1
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Hirao K, Nakajima T, Chan B. Exploiting the Correlation between the 1s, 2s, and 2p Energies for the Prediction of Core-Level Binding Energies of Si, P, S, and Cl species. J Phys Chem A 2024; 128:6879-6897. [PMID: 39120958 DOI: 10.1021/acs.jpca.4c03252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
The binding energies (BEs) of the 1s, 2s, and 2p core electrons of third-period elements (Si, P, S, Cl) were calculated using Hartree-Fock (HF) and B3LYP, BH&HLYP, and LC-BOP ΔSCF, and the shifted KS ΔSCF methods. Linear relationships between two BEs were derived and compared with the Auger parameter. The derived lines are essentially parallel, with only the intercepts differing. The difference in intercepts is due to the lack of electron correlation effects in HF and the self-interaction errors (SIEs) of the functional. The slope is the slope of the linear relationship between the chemical shifts. The straight lines between the 2s and 2p BEs also coincided with the Auger parameter lines, which have a slope of 1 by definition and an intercept being the difference between the 2s and 2p BEs. The shifted KS ΔSCF scheme compensates for SIEs, yielding equations that are approximately invariant. The calculated average gaps for the 2s and 2p BEs are 51.21 eV for Si, 57.48 eV for P, 63.85 eV for S, and 70.48 eV for Cl. The straight lines representing the relationships between the BEs of the 1s and 2s and 1s and 2p electrons are also parallel to each other in ΔSCF and converge into a single line in the shifted ΔSCF scheme. However, these lines are steeper than the Auger parameter line. The derived relationships can be used to predict unknown BEs, which we have applied to many molecules. The results are highly accurate, with mean absolute errors (MAEs) of less than 0.2 eV compared to experimental values.
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Affiliation(s)
- Kimihiko Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Bun Chan
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
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2
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Hirao K, Nakajima T, Chan B. Core-Level 2s and 2p Binding Energies of Third-Period Elements (P, S, and Cl) Calculated by Hartree-Fock and Kohn-Sham Δ SCF Theory. J Phys Chem A 2023; 127:7954-7963. [PMID: 37703090 DOI: 10.1021/acs.jpca.3c04783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
In the present study, we investigate the use of the ΔSCF method and Slater's transition state (STS) theory to calculate the binding energies of the 2s and 2p electrons of third-period elements (P, S, and Cl). Both the Hartree-Fock (HF) and Kohn-Sham (KS) approximations are examined. The STS approximation performs well in reproducing the ΔSCF values. However, for the ΔSCF method itself, while the binding energy of the 2p electrons is accurately predicted, the results for 2s are fairly sensitive to the functional, exhibiting significant variations due to self-interaction errors (SIE). Nonetheless, the variations in chemical shifts between different species remain relatively small, and the values agree with experiments due to the cancellation of SIE. A notable observation is that the chemical shifts of the 2s and 2p electrons are similar, indicating a perturbation caused by the valence electrons. The error in the absolute binding energy of KS ΔSCF against the experiment is nearly constant for the same element in different molecules, and it depends largely on the functional owing to SIE. A shifting scheme previously developed can be employed to reproduce the experimental 2s and 2p binding energies, with dependence on the functional and atom but not on the molecule even for 2s KS ΔSCF binding energies. Upon obtaining the corrected binding energies, we find that the gap between 2s and 2p binding energy is nearly independent of chemical environment for a given element: 57.5, 63.9, and 70.9 eV for the elements P, S, and Cl, respectively.
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Affiliation(s)
- Kimihiko Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
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3
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Jana S, Herbert JM. Fractional-Electron and Transition-Potential Methods for Core-to-Valence Excitation Energies Using Density Functional Theory. J Chem Theory Comput 2023; 19:4100-4113. [PMID: 37312236 DOI: 10.1021/acs.jctc.3c00202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Methods for computing X-ray absorption spectra based on a constrained core hole (possibly containing a fractional electron) are examined. These methods are based on Slater's transition concept and its generalizations, wherein core-to-valence excitation energies are determined using Kohn-Sham orbital energies. Methods examined here avoid promoting electrons beyond the lowest unoccupied molecular orbital, facilitating robust convergence. Variants of these ideas are systematically tested, revealing a best-case accuracy of 0.3-0.4 eV (with respect to experiment) for K-edge transition energies. Absolute errors are much larger for higher-lying near-edge transitions but can be reduced below 1 eV by introducing an empirical shift based on a charge-neutral transition-potential method, in conjunction with functionals such as SCAN, SCAN0, or B3LYP. This procedure affords an entire excitation spectrum from a single fractional-electron calculation, at the cost of ground-state density functional theory and without the need for state-by-state calculations. This shifted transition-potential approach may be especially useful for simulating transient spectroscopies or in complex systems where excited-state Kohn-Sham calculations are challenging.
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Affiliation(s)
- Subrata Jana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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4
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van Horn M, List NH, Saue T. Transition moments beyond the electric-dipole approximation: Visualization and basis set requirements. J Chem Phys 2023; 158:2889486. [PMID: 37154286 DOI: 10.1063/5.0147105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
In the simulation of x-ray absorption spectroscopy, the validity of the electric-dipole approximation comes into question. Three different schemes exist to go beyond this approximation: the first scheme is based on the full semi-classical light-matter interaction, whereas the latter two schemes, referred to as the generalized length and velocity representation, are based on truncated multipole expansions. Even though these schemes have been successfully implemented in several quantum chemistry codes, their basis set requirements remained largely unknown. Here, we assess basis set requirements of these three schemes. We have considered 1s1/2 and 7s1/2 → 7p1/2 transitions in the radium atom, representative of core and valence excitations, respectively, and carried out calculations with dyall.aeXz (X = 2, 3, 4) basis sets at the four-component relativistic TD-HF level of theory. Our basis set study was greatly facilitated by the generation and visualization of radial distributions of transition moment densities, allowing for a straightforward comparison with equivalent finite-difference calculations. Pertaining to the truncated interaction, we find that the length representation electric multipole is the easiest to converge, requiring the dyall.ae2z basis for low-order multipoles and the dyall.ae4z basis at higher orders. The magnetic multipole moments follow a similar trend although they are more difficult to converge. The velocity representation electric multipoles are the most difficult to converge: at high orders, the dyall.ae3z and dyall.ae4z basis sets introduce artificial peaks and oscillations, which increase the overall error. These artifacts are associated with linear dependence issues in the small component space of larger basis sets. The full interaction operator, however, does not suffer from these problems, and we therefore recommend its use in the simulation of x-ray spectroscopy.
