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  • Blackwell Publishing Ltd  (182,057)
  • International Union of Crystallography (IUCr)
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  • 1
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    Toward an adequate level of detail in flood risk assessments (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-01-24
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Flood risk assessments require different disciplines to understand and model the underlying components hazard, exposure, and vulnerability. Many methods and data sets have been refined considerably to cover more details of spatial, temporal, or process information. We compile case studies indicating that refined methods and data have a considerable effect on the overall assessment of flood risk. But are these improvements worth the effort? The adequate level of detail is typically unknown and prioritization of improvements in a specific component is hampered by the lack of an overarching view on flood risk. Consequently, creating the dilemma of potentially being too greedy or too wasteful with the resources available for a risk assessment. A “sweet spot” between those two would use methods and data sets that cover all relevant known processes without using resources inefficiently. We provide three key questions as a qualitative guidance toward this “sweet spot.” For quantitative decision support, more overarching case studies in various contexts are needed to reveal the sensitivity of the overall flood risk to individual components. This could also support the anticipation of unforeseen events like the flood event in Germany and Belgium in 2021 and increase the reliability of flood risk assessments.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: BMBF http://dx.doi.org/10.13039/501100002347
    Description: Federal Environment Agency http://dx.doi.org/10.13039/501100010809
    Description: http://howas21.gfz-potsdam.de/howas21/
    Description: https://www.umwelt.niedersachsen.de/startseite/themen/wasser/hochwasser_amp_kustenschutz/hochwasserrisikomanagement_richtlinie/hochwassergefahren_und_hochwasserrisikokarten/hochwasserkarten-121920.html
    Description: https://download.geofabrik.de/europe/germany.html
    Description: https://emergency.copernicus.eu/mapping/list-of-components/EMSN024
    Description: https://data.jrc.ec.europa.eu/collection/id-0054
    Description: https://oasishub.co/dataset/surface-water-flooding-footprinthurricane-harvey-august-2017-jba
    Description: https://www.wasser.sachsen.de/hochwassergefahrenkarte-11915.html
    Keywords: ddc:551.48 ; decision support ; extreme events ; integrated flood risk management ; risk assessment
    Language: English
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  • 2
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    Small lateral air pressure gradients generated by a large chamber system have a strong effect on CO2 transport in soil (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-02-09
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Gas transport in soils is usually assumed to be purely diffusive, although several studies have shown that non‐diffusive processes can significantly enhance soil gas transport. These processes include barometric air pressure changes, wind‐induced pressure pumping and static air pressure fields generated by wind interacting with obstacles. The associated pressure gradients in the soil can cause advective gas fluxes that are much larger than diffusive fluxes. However, the contributions of the respective transport processes are difficult to separate. We developed a large chamber system to simulate pressure fields and investigate their influence on soil gas transport. The chamber consists of four subspaces in which pressure is regulated by fans that blow air in or out of the chamber. With this setup, we conducted experiments with oscillating and static pressure fields. CO〈sub〉2〈/sub〉 concentrations were measured along two soil profiles beneath the chamber. We found a significant relationship between static lateral pressure gradients and the change in the CO〈sub〉2〈/sub〉 profiles (R〈sup〉2〈/sup〉 = 0.53; 〈italic toggle="no"〉p〈/italic〉‐value 〈2e‐16). Even small pressure gradients between −1 and 1 Pa relative to ambient pressure resulted in an increase or decrease in CO〈sub〉2〈/sub〉 concentrations of 8% on average in the upper soil, indicating advective flow of air in the pore space. Positive pressure gradients resulted in decreasing, negative pressure gradients in increasing CO〈sub〉2〈/sub〉 concentrations. The concentration changes were probably caused by an advective flow field in the soil beneath the chamber generated by the pressure gradients. No effect of oscillating pressure fields was observed in this study. The results indicate that static lateral pressure gradients have a substantial impact on soil gas transport and therefore are an important driver of gas exchange between soil and atmosphere. Lateral pressure gradients in a comparable range can be induced under windy conditions when wind interacts with terrain features. They can also be caused by chambers used for flux measurements at high wind speed or by fans used for head‐space mixing within the chambers, which yields biased flux estimates.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; advective flux ; chamber flux measurements ; static air pressure fields ; wind‐induced pressure pumping
    Language: English
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  • 3
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    Redoxtrons – An experimental system to study redox processes within the capillary fringe (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2023-11-18
    Description: Spatiotemporal characterisation of the soil redox status within the capillary fringe (CF) is a challenging task. Air‐filled porosities (ε), oxygen concentration (O〈sub〉2〈/sub〉) and soil redox potential (EH) are interrelated soil variables within active biogeochemical domains such as the CF. We investigated the impact of water table (WT) rise and drainage in an undisturbed topsoil and subsoil sample taken from a Calcaric Gleysol for a period of 46 days. We merged 1D (EH and matric potential) and 2D (O〈sub〉2〈/sub〉) systems to monitor at high spatiotemporal resolution redox dynamics within self‐constructed redoxtron housings and complemented the data set by a 3D pore network characterization using X‐ray microtomography (X‐ray μCT). Depletion of O〈sub〉2〈/sub〉 was faster in the organic matter‐ and clay‐rich aggregated topsoil and the CF extended 〉10 cm above the artificial WT. The homogeneous and less‐aggregated subsoil extended only 4 cm above the WT as indicated by ε–O〈sub〉2〈/sub〉–EH data during saturation. After drainage, 2D O〈sub〉2〈/sub〉 imaging revealed a fast aeration towards the lower depths of the topsoil, which agrees with the connected ε derived by X‐ray μCT (ε〈sub〉CT_conn〈/sub〉) of 14.9% of the total porosity. However, small‐scaled anoxic domains with O〈sub〉2〈/sub〉 saturation 〈5% were apparent even after lowering the WT (down to 0.25 cm〈sup〉2〈/sup〉 in size) for 23 days. These domains remained a nucleus for reducing soil conditions (E〈sub〉H〈/sub〉 〈 −100 mV), which made it challenging to characterise the soil redox status in the CF. In contrast, the subsoil aeration reached O〈sub〉2〈/sub〉 saturation after 8 days for the complete soil volume. Values of ε〈sub〉CT_conn〈/sub〉 around zero in the subsoil highlighted that soil aeration was independent of this parameter suggesting that other variables such as microbial activity must be considered when predicting the soil redox status from ε alone. The use of redoxtrons in combination with localised redox‐measurements and image based pore space analysis resulted in a better 2D/3D characterisation of the pore system and related O〈sub〉2〈/sub〉 transport properties. This allowed us to analyse the distribution and activity of microbiological niches highly associated with the spatiotemporal variable redox dynamics in soil environments. Highlights: The time needed to turn from reducing to oxidising (period where all platinum electrodes feature E〈sub〉H〈/sub〉 〉 300 mV) condition differ for two samples with contrasting soil structure. The subsoil with presumably low O〈sub〉2〈/sub〉 consumption rates aerated considerably faster than the topsoil and exclusively by O〈sub〉2〈/sub〉 diffusion through medium‐ and fine‐sized pores. To derive the soil redox status based upon the triplet ε–O〈sub〉2〈/sub〉–E〈sub〉H〈/sub〉 is challenging at present in heterogeneous soil domains and larger soil volumes than 250 cm〈sup〉3〈/sup〉. Undisturbed soil sampling along with 2D/3D redox measurement systems (e.g., redoxtrons) improve our understanding of redox dynamics within the capillary fringe.
