The first 27 years of Reverse Monte Carlo Modelling
Budapest, Hungary 17-19 September, 2015


Marco Amores: Fast microwave-assisted solid-state synthesis of lithium containing garnets and local structure characterization by total scattering (poster)
Mona Bahout: Stability under hydrogen and humid conditions of potential SOFC electrodes investigated by high-temperature in situ neutron powder diffraction (talk)
Imre Bakó: A new approach to the determination of the uncertainty in neutron diffraction experiments with isotopic substitution method (talk)
Rafal Babilas: Reverse Monte Carlo modeling of local atomic structure in binary Fe-based metallic glasses (poster)
Dominic Carter: The local structure of beta-cristobalite as a composite of low symmetry domains (talk)
Viviana Cristiglio: Structure investigation of molecular liquids and liquid solutions by small angle neutron scattering (talk)
Kaustuv Datta: Local structures of perovskite based ferroelectric solid solutions containing morphotropic phase boundary (talk)
Juan Du: After RMC refinement: new tools for analysing refined configurations (with case study BiFeO3) (talk)
William Fletcher: A Bayesian route to protein structure without crystals (talk)
Giles Flowitt-Hill: Local order of small organic molecules in crystals (talk)
Nick Funnell: RMC and the Nanoscale (talk)
Orsolya Gereben: Characterization of the hydrogen-bonded network in ethanol-water mixtures (talk)
Andrew Goodwin: RMC in magnets (talk)
Ilkyoung Jeong: Separation of thermal disorder from static displacements in RMC modeling (talk)
Andrew J. Johnston: The Atomic Structure of Pharmaceuticals in Solution: Penetrating the Blood-brain Barrier (talk)
Pál Jóvári: Short range order in CuZr-based metallic glasses (talk)
David Keen: The first 27 years of reverse Monte Carlo (talk)
J. Vidal Laveda: Microwave synthesis of LiFe1-xMnxPO4 nanostructures for use as positive insertion electrodes in Li-ion batteries (poster)
Huw Marchbank: Understanding how different synthetic procedures influence the short, medium and long range atomic arrangement in ceria (talk)
Serena Ada Maugeri: Modelling nanoparticles structure using PDFgui and RMCprofile (talk)
Sylvia McLain: Probing biomolecular structure in aqueous solution: Insights from neutron diffraction and computation (talk)
Bahout Mona: Stability under hydrogen and humid conditions of potential SOFC electrodes investigated by high-temperature in situ neutron powder diffraction (talk)
Koji Ohara: Liquid structure of the electrolyte material Li/Mg/Cs-TFSA molten salt (talk)
Yohei Onodera: Reverse Monte Carlo methods for superionic conductors (talk)
Alistar Overy: Disorder-phonon coupling in crystal-like aperiodic solids (talk)
Lewis Owen: Short range order in alloys (talk)
Luis Alberto Rodríguez Palomino: The structure factor of liquid propanol studied by polarized neutron diffraction and RMC (talk)
Anthony E. Phillips: Phase transitions in molecule-containing crystals (talk)
Helen Playford: How long is long enough? (talk)
Ildikó Pethes: Chemical order in chalcogenide glasses (talk)
Szilvia Pothoczki: Intermolecular correlations in liquid acetonitrile (talk)
László Pusztai: Determining the structure of molecular liquids by combining molecular dynamics and RMC (talk)
Vicente Sanchez Gil: N-RMC method: Reverse Monte Carlo modeling in confined systems (talk)
Arkadiy Simonov: 3D-∆PDF + RMC: a microscopic model of orientational frustration in an organic single crystal (talk)
Alan Soper: Recent developments in EPSR (talk)
Nicola Steinke: Atomic level insights into urea induced protein unfolding (talk)
László Temleitner: H-bonded and non-H bonded liquids: removing the incoherent scattering of 1H polarized neutrons (talk)
Janis Timoshenko: Reverse Monte Carlo/evolutionary algorithm approach for the analysis of EXAFS data from distant coordination shells of crystalline materials (talk)
Rupert Tscheließnig: Interfacial forces of proteins and surfaces (talk)
Phillip Tucciarone: NTE, spaghetti dynamics, and hydration-driven volume collapse in ZrW2O8 (talk)
Matt Tucker: The new XPDF beam line at Diamond (talk)
Peter Thygesen: Small displacements, big effect: correlated orbital disorder drives spin-glass state in Y2Mo2O7 (talk)
Hans Weber: Atomic structure of liquid GeTe (poster)


Stability in humid conditions of potential SOFC electrodes investigated by high-temperature in situ neutron powder diffraction