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Affiliation(s)
- Martin van Horn
- Laboratoire de Chimie et Physique Quantiques, UMR 5626 CNRS - Université Toulouse III-Paul Sabatier, 118 route de Narbonne, F-31062 Toulouse, France
| | - Nanna Holmgaard List
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Trond Saue
- Laboratoire de Chimie et Physique Quantiques, UMR 5626 CNRS - Université Toulouse III-Paul Sabatier, 118 route de Narbonne, F-31062 Toulouse, France
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5
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Jana S, Herbert JM. Slater transition methods for core-level electron binding energies. J Chem Phys 2023; 158:094111. [PMID: 36889976 DOI: 10.1063/5.0134459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Methods for computing core-level ionization energies using self-consistent field (SCF) calculations are evaluated and benchmarked. These include a "full core hole" (or "ΔSCF") approach that fully accounts for orbital relaxation upon ionization, but also methods based on Slater's transition concept in which the binding energy is estimated from an orbital energy level that is obtained from a fractional-occupancy SCF calculation. A generalization that uses two different fractional-occupancy SCF calculations is also considered. The best of the Slater-type methods afford mean errors of 0.3-0.4 eV with respect to experiment for a dataset of K-shell ionization energies, a level of accuracy that is competitive with more expensive many-body techniques. An empirical shifting procedure with one adjustable parameter reduces the average error below 0.2 eV. This shifted Slater transition method is a simple and practical way to compute core-level binding energies using only initial-state Kohn-Sham eigenvalues. It requires no more computational effort than ΔSCF and may be especially useful for simulating transient x-ray experiments where core-level spectroscopy is used to probe an excited electronic state, for which the ΔSCF approach requires a tedious state-by-state calculation of the spectrum. As an example, we use Slater-type methods to model x-ray emission spectroscopy.
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Affiliation(s)
- Subrata Jana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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6
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Hirao K, Nakajima T, Chan B, Lee HJ. The core ionization energies calculated by delta SCF and Slater's transition state theory. J Chem Phys 2023; 158:064112. [PMID: 36792520 DOI: 10.1063/5.0140032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The core ionization energies of the second-period and third-period elements are studied by ΔSCF and Slater's transition state (STS) theory by using Hartree-Fock (HF) and Kohn-Sham (KS) approximations. Electron correlation increases the estimated core ionization energies, while the self-interaction error (SIE) decreases them, especially for the third-period elements and is a more significant factor. As a result, while HF lacks electron correlation, it is free of SIE and reasonably predicts the core ionization energies. The core ionization energies calculated by HF STS are very close to those calculated by HF ΔSCF, showing that STS reasonably describes the relaxation of the core hole. The core ionization energies calculated by KS are particularly sensitive to the SIE of the functional used, with functionals having less SIE yielding more accurate ΔSCF core ionization energies. Consequently, BH&HLYP gives better results than B3LYP and LC-BOP since BH&HLYP is the hybrid functional with high proportion of the exact HF exchange. Although the core ionization energies are underestimated by ΔSCF due to SIE, STS gives larger core ionization energies than ΔSCF due to a concave behavior of the error curves of STS, which is also related to SIE. The mean absolute deviations of STS relative to ΔSCF, and relative to the experiment, are almost constant regardless of the nuclei among the element in the second period, and likewise among those in the third period. The systematic nature suggests that shifting the STS core ionization energies may be useful. We propose the shifted STS (1) for reproducing ΔSCF values, and the shifted STS (2) to reproduce the observed ones for KS calculations. Both schemes work quite well. The calculated results of KS ΔSCF and STS vary depending on the functional. However, the variation of each species' shifted STS (2) is very small, and all shifted STS (2) values are close to the observed ones. As the shifted STS require only one SCF calculation, they are simple and practical for predicting the core ionization energies.
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Affiliation(s)
- Kimihiko Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
| | - Ho-Jin Lee
- Department of Natural Sciences, Southwest Tennessee Community College, Memphis, Tennessee 38015, USA
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7
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Bruggeman M, Zelzer M, Dong H, Stamboulis A. Processing and interpretation of core-electron XPS spectra of complex plasma-treated polyethylene-based surfaces using a theoretical peak model. SURF INTERFACE ANAL 2022; 54:986-1007. [PMID: 38617442 PMCID: PMC11010728 DOI: 10.1002/sia.7125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
Abstract
Interpretation of X-ray photoelectron spectroscopy (XPS) spectra of complex material surfaces, such as those obtained after surface plasma treatment of polymers, is confined by the available references. The limited understanding of the chemical surface composition may impact the ability to determine suitable coupling chemistries used for surface decoration or assess surface-related properties like biocompatibility. In this work, XPS is used to investigate the chemical composition of various ultra-high-molecular-weight polyethylene (UHMWPE) surfaces. UHMWPE doped with α-tocopherol or functionalised by active screen plasma nitriding (ASPN) was investigated as a model system. Subsequently, a more complex combined system obtained by ASPN treatment of α-tocopherol doped UHMWPE was investigated. Through ab initio orbital calculations and by employing Koopmans' theorem, the core-electron binding energies (CEBEs) were evaluated for a substantial number of possible chemical functionalities positioned on PE-based model structures. The calculated ΔCEBEs showed to be in reasonable agreement with experimental reference data. The calculated ΔCEBEs were used to develop a material-specific peak model suitable for the interpretation of merged high-resolution C 1 s, N 1 s and O 1 s XPS spectra of PE-based materials. In contrast to conventional peak fitting, the presented approach allowed the distinction of functionality positioning (i.e. centred or end-chain) and evaluation of the long-range effects of the chemical functionalities on the PE carbon backbone. Altogether, a more detailed interpretation of the modified UHMWPE surfaces was achieved whilst reducing the need for manual input and personal bias introduced by the spectral analyst.