    Keywords: ddc:631.4 ; environmental monitoring ; incubation experiments ; redox processes ; soil reducing conditions ; undisturbed soil ; X‐ray microtomography
    Language: English
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  • 4
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    The dilemma of analytical method changes for soil organic carbon in long‐term experiments (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2023-11-17
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈sec xmlns:mml="http://www.w3.org/1998/Math/MathML" id="ejss13362-sec-1003" xml:lang="en"〉 〈p xml:lang="en"〉Long‐term experiments (LTEs) have provided data to modellers and agronomists to investigate changes and dynamics of soil organic carbon (SOC) under different cropping systems. As treatment changes have occurred due to agricultural advancements, so too have analytical soil methods. This may lead to method bias over time, which could affect the robust interpretation of data and conclusions drawn. This study aims to quantify differences in SOC due to changes in dry combustion methods over time, using soil samples of a LTE established in 1963 that focuses on mineral and organic fertilizer management in the temperate zone of Northeast Germany. For this purpose, 1059 soil samples, collected between 1976 and 2008, have been analysed twice, once with their historical laboratory method right after sampling, and a second time in 2016 when all samples were analysed using the same elementary analyser. In 9 of 11 soil sampling campaigns, a paired 〈italic toggle="no"〉t〈/italic〉‐test provided evidence for significant differences in the historical SOC values when compared with the re‐analysed concentrations of the same LTE sample. In the sampling years 1988 and 2004, the historical analysis obtained about 0.9 g kg〈sup〉−1〈/sup〉 lower SOC compared with the re‐analysed one. For 1990 and 1998, this difference was about 0.4 g kg〈sup〉−1〈/sup〉. Correction factors, an approach often used to correct for different analytical techniques, could only be applied for 5 of 11 sampling campaigns to account for constant and proportional systematic method error. For this particular LTE, the interpretation of SOC changes due to agronomic management (here fertilization) deviates depending on the analytical method used, which may weaken the explanatory power of the historical data. We demonstrate that analytical method changes over time present one of many challenges in the interpretation of time series data of SOC dynamics. Therefore, LTE site managers need to ensure providing all necessary protocols and data in order to retrace method changes and if necessary recalculate SOC.〈/p〉 〈/sec〉〈sec xmlns:mml="http://www.w3.org/1998/Math/MathML" id="ejss13362-sec-0003" xml:lang="en"〉 〈title〉Highlights〈/title〉 〈p xml:lang="en"〉〈list list-type="bullet" id="ejss13362-list-0001"〉 〈list-item id="ejss13362-li-0001"〉〈p〉A total of 1059 LTE soil samples taken between 1976 and 2008 were re‐analysed for SOC in 2016〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0002"〉〈p〉Several methodological changes for SOC determination led to significant different SOC concentration in the same sample〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0003"〉〈p〉Interpretation and time series of LTE soil data suffer from consideration of analytical method changes and poor documentation of the same〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0004"〉〈p〉Soil archive establishment, thorough method protocols and diligent proficiency testing after soil method changes ameliorate the dilemma〈/p〉〈/list-item〉 〈/list〉〈/p〉 〈/sec〉
    Description: Brandenburger Staatsministerium für Wissenschaft, Forschung und Kultur http://dx.doi.org/10.13039/501100004581
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100004937
    Description: https://doi.org/10.4228/zalf-acge-b683
    Keywords: ddc:631.4 ; Bland–Altman ; carbon stocks ; data trueness ; Deming regression ; method bias ; soil archive ; soil survey
    Language: English
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  • 5
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    Optimised use of data fusion and memory‐based learning with an Austrian soil library for predictions with infrared data (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2023-12-12
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Infrared spectroscopy in the visible to near‐infrared (vis–NIR) and mid‐infrared (MIR) regions is a well‐established approach for the prediction of soil properties. Different data fusion and training approaches exist, and the optimal procedures are yet undefined and may depend on the heterogeneity present in the set and on the considered scale. The objectives were to test the usefulness of partial least squares regressions (PLSRs) for soil organic carbon (SOC), total carbon (C〈sub〉t〈/sub〉), total nitrogen (N〈sub〉t〈/sub〉) and pH using vis–NIR and MIR spectroscopy for an independent validation after standard calibration (use of a general PLSR model) or using memory‐based learning (MBL) with and without spiking for a national spectral database. Data fusion approaches were simple concatenation of spectra, outer product analysis (OPA) and model averaging. In total, 481 soils from an Austrian forest soil archive were measured in the vis–NIR and MIR regions, and regressions were calculated. Fivefold calibration‐validation approaches were carried out with a region‐related split of spectra to implement independent validations with n ranging from 47 to 99 soils in different folds. MIR predictions were generally superior over vis–NIR predictions. For all properties, optimal predictions were obtained with data fusion, with OPA and spectra concatenation outperforming model averaging. The greatest robustness of performance was found for OPA and MBL with spiking with 〈italic toggle="no"〉R〈/italic〉〈sup〉2〈/sup〉 ≥ 0.77 (N), 0.85 (SOC), 0.86 (pH) and 0.88 (C〈sub〉t〈/sub〉) in the validations of all folds. Overall, the results indicate that the combination of OPA for vis–NIR and MIR spectra with MBL and spiking has a high potential to accurately estimate properties when using large‐scale soil spectral libraries as reference data. However, the reduction of cost‐effectiveness using two spectrometers needs to be weighed against the potential increase in accuracy compared to a single MIR spectroscopy approach.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; data fusion ; independent validation ; infrared spectroscopy ; MBL ; nitrogen ; outer product analysis ; pH ; soil organic carbon ; spiking ; total carbon
    Language: English
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  • 6
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    Importance of catchment hydrological processes and calibration of hydrological‐hydrodynamic rainfall‐runoff models in small rural catchments (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-01-19
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉In recent years, many two‐dimensional (2D) hydrodynamic models have been extended to include the direct rainfall method (DRM). This allows their application as a hydrological‐hydrodynamic model for the determination of floodplains in one model system. In previous studies on DRM, the role of catchment hydrological processes (CaHyPro) and its interaction with the calibration process was not investigated in detail. In the present, case‐oriented study, the influence of the spatiotemporal distribution of the processes precipitation and runoff formation in combination with the 2D model HEC‐RAS is investigated. In a further step, a conceptual approach for event‐based interflow is integrated. The study is performed on the basis of a single storm event in a small rural catchment (low mountain range, 38 km〈sup〉2〈/sup〉) in Hesse (Germany). The model results are evaluated against six quality criteria and compared to a simplified baseline model. Finally, the calibrated improved model is contrasted with a calibrated baseline model. The results show the enhancement of the model results due to the integration of the CaHyPro and highlight its interplay with the calibrated model parameters.〈/p〉
    Keywords: ddc:551.48 ; 2D hydrodynamic modeling ; calibration ; direct rainfall modeling ; hydrological processes ; radar data ; runoff formation
    Language: English
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  • 7
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    BODIUM—A systemic approach to model the dynamics of soil functions (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-01-26