Mona BAHOUT1, Stevin S. Pramana2, James M. Hanlon1, Vincent Dorcet1, Ron Smith3, Serge Paofai1 and Stephen J. Skinner2

1Institut des Sciences Chimiques de Rennes, UMR CNRS 6226, Université de Rennes 1, 263 Av. Général Leclerc, 35042 Rennes, France, 2Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom, 3The ISIS Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK.
Standard Solid Oxide fuel cells (SOFCs) based on an oxide ion conducting electrolyte require high operating temperatures, typically 800-1000 °C, which can affect the stability and durability of SOFC materials. Because of this, research is being directed towards reducing the operating temperature of SOFCs. A promising answer could be the use of a proton-conducting solid oxide fuel cells (H+-SOFC as these devices operate at lower temperatures of around 500-700 °C. The search for air electrode (cathode) materials with fast transfer kinetics is an important issue in developing H+-SOFCs. The air electrode plays a critical role in proton conducting fuel cells because the electrochemical reaction that combines protons (H+), electrons from the external circuit (which gives the electrical power) and oxygen (from the air) occurs here - producing water as the waste product.
Cobalt-based double perovskite oxides possess excellent electrochemical properties correlated with their mixed ionic and electronic conductivity and are being considered as potential cathodes in H+-SOFCs. Their fast oxygen transport kinetics and the high level of oxygen vacancies they can accommodate are needed to allow the dissociation of water gas molecules and the formation of protonic defects; however the presence of structural protons in these systems has not yet been demonstrated.
In situ neutron diffraction data collected on the high-flux POLARIS diffractometer at ISIS (RAL, UK) exploited the sensitivity of neutron diffraction to light atoms to determine atomic positions and site occupancies. The double perovskites NdBaCo2-xMnxO5+δ (x = 0 and 0.5) were investigated using high temperature neutron powder diffraction in dry argon and wet atmospheres [1]. This enabled us to search for the presence of protons, monitor the oxygen vacancy formation and assess the stability and structural behaviour of NdBaCo2-xMnxO5+δ under operating conditions consistent with cathodes in H+-SOFCs.
References:[1] M. Bahout, S. S. Pramana, J. M. Hanlon, V. Dorcet, R. I. Smith, S. Paofai and S. J. Skinner, Journal of Materials Chemistry A, 3 15420 (2015)
Back to the Top

A new approach to the determination of the uncertainty in neutron diffraction experiments with isotopic substitution method

Imre BAKÓ 1, Gábor Pálinkás , Tamás Grósz 2, Szabolcs Bálint 2, Gergely Tóth 3

1Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary 2 Institute of Institute of Materials and Environmental, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary 3 Eötvös Loránd University, Institute of Chemistry, H-1518 Budapest, Hungary
Corresponding author: Imre Bakó ,, 003614883891,

Keywords: neutron diffraction isotopic substitution, experimental uncertainty, systems of linear equations, estimation of uncertainty
Neutron diffraction experiment with isotopically substituted substances is a powerful approach claiming to yield unambiguous information about the local atomic structure in disordered materials. This information is expressed in the partial structure factors, and extracting them from a series of measurements requires solution of a set of linear equations that is affected by experimental errors. In this article, we suggest a method for the determination of the optimal set of H/D compositions with or without taking into account the experimental error. For the case of water, our investigations show that the selection of the isotope concentrations and the distribution of measurement time among the various samples have critical role if one wants to utilize the limited neutron beam time efficiently. It is well known that measurements of pure H2O introduce fairly large errors in the partial structure factors due to its very strong incoherent scattering. On water and methanol as examples, we investigated the propagation of random errors to the partial structure factors using partial pair-correlation functions from molecular dynamics simulation. We investigated the effect of incorrect normalisation and subtraction of multiple scattering contribution to the quality of partial structure functions. It is shown on the example of water that it is not worthwhile to measure pure H2O.
Back to the Top

Reverse Monte Carlo modeling of local atomic structure in binary Fe-and Co-based metallic glasses