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Affiliation(s)
- Marc Bruggeman
- Biomaterials Group, School of Metallurgy and MaterialsUniversity of Birmingham, EdgbastonBirminghamUK
| | - Mischa Zelzer
- School of Pharmacy, Biodiscovery Institute, University ParkUniversity of NottinghamNottinghamUK
| | - Hanshan Dong
- Surface Engineering Group, School of Metallurgy and MaterialsUniversity of BirminghamBirminghamUK
| | - Artemis Stamboulis
- Biomaterials Group, School of Metallurgy and MaterialsUniversity of Birmingham, EdgbastonBirminghamUK
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8
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Brigiano FS, Bazin D, Tielens F. Peculiar opportunities given by XPS spectroscopy for the clinician. CR CHIM 2022. [DOI: 10.5802/crchim.154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Nakajima T, Hirao K, Chan B. Higher-order transition state approximation. J Chem Phys 2022; 156:114112. [DOI: 10.1063/5.0086173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We generalize Slater’s transition state concept by deriving systematic higher-order transition state approximations. Numerical validation is performed by the calculation of transition energies for various excitations, including core, valence, and charge-transfer excitations, at Hartree–Fock and Kohn–Sham density functional theory levels. All higher-order transition state approximations introduced in this study accurately reproduce the results from delta self-consistent-field calculations. In particular, we demonstrate that the third-order generalized transition state (GTS3) approximation is a promising alternative to the original, owing to a good balance between the accuracy and computational cost. We also demonstrate that accurate and reliable results can be obtained with a low computational cost by combining the GTS3 approximation with the transition potential scheme.
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Affiliation(s)
- Takahito Nakajima
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minami, Cyuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kimihiko Hirao
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minami, Cyuo-ku, Kobe, Hyogo 650-0047, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Bun Chan
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minami, Cyuo-ku, Kobe, Hyogo 650-0047, Japan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
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10
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Hirao K, Bae HS, Song JW, Chan B. Vertical ionization potential benchmarks from Koopmans prediction of Kohn-Sham theory with long-range corrected (LC) functional. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:194001. [PMID: 35158348 DOI: 10.1088/1361-648x/ac54e3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
The Kohn-Sham density functional theory (KS-DFT) with the long-range corrected (LC) functional is applied to the benchmark dataset of 401 valence ionization potentials (IPs) of 63 small molecules of Chong, Gritsenko and Baerends (the CGB set). The vertical IP of the CGB set are estimated as negative orbital energies within the context of the Koopmans' prediction using the LCgau-core range-separation scheme in combination with PW86-PW91 exchange-correlation functional. The range separation parameterμof the functional is tuned to minimize the error of the negative HOMO orbital energy from experimental IP. The results are compared with literature data, includingab initioIP variant of the equation-of-motion coupled cluster theory with singles and doubles (IP-EOM-CCSD), the negative orbital energies calculated by KS-DFT with the statistical averaging of orbital potential, and those with the QTP family of functionals. The optimally tuned LC functional performs better than other functionals for the estimation of valence level IP. The mean absolute deviations (MAD) from experiment and from IP-EOM-CCSD are 0.31 eV (1.77%) and 0.25 eV (1.46%), respectively. LCgau-core performs quite well even with fixedμ(not system-dependent). Aμvalue around 0.36 bohr-1gives MAD of 0.40 eV (2.42%) and 0.33 eV (1.96%) relative to experiment and IP-EOM-CCSD, respectively. The LCgau-core-PW86-PW91 functional is an efficient alternative to IP-EOM-CCSD and it is reasonably accurate for outer valence orbitals. We have also examined its application to core ionization energies of C(1s), N(1s), O(1s) and F(1s). The C(1s) core ionization energies are reproduced reasonably [MAD of 46 cases is 0.76 eV (0.26%)] but N(1s), O(1s) and F(1s) core ionization energies are predicted less accurately.
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Affiliation(s)
- Kimihiko Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto, 606-8103, Japan
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
| | - Han-Seok Bae
- Department of Chemistry Education, Daegu University, Gyeongsan, 113-8656, Korea
| | - Jong-Won Song
- Department of Chemistry Education, Daegu University, Gyeongsan, 113-8656, Korea
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
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11
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Qian J, Crumlin EJ, Prendergast D. Efficient basis sets for core-excited states motivated by Slater's rules. Phys Chem Chem Phys 2022; 24:2243-2250. [PMID: 35014633 DOI: 10.1039/d1cp03931h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-Ray photoemission spectroscopy is a commonly applied characterization technique that probes the local chemistry of atoms in molecules and materials via the photoexcitation of electrons from atomic core orbitals. These measurements can be interpreted by comparison with previous literature or through the calculation of core-electron binding energies (CEBEs) for model systems. However, physically and numerically accurate description of the core-excited electronic structures demands specializations beyond routine ground state setups. Inspired by Slater's rules, we focus on developing computationally efficient and physically motivated contractions to reproduce the core-excited atomic orbitals which led to improved numerical accuracy of calculated CEBEs. When applied to carbon 1s excitations in a wide range of molecules, these core-excited basis sets produce total energy differences (ΔSCF) using a hybrid exact-exchange density functional (B3LYP) that can reproduce core-excitation energies within experimental accuracy (∼0.1 eV). Due to missing relativistic effects, heavier elements (N, O) exhibit slightly larger systematic absolute errors, but still maintain a satisfactory 0.2 eV mean average error for relative CEBEs. We also connect the known variability in the core level binding energy with local atomic charge to demonstrate how the transferability of a given model should be measured against a diverse test set. We conclude by exploring one outlier, CO, and the outlook for extending this approach to other elements.
