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Structure, Dynamics and Thermodynamics of Liquid Water: Insights from Molecular Simulations
Stockholm University, Faculty of Science, Department of Physics. (Kvantkemi)
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Water is a complex liquid with many unusual properties. Our understanding of its physical, chemical and biological properties is greatly advanced after a century of dedicated research but there are still many unresolved questions. If answered, they could have important long-term consequences for practical applications ranging from drug design to water purification. This thesis presents results on the structure, dynamics and thermodynamics of liquid water. The focus is on theoretical simulations applied to interpret experimental data from mainly x-ray and neutron scattering and spectroscopy techniques. The structural sensitivity of x-ray and neutron diffraction is investigated using reverse Monte Carlo simulations and information on the pair-correlation functions of water is derived. A new method for structure modeling of computationally demanding data sets is presented and used to resolve an inconsistency between experimental extended x-ray absorption fine-structure and diffraction data regarding oxygen-oxygen pair-correlations. Small-angle x-ray scattering data are modeled using large-scale classical molecular dynamics simulations, and the observed enhanced scattering at supercooled temperatures is connected to the presence of a Widom line emanating from a liquid-liquid critical point in the deeply supercooled high pressure regime. An investigation of inherent structures reveals an underlying structural bimodality in the simulations connected to disordered high-density and ordered low-density molecules, providing a clearer interpretation of experimental small-angle scattering data. Dynamical anomalies in supercooled water observed in inelastic neutron scattering experiments, manifested by low-frequency collective excitations resembling a boson peak, are investigated and found to be connected to the thermodynamically defined Widom line. Finally, x-ray absorption spectra are calculated for simulated water structures using density functional theory. An approximation of intra-molecular zero-point vibrational effects is found to significantly improve the relative spectral intensities but a structural investigation indicates that the classical simulations underestimate the amount of broken hydrogen bonds.

Abstract [sv]

Vatten är en komplex vätska med flera ovanliga egenskaper. Vår förståelse av dess fysiska, kemiska och biologiska egenskaper har utvecklats mycket sedan systematiska vetenskapliga studier började genomföras för mer än ett sekel sedan, men många viktiga frågor är fortfarande obesvarade. En ökad förståelse skulle på sikt kunna leda till framsteg inom viktiga områden så som medicinutveckling och vattenrening. Denna avhandling presenterar resultat kring vattnets struktur, dynamik och termodynamik. Fokusen ligger på teoretiska simuleringar som använts för att tolka experimentella data från huvudsakligen röntgen- och neutronspridning samt spektroskopier. Den strukturella känsligheten i röntgen- och neutrondiffraktionsdata undersöks via reverse Monte Carlo metoden och information om de partiella parkorrelationsfunktionerna erhålls. En ny metod för strukturmodellering av beräkningsintensiva data presenteras och används för att lösa en motsägelse mellan experimentell diffraktion och EXAFS angående syre- syre parkorrelationsfunktionen. Data från röntgensmåvinkelspridning modelleras med storskaliga klassiska molekyldynamiksimuleringar, och den observerade förhöjda småvinkelspridningen vid underkylda temperaturer kopplas till existensen av en Widomlinje härrörande från en vätske- vätske kritisk punkt i det djupt underkylda området vid höga tryck. En undersökning av inherenta strukturer i simuleringarna påvisar en underliggande strukturell bimodalitet mellan molekyler i oordnade högdensitetsregioner respektive ordnade lågdensitetsregioner, vilket ger en tydligare tolkning av den experimentella småvinkelspridningen. Dynamiska anomalier i underkylt vatten som har observerats i inelastisk neutronspridning, speciellt förekomsten av lågfrekventa excitationer som liknar en bosontopp, undersöks och kopplas till den termodynamiskt definierade Widomlinjen. Slutligen presenteras densitetsfunktionalberäkningar av röntgenabsorptionsspektra för simulerade vattenstrukturer. En approximation av intramolekylära nollpunktsvibrationseffekter förbättrar relativa intensiteteri spektrumen avsevärt, men en strukturanalys visar att klassiska simuleringar av vatten underskattar andelen brutna vätebindningar.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University , 2011. , 102 p.
Keyword [en]
Liquid water, supercooled water, diffraction, structure modeling, molecular dynamics, x-ray spectroscopy, EXAFS, SAXS
National Category
Physical Sciences
Research subject
Theoretical Physics
Identifiers
URN: urn:nbn:se:su:diva-56711ISBN: 978-91-7447-287-5OAI: oai:DiVA.org:su-56711DiVA: diva2:412365
Public defence
2011-05-27, lecture room FA31, AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 6: Submitted. Paper 7: Submitted. Paper 8: Manuscript. Paper 9: Submitted. Available from: 2011-05-05 Created: 2011-04-22 Last updated: 2011-04-26Bibliographically approved
List of papers
1. 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
2. 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
3. The Inhomogeneous Structure of Water at Ambient Conditions
Open this publication in new window or tab >>The Inhomogeneous Structure of Water at Ambient Conditions
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2009 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, 15214-15218 p.Article in journal (Refereed) Published
Abstract [en]

Small-angle X-ray scattering (SAXS) is used to demonstrate the presence of density fluctuations in ambient water on a physical length-scale of ≈1 nm; this is retained with decreasing temperature while the magnitude is enhanced. In contrast, the magnitude of fluctuations in a normal liquid, such as CCl4, exhibits no enhancement with decreasing temperature, as is also the case for water from molecular dynamics simulations under ambient conditions. Based on X-ray emission spectroscopy and X-ray Raman scattering data we propose that the density difference contrast in SAXS is due to fluctuations between tetrahedral-like and hydrogen-bond distorted structures related to, respectively, low and high density water. We combine our experimental observations to propose a model of water as a temperature-dependent, fluctuating equilibrium between the two types of local structures driven by incommensurate requirements for minimizing enthalpy (strong near-tetrahedral hydrogen-bonds) and maximizing entropy (nondirectional H-bonds and disorder). The present results provide experimental evidence that the extreme differences anticipated in the hydrogen-bonding environment in the deeply supercooled regime surprisingly remain in bulk water even at conditions ranging from ambient up to close to the boiling point.