R. BABILAS1, A. Burian2, L. Hawelek3 and L. Temleitner4

1Institute of Engineering Materials and Biomaterials, Silesian University of Technology, Gliwice, Poland; 2A. Chekowski Institute of Physics, University of Silesia, Katowice, Poland; 3Institute of Non-Ferrous Metals, Gliwice, Poland; 4Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Budapest, Hungary
The atomic scale structure of Fe80B20 and Co80B20 metallic glasses has been studied using the wide-angle X-ray scattering and reverse Monte Carlo (RMC) methods. The Fe80B20 and Co80B20 samples were prepared in the form of amorphous ribbons by the melt spinning technique under the argon protective atmosphere. The wide-angle X-ray scattering measurements were performed on the ID31 beam-line at the European Synchrotron Radiation Facility, Grenoble, France. The incident beam energy of 31 keV yielding the wavelength of 0.4 Å was used in this experiment. RMC simulation was carried out through fitting to the X-ray structure factors. A starting configuration of 8000 atoms with appropriate composition, randomly distributed in a cube box of length of 44 Å, was used. The initial configuration was obtained by a hard sphere simulation satisfying the above constraints. RMC uses a standard Metropolis Monte Carlo algorithm to move atoms within the simulation box. The Reverse Monte Carlo method applied for the Fe80B20 and Co80B20 metallic glasses allowed obtaining good fit to the experimental structure factors. The structural information obtained form RMC simulation was also utilized to calculate the coordination numbers enclosed in the first coordination shell. Resemblance of the local structure, which extends up to approximately 17 Å, to the icosahedral and trigonal prism configurations are discussed.
The work was supported by National Science Centre under research project no.: 2011/03/D/ST8/04138.
Back to the Top

Structure investigation of molecular liquids and liquid solutions by small angle neutron scattering


Institut Laue-Langevin, Grenoble, France
In this talk two studies of liquids structure determination investigated by neutron scattering techniques will be presented. In the first part of the talk the structure of deuterated liquid n-butanol (C4D10O) by neutron diffraction (ND) with isotopic substitution will be presented. The aim of this study is to explore the physical nature of the observed pre-peak in the structure factor. The experiment was conducted at ILL (Grenoble, France) using two neutron diffractometers: D16 to get a detailed structure factor in the low-Q range, and D4 for a high precision structure factor and proper normalization. In this way a total structure factor was determined covering an extended Q-range from 0.04 to 23.4 Å-1. For data interpretation in real space, a molecular dynamics simulation using the general all-atom ab initio force field Condensed-phase Optimized Molecular Potentials for Atomic Simulation Studies (COMPASS) was also carried out. Using this detailed information we are able to interpret the origin of the prepeak observed at 0.6 Å-1 as coming from the intermolecular ordering in the liquid, also in function of the temperature.
The second part of the talk will concern the investigation of changes in protein-protein interaction distances of a model protein/cryoprotectant system based on lysozyme/sorbitol/water liquid solution using small-angle neutron scattering at D22 instrument at ILL. Many protein drugs are either stored as frozen solutions, or converted into the solid state by freeze-drying, in order to improve the long-term stability. Aggregation is often observed after freeze-thaw or reconstitution of freeze-dried powder and the stability is no longer assured. These neutrons results demonstrate the utility of SANS methods to monitor the protein crowding at different stages of freezing and drying and the role of the carbohydrates in the protein aggregation.
The organization of the molecular structures in these liquids systems is not fully understood and a possible integration of RMC refinement in these data sets could be really helpful in data interpretation at the nanoscale range order.
Back to the Top

A Bayesian route to protein structure without crystals


The biggest problem with RMC for amorphous systems is that a pair distribution function (PDF) is not specific to the structure that generated it: many wrong models can replicate the correct PDF perfectly [1]. But it has been shown [2] that including only a little extra information suddenly makes some problems tractable. A C60 buckyball, for example, can be reproduced by fitting an atomic model to its PDF with the added clue from NMR that all carbon environments are equivalent. Turning our attention to a different nanostructure problem that of proteins in solution the same thinking suggests that with the right set of prior knowledge, a protein's native fold might be found using a PDF technique. Bayes formula gives us a way to inform a protein model space with a pre-existing idea of model likelihood. There are many appealing sources of this information from theory, experiment or databases; if all are exploited at once then we get a very clear idea of what our protein should look like before we even begin to match the PDF. We have created a Bayesian RMC that succeeds in reconstructing small protein folds from simulated PDFs by applying a conformation bias in the form of Ramachandran distributions. We also explore how using further information will allow larger protein structures to be determined from relatively cheap and easy experiments and in biologically relevant environments.
References: [1] Y. Jiao, F. H. Stillinger and S. Torquato, Phys. Rev. E, 81, 11105 (2010) [2] M. J. Cliffe, M. T. Dove, D. A. Drabold and A. L. Goodwin, Phys. Rev. Lett., 16, 2654 (2010)
Back to the Top

RMC and the Nanoscale

Nick FUNNELL, Qiang Wang, Matt Tucker, Leigh Connor, Dermot O’Hare, Max Fulford, Alex Ha and Andrew Goodwin

