Detailed study of pyridine at the C 1<i>s</i> and N 1<i>s</i> ionization thresholds: The influence of the vibrational fine structure

Kolczewski, Christine; Püttner, R.; Plashkevych, Oleksandr; Ågren, Hans; Staemmler, Volker; Martins, M.; Snell, G.; Schlachter, A. S.; Sant’Anna, M. M.; Kaindl, G.; Pettersson, Lars G. M.

doi:10.1063/1.1397797

Cited by 250 publications

(287 citation statements)

References 31 publications

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“…This can be done by computing the difference in the total energy of the first core-excited state (XCH) § § and the ground state for each configuration or nonequivalent center. [132] The first TP transition is then set to occur at this energy. [132,133] After an absolute energy scale has been established, the resulting spectra need still to be shifted to account for, for example, deficiencies in the approximate DFT functional as well as relativistic and basis set incompleteness effects.…”

Section: Core Electron Excitationsmentioning

confidence: 99%

“…[132] The first TP transition is then set to occur at this energy. [132,133] After an absolute energy scale has been established, the resulting spectra need still to be shifted to account for, for example, deficiencies in the approximate DFT functional as well as relativistic and basis set incompleteness effects. [134] The determination of the excited core state is performed dynamically in ERKALE during the SCF iteration process by computing the centers r i and rms widths r i of each occupied orbital ψ σ i of the excited spin σ…”

Section: Core Electron Excitationsmentioning

confidence: 99%

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ERKALE—A flexible program package for X‐ray properties of atoms and molecules

et al. 2012

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ERKALE is a novel software program for computing X-ray properties, such as ground-state electron momentum densities, Compton profiles, and core and valence electron excitation spectra of atoms and molecules. The program operates at Hartree-Fock or density-functional level of theory and supports Gaussian basis sets of arbitrary angular momentum and a wide variety of exchange-correlation functionals. ERKALE includes modern convergence accelerators such as Broyden and ADIIS and it is suitable for general use, as calculations with thousands of basis functions can routinely be performed on desktop computers. Furthermore, ERKALE is written in an object oriented manner, making the code easy to understand and to extend to new properties while being ideal also for teaching purposes.

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Section: Core Electron Excitationsmentioning

confidence: 99%

Section: Core Electron Excitationsmentioning

confidence: 99%

ERKALE—A flexible program package for X‐ray properties of atoms and molecules

et al. 2012

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“…27 The experimental spectra measured in the gas phase can be simulated with excellent agreement by including specific corrections to the NEXAFS computations for addressing fine details such as the coupling to vibrational states. 28 Time dependent DFT calculations have been successfully extended to treat also core level excitations in heterocyclic aromatics. 29 On the other hand, the renovated interest in NEXAFS simulations of poly-and heterocyclic aromatics is associated with the study of their interaction with substrates of technological interest.…”

Section: Introductionmentioning

confidence: 99%

High resolution NEXAFS of perylene and PTCDI: a surface science approach to molecular orbital analysis

Fratesi

Lanzilotto

Stranges

et al. 2014

Phys. Chem. Chem. Phys.

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We made use of synchrotron radiation to perform near edge X-ray absorption fine structure spectroscopy, NEXAFS, at the carbon K-edge of perylene and perylene-tetracarboxylic-diimide, PTCDI. Reference spectra measured for isolated molecules in the gas phase are compared with polarization dependent NEXAFS spectra measured on highly oriented thin films in order to study the symmetry of the molecular orbitals. The molecular overlayers are grown onto the rutile TiO 2 (110) surface for which the large anisotropic corrugation effectively drives the molecular orientation, while its dielectric nature prevents the rehybridization of the molecular orbitals. We employed density functional theory, DFT, calculations to disentangle the contribution of specific carbon atoms to the molecular density of states. Numerical simulations correctly predict the observed NEXAFS azimuthal dichroism of the s* resonances above the ionization threshold, from which we determine the full geometric orientation of the overlayer molecules. A discrepancy observed for the spectral contribution of the imide carbon atom to the calculated unoccupied molecular orbitals has been explained in terms of initial state effects, as determined by Hartree-Fock corrections and in full agreement with the corresponding shift of the C 1s core level measured by X-ray photoelectron spectroscopy, XPS.