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The increasing demand for biomass for food, animal feed, fibre and bioenergy requires optimization of soil productivity, while at the same time, protecting other soil functions such as nutrient cycling and buffering, carbon storage, habitat for biological activity and water filter and storage. Therefore, one of the main challenges for sustainable agriculture is to produce high yields while maintaining all the other soil functions. Mechanistic simulation models are an essential tool to fully understand and predict the complex interactions between physical, biological and chemical processes of soils that generate those functions. We developed a soil model to simulate the impact of various agricultural management options and climate change on soil functions by integrating the relevant processes mechanistically and in a systemic way. As a special feature, we include the dynamics of soil structure induced by tillage and biological activity, which is especially relevant in arable soils. The model operates on a 1D soil profile consisting of a number of discrete layers with dynamic thickness. We demonstrate the model performance by simulating crop growth, root growth, nutrient and water uptake, nitrogen cycling, soil organic matter turnover, microbial activity, water distribution and soil structure dynamics in a long‐term field experiment including different crops and different types and levels of fertilization. The model is able to capture essential features that are measured regularly including crop yield, soil organic carbon, and soil nitrogen. In this way, the plausibility of the implemented processes and their interactions is confirmed. Furthermore, we present the results of explorative simulations comparing scenarios with and without tillage events to analyse the effect of soil structure on soil functions. Since the model is process‐based, we are confident that the model can also be used to predict quantities that have not been measured or to estimate the effect of management measures and climate states not yet been observed. The model thus has the potential to predict the site‐specific impact of management decisions on soil functions, which is of great importance for the development of a sustainable agriculture that is currently also on the agenda of the ‘Green Deal’ at the European level.〈/p〉
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: https://git.ufz.de/bodium/bodium_v1.0
    Keywords: ddc:631.4 ; agriculture ; computational model ; simulation ; soil microbiology ; soil structure ; sustainable soil
    Language: English
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  • 8
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    Temperature and soil moisture change microbial allocation of pesticide‐derived carbon (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-03-18
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Temperature and soil moisture are known to control pesticide mineralization. Half‐life times (DT〈sub〉50〈/sub〉) derived from pesticide mineralization curves generally indicate longer residence times at low soil temperature and moisture but do not consider potential changes in the microbial allocation of pesticide‐derived carbon (C). We aimed to determine carbon use efficiency (CUE, formation of new biomass relative to total C uptake) to better understand microbial utilization of pesticide‐derived C under different environmental conditions and to support the conventional description of degradation dynamics based on mineralization. We performed a microcosm experiment at two MCPA (2‐methyl‐4‐chlorophenoxyacetic acid) concentrations (1 and 20 mg kg〈sup〉−1〈/sup〉) and defined 20°C/pF 1.8 as optimal and 10°C/pF 3.5 as limiting environmental conditions. After 4 weeks, 70% of the initially applied MCPA was mineralized under optimal conditions but MCPA mineralization reached less than 25% under limiting conditions. However, under limiting conditions, an increase in CUE was observed, indicating a shift towards anabolic utilization of MCPA‐derived C. In this case, increased C assimilation implied C storage or the formation of precursor compounds to support resistance mechanisms, rather than actual growth since we did not find an increase in the 〈italic toggle="no"〉tfdA〈/italic〉 gene relevant to MCPA degradation. We were able to confirm the assumption that under limiting conditions, C assimilation increases relative to mineralization and that C redistribution, may serve as an explanation for the difference between mineralization and MCPA dissipation‐derived degradation dynamics. In addition, by introducing CUE to the temperature‐ and moisture‐dependent degradation of pesticides, we can capture the underlying microbial constraints and adaptive mechanisms to changing environmental conditions.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Changing environmental conditions alter the MCPA degradation dynamics and the allocation of pesticide‐derived carbon to anabolic or catabolic metabolism.〈boxed-text position="anchor" content-type="graphic" id="ejss13417-blkfxd-0001" xml:lang="en"〉 〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:13510754:media:ejss13417:ejss13417-toc-0001"〉 〈/graphic〉 〈/boxed-text〉〈/p〉
    Description: Collaborative Research Center 1253 CAMPOS (DFG)
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: DFG Priority Program 2322 “Soil System”
    Description: Ellrichshausen Foundation
    Description: Research Training Group “Integrated Hydrosystem modeling”
    Description: https://doi.org/10.5281/zenodo.5081655
    Keywords: ddc:631.4 ; anabolism ; carbon use efficiency ; catabolism ; effect of soil moisture and temperature ; gene‐centric process model ; MCPA biodegradation
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  • 9
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    Inspecting the Reliability of Geochemical Facies Identified for the Waterworks' Capture Zone in Germany (2022)
    Blackwell Publishing Ltd | Malden, US
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    Publication Date: 2022-09-27
    Description: Little research attention has been given to validating clusters obtained from the groundwater geochemistry of the waterworks' capture zone with a prevailing lake‐groundwater exchange. To address this knowledge gap, we proposed a new scheme whereby Gaussian finite mixture modeling (GFMM) and Spike‐and‐Slab Bayesian (SSB) algorithms were utilized to cluster the groundwater geochemistry while quantifying the probability of the resulting cluster membership against each other. We applied GFMM and SSB to 13 geochemical parameters collected during different sampling periods at 13 observation points across the Barnim Highlands plateau located in the northeast of Berlin, Germany; this included 10 observation wells, two lakes, and a gallery of drinking production wells. The cluster analysis of GFMM yielded nine clusters, either with a probability ≥0.8, while the SSB produced three hierarchical clusters with a probability of cluster membership varying from 〈0.2 to 〉0.8. The findings demonstrated that the clustering results of GFMM were in good agreement with the classification as per the principal component analysis and Piper diagram. By superimposing the parameter clustering onto the observation clustering, we could identify discrepancies that exist among the parameters of a certain cluster. This enables the identification of different factors that may control the geochemistry of a certain cluster, although parameters of that cluster share a strong similarity. The GFMM results have shown that from 2002, there has been active groundwater inflow from the lakes towards the capture zone. This means that it is necessary to adopt appropriate measures to reverse the inflow towards the lakes.
    Description: Article impact statement: The probability of cluster membership quantified using an algorithm should be validated against another probabilistic‐based classifier.
    Description: Federal Ministry of Education and Research http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:551.9 ; ddc:551.49
    Language: English
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  • 10
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    Application of mixed‐effects modelling and rule‐based models to explain copper variation in soil profiles of southern Germany (2022)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2022-10-01
    Description: Copper (Cu) is an essential element for plants and microorganisms and at larger concentrations a toxic pollutant. A number of factors controlling Cu dynamics have been reported, but information on quantitative relationships is scarce. We aimed to (i) quantitatively describe and predict soil Cu concentrations (CuAR) in aqua regia considering site‐specific effects and effects of pH, soil organic carbon (SOC) and cation exchange capacity (CEC), and (ii) study the suitability of mixed‐effects modelling and rule‐based models for the analysis of long‐term soil monitoring data. Thirteen uncontaminated long‐term monitoring soil profiles in southern Germany were analysed. Since there was no measurable trend of increasing CuAR concentrations with time in the respective depth ranges of the sites, data from different sampling dates were combined and horizon‐specific regression analyses including model simplifications were carried out for 10 horizons. Fixed‐ and mixed‐effects models with the site as a random effect were useful for the different horizons and significant contributions (either of main effects or interactions) of SOC, CEC and pH were present for 9, 8 and 7 horizons, respectively. Horizon‐specific rule‐based cubist models described the CuAR data similarly well. Validations of cubist models and mixed‐effects models for the CuAR concentrations in A horizons were successful for the given population after random splitting into calibration and validation samples, but not after independent validations with random splitting according to sites. Overall, site, CEC, SOC and pH provide important information for a description of CuAR concentrations using the different regression approaches. Highlights: Information on quantitative relationships for factors controlling Cu dynamics is scarce. Site, CEC, SOC and pH provide important information for a description of Cu concentrations. Validations of cubist models and mixed‐effects models for A horizons were successful for a closed population of sites.
