| 1. |
- Ekström, Ulf, et al.
(författare)
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Characterization of the chemisorption of methylsilane on a au(1,1,1) surface from the silicon K- And L-edge spectra : A theoretical study using the four-component static exchange approximation
- 2007
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 111:37, s. 13846-13850
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Tidskriftsartikel (refereegranskat)abstract
- X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectra (NEXAFS) of methylsilane, isolated and chemisorbed to a Au(1,1,1) surface, are determined in the fully relativistic four-component static exchange approximation - both the K- and the L-edge of silicon are addressed in this investigation. In the fully chemisorbed structure, three H(Si) atoms have been cleaved off when Si binds in the hollow site of Au forming three Si - Au bonds of normal length. As due to die tri-coordinated chemisorption, the onsets of the K- and L-edge NEXAFS absorption bands occur some 2.0 and 2.5 eV lower in energy, respectively. The spin-orbit splittings in the silicon 2p-shell are not significantly changed due to adsorption. A partly chemisorbed methylsilane with only one H(Si) bond cleaved was also studied, and it is shown that the polarization dependence in the surface spectra contains details that can be used experimentally to identify the surface coordination of silicon. The red-shifts in the XPS silicon 1s (2p) spectra upon surface binding are 0.95 (0.65) and 1.15 (0.83) eV for the mono- and tricoordinated system, respectively.
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| 2. |
- Falklöf, Olle, et al.
(författare)
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Inter-Excited-State Phosphorescence in the Four-Component Relativistic Kohn-Sham Approximation : A Case Study on Lumiflavin
- 2015
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 119:49, s. 11911-11921
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Tidskriftsartikel (refereegranskat)abstract
- Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states can be supplemented by the ability to also describe inter-excited-state phosphorescence. Specifically, by performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL∗) singlet state of lumiflavin to the 3(πHπL∗), 3(nN2πL∗), and 3(πH-1πL∗) triplet states, and subsequently, we compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically 2 to 5 orders of magnitude smaller than the nonradiative ones.
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| 3. |
- da Cruz, Vinicius Vaz, et al.
(författare)
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Nuclear dynamics in resonant inelastic X-ray scattering and X-ray absorption of methanol
- 2019
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 150:23
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Tidskriftsartikel (refereegranskat)abstract
- We report on a combined theoretical and experimental study of core-excitation spectra of gas and liquid phase methanol as obtained with the use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). The electronic transitions are studied with computational methods that include strict and extended second-order algebraic diagrammatic construction [ADC(2) and ADC(2)-x], restricted active space second-order perturbation theory, and time-dependent density functional theory-providing a complete assignment of the near oxygen K-edge XAS. We show that multimode nuclear dynamics is of crucial importance for explaining the available experimental XAS and RIXS spectra. The multimode nuclear motion was considered in a recently developed "mixed representation" where dissociative states and highly excited vibrational modes are accurately treated with a time-dependent wave packet technique, while the remaining active vibrational modes are described using Franck-Condon amplitudes. Particular attention is paid to the polarization dependence of RIXS and the effects of the isotopic substitution on the RIXS profile in the case of dissociative core-excited states. Our approach predicts the splitting of the 2a RIXS peak to be due to an interplay between molecular and pseudo-atomic features arising in the course of transitions between dissociative core- and valence-excited states. The dynamical nature of the splitting of the 2a peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical results are in good agreement with our liquid phase measurements and gas phase experimental data available from the literature. (C) 2019 Author(s).
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| 4. |
- Linares, Mathieu, et al.