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Affiliation(s)
- Jin Qian
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ethan J Crumlin
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Prendergast
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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12
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Kahk JM, Lischner J. Predicting Core Electron Binding Energies in Elements of the First Transition Series Using the Δ-Self-Consistent-Field Method. Faraday Discuss 2022; 236:364-373. [DOI: 10.1039/d1fd00103e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Δ-Self-Consistent-Field (ΔSCF) method has been established as an accurate and computationally efficient approach for calculating absolute core electron binding energies for light elements up to chlorine, but relatively little...
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13
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Hill A, Sa'adeh H, Cameron D, Wang F, Trofimov AB, Larionova EY, Richter R, Prince KC. Positional and Conformational Isomerism in Hydroxybenzoic Acid: A Core-Level Study and Comparison with Phenol and Benzoic Acid. J Phys Chem A 2021; 125:9877-9891. [PMID: 34752704 DOI: 10.1021/acs.jpca.1c07523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three positional isomers of hydroxybenzoic acid, as well as phenol and benzoic acid, were studied using core-level photoemission and X-ray absorption spectroscopies, supported by quantum chemical calculations. While 2-hydroxybenzoic (salicylic) acid exists as a single conformer with an internal hydrogen bond, 3- and 4-hydroxybenzoic acids are mixtures of multiple conformers. The effects due to isomerism are clearly seen in the C 1s and O 1s photoelectron spectra, whereas the conformational effects on the binding energies are less pronounced. The O 1s photoelectron spectrum of salicylic acid is significantly different from that of the other two isomers, providing a signature of the hydrogen bond. In contrast, the oxygen K edge X-ray absorption spectra of the three hydroxybenzoic acids show only minor differences. The salicylic acid absorption spectrum at the carbon K edge shows a more resolved vibrational structure than the spectra of the other molecules, which can be explained in part by the existence of a single conformer. Our theoretical study of vibrational excitations in the lowest C 1s absorption bands of salicylic and 4-hydroxybenzoic acids indicates that the observed structure can be assigned to 0-0 lines of various electronic transitions since most of the totally symmetric vibrational modes with sufficiently large frequencies to be resolved are predicted to be inactive. Significant sensitivity of the C 1s excitations in 3-hydroxybenzoic acid to rotational conformerism was predicted but not observed due to spectral crowding.
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Affiliation(s)
- Alexander Hill
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Melbourne 3122, Australia
| | - Hanan Sa'adeh
- Department of Physics, The University of Jordan, Amman 11942, Jordan.,Elettra Sincrotrone Trieste, in Area Science Park, Basovizza, Trieste 34149, Italy
| | - David Cameron
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Melbourne 3122, Australia
| | - Feng Wang
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Melbourne 3122, Australia
| | - Alexander B Trofimov
- Laboratory of Quantum Chemistry, Irkutsk State University, Karl Marx Str. 1, Irkutsk 664003, Russia.,A. E. Favorsky Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky Str. 1, Irkutsk 664033, Russia
| | - Elena Yu Larionova
- Laboratory of Quantum Chemistry, Irkutsk State University, Karl Marx Str. 1, Irkutsk 664003, Russia.,East-Siberian Institute of the MIA of Russia, Lermontov Str. 110, Irkutsk 664074, Russia
| | - Robert Richter
- Elettra Sincrotrone Trieste, in Area Science Park, Basovizza, Trieste 34149, Italy
| | - Kevin C Prince
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Melbourne 3122, Australia.,Elettra Sincrotrone Trieste, in Area Science Park, Basovizza, Trieste 34149, Italy
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14
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Hirao K, Nakajima T, Chan B. An improved Slater's transition state approximation. J Chem Phys 2021; 155:034101. [PMID: 34293872 DOI: 10.1063/5.0059934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have extended Slater's transition state concept for the approximation of the difference in total energies of the initial and final states by three orbital energies of initial, final, and half-way Slater's transition states of the system. Numerical validation was performed with the ionization energies for H2O, CO, and pyrrole by calculation using Hartree-Fock (HF) and Kohn-Sham (KS) theories with the B3LYP and LCgau-core-BOP functionals. The present extended method reproduces full ΔSCF very accurately for all occupied orbitals obtained with HF and for valence orbitals obtained with KS. KS core orbitals have some errors due to the self-interaction errors, but the present method significantly improves the core electron binding energies. In its current form, the newly derived theory may not yet be practically useful, but it is simple and conceptually useful for gaining improved understanding of SCF-type orbital theories.
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Affiliation(s)
- Kimihiko Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
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15
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Besley NA. Density Functional Theory Calculations of Core-Electron Binding Energies at the K-Edge of Heavier Elements. J Chem Theory Comput 2021; 17:3644-3651. [PMID: 34042434 DOI: 10.1021/acs.jctc.1c00171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The capability to determine core-electron binding energies (CEBEs) is vital in the analysis of X-ray photoelectron spectroscopy, and the continued development of light sources has made inner shell spectroscopy of heavier elements increasingly accessible. Density functional theory is widely used to determine CEBEs of lighter elements (boron-fluorine). It is shown that good performance of exchange-correlation functionals for these elements does not necessarily translate to the calculation of CEBEs for the heavier elements from the next row of the periodic table, and in general, larger errors are observed. Two strategies are explored that improve the accuracy of the calculated CEBEs. The first is to apply element and functional dependent energy corrections, and the second is a reparametrization of a short-range corrected functional. This functional is able to reproduce experimental phosphorus and sulfur K-edge CEBEs with an average error of 0.15 eV demonstrating the importance of reducing the self-interaction error associated with the core electrons and represents progress toward a density functional theory calculation that performs equally well for ionization at the K-edge of all elements.