    Description: Bavarian State Ministry of the Environment and Consumer Protection http://dx.doi.org/10.13039/501100010219
    Description: Ministry of Agriculture and Environment Mecklenburg‐Western Pomerania
    Keywords: ddc:631.4
    Language: English
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  • 11
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    Millimetre scale aeration of the rhizosphere and drilosphere (2022)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2022-10-04
    Description: Soil aeration is a critical factor for oxygen‐limited subsoil processes, as transport by diffusion and advection is restricted by the long distance to the free atmosphere. Oxygen transport into the soil matrix is highly dependent on its connectivity to larger pore channels like earthworm and root colonised biopores. Here we hypothesize that the soil matrix around biopores represents different connectivity depending on biopore genesis and actual coloniser. We analysed the soil pore system of undisturbed soil core samples around biopores generated or colonised by roots and earthworms and compared them with the pore system of soil, not in the immediacy of a biopore. Oxygen partial pressure profiles and gas relative diffusion was measured in the rhizosphere and drilosphere from the biopore wall into the bulk soil with microelectrodes. The measurements were linked with structural features such as porosity and connectivity obtained from X‐ray tomography and image analysis. Aeration was enhanced in the soil matrix surrounding biopores in comparison to the bulk soil, shown by higher oxygen concentrations and higher relative diffusion coefficients. Biopores colonised by roots presented more connected lateral pores than earthworm colonised ones, which resulted in enhanced aeration of the rhizosphere compared to the drilosphere. This has influenced biotic processes (microbial turnover/mineralization or root respiration) at biopore interfaces and highlights the importance of microstructural features for soil processes and their dependency on the biopore's coloniser.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4
    Language: English
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  • 12
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    Response of subsoil organic matter contents and physical properties to long‐term, high‐rate farmyard manure application (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-07-26
    Description: Application of farmyard manure (FYM) is common practice to improve physical and chemical properties of arable soil and crop yields. However, studies on effects of FYM application mainly focussed on topsoils, whereas subsoils have rarely been addressed so far. We, therefore, investigated the effects of 36‐year FYM application with different rates of annual organic carbon (OC) addition (0, 469, 938 and 1875 g C m−2 a−1) on OC contents of a Chernozem in 0–30 cm (topsoil) and 35–45 cm (subsoil) depth. We also investigated its effects on soil structure and hydraulic properties in subsoil. X‐ray computed tomography was used to analyse the response of the subsoil macropore system (≥19 μm) and the distribution of particulate organic matter (POM) to different FYM applications, which were related to contents in total OC (TOC) and water‐extractable OC (WEOC). We show that FYM‐C application of 469 g C m−2 a−1 caused increases in TOC and WEOC contents only in the topsoil, whereas rates of ≥938 g C m−2 a−1 were necessary for TOC enrichment also in the subsoil. At this depth, the subdivision of TOC into different OC sources shows that most of the increase was due to fresh POM, likely by the stimulation of root growth and bioturbation. The increase in subsoil TOC went along with increases in macroporosity and macropore connectivity. We neither observed increases in plant‐available water capacity nor in unsaturated hydraulic conductivity. In conclusion, only very high application of FYM over long periods can increase OC content of subsoil at our study site, but this increase is largely based on fresh, easily degradable POM and likely accompanied by high C losses when considering the discrepancy between OC addition rate by FYM and TOC response in soil. Highlights A new image processing procedure to distinguish fresh and decomposed POM. The increase of subsoil C stock based to a large extend on fresh, labile POM. Potential of arable subsoils for long‐term C storage by large FYM application rates is limited. The increase in TOC has no effect on hydraulic properties of the subsoil.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4
    Language: English
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    Non‐exchangeable stable hydrogen isotope ratios in clay minerals and soil clay fractions: A method test (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-01-20
    Description: Stable hydrogen isotope ratios (δ2H values) in structural hydroxyl groups of pedogenic clay minerals are inherited from the surrounding water at the time of their formation. Only non‐exchangeable H preserves the environmental forensic and paleoclimate information (δ2Hn value). To measure δ2Hn values in structural H of clay minerals and soil clay fractions, we adapted a steam equilibration method by accounting for high hygroscopicity. Our δ2Hn values for USGS57 biotite (−95.3 ± SD 0.9‰) and USGS58 muscovite (30.7 ± 1.4‰) differed slightly but significantly from the reported δ2H values (−91.5 ± 2.4‰ and −28.4 ± 1.6‰), because the minerals contained 1.1%–4.4% of exchangeable H. The low SD of replicate measurements (n = 3) confirmed a high precision. The clay separation method including destruction of Fe oxides, carbonates and soil organic matter, and dispersion did not significantly change the δ2Hn values of five different clay minerals. However, we were unable to remove all organic matter from the soil clay fractions resulting in an estimated bias of 1‰ in two samples and 15‰ in the carbon‐richest sample. Our results demonstrate that δ2Hn values of structural H of clay minerals and soil clay fractions can be reliably measured without interference from atmospheric water and the method used to separate the soil clay fraction. Highlights We tested steam equilibration to determine stable isotope ratios of structural H in clay. Gas‐tight capsule sealing in Ar atmosphere was necessary to avoid remoistening. Our steam equilibration method showed a high accuracy and precision. The clay separation method did not change stable isotope ratios of structural H in clay.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:549 ; controlled isotope exchange technique ; deuterium ; montmorillonite ; soil clay separation ; soil organic matter removal ; steam equilibration ; structural H ; USGS57 biotite ; vermiculite ; δ2H
    Language: English
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    Potential erodibility of semi‐arid steppe soils derived from aggregate stability tests (2022)
    Koza, Moritz ; Pöhlitz, Julia ; Prays, Aleksey ; [et al.]
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-01-26
    Description: Erosion is a severe threat to the sustainable use of agricultural soils. However, the structural resistance of soil against the disruptive forces steppe soils experience under field conditions has not been investigated. Therefore, 132 topsoils under grass‐ and cropland covering a large range of physico‐chemical soil properties (sand: 2–76%, silt: 18–80%, clay: 6–30%, organic carbon: 7.3–64.2 g kg−1, inorganic carbon: 0.0–8.5 g kg−1, pH: 4.8–9.5, electrical conductivity: 32–946 μS cm−1) from northern Kazakhstan were assessed for their potential erodibility using several tests. An adjusted drop‐shatter method (low energy input of 60 Joule on a 250‐cm3 soil block) was used to estimate the stability of dry soil against weak mechanical forces, such as saltating particles striking the surface causing wind erosion. Three wetting treatments with various conditions and energies (fast wetting, slow wetting, and wet shaking) were applied to simulate different disruptive effects of water. Results indicate that aggregate stability was higher for grassland than cropland soils and declined with decreasing soil organic carbon content. The results of the drop‐shatter test suggested that 29% of the soils under cropland were at risk of wind erosion, but only 6% were at high risk (i.e. erodible fraction 〉60%). In contrast, the fast wetting treatment revealed that 54% of the samples were prone to become “very unstable” and 44% “unstable” during heavy rain or snowmelt events. Even under conditions comparable to light rain events or raindrop impact, 53–59% of the samples were “unstable.” Overall, cropland soils under semi‐arid conditions seem much more susceptible to water than wind erosion. Considering future projections of increasing precipitation in Kazakhstan, we conclude that the risk of water erosion is potentially underestimated and needs to be taken into account when developing sustainable land use strategies. Highlights Organic matter is the important binding agent enhancing aggregation in steppe topsoils. Tillage always declines aggregate stability even without soil organic carbon changes. All croplands soil are prone to wind or water erosion independent of their soil properties. Despite the semi‐arid conditions, erosion risk by water seems higher than by wind.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:631.4 ; climate change ; land use ; soil organic carbon ; soil texture ; water erosion ; wind erosion
    Language: English
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    Vertical SOC distribution and aromatic carbon in centuries old charcoal‐rich Technosols (2022)
    Bonhage, Alexander ; Raab, Thomas ; Schneider, Anna ; [et al.]