National Category
Atom and Molecular Physics and Optics
Research subject
Chemical Physics
Identifiers
urn:nbn:se:su:diva-32156 (URN)10.1073/pnas.0904743106 (DOI)000269632400025 ()
Available from: 2009-12-04 Created: 2009-12-04 Last updated: 2011-04-26Bibliographically approved
4. 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: 2011-04-26Bibliographically approved
5. 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
6. Enhanced small-angle scattering connected to the Widom line in simulations of supercooled water
Open this publication in new window or tab >>Enhanced small-angle scattering connected to the Widom line in simulations of supercooled water
(English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690Article in journal (Refereed) Submitted
Abstract [en]

We present extensive simulation results on the TIP4P/2005 water model and show that it displays significantly enhanced small-angle scattering in the supercooled regime. The simulations exhibit a Widom line (TW), emanating from a liquid-liquid critical point (LLCP) in the supercooled region; TW is characterized by a maximal Ornstein-Zernike correlation length and strong small-angle scattering. The good agreement between the simulated small-angle scattering and recent experimental SAXS data [Huang et al., J. Chem. Phys. 133, 134504 (2010)] thus provides indirect evidence for the existence of a Widom line in supercooled water; both the LLCP and singularity-free (SF) scenarios are however consistent with the presence of TW. Simulations performed at 1, 1,000 and 1,500 bar show an increasing abruptness of a high-density (HDL) to low-density (LDL) liquid crossover associated with crossing TW, while simulations at 2,000 bar show a very gradual transition at lower temperatures indicating that the critical pressure (whether at T=0, as in the SF scenario, or above as in the LLCP scenario) is below 2,000 bar in this simulation model. Maxima in the isothermal compressibility and negative thermal expansion coefficient nearly coincide with TW at 1, 1,000 and 1,500 bar. Analysis of the tetrahedrality parameter Q reveals that the HDL-LDL structural transition is very sharp at 1,000 and 1,500 bar, and that structural fluctuations become strongly coupled to density fluctuations upon approaching TW. Furthermore, the tetrahedrality distribution becomes bimodal at ambient temperatures, an observation that possibly provides a link between the HDL-LDL transition and the structural bimodality in liquid water indicated by x-ray spectroscopic techniques.

National Category
Physical Sciences
Identifiers
urn:nbn:se:su:diva-47122 (URN)
Available from: 2010-11-29 Created: 2010-11-29 Last updated: 2011-04-26Bibliographically approved
7. X-ray diffraction study of temperature dependent structure of liquid water
Open this publication in new window or tab >>X-ray diffraction study of temperature dependent structure of liquid water
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(English)Article in journal (Refereed) Submitted
Abstract [en]

We have developed x-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 °C) under normal pressure. Using a spherically curved Ge crystal an energy resolution better than 15 eV has been achieved which eliminates influence from Compton scattering. The high quality of the data allows a precise oxygen-oxygen pair correlation function (PCF) to be directly derived from the Fourier transform of the experimental data resolving shell structure out to ~12 Å, i.e. 5 hydration shells. Large-scale molecular dynamics (MD) simulations using the TIP4P/2005 force-field reproduce excellently the experimental shell structure in the range 4-12 Å although less agreement is seen for the first peak in the PCF. The Local Structure Index (LSI) [J. Chem. Phys. 104, 7671 (1996)] identifies a tetrahedral minority giving the long-range oscillations in the PCF and a disordered majority providing a more featureless background in this range. The current study supports the proposal that the structure of liquid water even under ambient conditions can be described in terms of a two-state fluctuation model involving local structures related to the high-density and low-density forms of liquid water as postulated in the liquid-liquid phase transition hypothesis.

National Category
Physical Sciences
Identifiers
urn:nbn:se:su:diva-56708 (URN)
Available from: 2011-04-22 Created: 2011-04-22 Last updated: 2011-04-26Bibliographically approved
8. Possible origin of low-frequency excitations in supercooled bulk and protein-hydration water
Open this publication in new window or tab >>Possible origin of low-frequency excitations in supercooled bulk and protein-hydration water
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(English)Manuscript (preprint) (Other academic)
National Category
Physical Sciences
Identifiers
urn:nbn:se:su:diva-56709 (URN)
Available from: 2011-04-22 Created: 2011-04-22 Last updated: 2011-04-26Bibliographically approved
9. Bimodal inherent structure in simulated water from 200 to 360 K
Open this publication in new window or tab >>Bimodal inherent structure in simulated water from 200 to 360 K
(English)Manuscript (preprint) (Other academic)
National Category
Physical Sciences
Identifiers
urn:nbn:se:su:diva-56491 (URN)
Available from: 2011-04-18 Created: 2011-04-18 Last updated: 2011-04-26Bibliographically approved

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