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Structure Modeling with X-ray Absorption and Reverse Monte Carlo: Applications to Water
Stockholm University, Faculty of Science, Department of Physics.
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Water is an important substance. It is part of us, of our environment, and is a fundamental prerequisite for the existence of life as we know it. The structure of water is still, after over 100 years of research on the subject, however under debate. In this thesis x-ray absorption spectroscopy (XAS) and reverse Monte Carlo (RMC) modeling are used to search for structural solutions of water consistent with many different experimental data sets, with emphasis on the combination of different experimental techniques for a reliable structure determination. Neutron and x-ray diffraction are analyzed in combination with the more recent synchrotron radiation based XAS. Geometrical criteria for H-bonding are implemented in RMC to drive the fits and allow to evaluate differently H-bonded structure models against the data. It is shown that the available diffraction data put little constraints on the type of H-bond topology or O-O-O tetrahedrality for the structure of liquid water. It is also demonstrated that classical MD simulations, using some of the most common interaction potentials for water, give rise to O-O and O-H pair-correlation functions with too sharp first peaks at too short distances to be in agreement with diffraction, and furthermore that requiring a large fraction of broken H-bonds is not in itself enough for a structure model to reproduce the experimental XAS. A contribution to the theoretical description of XAS is made by an in-depth investigation of important technical aspects of the TP-DFT spectrum calculations. A novel approach to RMC, applicable also to data that require a significant amount of computer time to evaluate, is developed which makes use of pre-computed properties from a large set of local geometries allowing RMC simulations directly on data from core-level spectroscopies such as XAS.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University , 2009. , 83 p.
Keyword [en]
water structure, x-ray absorption, spectroscopy, diffraction, reverse monte carlo, XAS, EXAFS, XANES, RMC, TP-DFT spectrum calculations
National Category
Physical Sciences
Research subject
Chemical Physics
Identifiers
URN: urn:nbn:se:su:diva-31475ISBN: 978-91-7155-972-2 (print)OAI: oai:DiVA.org:su-31475DiVA: diva2:277117
Public defence
2009-12-11, FB53 AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4, 5 and 6: SubmittedAvailable from: 2009-11-19 Created: 2009-11-16 Last updated: 2011-04-26Bibliographically approved
List of papers
1. Are Recent Water Models Obtained by Fitting Diffraction Data Consistent with IR/Raman and X-ray Absorption Spectra?
Open this publication in new window or tab >>Are Recent Water Models Obtained by Fitting Diffraction Data Consistent with IR/Raman and X-ray Absorption Spectra?
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2006 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 125, 244510- p.Article in journal (Refereed) Published
Abstract [en]

X-ray absorption (XA) spectra have been computed based on water structures obtained from a recent fit to x-ray and neutron diffraction data using models ranging from symmetrical to asymmetrical local coordination of the water molecules [A. K. Soper, J. Phys.: Condens. Matter 17, S3273 (2005)]. It is found that both the obtained symmetric and asymmetric structural models of water give similar looking XA spectra, which do not match the experiment. The fitted models both contain unphysical structures that are allowed by the diffraction data, where, e.g., hydrogen-hydrogen interactions may occur. A modification to the asymmetric model, in which the non-hydrogen-bonded OH intramolecular distance is allowed to become shorter while the bonded OH distance becomes longer, improves the situation somewhat, but the overall agreement is still unsatisfactory. The electric field (E-field) distributions and infrared (IR) spectra are also calculated using two established theoretical approaches, which, however, show significant discrepancies in their predictions for the asymmetric structural models. Both approaches predict the Raman spectrum of the symmetric model fitted to the diffraction data to be significantly blueshifted compared to experiment. At the moment no water model exists that can equally well describe IR/Raman, x-ray absorption spectroscopy, and diffraction data. ©2006 American Institute of Physics

Identifiers
urn:nbn:se:su:diva-12384 (URN)10.1063/1.2408419 (DOI)
Available from: 2008-01-15 Created: 2008-01-15 Last updated: 2010-05-07Bibliographically approved
2. Diffraction and IR/Raman Data do not Prove Tetrahedral Water
Open this publication in new window or tab >>Diffraction and IR/Raman Data do not Prove Tetrahedral Water
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2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 8, 084502- p.Article in journal (Refereed) Published
Abstract [en]

