ORCID Profile
0000-0002-4192-6577
Current Organisations
University of Tsukuba
,
National University of Science and Technology
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Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3TA90280C
Publisher: International Union of Crystallography (IUCr)
Date: 16-04-2021
DOI: 10.1107/S1600576721001126
Abstract: Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide L-alanyl-glycyl-L-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.
Publisher: American Chemical Society (ACS)
Date: 14-02-2019
DOI: 10.1021/JACS.8B12927
Abstract: High-resolution synchrotron and neutron single-crystal diffraction data of 18-crown-6/(pentakis)urea measured at 30 K are combined, with the aim of better appreciating the electrostatics associated with intermolecular interactions in condensed matter. With two 18-crown-6 molecules and five different urea molecules in the crystal, this represents the most ambitious combined X-ray/synchrotron and neutron experimental charge density analysis to date on a cocrystal or host-guest system incorporating such a large number of unique molecules. The dipole moments of the five urea guest molecules in the crystal are enhanced considerably compared to values determined for isolated molecules, and 2D maps of the electrostatic potential and electric field show clearly how the urea molecules are oriented with dipole moments aligned along the electric field exerted by their molecular neighbors. Experimental electric fields in the range of 10-19 GV m
Publisher: AIP Publishing
Date: 02-09-2004
DOI: 10.1063/1.1781762
Abstract: We present neutron and synchrotron powder-diffraction investigations as well as ab initio calculations to elucidate delicate structural features in doped skutterudites. S les with assumed Fe doping were investigated (FeyCo4Sb12, y=0.4, 0.8, 1.0, and 1.6), as well as s les with formal Ni substitution (Co4−xNixSb12, x=0, 0.4, 0.8, and 1.2). The present study serves as a case story for the determination of fine structural details of thermoelectric skutterudites by diffraction methods in combination with ab initio calculations. We illustrate the problem of fluorescence in the conventional x-ray powder diffraction on the Fe-doped s les by a comparison with the neutron powder-diffraction data. On the series of the Ni-substituted s les, the neutron powder-diffraction data were collected to investigate the exact sitting of the Ni. The s le with the highest Ni substitution (Co2.8Ni1.2Sb12) was also used for high resolution, high-energy synchrotron powder diffraction measurements. These revealed that the s le consists of two skutterudite phases. A complete description of the Ni-substituted s les was obtained in tandem with ab initio calculations, which show that the system contains a Ni-rich (Co0.38Ni3.62Sb12) and a Ni-poor (Co3.76Ni0.24Sb12)) skutterudite phases.
Publisher: Royal Society of Chemistry (RSC)
Date: 2010
DOI: 10.1039/C0DT00742K
Abstract: Phase pure s les of the half-Heusler material TiCoSb were synthesised and investigated. Multi-temperature synchrotron powder X-ray diffraction (PXRD) data measured between 90 and 1000 K in atmospheric air confirm the phase purity, but they also reveal a decomposition reaction starting at around 750 K. This affects the high temperature properties since TiCoSb is semiconducting, whereas CoSb is metallic. Between 90 K and 300 K the linear thermal expansion coefficient is estimated to be 10.5 × 10(-6) K(-1), while it is 8.49 10(-6) K(-1) between 550 K and 1000 K. A fit of a Debye model to the Atomic Displacement Parameters obtained from Rietveld refinement of the PXRD data gives a Debye temperature of 395(4) K. The heat capacity was measured between 2 K and 300 K and a Debye temperature of 375(5) K was obtained from modelling of the data. Coming from low temperatures the electrical resistivity shows a metallic to semiconducting transition at 113 K. A relatively high Seebeck coefficient of ∼-250 μV K(-1) was found at 400 K, but the substantial thermal conductivity (∼10 W mK(-1) at 400 K) leads to a moderate thermoelectric figure of merit of 0.025 at 400 K.