Manufacturing materials on the nanoscale often leads to enhanced material performance, however their lack of periodic, three-dimensional order precludes the use of conventional crystallographic techniques for characterisation. Although analysis of total scattering/PDF data is an ideal approach for studying nanostructure-showing sensitivity to the atom-atom correlations, in contrast to conventional Bragg data-it is still far from routine. This talk explores the extension of RMCProfile to enable structural refinement of nanomaterials, fitting atomistic models against real and reciprocal space data and exploiting the information content of both [1,2].
References: [1] M. Tucker, D. Keen, M. Dove, A. Goodwin and Q. Hui, J. Phys.: Condens. Matter, 2007, 19, 335218 [2] N. Funnell, Q. Wang, L. Connor, M. Tucker, D. O’Hare and A. Goodwin, Nanoscale, 2014, 6, 8032
Back to the Top

Characterization of the hydrogen-bonded network in ethanol-water mixtures


Systematic molecular dynamics studies of ethanol-water mixtures with 20-80 mol % ethanol content and of pure ethanol and water, using three different water models and the OPLS-AA ethanol force field for ethanol, have been performed. The systems displaying the best agreement with experimental total scattering X-ray structure factors were selected at each composition for further analyses. Morphological characterization of the hydrogen-bonded clusters reveals that 60-95% of their molecules are involved in ring formation. The average number of rings necessary to describe the ring structure in the main, percolating cluster is ~2200 for pure water for the investigated system size. Only 6% of this is found for 80 mol % ethanol content, which is increasing with decreasing ethanol concentration to 56% for the 20 mol % ethanol-water mixture. In the mixtures rings with 5 molecules, while in pure water, 6-membered rings occur with the highest probability. A few pure ethanol rings exist only above 60 mol % ethanol concentration, with the most popular ring size of 5 molecules. Pure water rings exist in the whole concentration range, with the most frequent ring size increasing from 4 to 5 molecules with increasing water concentration. Lacunarity analysis revealed that the placement of the one-component clusters at low concentration can be described by a multifractal distribution, especially in case of ethanol.
Back to the Top

Separation of thermal disorder from static displacements in RMC modeling

Ilkyoung JEONG

Research Center for Dielectrics and Advanced Matter Physics, Pusan National University, Busan 609-735, Korea (ROK);
Local atomic displacements and nano-scale ordering are important features of mixed-ion ferroelectric perovskite and play a key role in their macroscopic properties. For example, a formation of nano-scale polar regions in the average cubic lattice has been reported in a relaxor ferroelectric Pb(Mg1/3Nb2/3)O3 (PMN). For a structural modeling of these complex materials, reverse Monte Carlo (RMC) method is often adopted to handle both local and the average structural features simultaneously. In this talk, I will discuss how the separation of thermal disorder affects atomic structure from RMC modeling by using DISCUS [2] and RMCprofile [3] software.
References: [1] I.-K. Jeong et al., Physical Review Letters 94, 147602 (2005). [2] Matt Tucker, Stefan Norberg, Andrew Goodwin, Martin Dove, Toby White, Victor Krayzman, Igor Levin, [3] Th. Proffen and Reinhard Neder,
Back to the Top

The Atomic Structure of Pharmaceuticals in Solution: Penetrating the Blood-brain Barrier

Andrew J. JOHNSTON, Sebastian Busch, Richard J. Gillams, Sam Callear and Sylvia E.McLain

Although successful in protecting the brain from noxious agents, the blood-brain barrier (BBB) also significantly hinders the delivery of therapeutics to the brain. In fact, around 98% of small molecules are unable to cross the BBB. A first step in determining how certain molecules are able to cross this membrane is understanding their structure in the environment at the BBB. Using neutron diffraction with isotopic substitution and computational techniques, such as EPSR, complemented by NMR, microscopic structural information has been extracted from simulations of solutions of cocaine, clondine and alprazolam dissolved in water and water/methanol solutions. Interatomic and intraatomic distances, as well as atomic density distributions and orientational information, have allowed a comprehensive picture to be formed of the behaviour of these molecules in solution and allowed an understanding to be gained of how these molecules interact with hydrophobic and hydrophilic groups. For instance, these analytical tools have uncovered clear evidence of an intramolecular hydrogren bond between the amine hydrogen and the carbonyl oxygen. Such intramolecular bonding is able to confer the property of lipophilicity to a drug by shielding the hydrogen bond from the solvent, offering a possible partial explanation for the mechanism by which cocaine crosses the BBB.
Back to the Top

Microwave synthesis of LiFe1-xMnxPO4 nanostructures for use as positive insertion electrodes in Li-ion batteries