We use the reverse Monte Carlo modeling technique to fit two extreme structure models for water to available x-ray and neutron diffraction data in q space as well as to the electric field distribution as a representation of the OH stretch Raman spectrum of dilue HOD in D2O; the internal geometries were fitted to a quantum distribution. Forcing the fit to maximize the number of hydrogen (H) bonds results in a tetrahedral model with 74% double H-bond donors (DD) and 21% single donors (SD). Maximizing instead the number of SD species gives 81% SD and 18% DD, while still reproducing the experimental data and losing only 0.7–1.8 kJ/mole interaction energy. By decomposing the simulated Raman spectrum we can relate the models to the observed ultrafast frequency shifts in recent pump-probe measurements. Within the tetrahedral DD structure model the assumed connection between spectrum position and H-bonding indicates ultrafast dynamics in terms of breaking and reforming H bonds while in the strongly distorted model the observed frequency shifts do not necessarily imply H-bond changes. Both pictures are equally valid based on present diffraction and vibrational experimental data. There is thus no strict proof of tetrahedral water based on these data. We also note that the tetrahedral structure model must, to fit diffraction data, be less structured than most models obtained from molecular dynamics simulations. ©2008 American Institute of Physics

National Category
Physical Sciences
Identifiers
urn:nbn:se:su:diva-14617 (URN)10.1063/1.2968550 (DOI)000259008900022 ()
Available from: 2008-12-05 Created: 2008-12-05 Last updated: 2011-04-26Bibliographically approved
3. On the Range of Water Structure Models Compatible with X-ray and Neutron Diffraction Data
Open this publication in new window or tab >>On the Range of Water Structure Models Compatible with X-ray and Neutron Diffraction Data
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2009 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 18, 6246-6255 p.Article in journal (Refereed) Published
Abstract [en]

We use the reverse Monte Carlo (RMC) method to critically evaluate the structural information content of diffraction data on bulk water by fitting simultaneously or separately to X-ray and neutron data; the O-H and H-H, but not the O-O, pair-correlation functions (PCFs) are well-described by the neutron data alone. Enforcing at the same time different H-bonding constraints, we generate four topologically different structure models of liquid water, including a simple mixture model, that all equally well reproduce the diffraction data. Although earlier work [Leetmaa, M.; et al. J. Chem. Phys. 2008, 129, 084502] has focused on tetrahedrality in the H-bond network in liquid water, we show here that, even for the O-O-O three-body correlation, tetrahedrality is not strictly defined by the data. We analyze how well two popular MD models (TIP4P-pol2 and SPC/E) reproduce the neutron data in q-space and find differences in important aspects from the experiment. From the RMC fits, we obtain pair-correlation functions (PCFs) that are in optimal agreement with the diffraction data but still show a surprisingly strong variability both in position and height of the first intermolecular (H-bonding) O-H peak. We conclude that, although diffraction data impose important constraints on the range of possible water structures, additional data are needed to narrow the range of possible structure models.

National Category
Physical Sciences
Identifiers
urn:nbn:se:su:diva-31446 (URN)10.1021/jp9007619 (DOI)000265687500010 ()
Available from: 2009-11-13 Created: 2009-11-13 Last updated: 2011-04-26Bibliographically approved
4. Theoretical Approximations to X-ray Absorption Spectroscopy of Liquid Water and Ice
Open this publication in new window or tab >>Theoretical Approximations to X-ray Absorption Spectroscopy of Liquid Water and Ice
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2010 (English)In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, Vol. 177, no 2-3, 135-157 p.Article in journal (Refereed) Published
Abstract [en]

We review methods to compute x-ray absorption spectra (XAS) with special focus on the transition potential approach of Triguero et al. [Phys. Rev. B 58, 8097 (1998)] and its application to calculations on water in condensed phase. We discuss the absolute energy scale, functional dependence, broadening versus sampling of intra- and intermolecular vibrational modes, treatment of the continuum, cluster size convergence as well as compare with periodic calculations and with experiment; periodic and cluster model calculations are found to agree very closely in the relevant near-edge region although neither reproduces the pre-edge and main-edge features in the experimental spectra of thin ice films. The real space grid representation of the wave function in the periodic calculations allows a more extended energy range to be described and we find satisfactory agreement with experiment for higher energy continuum resonances. Two proposed alternative approaches using either the potential from a full core-hole (FCH) or the full core-hole with an excited electron in the lowest state (XCH) are shown to lead to spectra that deviate significantly from experiment.