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Affiliation(s)
- Nicholas A Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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16
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Hirao K, Bae HS, Song JW, Chan B. Koopmans'-Type Theorem in Kohn-Sham Theory with Optimally Tuned Long-Range-Corrected (LC) Functionals. J Phys Chem A 2021; 125:3489-3502. [PMID: 33874719 DOI: 10.1021/acs.jpca.1c01593] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present study, we have investigated the applicability of long-range-corrected (LC) functionals to a Kohn-Sham (KS) Koopmans'-type theorem. Specifically, we have examined the performance of optimally tuned LCgau-core functionals (in combination with BOP and PW86-PW91 exchange-correlation functionals) by calculating the ionization potential (IP) within the context of Koopmans' prediction. In the LC scheme, the electron repulsion operator, 1/r12, is divided into short-range and long-range components using a standard error function, with a range separation parameter μ determining the weight of the two ranges. For each system that we have examined (H2O, CO, benzene, N2, HF, H2CO, C2H4, and five-membered ring compounds cyclo-C4H4X, with X = CH2, NH, O, and S, and pyridine), the value of μ is optimized to minimize the deviation of the negative HOMO energy from the experimental IP. Our results demonstrate the utility of optimally tuned LC functionals in predicting the IP of outer valence levels. The accuracy is comparable to that of highly accurate ab initio theory. However, our Koopmans' method is less accurate for the inner valence and core levels. Overall, our results support the notion that orbitals in KS-DFT, when obtained with the LC functional, provide an accurate one-electron energy spectrum. This method represents a one-electron orbital theory that is attractive in its simple formulation and effective in its practical application.
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Affiliation(s)
- Kimihiko Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto 606-8103, Japan.,RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe 650-0047, Japan
| | - Han-Seok Bae
- Department of Chemistry Education, Daegu University, Gyeongsan 113-8656, Korea
| | - Jong-Won Song
- Department of Chemistry Education, Daegu University, Gyeongsan 113-8656, Korea
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
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17
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Chong DP. Computational Study of the Electron Spectra of Vapor-Phase Indole and Four Azaindoles. Molecules 2021; 26:1947. [PMID: 33808397 PMCID: PMC8037839 DOI: 10.3390/molecules26071947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 11/19/2022] Open
Abstract
After geometry optimization, the electron spectra of indole and four azaindoles are calculated by density functional theory. Available experimental photoemission and excitation data for indole and 7-azaindole are used to compare with the theoretical values. The results for the other azaindoles are presented as predictions to help the interpretation of experimental spectra when they become available.
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Affiliation(s)
- Delano P Chong
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, BC V6T 1Z1, Canada
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18
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Besley NA. Modeling of the spectroscopy of core electrons with density functional theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1527] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nicholas A. Besley
- School of Chemistry, University of Nottingham University Park Nottingham UK
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19
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Chong DP. Calculation of reliable non-resonant Kα X-ray emission spectra of organic molecules and other small molecules. CAN J CHEM 2020. [DOI: 10.1139/cjc-2020-0186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
For reliable calculation of vertical ionization energies (VIEs) of both core and valence electrons of gas-phase organic molecules and other small molecules, we developed DFT procedures in 1999 and 2009. The difference between core and valence VIEs give the energies for X-ray emission spectra (XES). The dipole matrix elements between core and valence electrons required for calculation of the XES intensities are now easily available. The simple procedure for calculation of reliable XES is demonstrated by comparison with known XES for H2O(g), NH3(g), CO(g), CO2(g), N2(g), and NNO(g). Consequently, the XES of H2CO(g), formamide(g), 1-nitrosamine(g), N-methylformamide(g), 1-nitrosoaziridine(g), and oxirane(g) are predicted with confidence.
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Affiliation(s)
- Delano P. Chong
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, BC V6T 1Z1, Canada
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, BC V6T 1Z1, Canada
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20
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Sarangi R, Vidal ML, Coriani S, Krylov AI. On the basis set selection for calculations of core-level states: different strategies to balance cost and accuracy. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1769872] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Ronit Sarangi
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Marta L. Vidal
- DTU Chemistry – Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry – Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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21
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Sa'adeh H, Backler F, Wang F, Piccirillo S, Ciavardini A, Richter R, Coreno M, Prince KC. Experimental and Theoretical Soft X-ray Study of Nicotine and Related Compounds. J Phys Chem A 2020; 124:4025-4035. [PMID: 32336097 DOI: 10.1021/acs.jpca.9b11586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The valence and core electronic structure of nicotine, nicotinic acid, and nicotinamide have been studied by photoelectron and soft X-ray absorption spectroscopy, supported by theoretical calculations, which take into account conformational isomerism. The core-level photoionization spectra of all molecules have been assigned, and theory indicates that the effects of conformational differences are small, generally less than the natural line widths of the core ionic states. However, in the case of nicotinamide, the theoretical valence ionization potentials of cis and trans conformers differ significantly in the outer valence space, and the experimental spectrum is in agreement with the calculated outer valence cis conformer spectrum. In addition, the C, N, and O K edge near-edge absorption fine structure spectra are reported and interpreted by comparison with reference compounds. We find evidence at the N and O K edges of interaction between the delocalized orbitals of the pyridine ring and the substituents for nicotinic acid and nicotinamide. The strength of the interaction varies because the first is planar, while the second is twisted, reducing the extent of orbital mixing.
