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Simulation of Core-Level Spectra of H-bonded Systems
Stockholm University, Faculty of Science, Department of Physics.
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The thesis consists of three related projects where attempts have been made to simulate X-Ray Absorption (XAS) spectra of water and hexagonal ice, static non-resonant X-ray Emission (XES) spectrum of water and to apply the semi-classical approximation to Kramers-Heisenberg formula (SCKH) formalism to calculate the non-resonant XES spectrum of water and methanol. The first project is devoted to an investigation of the performance of damped response theory in combination with the DFT electronic structure method (CPP-DFT) in XAS spectrum simulations of liquid water. Based on this study the basis set and cluster size have been determined. The summed CPP-DFT XAS water spectrum was able to reproduce well the three main water absorption spectrum features - pre, main and post edge.

The investigation of the CPP-DFT approach in case of hexagonal ice reveals that neither of four tested ice models with gradually increased degree of structural disorder can reproduce correctly the hexagonal ice spectrum features. A critical investigation of the available experimental ice spectra showed that those spectra are quite different depending on the sample preparation procedure and registration mode. This leads to questioning which ice structures have been actually measured. This was investigated using a Reverse Monte-Carlo based technique which fits the reference spectra using a library of pre-computed structures and assigns weights to each structure. The obtained weights were then used to generate the corresponding radial distribution functions (RDFs). The calculated RDFs have peaks corresponding to perfect lattice distances, but significantly broader than expected for the ideal lattice. In conclusion it was suggested that the available XAS ice spectra do not correspond to the perfect hexagonal ice, but rather samples with varying fraction of defects and possible impurity of amorphous ice.

Simulation of the static non-resonant XES spectrum of water has been performed based on time-dependent density functional theory with the Tamm-Dancoff approximation (TD-DFT/TDA) level of theory. The simulation reveals that the 1b1 peak position is sensitive to the number of H-bonds and to the tetrahedrality of the environment as measured by the local structure index (LSI). The 1b1 peak splitting is observed between two structure sets - tetrahedrally coordinated, low density liquid (LDL) like, structures and asymmetric, high density liquid (HDL) like, structures. The magnitude of the peak splitting depends also on the H-bond lengths. A maximum value 0.6 eV is obtained between LDL structures with short bonds (< 2.68 Å) and HDL structures with long bonds (> 2.8 Å).

The influence of core-hole induced dynamics on the spectrum profile has been studied based on the SCKH approximation for liquid water and methanol. The lone pair 2aʺ peak splitting in liquid methanol was explained based on methanol molecules in different H-bond coordination. The low energy 2aʺ peak is assigned to strongly H-bonded methanol molecules while weakly bonded or non-bonded methanol molecules contribute mainly to the high energy 2aʺ peak. The 2aʺ peak splitting is observed in the static XES spectrum, while inclusion of the core-hole induced dynamics preserves the split and does not generate additional spectrum features, but broadens and smears out spectrum features seen in the static case. Inclusion of the dynamical effects in the water case has revealed that the 1b1 peak splitting is preserved for LDL structures with short bonds and HDL structures with long bonds while unbalanced water structures with odd number of H-bonds generate peaks in between these two extreme cases.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University , 2019. , p. 92
Keywords [en]
water, x-ray absorption, non-resonant x-ray emission, damped linear response theory, time-dependent density functional theory, semi-classical approximation to Kramers-Heisenberg formula, Reverse Monte-Carlo
National Category
Chemical Sciences Physical Sciences
Research subject
Chemical Physics
Identifiers
URN: urn:nbn:se:su:diva-167432ISBN: 978-91-7797-672-1 (print)ISBN: 978-91-7797-673-8 (electronic)OAI: oai:DiVA.org:su-167432DiVA, id: diva2:1300747
Public defence
2019-05-17, sal FP21, hus 1, AlbaNova universitetscentrum, Roslagstullsbacken 33, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.

Available from: 2019-04-24 Created: 2019-03-29 Last updated: 2019-04-24Bibliographically approved
List of papers
1. Requirements of first-principles calculations of X-ray absorption spectra of liquid water
Open this publication in new window or tab >>Requirements of first-principles calculations of X-ray absorption spectra of liquid water
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2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 1, p. 566-583Article in journal (Refereed) Published
Abstract [en]

A computational benchmark study on X-ray absorption spectra of water has been performed by means of transition-potential density functional theory (TP-DFT), damped time-dependent density functional theory (TDDFT), and damped coupled cluster (CC) linear response theory. For liquid water, using TDDFT with a tailored CAM-B3LYP functional and a polarizable embedding, we find that an embedding with over 2000 water molecules is required to fully converge spectral features for individual molecules, but a substantially smaller embedding can be used within averaging schemes. TP-DFT and TDDFT calculations on 100 MD structures demonstrate that TDDFT produces a spectrum with spectral features in good agreement with experiment, while it is more difficult to fully resolve the spectral features in the TP-DFT spectrum. Similar trends were also observed for calculations of bulk ice. In order to further establish the performance of these methods, small water clusters have been considered also at the CC2 and CCSD levels of theory. Issues regarding the basis set requirements for spectrum simulations of liquid water and the determination of gas-phase ionization potentials are also discussed.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-127281 (URN)10.1039/c5cp03919c (DOI)000368755500059 ()
Available from: 2016-06-28 Created: 2016-03-01 Last updated: 2019-08-30Bibliographically approved
2. X-ray absorption spectrum simulations of hexagonal ice
Open this publication in new window or tab >>X-ray absorption spectrum simulations of hexagonal ice
2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 3, article id 034501Article in journal (Refereed) Published
Abstract [en]