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-01-21
    Description: Charcoal‐rich Technosols on century‐old relict charcoal hearths (RCHs) are the subject of ongoing research regarding potential legacy effects that result from historic charcoal production and subsequent charcoal amendments on forest soil properties and forest ecosystems today. RCHs consist mostly of Auh horizons that are substantially enriched in soil organic carbon (SOC), of which the largest part seems to be of pyrogenic origin (PyC). However, the reported range of SOC and PyC contents in RCH soil also suggests that they are enriched in nonpyrogenic SOC. RCH soils are discussed as potential benchmarks for the long‐term influence of biochar amendment and the post‐wildfire influences on soil properties. In this study, we utilised a large soil sample dataset (n = 1245) from 52 RCH sites in north‐western Connecticut, USA, to quantify SOC contents by total element analysis. The contents of condensed highly aromatic carbon as a proxy for black carbon (BC) were predicted by using a modified benzene polycarboxylated acid (BPCA) marker method in combination with diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy‐based partial least square regression (r2 = 0.89). A high vertical spatial sampling resolution allowed the identification of soil organic matter (SOM) enrichment and translocation processes. The results show an average 75% and 1862% increase in TOC and BPCA‐derived carbon, respectively, for technogenic Auh horizons compared to reference soils. In addition to an increase in aromatic properties, increased carboxylic properties of the RCH SOC suggest self‐humification effects of degrading charcoal and thereby the continuing formation of leachable aromatic carbon compounds, which could have effects on pedogenic processes in buried soils. Indeed, we show BPCA‐derived carbon concentrations in intermediate technogenic Cu horizons and buried top/subsoils that suggest vertical translocation of highly aromatic carbon originating in RCH Auh horizons. Topmost Auh horizons showed a gradual decrease in total organic carbon (TOC) contents with increasing depth, suggesting accumulation of recent, non‐pyrogenic SOM. Lower aliphatic absorptions in RCH soil spectra suggest different SOM turnover dynamics compared to reference soils. Furthermore, studied RCH soils featured additional TOC enrichment, which cannot be fully explained now. Highlights BC to TOC ratio and high resolution vertical SOC distribution in 52 RCH sites were studied. RCH soils non‐BC pool was potentially different to reference soils. RCH soils feature TOC accumulation in the topmost horizon. There is BC translocation into buried soils on RCH sites.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; benzene polycarboxylated acid marker (BPCA) ; black carbon ; charcoal degradation ; charcoal kiln ; pyrogenic carbon ; relict charcoal hearth ; biochar
    Language: English
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    Defining Hydrogeological Site Similarity with Hierarchical Agglomerative Clustering (2022)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2024-02-28
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Hydrogeological information about an aquifer is difficult and costly to obtain, yet essential for the efficient management of groundwater resources. Transferring information from sampled sites to a specific site of interest can provide information when site‐specific data is lacking. Central to this approach is the notion of site similarity, which is necessary for determining relevant sites to include in the data transfer process. In this paper, we present a data‐driven method for defining site similarity. We apply this method to selecting groups of similar sites from which to derive prior distributions for the Bayesian estimation of hydraulic conductivity measurements at sites of interest. We conclude that there is now a unique opportunity to combine hydrogeological expertise with data‐driven methods to improve the predictive ability of stochastic hydrogeological models.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉Article impact statement〈/italic〉: This article introduces hierarchical clustering as a method for defining a notion of site similarity; the aim of this method is to improve the derivation of prior distributions in Bayesian methods in hydrogeology.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: https://github.com/GeoStat-Bayesian/geostatDB
    Description: https://github.com/GeoStat-Bayesian/exPrior
    Description: https://github.com/GeoStat-Bayesian/siteSimilarity
    Keywords: ddc:551.49 ; hydrogeological sites ; hydrogeological modeling
    Language: English
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    Reducing tillage intensity benefits the soil micro‐ and mesofauna in a global meta‐analysis (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-03-22
    Description: Soil fauna drives crucial processes of energy and nutrient cycling in agricultural systems, and influences the quality of crops and pest incidence. Soil tillage is the most influential agricultural manipulation of soil structure, and has a profound influence on soil biology and its provision of ecosystem services. The objective of this study was to quantify through meta‐analyses the effects of reducing tillage intensity on density and diversity of soil micro‐ and mesofaunal communities, and how these effects vary among different pedoclimatic conditions and interact with concurrent management practices. We present the results of a global meta‐analysis of available literature data on the effects of different tillage intensities on taxonomic and functional groups of soil micro‐ and mesofauna. We collected paired observations (conventional vs. reduced forms of tillage/no‐tillage) from 133 studies across 33 countries. Our results show that reduced tillage intensity or no‐tillage increases the total density of springtails (+35%), mites (+23%), and enchytraeids (+37%) compared to more intense tillage methods. The meta‐analyses for different nematode feeding groups, life‐forms of springtails, and taxonomic mite groups showed higher densities under reduced forms of tillage compared to conventional tillage on omnivorous nematodes (+53%), epedaphic (+81%) and hemiedaphic (+84%) springtails, oribatid (+43%) and mesostigmatid (+57%) mites. Furthermore, the effects of reduced forms of tillage on soil micro‐ and mesofauna varied with depth, climate and soil texture, as well as with tillage method, tillage frequency, concurrent fertilisation, and herbicide application. Our findings suggest that reducing tillage intensity can have positive effects on the density of micro‐ and mesofaunal communities in areas subjected to long‐term intensive cultivation practices. Our results will be useful to support decision making on the management of soil faunal communities and will facilitate modelling efforts of soil biology in global agroecosystems. HIGHLIGHTS Global meta‐analysis to estimate the effect of reducing tillage intensity on micro‐ and mesofauna Reduced tillage or no‐tillage has positive effects on springtail, mite and enchytraeid density Effects vary among nematode feeding groups, springtail life forms and mite suborders Effects vary with texture, climate and depth and depend on the tillage method and frequency
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: https://doi.org/10.20387/bonares-eh0f-hj28
    Keywords: ddc:631.4 ; agricultural land use ; conservation agriculture ; conventional agriculture ; soil biodiversity ; soil cultivation
    Language: English
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    Evaluating learning spaces in flood risk management in Germany: Lessons for governance research (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-06-28
    Description: Efforts to collaboratively manage the risk of flooding are ultimately based on individuals learning about risks, the decision process, and the effectiveness of decisions made in prior situations. This article argues that much can be learned about a governance setting by explicitly evaluating the relationships through which influential individuals and their immediate contacts receive and send information to one another. We define these individuals as “brokers,” and the networks that emerge from their interactions as “learning spaces.” The aim of this article is to develop strategies to identify and evaluate the properties of a broker's learning space that are indicative of a collaborative flood risk management arrangement. The first part of this article introduces a set of indicators, and presents strategies to employ this list so as to systematically identify brokers, and compare their learning spaces. The second part outlines the lessons from an evaluation that explored cases in two distinct flood risk management settings in Germany. The results show differences in the observed brokers' learning spaces. The contacts and interactions of the broker in Baden‐Württemberg imply a collaborative setting. In contrast, learning space of the broker in North Rhine‐Westphalia lacks the same level of diversity and polycentricity.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: MWK Baden‐Württemberg
    Keywords: 333.91 ; brokerage ; collaborative water governance ; comanagement ; comparative analysis ; social networks
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    Synthetic resampling strategies and machine learning for digital soil mapping in Iran (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-07-04
    Description: Most common machine learning (ML) algorithms usually work well on balanced training sets, that is, datasets in which all classes are approximately represented equally. Otherwise, the accuracy estimates may be unreliable and classes with only a few values are often misclassified or neglected. This is known as a class imbalance problem in machine learning and datasets that do not meet this criterion are referred to as imbalanced data. Most datasets of soil classes are, therefore, imbalanced data. One of our main objectives is to compare eight resampling strategies that have been developed to counteract the imbalanced data problem. We compared the performance of five of the most common ML algorithms with the resampling approaches. The highest increase in prediction accuracy was achieved with SMOTE (the synthetic minority oversampling technique). In comparison to the baseline prediction on the original dataset, we achieved an increase of about 10, 20 and 10% in the overall accuracy, kappa index and F‐score, respectively. Regarding the ML approaches, random forest (RF) showed the best performance with an overall accuracy, kappa index and F‐score of 66, 60 and 57%, respectively. Moreover, the combination of RF and SMOTE improved the accuracy of the individual soil classes, compared to RF trained on the original dataset and allowed better prediction of soil classes with a low number of samples in the corresponding soil profile database, in our case for Chernozems. Our results show that balancing existing soil legacy data using synthetic sampling strategies can significantly improve the prediction accuracy in digital soil mapping (DSM). Highlights Spatial distribution of soil classes in Iran can be predicted using machine learning (ML) algorithms. The synthetic minority oversampling technique overcomes the drawback of imbalanced and highly biased soil legacy data. When combining a random forest model with synthetic sampling strategies the prediction accuracy of the soil model improves significantly. The resulting new soil map of Iran has a much higher spatial resolution compared to existing maps and displays new soil classes that have not yet been mapped in Iran.