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Affiliation(s)
- Hanan Sa'adeh
- Department of Physics, The University of Jordan, 11942 Amman, Jordan.,Elettra Sincrotrone Trieste, in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Frederick Backler
- Centre for Translational Atomaterials and Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Feng Wang
- Centre for Translational Atomaterials and Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Susanna Piccirillo
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", 00133 Rome, Italy
| | | | - Robert Richter
- Elettra Sincrotrone Trieste, in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marcello Coreno
- ISM-CNR, in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra Sincrotrone Trieste, in Area Science Park, 34149 Basovizza, Trieste, Italy.,Centre for Translational Atomaterials and Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
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22
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Pi JM, Stella M, Fernando NK, Lam AY, Regoutz A, Ratcliff LE. Predicting Core Level Photoelectron Spectra of Amino Acids Using Density Functional Theory. J Phys Chem Lett 2020; 11:2256-2262. [PMID: 32125160 DOI: 10.1021/acs.jpclett.0c00333] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Core level photoelectron spectroscopy is a widely used technique to study amino acids. Interpretation of the individual contributions from functional groups and their local chemical environments to overall spectra requires both high-resolution reference spectra and theoretical insights, for example, from density functional theory calculations. This is a particular challenge for crystalline amino acids due to the lack of experimental data and the limitation of previous calculations to gas phase molecules. Here, a state of the art multiresolution approach is used for high-precision gas phase calculations and to validate core hole pseudopotentials for plane-wave calculations. This powerful combination of complementary numerical techniques provides a framework for accurate ΔSCF calculations for molecules and solids in systematic basis sets. It is used to successfully predict C and O 1s core level spectra of glycine, alanine, and serine and identify chemical state contributions to experimental spectra of crystalline amino acids.
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Affiliation(s)
- Jo M Pi
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Martina Stella
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Nathalie K Fernando
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Aaron Y Lam
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Anna Regoutz
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Laura E Ratcliff
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
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23
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Fouda AAE, Besley NA. Improving the predictive quality of time‐dependent density functional theory calculations of the X‐ray emission spectroscopy of organic molecules. J Comput Chem 2020; 41:1081-1090. [DOI: 10.1002/jcc.26153] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 12/20/2022]
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24
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Abstract
The molecular structures of 12 azabenzenes have been optimized with the Gaussian09 package at the level of coupled cluster singles and doubles with the basis set cc-pVTZ. The optimized geometry of each is used in the ADF13 program for the calculation of the vertical ionization energies of all the electrons. For both outer-shell and inner-shell valence electrons, the 2009 method of ΔPBE0(SAOP) is used, whereas the 1999 method of ΔPW86PW91 + Crel is employed for the core electrons. For degenerate orbitals, the alternative method chosen is to use localized orbitals, keeping the integer number of electrons, while giving up proper symmetry, rather than to keep symmetry with fractional electrons. The success of the computed results of valence ionization potentials of pyridine and the diazabenzenes gives confidence for the predicted values for the higher azabenzenes. The calculated results for core-electron binding energies provide incentive to experimentalists to measure them with X-ray photoelectron spectrometers and (or) synchrotron facilities.
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Affiliation(s)
- Delano P. Chong
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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25
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Hanson-Heine MWD, George MW, Besley NA. A scaled CIS(D) based method for the calculation of valence and core electron ionization energies. J Chem Phys 2019; 151:034104. [DOI: 10.1063/1.5100098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
| | - Michael W. George
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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26
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Ambroise MA, Jensen F. Probing Basis Set Requirements for Calculating Core Ionization and Core Excitation Spectroscopy by the Δ Self-Consistent-Field Approach. J Chem Theory Comput 2018; 15:325-337. [DOI: 10.1021/acs.jctc.8b01071] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Frank Jensen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
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27
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Islam S, Ganesan A, Auchettl R, Plekan O, Acres RG, Wang F, Prince KC. Electronic structure and intramolecular interactions in three methoxyphenol isomers. J Chem Phys 2018; 149:134312. [DOI: 10.1063/1.5048691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shawkat Islam
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, School of Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Aravindhan Ganesan
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, School of Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Rebecca Auchettl
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, School of Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Oksana Plekan
- Elettra Sincrotrone Trieste, SS 14-km 163,5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Robert G. Acres
- Elettra Sincrotrone Trieste, SS 14-km 163,5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Feng Wang
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, School of Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Kevin C. Prince
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, School of Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
- Elettra Sincrotrone Trieste, SS 14-km 163,5 in Area Science Park, 34149 Basovizza, Trieste, Italy
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28
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29
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Viñes F, Sousa C, Illas F. On the prediction of core level binding energies in molecules, surfaces and solids. Phys Chem Chem Phys 2018. [PMID: 29527610 DOI: 10.1039/c7cp08503f] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Core level binding energies, directly measured by X-ray photoelectron spectroscopy (XPS), provide unique information regarding the chemical environment of atoms in a given system. However, interpretation of XPS in extended systems may not be straightforward and requires assistance from theory. The different state-of-the-art theoretical methods commonly used to approach core level binding energies and their shifts with respect to a given reference are reviewed and critically assessed with special emphasis on recently developed theoretical methods and with a focus on future applications in materials and surface sciences.
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Affiliation(s)
- Francesc Viñes
- Departament de Ciència de Materials i Química Física & Institut de Quimica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1, 08028 Barcelona, Catalunya, Spain.
| | - Carmen Sousa
- Departament de Ciència de Materials i Química Física & Institut de Quimica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1, 08028 Barcelona, Catalunya, Spain.
| | - Francesc Illas
- Departament de Ciència de Materials i Química Física & Institut de Quimica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1, 08028 Barcelona, Catalunya, Spain.
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30
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Kahk JM, Lischner J. Core electron binding energies of adsorbates on Cu(111) from first-principles calculations. Phys Chem Chem Phys 2018; 20:30403-30411. [DOI: 10.1039/c8cp04955f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
C1s and O1s core level binding energy shifts have been calculated for various adsorbates on Cu(111) using the ΔSCF method.