Keyword
X-ray absorption spectroscopy; DFT; NEXAFS; Water structure; Transition-potential
National Category
Natural Sciences
Identifiers
urn:nbn:se:su:diva-31447 (URN)10.1016/j.elspec.2010.02.004 (DOI)000277949100007 ()
Available from: 2009-11-13 Created: 2009-11-13 Last updated: 2011-11-22Bibliographically approved
5. SpecSwap-RMC: A novel reverse Monte Carlo approach using a discrete set of local configurations and pre-computed properties
Open this publication in new window or tab >>SpecSwap-RMC: A novel reverse Monte Carlo approach using a discrete set of local configurations and pre-computed properties
2010 (English)In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 22, no 13, 135001- p.Article in journal (Refereed) Published
Abstract [en]

We present a novel approach to reverse Monte Carlo (RMC) modeling, SpecSwap-RMC, specifically applicable to structure modeling based on properties that require significant computer time to evaluate. In this approach pre-computed property data from a discrete set of local configurations are used and the configuration space is expressed in this basis. Atomistic moves are replaced with swap moves of contributions to a sample set representing the state of the simulated system. We demonstrate the approach by fitting jointly and separately the EXAFS signal and x-ray absorption spectrum (XAS) of ice Ih using a SpecSwap sample set of 80 configurations from a library of 1382 local structures with associated pre-computed spectra. As an additional demonstration we compare SpecSwap and FEFFIT fits of EXAFS data on crystalline copper, finding excellent agreement. SpecSwap-RMC thus extends RMC structure modeling to any property that can be computed from a structure irrespective of computational expense, but at the cost of a reduced configuration space. The method is general enough that it can be applied to any sets of computed properties, not necessarily limited to structure determination.

National Category
Physical Sciences
Identifiers
urn:nbn:se:su:diva-47088 (URN)10.1088/0953-8984/22/13/135001 (DOI)
Available from: 2010-11-29 Created: 2010-11-29 Last updated: 2017-12-12Bibliographically approved
6. Oxygen-oxygen correlations in liquid water: Addressing the discrepancy between diffraction and EXAFS using a novel multiple –data set fitting technique
Open this publication in new window or tab >>Oxygen-oxygen correlations in liquid water: Addressing the discrepancy between diffraction and EXAFS using a novel multiple –data set fitting technique
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2010 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 132, no 10Article in journal (Refereed) Published
Abstract [en]

The first peak of the oxygen-oxygen pair-correlation function (O-O PCF) is a critical measure of the first coordination shell distances in liquid water. Recently, a discrepancy has been uncovered between diffraction and extended x-ray absorption fine-structure (EXAFS) regarding the height and position of this peak, where EXAFS gives a considerably more well-defined peak at a shorter distance compared with diffraction results. This discrepancy is here investigated through a new multiple data set structure modeling technique, SpecSwap-RMC, based on the reverse Monte Carlo (RMC) method. Fitting simultaneously to both EXAFS and a diffraction-based O-O PCF shows that, even though the reported EXAFS results disagree with diffraction, the two techniques can be reconciled by taking into account a strong contribution from the focusing effect originating from nearly linear hydrogen bonds. This many-body contribution, which is usually neglected in RMC modeling of EXAFS data, is included in the fits by precomputing and storing EXAFS signals from real-space multiple-scattering calculations on a large number of unique water clusters. On the other hand, fitting also the O-O PCF from diffraction is seen to enhance the amount of structural disorder in the joint fit. Thus, both nearly linear hydrogen bonds and local structural disorder are important to reproduce diffraction and EXAFS simultaneously. This work also illustrates a few of many possible uses of the SpecSwap-RMC method in modeling disordered materials, particularly for fitting computationally demanding techniques and combining multiple data sets.

Keyword
EXAFS, hydrogen bonds, water, X-ray diffraction
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:su:diva-31450 (URN)10.1063/1.3330752 (DOI)
Available from: 2009-11-13 Created: 2009-11-13 Last updated: 2015-01-22Bibliographically approved

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