(författare)
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Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra
- 2019
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 21:7, s. 3637-3643
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Tidskriftsartikel (refereegranskat)abstract
- DNA binding modes of the stereoisomeric rotamers of two dithenylethene derivatives (DTE1 and DTE2) representing candidate molecular photoswitches of great promise for photopharmacology and nanotechnology have been identified and characterized in terms of their binding energies and electronic circular dichroism (CD) responses. In the open form, two binding modes are identified namely minor-groove binding of the lowest-energy conformer with an anti-parallel arrangement of methyl groups and major-groove double-intercalation of the P-enantiomers of an intermediate-state rotamer. Only the latter binding mode is found to be enantiomerically selective and expected to have an overall negative linear dichroism (LD) as observed in the experiment for DTE1 (Angew. Chem., Int. Ed., 2013, 52, 4393). In the closed form, the most favorable binding mode is found to be minor groove binding. Also this binding mode is found to be enantiomerically selective and for DTE1, it is the M-enantiomer that binds the strongest, showing a positive theoretical signature CD band in the long wavelength region with origin in pyridinium ligands. The theoretical CD spectrum is found to be in good agreement with the experimental one, which provides an indirect evidence for a correct identification of the binding mode in the closed form.
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| 5. |
- Fransson, Thomas, et al.
(författare)
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XABOOM : An X-ray Absorption Benchmark of Organic Molecules Based on Carbon, Nitrogen, and Oxygen 1s -> π* Transitions
- 2021
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 17:3, s. 1618-1637
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Tidskriftsartikel (refereegranskat)abstract
- The performance of several standard and popular approaches for calculating X-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges of 40 primarily organic molecules up to the size of guanine has been evaluated, focusing on the low-energy and intense 1s -> pi* transitions. Using results obtained with CVS-ADC(2)-x and fc-CVS-EOM-CCSD as benchmark references, we investigate the performance of CC2, ADC(2), ADC(3/2), and commonly adopted density functional theory (DFT)-based approaches. Here, focus is on precision rather than on accuracy of transition energies and intensities-in other words, we target relative energies and intensities and the spread thereof, rather than absolute values. The use of exchange-correlation functionals tailored for time-dependent DFT calculations of core excitations leads to error spreads similar to those seen for more standard functionals, despite yielding superior absolute energies. Long-range corrected functionals are shown to perform particularly well compared to our reference data, showing error spreads in energy and intensity of 0.2-0.3 eV and similar to 10%, respectively, as compared to 0.3-0.6 eV and similar to 20% for a typical pure hybrid. In comparing intensities, state mixing can complicate matters, and techniques to avoid this issue are discussed. Furthermore, the influence of basis sets in high-level ab initio calculations is investigated, showing that reasonably accurate results are obtained with the use of 6-311++G**. We name this benchmark suite as XABOOM (X-ray absorption benchmark of organic molecules) and provide molecular structures and ground-state self-consistent field energies and spectroscopic data. We believe that it provides a good assessment of electronic structure theory methods for calculating X-ray absorption spectra and will become useful for future developments in this field.
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| 6. |
- Norman, Patrick, et al.
(författare)
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On the interplay between chirality and exciton coupling : A DFT calculation of the circular dichroism in π-stacked ethylene
- 2014
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Ingår i: Chirality. - : Wiley-Blackwell. - 0899-0042 .- 1520-636X. ; 26:9, s. 483-489
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Tidskriftsartikel (refereegranskat)abstract
- The chirality of stacked weakly interacting π-systems was interpreted in terms of Frenkel exciton states and the formation of excitonic circular dichroism (CD) bands was monitored for ethylene stacks of varying sizes. Convergence of CD bands with respect to the system size was observed for stacks involving around 10 molecules. By means of rotation around the C-C double bond in ethylene, chirality was induced in the monomeric system and which was shown to dominate the spectral responses, even for polymer aggregates. In helical assemblies of chiral entities, there will always be a mix of excitonic and monomeric contributions to the CD signal and it is demonstrated that the complex polarization propagator approach in combination with Density Functional Theory is a suitable method to address this situation. Chirality 26:123-129, 2014.
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| 7. |
- Rubio-Magnieto, J., et al.