J. Vidal LAVEDA1, M. Tucker2, H. Playford2 and S. A. Corr1

1School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom; 2ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
Nowadays, Li-ion batteries play a key role in the growing demand of portable electronics and hybrid electric vehicles (HEVs).[1] Amongst new positive insertion electrodes, olivine-structured lithium transition metal phosphates such as LiFePO4 have been recognized as a low cost, non-toxic and safe alternative exhibiting thermal stability, high specific charge capacity and good cyclability. However, the higher energy density exhibited by LiMnPO4 compared to its Fe analogue due to the higher Mn2+/3+ redox potentials compared to the Fe2+/3+ pair, has produced a growing interest on the mixed-metal phosphates LiFe1-xMnxPO4.[2, 3] Especially, nanostructured materials are of particular interest due to the potential improvements in the electrochemical performance obtained by shrinking the particle size, as smaller sizes allow shorter path lengths for the Li+ to diffuse while the increased surface areas improve the electron-electrolyte interactions.[4,5]
Here, we present two microwave-assisted synthetic approaches for the preparation of LiFe1-xMnxPO4 nanoparticles, one using commercial starting materials and other employing a new class of heterometallic alkoxide precursors. Co-location of two transition metals in these metalorganic precursors is believed to bypass the need of diffusional mixing and allow the reactions to proceed faster and at lower temperatures generating highly crystalline materials. To fully characterize and have a better understanding of the structure-property relationship of these nanocrystalline phases, we show neutron pair distribution function (PDF) analyses of these materials, which allow elucidation of the local structure, cation distribution, presence of defects and Li content. Future work involves modeling this neutron PDF data using the Reverse Monte Carlo method. Finally, we also include cycling studies in an effort to probe the relationship between the synthetic route, composition and electrochemical performance.

Figure 1. Neutron PDF fits at room temperature of LiFe1-xMnxPO4 (x=0, 0.25, 0.5, 0.75 and 1) nanostructures prepared from commercial starting materials.
References: [1] Tarascon, Armand, Nature, 2001, 414, 359. [2] Kang, Ceder, Nature, 2009, 458, 190 [3] Aravindan, Gnanaraj, Lee, Madhavi, J. Mater. Chem. A, 2013, 1, 3518. [4] Manthiram, Murugan, Sarkar, Muraliganth, Energy Environ. Sci., 2008, 1, 621. [5] Ashton, Vidal Laveda, MacLaren, Baker, Porch, Jones, Corr, J. Mater. Chem. A, 2014, 2, 623
Back to the Top

Understanding how different synthetic procedures influence the short, medium and long range atomic arrangement in ceria


A majority of nano-metal catalysts are comprised of small particles on supports that have a high surface area, such as alumina [1], ceria etc. These high surface area supports for the catalysts ensure that there is an efficient use of the metal particles due to most catalytic reactions only occurs on the surface of the metal particles. The size of the metal catalyst particles and structure of the support can have an effect on the catalytic properties [2] of the respective metal particles. In particular, the support oxide may interact with the metal particles in various ways. In some cases it is believed that defect structures present in the support allow convenient migration of ligands thereby facilitating not only metal-support interactions but also catalytic functionality. To understand how the nanostructure of these defects are distributed [3] or created within the structure of the oxide support, it is important to use a suite of techniques e.g. Pair distribution function (PDF), XAFS, x-ray or neutron diffraction, to gain as much information. In particular it would be beneficial in seeing the type of defect sites present in the oxides which may contribute to the catalytic properties of the materials and if different synthetic procedures create different defect structures.
The use of both in-situ x-ray and neutron PDF techniques have been successfully used to characterise both lanthanum-doped ceria [4] allowing greater understanding of local deviations from the average structure. Similarly the use of neutron PDF techniques have been used to investigate the effect of temperature treatment of ceria based materials [5].
Ex-situ XAFS, x-ray and neutron total scattering techniques have been used to investigate the ceria in order to show how the crystalline structure varies from the short through to long range e.g. different syntheses and how these influence the defect chemistry, different techniques and their respective view of the materials. These materials were studied further by the use of RMCProfile [6] in order to combine all these methodologies to gain a thorough understanding of the crystal structure under reaction conditions.
References: [1] T. Bunluesin, R.J. Gorte and G.W. Graham, Appl. Catal., B, 1998, 15, 107-114 [2] C. Tyrsted, K.M. Ørnsberg Jensen, E. D. Bøjesen, N. Lock, M. Christensen, S. J. L. Billange and B. B. Iversen, Angew. Chem. Int. Ed., 2012, 51, 9030-9033 [3] P. Li, I.W. Chen, J. E. Penner-Hahn, and T.Y. Tien, J. Am. Ceram. Soc., 1991,74, 958–967. [4] M. Coduri, M. Scavini, M. Brunellic, and P. Masalaa, Phys.Chem.Chem.Phys.,2013, 15, 8495. [5] E. Mamontov and T. Egami, J. Phys Chem. Solids, 2000, 61, 1345-1356. [6] M.G. Tucker, D.A. Keen, M.T. Dove, A.L. Goodwin, and Q. Hui, J. Phys. Condens. Matter, 2007, 19, 335218.
Back to the Top