    Description: Alexander von Humboldt‐Stiftung http://dx.doi.org/10.13039/100005156
    Description: German Research Foundation http://dx.doi.org/10.13039/501100001659
    Description: Soil and Water Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
    Keywords: 631.4 ; covariates ; imbalanced data ; machine learning ; random forest ; soil legacy data
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    Impact of biochar on nutrient supply, crop yield and microbial respiration on sandy soils of northern Germany (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-06-16
    Description: The application of biochar to agricultural soils to increase nutrient availability, crop production and carbon sequestration has gained increasing interest but data from field experiments on temperate, marginal soils are still under‐represented. In the current study, biochar, produced from organic residues (digestates) from a biogas plant, was applied with and without digestates at low (3.4 t ha−1) and intermediate (17.1 t ha−1) rates to two acidic and sandy soils in northern Germany that are used for corn (Zea mays L.) production. Soil nutrient availability, crop yields, microbial biomass and carbon dioxide (CO2) emissions from heterotrophic respiration were measured over two consecutive years. The effects of biochar application depended on the intrinsic properties of the two tested soils and the biochar application rates. Although the soils at the fallow site, with initially low nutrient concentrations, showed a significant increase in pH, soil nutrients and crop yield after low biochar application rates, a similar response was found at the cornfield site only after application of substantially larger amounts of biochar. The effect of a single dose of biochar at the beginning of the experiment diminished over time but was still detectable after 2 years. Whereas plant available nutrient concentrations increased after biochar application, the availability of potentially phytotoxic trace elements (Zn, Pb, Cd, Cr) decreased significantly, and although slight increases in microbial biomass carbon and heterotrophic CO2 fluxes were observed after biochar application, they were mostly not significant. The results indicate that the application of relatively small amounts of biochar could have positive effects on plant available nutrients and crop yields of marginal arable soils and may decrease the need for mineral fertilizers while simultaneously increasing the sequestration of soil organic carbon. Highlights A low rate of biochar increased plant available nutrients and crop yield on marginal soils. Biochar application reduced the availability of potentially harmful trace elements. Heterotrophic respiration showed no clear response to biochar application. Biochar application may reduce fertilizer need and increase carbon sequestration on marginal soils.
    Description: German Academic Exchange Service http://dx.doi.org/10.13039/501100001655
    Description: Institute Strategic Programme grants, “Soils to Nutrition”
    Keywords: 631.4 ; black carbon ; carbon sequestration ; corn ; digestate ; heterotrophic respiration ; marginal soils ; microbial biomass
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    Self‐stated recovery from flooding: Empirical results from a survey in Central Vietnam (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-06-27
    Description: Social inequalities lead to flood resilience inequalities across social groups, a topic that requires improved documentation and understanding. The objective of this paper is to attend to these differences by investigating self‐stated flood recovery across genders in Vietnam as a conceptual replication of earlier results from Germany. This study employs a regression‐based analysis of 1,010 respondents divided between a rural coastal and an urban community in Thua Thien‐Hue province. The results highlight an important set of recovery process‐related variables. The set of relevant variables is similar across genders in terms of inclusion and influence, and includes age, social capital, internal and external support after a flood, perceived severity of previous flood impacts, and the perception of stress‐resilience. However, women were affected more heavily by flooding in terms of longer recovery times, which should be accounted for in risk management. Overall, the studied variables perform similarly in Vietnam and Germany. This study, therefore, conceptually replicates previous results suggesting that women display slightly slower recovery levels as well as that psychological variables influence recovery rates more than adverse flood impacts. This provides an indication of the results' potentially robust nature due to the different socio‐environmental contexts in Germany and Vietnam.
    Keywords: 333.7 ; flood recovery ; resilience ; societal equity ; vulnerability
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    The potential of ryegrass as cover crop to reduce soil N2O emissions and increase the population size of denitrifying bacteria (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-07-05
    Description: Nitrogen (N) fertilization is the major contributor to nitrous oxide (N2O) emissions from agricultural soil, especially in post‐harvest seasons. This study was carried out to investigate whether ryegrass serving as cover crop affects soil N2O emissions and denitrifier community size. A microcosm experiment was conducted with soil planted with perennial ryegrass (Lolium perenne L.) and bare soil, each with four levels of N fertilizer (0, 5, 10 and 20 g N m−2; applied as calcium ammonium nitrate). The closed‐chamber approach was used to measure soil N2O fluxes. Real‐time PCR was used to estimate the biomass of bacteria and fungi and the abundance of genes involved in denitrification in soil. The results showed that the presence of ryegrass decreased the nitrate content in soil. Cumulative N2O emissions of soil with grass were lower than in bare soil at 5 and 10 g N m−2. Fertilization levels did not affect the abundance of soil bacteria and fungi. Soil with grass showed greater abundances of bacteria and fungi, as well as microorganisms carrying narG, napA, nirK, nirS and nosZ clade I genes. It is concluded that ryegrass serving as a cover crop holds the potential to mitigate soil N2O emissions in soils with moderate or high NO3− concentrations. This highlights the importance of cover crops for the reduction of N2O emissions from soil, particularly following N fertilization. Future research should explore the full potential of ryegrass to reduce soil N2O emissions under field conditions as well as in different soils. Highlights This study was to investigate whether ryegrass serving as cover crop affects soil N2O emissions and denitrifier community size; Plant reduced soil N substrates on one side, but their root exudates stimulated denitrification on the other side; N2O emissions were lower in soil with grass than bare soil at medium fertilizer levels, and growing grass stimulated the proliferation of almost all the denitrifying bacteria except nosZ clade II; Ryegrass serving as a cover crop holds the potential to mitigate soil N2O emissions.
    Description: China Scholarship Council http://dx.doi.org/10.13039/501100004543
    Description: The National Science Project for University of Anhui Province
    Keywords: 551.9 ; 631.4 ; denitrification ; perennial ryegrass (Lolium perenne L.) ; soil bacteria ; soil CO2 emissions ; soil N2O emissions
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    ogs5py: A Python‐API for the OpenGeoSys 5 Scientific Modeling Package (2021)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2021-07-04
    Description: High‐performance numerical codes are an indispensable tool for hydrogeologists when modeling subsurface flow and transport systems. But as they are written in compiled languages, like C/C++ or Fortran, established software packages are rarely user‐friendly, limiting a wider adoption of such tools. OpenGeoSys (OGS), an open‐source, finite‐element solver for thermo‐hydro‐mechanical–chemical processes in porous and fractured media, is no exception. Graphical user interfaces may increase usability, but do so at a dramatic reduction of flexibility and are difficult or impossible to integrate into a larger workflow. Python offers an optimal trade‐off between these goals by providing a highly flexible, yet comparatively user‐friendly environment for software applications. Hence, we introduce ogs5py, a Python‐API for the OpenGeoSys 5 scientific modeling package. It provides a fully Python‐based representation of an OGS project, a large array of convenience functions for users to interact with OGS and connects OGS to the scientific and computational environment of Python.
