Time-dependent density functional theory study of the X-ray emission spectroscopy of amino acids and proteins

Foerster, Aleksandra; Besley, Nicholas A.

doi:10.1016/j.cplett.2020.137860

Cited by 7 publications

(4 citation statements)

References 50 publications

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“…The electronic relaxation in the core-ionized states is captured by the reference determinant and the approach is straightforward to apply. This strategy to simulating X-ray emission spectra was originally proposed in the context of EOM-CCSD calculations, 169 and has also been adapted within ADC calculations 170 and applied with TDDFT to study organic molecules, 171,172 water, 64 and transition metal complexes. [173][174][175][176][177] There have been relatively few studies that directly compare these different approaches to computing X-ray emission spectra.…”

Section: X-ray Emission Spectroscopymentioning

confidence: 99%

Modeling of the spectroscopy of core electrons with density functional theory

Besley

2021

WIREs Comput Mol Sci

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100

104

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The availability of X‐ray light sources with increased resolution and intensity has provided a foundation for increasingly sophisticated experimental studies exploiting the spectroscopy of core electrons to probe fundamental chemical, physical, and biological processes. Quantum chemical calculations can play a critical role in the analysis of these experimental measurements. The relatively low computational cost of density functional theory (DFT) and time‐dependent density functional theory (TDDFT) make them attractive choices for simulating the spectroscopy of core electrons. An overview of current developments to apply DFT and TDDFT to study the key techniques of X‐ray photoelectron spectroscopy, X‐ray absorption spectroscopy, X‐ray emission spectroscopy, and resonant inelastic X‐ray scattering is presented. Insight into the accuracy that can be achieved, in conjunction with an examination of the limitations and challenges to modeling the spectroscopy of core electrons with DFT is provided. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy Electronic Structure Theory > Density Functional Theory

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Section: X-ray Emission Spectroscopymentioning

confidence: 99%

Modeling of the spectroscopy of core electrons with density functional theory

Besley

2021

WIREs Comput Mol Sci

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100

104

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“…the approximate alternative to ΔDFT for XES; Section ). Besley et al have used LR-TDDFT to support experiment by calculating the XES spectra of ionic liquids ([C 8 C 1 Im]X/ZnX 2 in different molar fractions, where X = Cl/Br) and simple (tri- to decaatomic organics, e.g., H 2 S, NH 3 , and CH 3 OH) and complex (amino acids in model α-helices and β-sheets) organic molecules, highlighting the wide applicability of the scheme across a spectrum of practical problems in XS. Reference .…”

Section: Electronic Structure Theory For Core-excited States and X-ra...mentioning

confidence: 99%

Progress in the Theory of X-ray Spectroscopy: From Quantum Chemistry to Machine Learning and Ultrafast Dynamics

Rankine

Penfold

2021

J. Phys. Chem. A

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The development of high-brilliance third- and fourth-generation light sources such as synchrotrons and X-ray free-electron lasers (XFELs), the emergence of laboratory-based X-ray spectrometers, and instrumental and methodological advances in X-ray absorption (XAS) and (non)resonant emission (XES and RXES/RIXS) spectroscopies have had far-reaching effects across the natural sciences. However, new kinds of experiments, and their ever-higher resolution and data acquisition rates, have brought acutely into focus the challenge of accurately, quickly, and cost-effectively analyzing the data; a far-from-trivial task that demands detailed theoretical calculations that are capable of capturing satisfactorily the underlying physics. The past decade has seen significant advances in the theory of core-hole spectroscopies for this purpose, driven by all of the developments above andcruciallya surge in demand. In this Perspective, we discuss the challenges of calculating core-excited states and spectra, and state-of-the-art developments in electronic structure theory, dynamics, and data-driven/machine-led approaches toward their better description.

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“…Experts on basis set design can typically advise on the strengths and limitations of particular basis sets; for example, that anions need diffuse functions, − the 6-311G family are not valence-triple-ζ basis sets, and property-specialized basis sets should be used for properties which have unusual basis set demands such as NMR parameters, − EPR parameters, − and X-ray − calculations, to name but a few. Such recommendations are based on a detailed understanding of basis sets design and being able to read and understand the composition of basis sets in terms of primitive exponents and contraction schemes.…”

Section: Introductionmentioning

confidence: 99%

Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided

Pitman,

Evans,

Ireland

et al. 2023

J. Phys. Chem. A

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Time-dependent density functional theory study of the X-ray emission spectroscopy of amino acids and proteins

Cited by 7 publications

References 50 publications

Modeling of the spectroscopy of core electrons with density functional theory

Modeling of the spectroscopy of core electrons with density functional theory

Progress in the Theory of X-ray Spectroscopy: From Quantum Chemistry to Machine Learning and Ultrafast Dynamics

Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided

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