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Affiliation(s)
| | - Johannes Lischner
- Department of Physics and Department of Materials
- and the Thomas Young Centre for Theory and Simulation of Materials
- Imperial College London
- London SW7 2AZ
- UK
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31
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Assessment of basis sets for density functional theory-based calculations of core-electron spectroscopies. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2181-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Benchmarking density functionals and Gaussian basis sets for calculation of core-electron binding energies in amino acids. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2115-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Abstract
Systems containing platinum (Pt) are more challenging for reliable computations, because Pt has 78 electrons and requires relativistic treatment. However, to reduce computational demands, most previous researchers used effective core potentials. In this investigation, we perform numerous computations on the cisplatin molecule with ab initio methods and density functional theory, some of which involve all electron and zero-order relativistic approximation. Tentative conclusions on the reliability of various methods are drawn from comparison of our results with previous calculations and available experimental data. Vibrational and electronic spectra are calculated and compared with previous studies and available experimental data.
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Affiliation(s)
- Delano P. Chong
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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34
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Bellafont NP, Illas F, Bagus PS. Validation of Koopmans' theorem for density functional theory binding energies. Phys Chem Chem Phys 2015; 17:4015-9. [PMID: 25566985 DOI: 10.1039/c4cp05434b] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both initial state effects, to a good approximation the electrostatic potential at the nucleus, and final state effects, due to the response of the electrons to the presence of the core-hole, contribute to core-level binding energies, BE's. For Hartree-Fock, HF, wavefunctions, Koopmans' theorem, KT, which states that the initial state BE = -ε ιs rigorous. However, the KT relationship is commonly used for Kohn-Sham, KS, ε's. We review that the KT relationship with KS ε's fails to give the absolute initial state contribution to the BE. However, we demonstrate that the shifts of initial state BE's from a reference value are accurately obtained from the shifts of the KS ε's. Thus the initial state contributions to BE shifts can be obtained from KT using KS ε's. This result validates a large body of work where KT has been used with KS ε's to define initial state contributions to BE shifts.
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Affiliation(s)
- Noèlia Pueyo Bellafont
- Departament de Química Física & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain.
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35
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Chong DP. Theoretical Study of Structures and Spectra of Small Anticancer Drugs: Fluorouracil, Hydroxyurea, and Tirapazamine. J CHIN CHEM SOC-TAIP 2015. [DOI: 10.1002/jccs.201400443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Delano P. Chong
- Department of Chemistry, 2036 Main Mall, University of British Columbia, Vancouver, B.C. Canada V6T 1Z1
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36
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Tolbatov I, Chipman DM. Comparative study of Gaussian basis sets for calculation of core electron binding energies in first-row hydrides and glycine. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1560-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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37
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Wang F, Ganesan A. Fragment based electronic structural analysis of l-phenylalanine using calculated ionization spectroscopy and dual space analysis. RSC Adv 2014. [DOI: 10.1039/c4ra09146a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fragmentation schemes in phenylalanine revealed using ionization spectroscopy and dual space analysis.
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Affiliation(s)
- Feng Wang
- Molecular Model Discovery Laboratory
- Department of Chemistry and Biotechnology
- Faculty of Sciences
- Engineering and Technology
- Swinburne University of Technology
| | - Aravindhan Ganesan
- Molecular Model Discovery Laboratory
- Department of Chemistry and Biotechnology
- Faculty of Sciences
- Engineering and Technology
- Swinburne University of Technology
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38
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Minasian SG, Keith JM, Batista ER, Boland KS, Clark DL, Kozimor SA, Martin RL, Shuh DK, Tyliszczak T. New evidence for 5f covalency in actinocenes determined from carbon K-edge XAS and electronic structure theory. Chem Sci 2014. [DOI: 10.1039/c3sc52030g] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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39
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Abstract
Allopurinol vapour is studied with density functional theory. Using the best method from past experience for each property, we predict the equilibrium geometry, vibrational spectrum, dipole moment, average dipole polarizability, UV absorption spectrum, vertical ionization energies of valence electrons, and core-electron binding energies.
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Affiliation(s)
- Delano P. Chong
- Department of Chemistry, 2036 Main Mall, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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40
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Giesbers M, Marcelis ATM, Zuilhof H. Simulation of XPS C1s spectra of organic monolayers by quantum chemical methods. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:4782-8. [PMID: 23548381 DOI: 10.1021/la400445s] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Several simple methods are presented and evaluated to simulate the X-ray photoelectron spectra (XPS) of organic monolayers and polymeric layers by density functional theory (DFT) and second-order Møller-Plesset theory (MP2) in combination with a series of basis sets. The simulated carbon (C1s) XPS spectra as obtained via B3LYP/6-311G(d,p) or M11/6-311G(d,p) calculations are in good agreement (average mean error <0.3 eV) with the experimental spectra, and good estimates of C1s spectra can be obtained via E(C1s)(exp) = 0.9698EC1s(theory) + 20.34 (in eV) (B3LYP/6-311G(d,p)). As a result, the simulated C1s XPS spectra can elucidate the binding energies of the different carbon species within an organic layer and, in this way, greatly aid the assignment of complicated C1s XPS spectra. The paper gives a wide range of examples, including haloalkanes, esters, (thio-)ethers, leaving groups, clickable functionalities, and bioactive moieties.