    Description: German Federal Environmental Foundation http://dx.doi.org/10.13039/100007636
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: 551.49 ; hydrogeology ; subsurface flow ; modeling ; software
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    High‐Resolution Integrated Transport Model for Studying Surface Water–Groundwater Interaction (2021)
    Blackwell Publishing Ltd | Malden, US
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    Publication Date: 2021-06-27
    Description: Transport processes that lead to exchange of mass between surface water and groundwater play a significant role for the ecological functioning of aquatic systems, for hydrological processes and for biogeochemical transformations. In this study, we present a novel integral modeling approach for flow and transport at the sediment–water interface. The model allows us to simultaneously simulate turbulent surface and subsurface flow and transport with the same conceptual approach. For this purpose, a conservative transport equation was implemented to an existing approach that uses an extended version of the Navier–Stokes equations. Based on previous flume studies which investigated the spreading of a dye tracer under neutral, losing and gaining flow conditions the new solver is validated. Tracer distributions of the experiments are in close agreement with the simulations. The simulated flow paths are significantly affected by in‐ and outflowing groundwater flow. The highest velocities within the sediment are found for losing condition, which leads to shorter residence times compared to neutral and gaining conditions. The largest extent of the hyporheic exchange flow is observed under neutral condition. The new solver can be used for further examinations of cases that are not suitable for the conventional coupled models, for example, if Reynolds numbers are larger than 10. Moreover, results gained with the integral solver provide high‐resolution information on pressure and velocity distributions at the rippled streambed, which can be used to improve flow predictions. This includes the extent of hyporheic exchange under varying ambient groundwater flow conditions.
    Description: Technische Universität Berlin, Germany
    Description: German Research Foundation http://dx.doi.org/10.13039/501100001659
    Keywords: 551.4 ; aquatic systems ; sediment-water interface ; transport model
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    Iron isotope fractionation in soil and graminaceous crops after 100 years of liming in the long‐term agricultural experimental site at Berlin‐Dahlem, Germany (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-07-05
    Description: Sustainable arable cropping relies on repeated liming. Yet, the associated increase in soil pH can reduce the availability of iron (Fe) to plants. We hypothesized that repeated liming, but not pedogenic processes such as lessivage (i.e., translocation of clay particles), alters the Fe cycle in Luvisol soil, thereby affecting Fe isotope composition in soils and crops. Hence, we analysed Fe concentrations and isotope compositions in soil profiles and winter rye from the long‐term agricultural experimental site in Berlin‐Dahlem, Germany, where a controlled liming trial with three field replicates per treatment has been conducted on Albic Luvisols since 1923. Heterogeneity in subsoil was observed at this site for Fe concentration but not for Fe isotope composition. Lessivage had not affected Fe isotope composition in the soil profiles. The results also showed that almost 100 years of liming lowered the concentration of the HCl‐extractable Fe that was potentially available for plant uptake in the surface soil (0–15 cm) from 1.03 (standard error (SE) 0.03) to 0.94 (SE 0.01) g kg−1. This HCl‐extractable Fe pool contained isotopically lighter Fe (δ56Fe = −0.05 to −0.29‰) than the bulk soil (δ56Fe = −0.08 to 0.08‰). However, its Fe isotope composition was not altered by the long‐term lime application. Liming resulted in relatively lower Fe concentrations in the roots of winter rye. In addition, liming led to a heavier Fe isotope composition of the whole plants compared with those grown in the non‐limed plots (δ56FeWholePlant_ + Lime = −0.12‰, SE 0.03 vs. δ56FeWholePlant_‐Lime = −0.21‰, SE 0.01). This suggests that the elevated soil pH (increased by one unit due to liming) promoted the Fe uptake strategy through complexation of Fe(III) from the rhizosphere, which favoured heavier Fe isotopes. Overall, the present study showed that liming and a related increase in pH did not affect the Fe isotope compositions of the soil, but may influence the Fe isotope composition of plants grown in the soil if they alter their Fe uptake strategy upon the change of Fe availability. Highlights Fe concentrations and stocks, but not Fe isotope compositions, were more heterogeneous in subsoil than in topsoil. Translocation of clay minerals did not result in Fe isotope fractionation in the soil profile of a Luvisol. Liming decreased Fe availability in topsoil, but did not affect its δ56Fe values. Uptake of heavier Fe isotopes by graminaceous crops was more pronounced at elevated pH.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: 551.9 ; liming ; plant‐available Fe pool in soil ; winter rye ; δ56Fe
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    How to Find Aquifer Statistics Utilizing Pumping Tests? Two Field Studies Using welltestpy (2021)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2022-04-01
    Description: We present a workflow to estimate geostatistical aquifer parameters from pumping test data using the Python package welltestpy. The procedure of pumping test analysis is exemplified for two data sets from the Horkheimer Insel site and from the Lauswiesen site, Germany. The analysis is based on a semi‐analytical drawdown solution from the upscaling approach Radial Coarse Graining, which enables to infer log‐transmissivity variance and horizontal correlation length, beside mean transmissivity, and storativity, from pumping test data. We estimate these parameters of aquifer heterogeneity from type‐curve analysis and determine their sensitivity. This procedure, implemented in welltestpy, is a template for analyzing any pumping test. It goes beyond the possibilities of standard methods, for example, based on Theis' equation, which are limited to mean transmissivity and storativity. A sensitivity study showed the impact of observation well positions on the parameter estimation quality. The insights of this study help to optimize future test setups for geostatistical aquifer analysis and provides guidance for investigating pumping tests with regard to aquifer statistics using the open‐source software package welltestpy.
    Description: Article impact statement: We present a workflow to infer parameters of subsurface heterogeneity from pumping test data exemplified at two sites using welltestpy.
    Description: German Federal Environmental Foundation (DBU) http://dx.doi.org/10.13039/100007636
    Keywords: ddc:551.49
    Language: English
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    Importance of sources of variability, scales and experimental design: A case study about the effects of biochar and slurry application on soil properties in agricultural silty loam soils (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-04-01
    Description: In designed experiments, different sources of variability and an adequate scale of measurement need to be considered, but not all approaches in common usage are equally valid. In order to elucidate the importance of sources of variability and choice of scale, we conducted an experiment where the effects of biochar and slurry applications on soil properties related to soil fertility were studied for different designs: (a) for a field‐scale sampling design with either a model soil (without natural variability) as an internal control or with composited soils, (b) for a design with a focus on amendment variabilities, and (c) for three individual field‐scale designs with true field replication and a combined analysis representative of the population of loess‐derived soils. Three silty loam sites in Germany were sampled and the soil macroaggregates were crushed. For each design, six treatments (0, 0.15 and 0.30 g slurry‐N kg−1 with and without 30 g biochar kg−1) were applied before incubating the units under constant soil moisture conditions for 78 days. CO2 fluxes were monitored and soils were analysed for macroaggregate yields and associated organic carbon (C). Mixed‐effects models were used to describe the effects. For all soil properties, results for the loess sites differed with respect to significant contributions of fixed effects for at least one site, suggesting the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils to be made and showed that site:slurry:biochar and site:slurry interactions were not negligible for macroaggregate yields. The use of a model soil as an internal control enabled observation of variabilities other than those related to soils or amendments. Experiments incorporating natural variability in soils or amendments resulted in partially different outcomes, indicating the need to include all important sources of variability. Highlights Effects of biochar and slurry applications were studied for different designs and mixed‐effects models were used to describe the effects. Including an internal control allowed observation of, e.g., methodological and analytical variabilities. The results suggested the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils. The results indicated the need to include all important sources of variability.