Probing biomolecular structure in aqueous solution: Insights from neutron diffraction and computation

Sylvia E. MCLAIN, Andrew J. Johnston, Nicola Steinke, Sebastian Busch, Luis Carlos Pardo, Christian D. Lorenz and Richard J. Gillams

Many natural life-giving chemical reactions take place in the liquid state or in the presence of some water. As humans, around 60% of our body weight is from water and the solutions in our bodies help to deliver oxygen and nutrients to our cells. Even though water is the medium of life, atomic scale details of water's role in these natural processes is still very poorly understood. Neutron diffraction with isotopic substitution is a key technique in understanding biomolecular structure in solution, given the relative intensity of hydrogen in a diffraction pattern when using neutrons as a probe. Using this technique in conjunction with NMR and computation (both EPSR and MD), yields details of how nature functions on an microscopic scale in solution, has provided valuble insights into the role that water plays in biology.
Back to the Top

Structural study of sulfide-based crystalline/glassy superionic conductors by RMC modeling


Sulfide-based glassy and crystalline materials with a high ionic conductivity have attracted much attention as one of promising candidates of solid electrolyte in all-solid-state batteries. Recently, it was found that Li-P-S and Na-P-S glass-ceramic obtained by annealing glassy materials show high ionic conductivities at room temperature (RT) [1,2]. Additionally, it was reported that Li10GeP2S12 crystal has the highest lithium conductivity in the order of 10-2 Scm-1 at RT [3]. In this study, I will report results of structural analysis of these crystalline/glassy superioic conductors by reverse Monte Carlo (RMC) modeling based on neutron/X-ray data and discuss a relationship between atomic structures and ionic conductivities.
References: [1] F. Mizuno, A. Hayashi, K. Tadanaga, M. Tatsumisago, Adv. Mater. 17 (2005) 918. [2] A. Hayashi, K. Noi, A. Sakuda, M. Tatsumisago, Nature communications 3 (2012) 856. [3] N. Kamaya, R. Kanno et al., Nature Materials 10 (2011) 684.
Back to the Top

The structure factor of liquid propanol studied by polarized neutron diffraction and RMC

L. A. Rodríguez PALOMINO1,2, G. J. Cuello1, A. Stunault1, J. Dawidowski2, L. Temleitner3

1Institut Laue Langevin, 71 Av. des Martyrs, PO Box 20156, F-38042, Grenoble, France; 2Centro Atómico Bariloche, CNEA-CONICET, Av. Bustillo 9500, R8402AGP Bariloche, Argentina; 3 Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly Thege út 29-33, H-1121 Budapest, Hungary
We present the experimental structure factor of liquid 1- and 2-propanol measured in the Polarized Hot Neutron Beam Facility (D3) at the Institut Laue Langevin (ILL, France). This neutron technique has the advantage of experimentally separating the coherent and incoherent scattering intensities. Using a linear combination of the non-spin-flip and spin-flip diffractograms, one can determine the coherent intensity, related with the coherent structure factor. We present a new procedure to perform the experimental correction using a hybrid Monte Carlo simulation code development for this kind of experiments. With this code, we evaluate the corrections by multiple scattering, attenuation and inelasticity (produced by the sample and the sample cell) as a whole and not as independent corrections, as it is usually done in the standard methods employed in neutron diffraction experiments. This hybrid simulation code is based on the combination of a modeled energy exchange and the experimental angular distribution, which are employed as input in the simulations. The good agreement observed between our simulation and the experimental results, confirm the goodness of this model. We performed RMC simulations using our corrected experimental structure factor. In doing this, we convoluted the ideal structure factor obtained from the RMC with the instrumental resolution in Q-space. We obtain a very good agreement between the simulated and experimental structure factor, which allows us to study the intermolecular structure in the simulation box.
Back to the Top