Publisher: MDPI AG
Date: 13-05-2022
DOI: 10.3390/SU14105927
Abstract: In this paper, we propose an agent-based approach for the evaluation of Multiple Unmanned Autonomous Vehicle (MUAV) wildfire monitoring systems for remote and hard-to-reach areas. Emerging environmental factors are causing a higher number of wildfires and keeping these fires in check is becoming a global challenge. MUAV deployment for the monitoring and surveillance of potential fires has already been established. However, most of the scholarly work is still focused on MUAV operations details. In wildfire surveillance and monitoring, evaluations of the system-level performance in terms of the analysis of the effects of in idual behavior on system surveillance has yet to be established. Especially in an MUAV system, the in idual and cooperative behaviors of the team affect the overall performance of the system. Such systems are dynamic and stochastic because of an ever-changing environment. Quantifying the emergent system behavior and general performance measures of such a system by analytical methods is challenging. In our work, we present an agent-based model for MUAV surveillance missions. This paper focuses on the overall system performance of cooperative UAVs performing forest fire surveillance. The principal theme is to present the effects of three behaviors on overall performance: (1) the area allocation and (2) dynamic coverage, and (3) the effects of forest density on team allocation. For area allocation, three behaviors are simulated: (1) randomized, (2) two-layer barrier sweep coverage, and (3) full sweep coverage. For dynamic coverage, the effects of communication and resource unavailability during the mission are studied by analyzing the agent’s downtime spent on refueling. Last, an extensive simulation is carried out on wildfire models with varying forest density. It is found that cooperative complete sweep coverage strategies perform better than the rest and the performance of the team is greatly affected by the forest density.
Publisher: Springer Science and Business Media LLC
Date: 30-12-2009
Publisher: Wiley
Date: 14-02-2023
Abstract: Loosely bonded (“rattling”) atoms with s 2 lone pair electrons are usually associated with strong anharmonicity and unexpectedly low thermal conductivity, yet their detailed correlation remains largely unknown. Here we resolve this correlation in thermoelectric InTe by combining chemical bonding analysis, inelastic X‐ray and neutron scattering, and first principles phonon calculations. We successfully probe soft low‐lying transverse phonons dominated by large In 1+ z‐ axis motions, and their giant anharmonicity. We show that the highly anharmonic phonons arise from the dynamic lone pair expression with unstable occupied antibonding states induced by the covalency between delocalized In 1+ 5 s 2 lone pair electrons and Te 5 p states. This work pinpoints the microscopic origin of strong anharmonicity driven by rattling atoms with stereochemical lone pair activity, important for designing efficient materials for thermoelectric energy conversion.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0CE00378F
Abstract: Hydrogen atom positions can be obtained accurately from X-ray diffraction data of hydrogen maleate salts via Hirshfeld atom refinement.
Publisher: American Physical Society (APS)
Date: 24-08-2011
Publisher: American Physical Society (APS)
Date: 28-08-2007
Publisher: Wiley
Date: 20-08-2004
Abstract: The experimental electron density of the high-performance thermoelectric material Zn4Sb3 has been determined by maximum entropy (MEM) analysis of short-wavelength synchrotron powder diffraction data. These data are found to be more accurate than conventional single-crystal data due to the reduction of common systematic errors, such as absorption, extinction and anomalous scattering. Analysis of the MEM electron density directly reveals interstitial Zn atoms and a partially occupied main Zn site. Two types of Sb atoms are observed: a free spherical ion (Sb3-) and Sb2(4-) dimers. Analysis of the MEM electron density also reveals possible Sb disorder along the c axis. The disorder, defects and vacancies are all features that contribute to the drastic reduction of the thermal conductivity of the material. Topological analysis of the thermally smeared MEM density has been carried out. Starting with the X-ray structure ab initio computational methods have been used to deconvolute structural information from the space-time data averaging inherent to the XRD experiment. The analysis reveals how interstitial Zn atoms and vacancies affect the electronic structure and transport properties of beta-Zn4Sb3. The structure consists of an ideal A12Sb10 framework in which point defects are distributed. We propose that the material is a 0.184:0.420:0.396 mixture of A12Sb10, A11BCSb10 and A10BCDSb10 cells, in which A, B, C and D are the four Zn sites in the X-ray structure. Given the similar density of states (DOS) of the A12Sb10, A11BCSb10 and A10BCDSb10 cells, one may electronically model the defective stoichiometry of the real system either by n-doping the 12-Zn atom cell or by p-doping the two 13-Zn atom cells. This leads to similar calculated Seebeck coefficients for the A12Sb10, A11BCSb10 and A10BCDSb10 cells (115.0, 123.0 and 110.3 microV K(-1) at T=670 K). The model system is therefore a p-doped semiconductor as found experimentally. The effect is dramatic if these cells are doped differently with respect to the experimental electron count. Thus, 0.33 extra electrons supplied to either kind of cell would increase the Seebeck coefficient to about 260 microV K(-1). Additional electrons would also lower sigma, so the resulting effect on the thermoelectric figure of merit of Zn4Sb3 challenges further experimental work.
