kondo-like so-called intertwined excitation.
{"title":"Impact of electron correlations on the k-resolved electronic structure of PdCrO2 revealed by Compton scattering","authors":"A. James, D. Billington, S. Dugdale","doi":"10.1088/2516-1075/acd28d","DOIUrl":"https://doi.org/10.1088/2516-1075/acd28d","url":null,"abstract":"Delafossite PdCrO2 is an intriguing material which displays nearly-free electron and Mott insulating behaviour in different layers. Both angle-resolved photoemission spectroscopy (ARPES) and Compton scattering measurements have established a hexagonal Fermi surface in the material’s paramagnetic phase. However, the Compton experiment detected an additional structure in the projected occupancy which was originally interpreted as an additional Fermi surface feature not seen by ARPES. Here, we revisit this interpretation of the Compton data. State-of-the-art density functional theory (DFT) with dynamical mean field theory (DMFT), the so-called DFT+DMFT method, predicts the Mott insulating state along with a single hexagonal Fermi surface in excellent agreement with ARPES and Compton. However, DFT+DMFT fails to predict the intensity of the additional spectral weight feature observed in the Compton data. We infer that this discrepancy may arise from the DFT+DMFT not being able to correctly predict certain features in the shape and dispersion of the unoccupied quasiparticle band near the Fermi level. Therefore, a theoretical description beyond our DFT+DMFT model is needed to incorporate vital electron interactions, such as inter-layer electron coupling interactions which for PdCrO2 gives rise to the Kondo-like so-called intertwined excitation.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42500810","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 : 2023-05-03DOI: 10.1088/2516-1075/acd234
Robert J. O’Reilly, A. Karton
The relative free energies of the isomers formed upon N-chlorination of each nitrogen atom within the DNA nucleobases (adenine, guanine, and thymine) have been obtained using the high-level G4(MP2) composite ab initio method (the free energies of the N-chlorinated isomers of cytosine have been reported at the same level of theory previously). Having identified the lowest energy N-chlorinated derivatives for each nucleobase, we have computed the free energies associated with chlorine transfer from N-chlorinated nucleobases to other unsubstituted bases. Our results provide quantitative support pertaining to the results of previous experimental studies, which demonstrated that rapid chlorine transfer occurs from N-chlorothymidine to cytidine or adenosine. The results of our calculations in the gas-phase reveal that chlorine transfer from N-chlorothymine to either cytosine, adenine, or guanine proceed via exergonic processes with ΔG o values of −50.3 (cytosine), −28.0 (guanine), and −6.7 (adenine) kJ mol–1. Additionally, we consider the effect of aqueous solvation by augmenting our gas-phase G4(MP2) energies with solvation corrections obtained using the conductor-like polarizable continuum model. In aqueous solution, we obtain the following G4(MP2) free energies associated with chlorine transfer from N-chlorothymine to the three other nucleobases: −58.4 (cytosine), −26.4 (adenine), and −18.7 (guanine) kJ mol–1. Therefore, our calculations, whether in the gas phase or in aqueous solution, clearly indicate that chlorine transfer from any of the N-chlorinated nucleobases to cytosine provides a thermodynamic sink for the active chlorine. This thermodynamic preference for chlorine transfer to cytidine may be particularly deleterious since previous experimental studies have shown that nitrogen-centered radical formation (via N–Cl bond homolysis) is more easily achieved in N-chlorinated cytidine than in other N-chlorinated nucleosides.
{"title":"A high-level quantum chemical study of the thermodynamics associated with chlorine transfer between N-chlorinated nucleobases","authors":"Robert J. O’Reilly, A. Karton","doi":"10.1088/2516-1075/acd234","DOIUrl":"https://doi.org/10.1088/2516-1075/acd234","url":null,"abstract":"The relative free energies of the isomers formed upon N-chlorination of each nitrogen atom within the DNA nucleobases (adenine, guanine, and thymine) have been obtained using the high-level G4(MP2) composite ab initio method (the free energies of the N-chlorinated isomers of cytosine have been reported at the same level of theory previously). Having identified the lowest energy N-chlorinated derivatives for each nucleobase, we have computed the free energies associated with chlorine transfer from N-chlorinated nucleobases to other unsubstituted bases. Our results provide quantitative support pertaining to the results of previous experimental studies, which demonstrated that rapid chlorine transfer occurs from N-chlorothymidine to cytidine or adenosine. The results of our calculations in the gas-phase reveal that chlorine transfer from N-chlorothymine to either cytosine, adenine, or guanine proceed via exergonic processes with ΔG o values of −50.3 (cytosine), −28.0 (guanine), and −6.7 (adenine) kJ mol–1. Additionally, we consider the effect of aqueous solvation by augmenting our gas-phase G4(MP2) energies with solvation corrections obtained using the conductor-like polarizable continuum model. In aqueous solution, we obtain the following G4(MP2) free energies associated with chlorine transfer from N-chlorothymine to the three other nucleobases: −58.4 (cytosine), −26.4 (adenine), and −18.7 (guanine) kJ mol–1. Therefore, our calculations, whether in the gas phase or in aqueous solution, clearly indicate that chlorine transfer from any of the N-chlorinated nucleobases to cytosine provides a thermodynamic sink for the active chlorine. This thermodynamic preference for chlorine transfer to cytidine may be particularly deleterious since previous experimental studies have shown that nitrogen-centered radical formation (via N–Cl bond homolysis) is more easily achieved in N-chlorinated cytidine than in other N-chlorinated nucleosides.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43957531","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 : 2023-04-28DOI: 10.1088/2516-1075/acd158