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Affiliation(s)
- Marcel Giesbers
- Laboratory of Organic Chemistry, Dreijenplein 8, Wageningen University, Wageningen, The Netherlands
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41
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Sindona A, Pisarra M, Naccarato F, Riccardi P, Plastina F, Cupolillo A, Ligato N, Caputi LS, Falcone G. Core-hole effects in fullerene molecules and small-diameter conducting nanotubes: a density functional theory study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:115301. [PMID: 23399885 DOI: 10.1088/0953-8984/25/11/115301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Core-hole induced electron excitations in fullerene molecules, and small-diameter conducting carbon nanotubes, are studied using density functional theory with minimal, split-valence, and triply-split-valence basis sets plus the generalized gradient approximation by Perdew-Burke-Ernzerhof for exchange and correlation. Finite-size computations are performed on the carbon atoms of a C(60) Bucky ball and a piece of (3, 3) armchair cylindrical network, terminated by hydrogen atoms, while periodically boundary conditions are imposed on a (3, 3) nanotube unit cell. Sudden creation of the core state is simulated by replacing a 1s electron pair, localized at a central site of the structures, with the effective pseudo-potentials of both neutral and ionized atomic carbon. Excited states are obtained from the ground-state (occupied and empty) electronic structure of the ionized systems, and their overlaps with the ground state of the neutral systems are computed. These overlaps enter Fermi's golden rule, which is corrected with lifetime and finite-temperature effects to simulate the many-electron response of the nanoobjects. A model based on the linked cluster expansion of the vacuum persistence amplitude of the neutral systems, in a parametric core-hole perturbation, is developed and found to be reasonably consistent with the density functional theory method. The simulated spectrum of the fullerene molecule is found to be in good agreement with x-ray photoemission experiments on thick C(60) films, reproducing the low energy satellites at excitation energies below 4 eV within a peak position error of ca. 0.3 eV. The nanotube spectra show some common features within the same experiments and describe well the measured x-ray photoelectron lineshape from nanotube bundles with an average diameter of 1.2 nm.
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Affiliation(s)
- A Sindona
- Dipartimento di Fisica dell'Università della Calabria, Rende (CS), Italy.
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CHONG DELANOP. DENSITY FUNCTIONAL THEORY STUDY OF THE PHOTOELECTRON SPECTRA OF 5-METHYLTETRAZOLE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633612500964] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The molecule 5-methyltetrazole (5MTZ) can exist in two taumeric forms. The vertical ionization energies (VIEs) of both valence and core electrons of both the tautomers are calculated with our established DFT procedures and compared with available experimental data. For the 2H-tautomer, the average absolute deviations (AADs) for the outer-valence VIEs and core-electron binding energies (CEBEs) from experiment are below 0.1 eV, while the AAD for the inner-valence VIEs is much larger at 0.4 eV. For the 1H-tautomer, no observed valence VIEs have been reported and the AAD for the calculated CEBEs is 0.2 eV. The assignment of the experimental core-electron ionization spectrum is confirmed, but our results suggest a slight modification of the assignment of the UV photoelectron spectrum of the 2H-tautomer.
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Affiliation(s)
- DELANO P. CHONG
- Department of Chemistry, 2036 Main Mall, University of British Columbia, Vancouver, B.C., V6T 1Z1, Canada
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Chong DP. Density functional theory study of the vertical ionization energies of the valence and core electrons of cyclopentadiene, pyrrole, furan, and thiophene. CAN J CHEM 2011. [DOI: 10.1139/v11-121] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The procedure abbreviated as ΔPBE0(SAOP)/et-pVQZ, based on density functional theory, was developed recently for the calculation of vertical ionization energies of the valence electrons of organic and other small molecules and succeeded in giving results with an average absolute deviation of 0.21 eV from experiment for a collection of 115 reliable test cases of nonperhalo molecules. The objective of this work is to add a number of test cases to the benchmark database. We chose the set of molecules cyclo-C4H4X, with X = CH2, NH, O, and S, previously studied by many workers both experimentally and theoretically. The results show that the ΔPBE0(SAOP)/et-pVQZ procedure is not only as good as ab initio methods such as SAC-CI, OVGF, and ADC(3) in performance, but also handles inner valence ionized cations more efficiently. Although the core-electron binding energies of the titled molecules have not been as well investigated theoretically, we apply the methods we developed in recent years to calculate the binding energies of C1s, N1s, O1s, S1s, and S2p, which compare well with available experimental data.
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Affiliation(s)
- Delano P. Chong
- Department of Chemistry, 2036 Main Mall, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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Holme A, Børve KJ, Sæthre LJ, Thomas TD. Accuracy of Calculated Chemical Shifts in Carbon 1s Ionization Energies from Single-Reference ab Initio Methods and Density Functional Theory. J Chem Theory Comput 2011; 7:4104-14. [PMID: 26598356 DOI: 10.1021/ct200662e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alf Holme
- Department of Chemistry, University of Bergen, NO-5007 Bergen, Norway
| | - Knut J. Børve
- Department of Chemistry, University of Bergen, NO-5007 Bergen, Norway
| | - Leif J. Sæthre
- Department of Chemistry, University of Bergen, NO-5007 Bergen, Norway
| | - T. Darrah Thomas
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, United States
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Affiliation(s)
- Delano P. Chong
- a Department of Chemistry, 2036 Main Mall , University of British Columbia , Vancouver , BC V6T 1Z1 , Canada
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46
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Besley NA, Gilbert ATB, Gill PMW. Self-consistent-field calculations of core excited states. J Chem Phys 2009; 130:124308. [DOI: 10.1063/1.3092928] [Citation(s) in RCA: 213] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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47
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Powis I. Photoelectron circular dichroism: Chiral asymmetry in the angular distribution of electrons emitted by (+)-S-carvone. Chirality 2008; 20:961-8. [DOI: 10.1002/chir.20537] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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48
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Takahata Y, Wulfman CE, Chong DP. Accurate calculation of N1s and C1s core electron binding energies of substituted pyridines. Correlation with basicity and with Hammett substituent constants. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Powis I. Photoelectron Circular Dichroism in Chiral Molecules. ADVANCES IN CHEMICAL PHYSICS 2008. [DOI: 10.1002/9780470259474.ch5] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ulrich V, Barth S, Joshi S, Hergenhahn U, Mikajlo E, Harding CJ, Powis I. Giant Chiral Asymmetry in the C 1s Core Level Photoemission from Randomly Oriented Fenchone Enantiomers. J Phys Chem A 2008; 112:3544-9. [DOI: 10.1021/jp709761u] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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