Publisher: International Union of Crystallography (IUCr)
Date: 19-05-2010
Publisher: Wiley
Date: 14-01-2021
Abstract: The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low‐molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non‐negligible consequences for derived properties.
Publisher: American Chemical Society (ACS)
Date: 28-07-2011
DOI: 10.1021/CM201330X
Publisher: International Union of Crystallography (IUCr)
Date: 17-10-2013
DOI: 10.1107/S0108767313024458
Abstract: CoSb 3 is an ex le of a highly challenging case for experimental charge-density analysis due to the heavy elements (suitability factor of ∼0.01), the perfect crystallinity and the high symmetry of the compound. It is part of a family of host–guest structures that are potential candidates for use as high-performance thermoelectric materials. Obtaining and analysing accurate charge densities of the undoped host structure potentially can improve the understanding of the thermoelectric properties of this family of materials. In a previous study, analysis of the electron density gave a picture of covalent Co–Sb and Sb–Sb interactions together with relatively low atomic charges based on state-of-the-art experimental and theoretical data. In the current study, several experimental X-ray diffraction data sets collected on the empty CoSb 3 framework are compared in order to probe the experimental requirements for obtaining data of high enough quality for charge-density analysis even in the case of very unsuitable crystals. Furthermore, the quality of the experimental structure factors is tested by comparison with theoretical structure factors obtained from periodic DFT calculations. The results clearly show that, in the current study, the data collected on high-intensity, high-energy synchrotron sources and very small crystals are superior to data collected at conventional sources, and in fact necessary for a meaningful charge-density study, primarily due to greatly diminished effects of extinction and absorption which are difficult to correct for with sufficient accuracy.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0DT02795B
Abstract: A range of experimental techniques is used to quantify how disorder varies with synthesis conditions in spinel ZnAl 2 O 4 .
Publisher: American Chemical Society (ACS)
Date: 16-11-2007
DOI: 10.1021/CM702247B
Publisher: Springer Science and Business Media LLC
Date: 18-11-2021
DOI: 10.1038/S41467-021-27007-Y
Abstract: Structural disorder, highly effective in reducing thermal conductivity, is important in technological applications such as thermal barrier coatings and thermoelectrics. In particular, interstitial, disordered, diffusive atoms are common in complex crystal structures with ultralow thermal conductivity, but are rarely found in simple crystalline solids. Combining single-crystal synchrotron X-ray diffraction, the maximum entropy method, diffuse scattering, and theoretical calculations, here we report the direct observation of one-dimensional disordered In 1+ chains in a simple chain-like thermoelectric InTe, which contains a significant In 1+ vacancy along with interstitial indium sites. Intriguingly, the disordered In 1+ chains undergo a static-dynamic transition with increasing temperature to form a one-dimensional diffusion channel, which is attributed to a low In 1+ -ion migration energy barrier along the c direction, a general feature in many other TlSe-type compounds. Our work provides a basis towards understanding ultralow thermal conductivity with weak temperature dependence in TlSe-type chain-like materials.