A. Banerjee, Edward F. Holby, A. Kohnert, S. Srivastava, M. Asta, B. Uberuaga
Point defect formation and migration in oxides governs a wide range of phenomena from corrosion kinetics and radiation damage evolution to electronic properties. In this study, we examine the thermodynamics and kinetics of anion and cation point defects using density functional theory in hematite ( α -Fe2O3), an important iron oxide highly relevant in both corrosion of steels and water-splitting applications. These calculations indicate that the migration barriers for point defects can vary significantly with charge state, particularly for cation interstitials. Additionally, we find multiple possible migration pathways for many of the point defects in this material, related to the low symmetry of the corundum crystal structure. The possible percolation paths are examined, using the barriers to determine the magnitude and anisotropy of long-range diffusion. Our findings suggest highly anisotropic mass transport in hematite, favoring diffusion along the c-axis of the crystal. In addition, we have considered the point defect formation energetics using the largest Fe2O3 supercell reported to date.
{"title":"Thermokinetics of point defects in α-Fe2O3","authors":"A. Banerjee, Edward F. Holby, A. Kohnert, S. Srivastava, M. Asta, B. Uberuaga","doi":"10.1088/2516-1075/acd158","DOIUrl":"https://doi.org/10.1088/2516-1075/acd158","url":null,"abstract":"Point defect formation and migration in oxides governs a wide range of phenomena from corrosion kinetics and radiation damage evolution to electronic properties. In this study, we examine the thermodynamics and kinetics of anion and cation point defects using density functional theory in hematite ( α -Fe2O3), an important iron oxide highly relevant in both corrosion of steels and water-splitting applications. These calculations indicate that the migration barriers for point defects can vary significantly with charge state, particularly for cation interstitials. Additionally, we find multiple possible migration pathways for many of the point defects in this material, related to the low symmetry of the corundum crystal structure. The possible percolation paths are examined, using the barriers to determine the magnitude and anisotropy of long-range diffusion. Our findings suggest highly anisotropic mass transport in hematite, favoring diffusion along the c-axis of the crystal. In addition, we have considered the point defect formation energetics using the largest Fe2O3 supercell reported to date.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41956639","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 : 2023-04-14DOI: 10.1088/2516-1075/accd33
Zhi-xing Liu, Chunfeng Zhang
In organic solar cells with non-fullerene acceptors (NFAs), an intra-moiety excited state, originating from intermolecular interactions in the acceptor domain, acts as a key immediate for charge separation. However, the nature of the intra-moiety state remains elusive. Here, we employ a model Hamiltonian with parameters derived from a model system of Y6 crystal to study the nature of low-lying excited states in NFAs. We find the intra-moiety excited state is mixed with local excitation and charge-transfer excitation (CTE) characters with nonnegligible contributions from extended CTEs with spatially-separated electrons and holes. The spatial extent of such a loosely bound state is susceptible to the intermolecular electronic interaction and electron–vibration interaction, which may be promoted by molecule engineering and morphology control. The findings provide an alternative strategy towards device optimization by manipulating the delocalization of intra-moiety state in organic photovoltaic materials.
{"title":"Extended-charge-transfer excitations in crystalline non-fullerene acceptors","authors":"Zhi-xing Liu, Chunfeng Zhang","doi":"10.1088/2516-1075/accd33","DOIUrl":"https://doi.org/10.1088/2516-1075/accd33","url":null,"abstract":"In organic solar cells with non-fullerene acceptors (NFAs), an intra-moiety excited state, originating from intermolecular interactions in the acceptor domain, acts as a key immediate for charge separation. However, the nature of the intra-moiety state remains elusive. Here, we employ a model Hamiltonian with parameters derived from a model system of Y6 crystal to study the nature of low-lying excited states in NFAs. We find the intra-moiety excited state is mixed with local excitation and charge-transfer excitation (CTE) characters with nonnegligible contributions from extended CTEs with spatially-separated electrons and holes. The spatial extent of such a loosely bound state is susceptible to the intermolecular electronic interaction and electron–vibration interaction, which may be promoted by molecule engineering and morphology control. The findings provide an alternative strategy towards device optimization by manipulating the delocalization of intra-moiety state in organic photovoltaic materials.","PeriodicalId":42419,"journal":{"name":"Electronic Structure","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48550616","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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