Chemical order in chalcogenide glasses


Ge-As-Se and Ge-Sb-Se glasses were studied by using the Reverse Monte Carlo method. Neutron and X-ray diffraction and extended x-ray fine structure (EXAFS) data sets were fitted simultaneously. It was found that the structure of the Ge-As-Se glasses does not show chemical order. These glasses behave as random covalent networks of the participant elements: Se-Se bonds can be found in Se-poor glasses and Ge-Ge, Ge-As or As-As bonds remain in Se-rich glasses. The structure of the Ge-Sb-Se glasses however can be described by the chemical ordered network model: Ge-Se and Sb-Se bonds are preferred. In Se-poor compositions Se-Se bonds can be avoided, in strongly Se-rich glasses metal-metal bonds are not needed. Some violation of the chemical order was observed in nearly stoichiometric compositions. The results were compared to amorphous tellurides (Ge-As-Te and Ge-Sb-Te systems) as well.
Back to the Top

Intermolecular correlations in liquid acetonitrile

Szilvia POTHOCZKI, László Pusztai

Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Budapest, Hungary
New structural studies of liquid acetonitrile (CH3CN) were motivated by an unexpected finding concerning liquid carbon tetrachloride: the presence of long range orientational correlations [1,2]. Based on the fact that these correlations appear already in some of the simplest molecular liquids, it may be expected that in more sophisticated systems even greater surprises would show up. Molecular Dynamics simulations have been performed. The partial radial distribution functions resulting from MD simulations together with the total scattering structure factors coming from neutron and X-ray diffraction have been interpreted by means of the Reverse Monte Carlo (RMC) simulation, thus providing sets of particle coordinates which were consistent with these ‘experimental’ data within their errors. From these particle configurations, partial radial distribution functions, as well as correlation functions characterizing mutual orientations of molecules as a function of distance between molecular centres have been calculated.
The following findings emerged from the present study: (1) Molecular Dynamics simulation is necessary to estimate the intermolecular correlations; (2) dipole-dipole correlations beyond the first coordination shell (where the molecules form typically antiparallel arrangements) show particular tendencies; (3) characteristics of partial radial distribution functions and distance-dependent orientational correlation functions exhibit well-recognizable structural features far beyond the first coordination shell.
References: [1] Sz. Pothoczki, L. Temleitner, P. Jóvári, S. Kohara, L. Pusztai, J. Chem. Phys. 130, 064503 (2009) [2] R. Rey, J. Chem. Phys. 126, 164506 (2007)
Back to the Top

Determining the structure of molecular liquids by combining molecular dynamics and RMC

O. Gereben1, I. Harsányi2, V. Mile2, A. Vrhovsek3, Sz. Pothoczki1, L. PUSZTAI1

1Wigner Research Centre for Physics, Hungarian Academy of Sciences, Budapest, Hungary; 2Centre for Energy Research, Hungarian Academy of Sciences, Budapest, Hungary;3 ‘Open Potato Fields’ Farming Centre of Malo Mrasevo, Slovenia The problem of information deficiency, i.e., when the number of available diffraction (and/or EXAFS) experiments is (in many cases, much) lower than the number of partial radial distribution function in the system, is considered, with a focus on molecular liquids. Two approaches, both relying heavily on Reverse Monte Carlo (RMC) modeling [1] are sketched: (1) molecular dynamics simulation, followed by RMC modeling (‘RMCMD’), and (2) RMC modeling that incorporates the extensive use of interatomic potential functions (‘RMC_POT’). We show that applying either method is useful, although the ‘RMCMD’ scheme appears to be more restricted to smaller molecules (unless the ’RMC_POT’ software, with potentials, is applied for the RMC modeling part). With larger molecules, the molecular structure begins to dominate the measurable total scattering structure factor and therefore, Reverse Monte Carlo is expected to play a more and more important role in conformational analyses in the liquid state (see, e.g., [2]). It will also be demonstrated that RMC may be a most effective way of assessing the performance of interatomic potential parameters used in classical MD simulations [3].
References [1] R.L. McGreevy, L. Pusztai, Molecular Simulation 1 359 (1988); [2] O. Gereben, L. Pusztai, J. Comput. Chem. 33 2285 (2012); [3] V. Mile, L. Pusztai, H. Dominguez, O. Pizio, J. Phys. Chem B 113 10760 (2009)
Back to the Top

Reverse Monte Carlo/evolutionary algorithm approach for the analysis of EXAFS data from distant coordination shells of crystalline materials