Publisher: American Chemical Society (ACS)
Date: 22-03-2022
Abstract: Static structure factors and charge density for metallic aluminum were investigated by periodic calculations using atom-centered Gaussian-type basis sets with the Perdew-Burke-Ernzerhof (PBE) functional implemented in the CRYSTAL14 package and X-ray constrained wave function (XCW) fitting. The effects of additional diffuse d and f basis functions on structure factors were compared with synchrotron powder X-ray diffraction and quantitative convergent electron beam diffraction data. Changes in structure factors from an independent atom model at 022, 113, and 222 reflections introduced d and f basis functions similar to those of the experimental data. The XCW fitting was applied to different sizes of aluminum clusters. The charge density features for a 50-atom cluster clearly demonstrated electron accumulation at tetrahedral sites and electron depletion at octahedral sites. The resolution dependence of the XCW study suggests that structure factors of the five lowest resolution reflections with 0.1% accuracy were indispensable for determining the detailed bonding description in the case of metallic aluminum.
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2DT30278K
Abstract: High resolution single crystal synchrotron X-ray diffraction data measured at 15(2) K were used to solve the structure of the complex intermetallic Zintl phase, Yb(11)AlSb(9) (space group Iba2), made up of Yb cations and polyanions along with isolated Sb anions. The 15(2) K cell parameters are a = 11.7383(4) Å, b = 12.3600(4) Å, c = 16.6796(6) Å. The temperature dependence of the structure was investigated through high resolution synchrotron powder X-ray diffraction (PXRD) data measured from 90 K to 1000 K. Rietveld refinements of the crystal structure revealed near linear thermal expansion of Yb(11)AlSb(9) with expansion coefficients of 1.49(2) × 10(-5) K(-1), 1.71(3) × 10(-5) K(-1), 1.13(1) × 10(-5) K(-1) for a, b and c, respectively. The chemical bonding in Yb(11)AlSb(9) was analyzed using atomic Hirshfeld surfaces, and the analysis supports the presence of the structural elements of Yb cations, [AlSb(4)](9-) tetrahedra, [Sb(2)](4-) dimers and isolated Sb(3-) anions. However, indications of interatomic interactions between the Zintl anions and the Yb cations were also observed.
Publisher: American Chemical Society (ACS)
Date: 30-05-2017
Publisher: International Union of Crystallography (IUCr)
Date: 2023
DOI: 10.1107/S2052252522011782
Abstract: Serial femtosecond crystallography for small-unit-cell systems has so far seen very limited application despite obvious scientific possibilities. This is because reliable data reduction has not been available for these challenging systems. In particular, important intensity corrections such as the partiality correction critically rely on accurate determination of the crystal orientation, which is complicated by the low number of diffraction spots for small-unit-cell crystals. A data reduction pipeline capable of fully automated handling of all steps of data reduction from spot harvesting to merged structure factors has been developed. The pipeline utilizes sparse indexing based on known unit-cell parameters, seed-skewness integration, intensity corrections including an overlap-based combined Ewald sphere width and partiality correction, and a dynamically adjusted post-refinement routine. Using the pipeline, data measured on the compound K 4 [Pt 2 (P 2 O 5 H 2 ) 4 ]·2H 2 O have been successfully reduced and used to solve the structure to an R 1 factor of ∼9.1%. It is expected that the pipeline will open up the field of small-unit-cell serial femtosecond crystallography experiments and allow investigations into, for ex le, excited states and reaction intermediate chemistry.
Publisher: International Union of Crystallography (IUCr)
Date: 30-08-2014
DOI: 10.1107/S2053273314012443
Abstract: High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first ex les of Z ′ 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O—H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body ( SHADE ) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.