(författare)
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Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes
- 2015
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Ingår i: Organic and biomolecular chemistry. - : Royal Society of Chemistry. - 1477-0520 .- 1477-0539. ; 13:8, s. 2453-2463
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Tidskriftsartikel (refereegranskat)abstract
- The molecular recognition of human telomeric G-quadruplexes by a novel cationic π-extended NiII-porphyrin (NiII-TImidP4) is studied in aqueous solutions via (chir)optical spectroscopy, Fluorescence Resonance Energy Transfer (FRET) melting assay, and computational molecular modeling. The results are systematically compared with the recognition by a conventional meso-substituted NiII-porphyrin (NiII-TMPyP4), which allows us to pinpoint the differences in binding modes depending on the G-quadruplex topology. Importantly, FRET melting assays show the higher selectivity of NiII-TImidP4 towards human telomeric G4 than that of NiII-TMPyP4.
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| 8. |
- Shirani, Hamid, et al.
(författare)
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A Palette of Fluorescent Thiophene-Based Ligands for the Identification of Protein Aggregates
- 2015
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Ingår i: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 21:43, s. 15133-15137
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Tidskriftsartikel (refereegranskat)abstract
- By replacing the central thiophene unit of an anionic pentameric oligothiophene with other heterocyclic moities, a palette of pentameric thiophene-based ligands with distinct fluorescent properties were synthesized. All ligands displayed superior selectivity towards recombinant amyloid fibrils as well as disease-associated protein aggregates in tissue sections.
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| 9. |
- Villaume, Sebastien, et al.
(författare)
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Near sulfur L-edge X-ray absorption spectra of methanethiol in isolation and adsorbed on a Au(111) surface : A theoretical study using the four-component static exchange approximation
- 2010
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 12:21, s. 5596-5601
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Tidskriftsartikel (refereegranskat)abstract
- The relativistic four-component static exchange approach for calculation of near-edge X-ray absorption spectra has been reviewed. Application of the method is made to the Au(111) interface and the adsorption of methanethiol by a study of the near sulfur L-edge spectrum. The binding energies of the sulfur 2p 1/2 and 2p3/2 sublevels in methanethiol are determined to be split by 1.2 eV due to spin-orbit coupling, and the binding energy of the 2p3/2 shell is lowered from 169.2 eV for the isolated system to 167.4 and 166.7-166.8 eV for methanethiol in mono- and di-coordinated adsorption sites, respectively (with reference to vacuum). In the near L-edge X-ray absorption fine structure spectrum only the σ*(S-C) peak at 166 eV remains intact by surface adsorption, whereas transitions of predominantly Rydberg character are largely quenched in the surface spectra. The σ*(S-H) peak of methanethiol is replaced by low-lying, isolated, σ*(S-Au) peak(s), where the number of peaks in the latter category and their splittings are characteristic of the local bonding situation of the sulfur.
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| 10. |
- Villaume, Sebastien, et al.
(författare)
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On circular dichroism and the separation between chromophore and chiral center : The near carbon K-Edge X-ray absorption and circular dichroism spectra of noradrenaline and L-DOPA
- 2009
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Ingår i: Chirality. - : Wiley. - 0899-0042 .- 1520-636X. ; 21:1 E, s. E13-E19
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Tidskriftsartikel (refereegranskat)abstract
- The near carbon K-edge X-ray absorption and circular dichroism spectra of noradrenaline (neutral and protonated forms) and L-DOPA (protonated form) have been determined with use of the complex polarization propagator method in conjunction with Kohn-Sham density functional theory. A Coulomb attenuated exchange-correlation functional and London atomic orbitals have been employed to address the issues of hole-electron interactions and gauge-origin dependence of the magnetic-dipole operator, respectively. Results show that the characteristics of the chromophore part of the circular dichroism spectra are shared for all three considered systems, whereas protonation qualitatively alters the part of the spectrum assigned to the chiral side chain. The comparatively larger spatial separation of chromophore and chiral center in L-DOPA inflicts larger differences in spectral intensities between the chromophore and chiral center part of the circular dichroism spectra.
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