Janis TIMOSHENKO*, Andris Anspoks, Alexandr Kalinko, Alexei Kuzmin

Institute of Solid State Physics, University of Latvia, Riga, Latvia; *
Extended X-ray absorption fine structure (EXAFS) spectroscopy is a modern element-specific method to study the local structure of a broad class of materials [1]. The analysis of EXAFS data from the first coordination shell around the absorbing atom to obtain distributions of distances to the nearest neighbours is a well-established technique. At the same time, the experimental EXAFS data, acquired at modern X-ray sources, contain much more information, especially for crystalline materials. In this case the total EXAFS consists of contributions from significantly more distant coordination shells (up to 10 Å and further). The precise analysis of EXAFS spectra beyond the first coordination shell using conventional methods is, however, often impossible since the total number parameters, required to completely describe the local structure, is exponentially increasing with the increase of the number of coordination shells, included in the analysis [2]. This problem may be treated by reverse Monte Carlo (RMC) method [3,4]. The existing RMC implementations for EXAFS analysis, nevertheless, are rather limited due to significant computational costs of ab-initio EXAFS simulations for large atomic clusters. Therefore, in the presented study we propose another approach for the advanced analysis of EXAFS data, where we complement the conventional RMC scheme with a powerful evolutionary algorithm for a very efficient structure model optimization [5]. In this study the potentiality of the method is demonstrated on the example of temperature-dependent EXAFS study of the local structure of copper nitride.
References: [1] Rehr J J and Albers R C 2000 Rev. Mod. Phys. 72 621 [2] Provost K, Beret E, Muller D, Marcos E S and Michalowicz A 2013 J. Phys.: Conf. Ser. 430 012015 [3] McGreevy R and Pusztai L 1988 Mol. Simul. 1 359 [4] Timoshenko J, Kuzmin A and Purans J 2012 Comput. Phys. Commun. 183 1237 [5] Timoshenko J, Kuzmin A and Purans J 2014 J. Phys.: Condens. Matter 26 055401
Back to the Top

Hydration-driven Volume Collapse in ZrW2O8: Microscopic Mechanism and Relation to Negative Thermal Expansion


The molar volume of ZrW2O8 H2O is reported to be ~10% smaller than anhydrous ZrW2O8. Here, we characterize the mechanism of this 'inverse sponge' behavior by ab initio calculations and subsequent mapping onto structural flexibility models. The hydration proceeds via a concerted formation of one-dimensional strings by non-unique choices of new W-O bonds; the same local changes in coordination can be propagated with a diverging number of different periodicities. This new connectivity contracts the unit cell via large shifts in the metal atom positions, and the superposition of all possible states gives an average structure with apparent Pa3 symmetry. By projecting this behavior onto the phonon modes, we compare those modes responsible for both negative thermal expansion (NTE) and the hydration-driven collapse.
Back to the Top

N-RMC method: Reverse Monte Carlo modeling in confined systems


N-RMC [1] method is a simple extension of the Reverse Monte Carlo [2] (RMC) method that enables the determination of the microscopic structure of fluids under confinement from Neutron or X-ray scattering measurements. The proposed method overcomes limitations induced by confinement in systems such as fluids adsorbed in microporous materials. N-RMC has been successfully tested in two zeolites with significantly different pore sizes and yields an adsorbate microscopic structure in good agreement with that of the model system even to the level of three body correlations, when these are induced by the confining media. Recently, this new approach has been applied to determine the structure of adsorbed Argon in ZSM-11 zeolite using both TOF neutron diffraction experimental data and volumetric adsorption experiments as input for the N-RMC.
References: [1] V. Sánchez-Gil, E. G. Noya and E. Lomba, J. Chem. Phys. 140, 024504 (2014) [2] R. L. McGreevy and L. Pusztai, Molec. Simul. 1, 359-367 (1988)
Back to the Top

Atomic level insights into urea induced protein unfolding

Nicola STEINKE, Christina Redfield, Christian D. Lorenz and Sylvia E. McLain

How do proteins fold and unfold in solution on the atomic scale? Although proteins in nature fold in the presence of water, very little is known about the contributions that water makes to these processes on the atomic scale. Similarly, urea is known to denature proteins in aqueous solutions, yet how urea interacts with proteins in order to affect this change is still the subject of debate.
Previous work on model peptides suggests that water and hydrogen bonding interactions may have a more direct role in mediating protein folding interactions than has been previously thought. In order to probe urea's specific role in protein denaturation a model peptide, glycyl-prolyl-glycineamide(GPG), which contains a sequence which occurs in protein turns in vivo, was characterized in aqueous urea solution using neutron diffraction in combination with computational techniques. From this study, site-specific interactions between water and urea and peptide side chains can be determined. Our results indicate a direct urea-peptide bonding. Urea often replaces hydrating water around the peptide backbone.
Back to the Top