Publisher: Springer Science and Business Media LLC
Date: 12-02-2018
DOI: 10.1038/S41563-017-0012-2
Abstract: Van der Waals (vdW) solids have attracted great attention ever since the discovery of graphene, with the essential feature being the weak chemical bonding across the vdW gap. The nature of these weak interactions is decisive for many extraordinary properties, but it is a strong challenge for current theory to accurately model long-range electron correlations. Here we use synchrotron X-ray diffraction data to precisely determine the electron density in the archetypal vdW solid, TiS
Publisher: Wiley
Date: 06-10-2023
Publisher: Springer Science and Business Media LLC
Date: 27-06-2004
DOI: 10.1038/NMAT1154
Publisher: Wiley
Date: 14-02-2023
Abstract: Loosely bonded (“rattling”) atoms with s 2 lone pair electrons are usually associated with strong anharmonicity and unexpectedly low thermal conductivity, yet their detailed correlation remains largely unknown. Here we resolve this correlation in thermoelectric InTe by combining chemical bonding analysis, inelastic X‐ray and neutron scattering, and first principles phonon calculations. We successfully probe soft low‐lying transverse phonons dominated by large In 1+ z‐ axis motions, and their giant anharmonicity. We show that the highly anharmonic phonons arise from the dynamic lone pair expression with unstable occupied antibonding states induced by the covalency between delocalized In 1+ 5 s 2 lone pair electrons and Te 5 p states. This work pinpoints the microscopic origin of strong anharmonicity driven by rattling atoms with stereochemical lone pair activity, important for designing efficient materials for thermoelectric energy conversion.
Publisher: American Physical Society (APS)
Date: 13-04-2005
Publisher: Springer Science and Business Media LLC
Date: 2006
DOI: 10.1557/PROC-0945-FF07-05
Abstract: The stability of high performance thermoelectric Zn 4 Sb 3 has been studied, by using synchrotron powder diffraction to establish differences in phase transition temperatures of two s les. High resolution multi temperature diffraction data has been collected, with a time interval of 13 months, and the phase transition temperature was determined based on the results of Rietveld refinements. The refinements show a difference in transition temperature from data collected the first time till data collected the second time. Furthermore the s les showed impurity peaks after being exposed to air for 13 months, indicating that the s le decomposes over time.
Publisher: American Chemical Society (ACS)
Date: 22-05-2019
Publisher: American Chemical Society (ACS)
Date: 20-01-2012
DOI: 10.1021/IC202231K
Abstract: The Mn atom in the cubic polymorph of CeMnNi(4) appears to be located in an oversized cage-like structure, and anomalously large atomic displacement parameters (ADPs) for the Mn atom indicate that it is a potential "rattler" atom. Here, multitemperature synchrotron powder X-ray diffraction data measured between 110 and 900 K are used to estimate ADPs for the Mn "guest" atom and the "host" structure atoms in cubic CeMnNi(4). The ADPs are subsequently fitted with Debye and Einstein models, giving Θ(D) = 301(2) K for the "host" structure and Θ(E) = 165(2) K for the Mn atom. This is higher than typical Einstein temperatures for rattlers in thermoelectric skutterudites and clathrates (Θ(E) = 50-80 K), indicating that the Mn atom in cubic CeMnNi(4) is more strongly bonded. In order to probe the chemical interactions of the potential Mn rattler atom, atomic Hirshfeld surface (AHS) analysis is carried out and compared with AHS analysis of well-established guest atom rattlers in archetypical skutterudites, MCoSb(3). Surprisingly, the skutterudite rattlers have more deformed AHSs than the Mn atom in cubic CeMnNi(4). This is related to the highly ionic nature of the skutterudite rattlers, which is not taken into account in the neutral spherical atom approach of the AHS. Additionally, visualization of void spaces in the two materials using the procrystal electron density shows that while the Mn atom is tightly fitting in the CeMnNi(4) structure then the La atom in the skutterudite is truly situated in an oversized cage of the host structure. Overall, we conclude that the Mn atom in cubic CeMnNi(4) cannot be coined a rattler.
No related grants have been discovered for Eiji Nishibori.