We calibrate basis sets and performance of two theoretical approaches to compute X-ray absorption spectra (XAS) of condensed water by comparison to experiments on hexagonal ice Ih. We apply both the transition-potential half-core-hole approach and the complex polarization propagator using four different models of the crystal with increasing oxygen and proton disorder but find poor agreement with experiments. We note that there are large variations in experimental spectra depending on detection mode and how the ice samples were prepared, which leads us to critically investigate what structures were actually prepared and measured in each case. This is done by using a Monte Carlo-based fitting technique which fits the spectra based on a library of precomputed spectra and assigns weights to contributions from different model structures. These are then used to generate O-O and O-H radial distribution functions and tetrahedrality parameters associated with each of the measured spectra. We find that all spectra are associated with sharp peaks at the oxygen positions in the perfect lattice, but with significant disorder around these positions. We suggest that presently available XAS of hexagonal ice are not fully representative of the perfect crystalline lattice, but contain varying amounts of defects and possible contributions from low-density amorphous ice.

Keywords
Crystal lattices, Density functional theory, Amorphous materials, Chemical elements, X-ray absorption spectroscopy, Hydrogen bonding, Correlation-consistent basis sets
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-166802 (URN)10.1063/1.5078385 (DOI)000456266100016 ()30660146 (PubMedID)
Available from: 2019-03-11 Created: 2019-03-11 Last updated: 2019-03-29Bibliographically approved
3. Relationship between x-ray emission and absorption spectroscopy and the local H-bond environment in water
Open this publication in new window or tab >>Relationship between x-ray emission and absorption spectroscopy and the local H-bond environment in water
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2018 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 148, no 14, article id 144507Article in journal (Refereed) Published
Abstract [en]

The connection between specific features in the water X-ray absorption spectrum and X-ray emission spectrum (XES) and the local H-bond coordination is studied based on structures obtained from path-integral molecular dynamics simulations using either the opt-PBE-vdW density functional or the MB-pol force field. Computing the XES spectrum using all molecules in a snapshot results in only one peak in the lone-pair (1b(1)) region, while the experiment shows two peaks separated by 0.8-0.9 eV. Different H-bond configurations were classified based on the local structure index (LSI) and a geometrical H-bond cone criterion. We find that tetrahedrally coordinated molecules characterized by high LSI values and two strong donated and two strong accepted H-bonds contribute to the lowenergy 1b(1) emission peak and to the post-edge region in absorption. Molecules with the asymmetric H-bond environment with one strong accepted H-bond and one strong donated H-bond and low LSI values give rise to the high energy 1b(1) peak in the emission spectrum and mainly contribute to the pre-edge and main-edge in the absorption spectrum. The 1b(1) peak splitting can be increased to 0.62 eV by imposing constraints on the H-bond length, i.e., for very tetrahedral structures short H-bonds (less than 2.68 angstrom) and for very asymmetric structures elongated H-bonds (longer than 2.8 angstrom). Such structures are present, but under-represented, in the simulations which give more of an average of the two extremes.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-155902 (URN)10.1063/1.5009457 (DOI)000430128600033 ()29655333 (PubMedID)
Available from: 2018-04-30 Created: 2018-04-30 Last updated: 2019-03-29Bibliographically approved
4. Core-hole-induced dynamical effects in the x-ray emission spectrum of liquid methanol
Open this publication in new window or tab >>Core-hole-induced dynamical effects in the x-ray emission spectrum of liquid methanol
2017 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 13, article id 134506Article in journal (Refereed) Published
Abstract [en]

We compute the x-ray emission spectrum of liquid methanol, with the dynamical effects that result from the creation of the core hole included in a semiclassical way. Our method closely reproduces a fully quantum mechanical description of the dynamical effects for relevant one-dimensional models of the hydrogen-bonded methanol molecules. For the liquid, we find excellent agreement with the experimental spectrum, including the large isotope effect in the first split peak. The dynamical effects depend sensitively on the initial structure in terms of the local hydrogen-bonding (H-bonding) character: non-donor molecules contribute mainly to the high-energy peak while molecules with a strong donating H-bond contribute to the peak at lower energy. The spectrum thus reflects the initial structure mediated by the dynamical effects that are, however, seen to be crucial in order to reproduce the intensity distribution of the recently measured spectrum.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-143601 (URN)10.1063/1.4979656 (DOI)000399073300035 ()28390372 (PubMedID)
Available from: 2017-05-31 Created: 2017-05-31 Last updated: 2019-03-29Bibliographically approved
5. X-ray Emission Spectrum Simulation of Liquid Water: The Origin of the Split Lone-Pair Peaks
Open this publication in new window or tab >>X-ray Emission Spectrum Simulation of Liquid Water: The Origin of the Split Lone-Pair Peaks
(English)Manuscript (preprint) (Other academic)
Keywords
water, non-resonant x-emission, time-dependent density functional theory, semi-classical approximation to Kramers-Heisenberg formula
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-167420 (URN)
Available from: 2019-03-29 Created: 2019-03-29 Last updated: 2019-03-29Bibliographically approved

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