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“…Effective core potentials (ECP) were used on all other oxygen atoms in order to simplify the definition of the core hole 29 . The HCH and FCH methods were compared by correcting the spectral energy scale through a Kohn-Sham approach 18,20,30 , where the XA spectrum is uniformly shifted by matching the lowest oscillator-strength to the energy difference between the total Kohn-Sham energies of the variationally obtained first resonant core-excited state and the ground state cluster. The revised value of +0.33 eV 31 for the relativistic correction for the oxygen atom is applied in the present work to all theoretical spectra.…”

mentioning

confidence: 99%

Half or full core hole in density functional theory X-ray absorption spectrum calculations of water?

Cavalleri

Odelius

Nordlund

et al. 2005

Phys. Chem. Chem. Phys.

111

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It was recently suggested, based on x-ray absorption (XAS) and x-ray Raman spectroscopy (XRS) combined with Density Functional Theory (DFT) calculations of spectra, that water in the liquid is in an asymmetric hydrogen bonding situation with only two strong H-bonds: one donating and one accepting with the remaining bonds weakened or broken through mainly bending off the H-bond angle 1 . This provocative result has attracted much attention and debate in the literature. Smith et al. 2 analyzed the temperature dependence of XAS spectra obtained on a liquid microjet and claimed agreement with fourcoordinated water. Their experimental data has, however, been shown to be flawed by saturation effects which invalidate their conclusions 3 . On the theory side Hetenyi et al. 4 computed spectra directly from their ab initio molecular dynamics (AIMD) simulations and claimed agreement with experiment by using a full core hole (FCH) in their spectrum calculations rather than the standard half core hole (HCH). In view of the predominance (80% at room temperature) of single-donor (SD) species reported in ref. 1 this is a surprising and contradictory result with respect to the XAS conclusions since the AIMD simulation only contained 19% SD species being instead dominated by doubledonor (DD), ice-like coordination. In view of the present debate on the structure of water it is important to analyze in depth the validity of the HCH and FCH approximations to the core-hole potential in DFT calculations of XAS spectra. XAS (elsewhere also NEXAFS or XANES) 5 and the corresponding non-resonant x-ray Raman spectroscopy (XRS) 6 are well-established experimental techniques that have recently been extended to measurements of the local electronic structure of liquid water 1,7-11 . Both XAS and XRS show major differences in the spectral profiles between bulk ice and liquid water 1,8,9 ; there is a well-defined pre-edge structure that can be seen in the spectrum of the liquid and is substantially reduced in the bulk ice spectrum; the remaining intensity is mainly due to proton disorder and minor defects 12 . The liquid water spectrum, with strong pre-edge (535 eV) and main-edge (537 eV) features, instead closely resembles that of the ice surface where a dominant fraction of the water molecules in the first half-bilayer has one free O-H bond 1,13 . The spectrum of bulk ice, in which each molecule is tetrahedrally coordinated, is instead characterized by weak main edge (537 eV) and strong post edge (540 eV) features 1,8 ; these experimental differences already indicate that the liquid cannot be dominated by fully coordinated molecules. In ref. 1 density functional theory (DFT) based spectrum calculations using the standard transition potential or HCH approximation were used to interpolate spectra between the two experimental extremes, i.e. bulk and surface of ice. This confirmed the experimental analysis in terms of coordination and furthermore lead to an operational H-bond definition relative to a geometrical cone at each of the donor hydrogens...

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Detailed study of pyridine at the C 1s and N 1s ionization thresholds: The influence of the vibrational fine structure

Cited by 250 publications

References 31 publications

ERKALE—A flexible program package for X‐ray properties of atoms and molecules

ERKALE—A flexible program package for X‐ray properties of atoms and molecules

High resolution NEXAFS of perylene and PTCDI: a surface science approach to molecular orbital analysis

Half or full core hole in density functional theory X-ray absorption spectrum calculations of water?

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