    Keywords: ddc:631.4
    Language: English
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    Do tree species affect decadal changes in soil organic carbon and total nitrogen stocks in Danish common garden experiments? (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-04-01
    Description: Temperate forest soils are often considered as an important sink for atmospheric carbon (C), thereby buffering anthropogenic CO2 emissions. However, the effect of tree species composition on the magnitude of this sink is unclear. We resampled a tree species common garden experiment (six sites) a decade after initial sampling to evaluate whether forest floor (FF) and topsoil organic carbon (Corg) and total nitrogen (Nt) stocks changed in dependence of tree species (Norway spruce—Picea abies L., European beech—Fagus sylvatica L., pedunculate oak—Quercus robur L., sycamore maple—Acer pseudoplatanus L., European ash—Fraxinus excelsior L. and small‐leaved lime—Tilia cordata L.). Two groups of species were identified in terms of Corg and Nt distribution: (1) Spruce with high Corg and Nt stocks in the FF developed as a mor humus layer which tended to have smaller Corg and Nt stocks and a wider Corg:Nt ratio in the mineral topsoil, and (2) the broadleaved species, of which ash and maple distinguished most clearly from spruce by very low Corg and Nt stocks in the FF developed as mull humus layer, had greater Corg and Nt stocks, and narrow Corg:Nt ratios in the mineral topsoil. Over 11 years, FF Corg and Nt stocks increased most under spruce, while small decreases in bulk mineral soil (esp. in 0–15 cm and 0–30 cm depth) Corg and Nt stocks dominated irrespective of species. Observed decadal changes were associated with site‐related and tree species‐mediated soil properties in a way that hinted towards short‐term accumulation and mineralisation dynamics of easily available organic substances. We found no indication for Corg stabilisation. However, results indicated increasing Nt stabilisation with increasing biomass of burrowing earthworms, which were highest under ash, lime and maple and lowest under spruce. Highlights We studied if tree species differences in topsoil Corg and Nt stocks substantiate after a decade. The study is unique in its repeated soil sampling in a multisite common garden experiment. Forest floors increased under spruce, but topsoil stocks decreased irrespective of species. Changes were of short‐term nature. Nitrogen was most stable under arbuscular mycorrhizal species.
    Description: Deutsche Forschungsgemeinschaff (DFG)
    Keywords: ddc:551.9 ; ddc:631.41
    Language: English
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    The ‘Flood Resilience Rose’: A management tool to promote transformation towards flood resilience (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-09-29
    Description: Coping with the growing impacts of flooding in EU countries, a paradigm shift in flood management can be observed, moving from safety‐based towards risk‐based approaches and holistic perspectives. Flood resilience is a common denominator of most of the approaches. In this article, we present the ‘Flood Resilience Rose’ (FRR), a management tool to promote harmonised action towards flood resilience in European regions and beyond. The FRR is a result of a two‐step process. First, based on scientific concepts as well as analysis of relevant policy documents, we identified three ‘levels of operation’. The first level refers to the EU Floods Directive and an extended multi‐layer safety approach, comprising the four different layers of protection, prevention, preparedness and recovery, and related measures to be taken. This level is not independent but depends both on the institutional (second level) and the wider (third level) context. Second, we used surveys, semi‐structured interviews and group discussions during workshops with experts from Belgium, Denmark, Germany, the Netherlands and the United Kingdom to validate the definitions and the FRR's practical relevance. The presented FRR is thus the result of rigorous theoretical and practical consideration and provides a tool capable to strengthen flood risk management practice.
    Description: European Regional Development Fund http://dx.doi.org/10.13039/501100008530
    Keywords: 551.48 ; flood defence measures ; governance and institutions ; integrated flood risk management ; resilience
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    Urban pluvial flood adaptation: Results of a household survey across four German municipalities (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-09-30
    Description: In recent years, German cities were heavily impacted by pluvial flooding and related damage is projected to increase due to climate change and urbanisation. It is important to ask how to improve urban pluvial flood risk management. To understand the current state of property level adaptation, a survey was conducted in four municipalities that had recently been impacted by pluvial flooding. A hybrid framework based on the Protection Motivation Theory (PMT) and the Protection Action Decision Model (PADM) was used to investigate drivers of adaptive behaviour through both descriptive and regression analyses. Descriptive statistics revealed that participants tended to instal more low‐ and medium‐cost measures than high‐cost measures. Regression analyses showed that coping appraisal increased protection motivation, but that the adaptive behaviour also depends on framing factors, particularly homeownership. We further found that, while threat appraisal solely affects protection motivation and responsibility appraisal affects solely maladaptive thinking, coping appraisal affects both. Our results indicate that PMT is a solid starting point to study adaptive behaviours in the context of pluvial flooding, but we need to go beyond that by, for instance, considering factors of the PADM, such as responsibility, ownership, or respondent age, to fully understand this complex decision‐making process.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:551.489 ; ddc:363.34
    Language: English
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    Framework disorder and its effect on selective hysteretic sorption of a T-shaped azole-based metal–organic framework (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-12-08
    Description: Metal–organic frameworks with highly ordered porosity have been studied extensively. In this paper, the effect of framework (pore) disorder on the gas sorption of azole-based isoreticular Cu(II) MOFs with rtl topology and characteristic 1D tubular pore channels is investigated for the first time. In contrast to other isoreticular rtl metal–organic frameworks, the Cu(II) metal–organic framework based on 5-(1H-imidazol-1-yl)isophthalate acid has a crystallographically identifiable disordered framework without open N-donor sites. The framework provides a unique example for investigating the effect of pore disorder on gas sorption that can be systematically evaluated. It exhibits remarkable temperature-dependent hysteretic CO2 sorption up to room temperature, and shows selectivity of CO2 over H2, CH4 and N2 at ambient temperature. The unique property of the framework is its disordered structure featuring distorted 1D tubular channels and DMF-guest-remediated defects. The results imply that structural disorder (defects) may play an important role in the modification of the performance of the material.
    Keywords: metal–organic frameworksT-shaped ligandsdisorderMOFssolid propertieschannel structuresgas separation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-12-08
    Description: SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns (`stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst. 45, 335–341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
    Keywords: serial crystallographyX-ray free-electron lasersXFELelectron diffractiondiffract-then-destroydynamical studiesauto-indexing algorithmsBragg peaks
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    The hydrocarbon-bearing clathrasil chibaite and its host–guest structure at low temperature (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-09
    Description: The natural sII-type clathrasil chibaite [chemical formula SiO2·(M12,M16), where Mx denotes a guest molecule] was investigated using single-crystal X-ray diffraction and Raman spectroscopy in the temperature range from 273 to 83 K. The O atoms of the structure at room temperature, which globally conforms to space group Fd{\overline 3}m [V = 7348.9 (17) Å3, a = 19.4420 (15) Å], have anomalous anisotropic displacement parameters indicating a static or dynamic disorder. With decreasing temperature, the crystal structure shows a continuous symmetry-lowering transformation accompanied by twinning. The intensities of weak superstructure reflections increase as temperature decreases. A monoclinic twinned superstructure was derived at 100 K [A2/n, V = 7251.0 (17) Å3, a′ = 23.7054 (2), b′ = 13.6861 (11), c′ = 23.7051 (2) Å, β′ = 109.47°]. The transformation matrix from the cubic to the monoclinic system is ai′ = (½ 1 ½ / ½ 0 −½ / ½ −1 ½). The A2/n host framework has Si—O bond lengths and Si—O—Si angles that are much closer to known values for stable silicate-framework structures compared with the averaged Fd{\overline 3}m model. As suggested from band splitting observed in the Raman spectra, the [512]-type cages (one crystallographically unique in Fd{\overline 3}m, four different in A2/n) entrap the hydrocarbon species (CH4, C2H6, C3H8, i-C4H10). The [51264]-type cage was found to be unique in both structure types. It contains the larger hydrocarbon molecules C2H6, C3H8 and i-C4H10.
    Keywords: chibaiteclathrasilshydrocarbonsRaman spectroscopyX-ray diffractionlow temperature
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-09
    Description: Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein–nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.
    Keywords: class II CPD photolyasesDNA repairDNA distortioncyclobutane pyrimidine dimercrystal structure
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-08-09
    Description: During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.
    Keywords: serial crystallographySIRAS phasinglipidic cubic phaseheavy-atom soakingde novo protein structure determination
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Conformational aspects of polymorphs and phases of 2-propyl-1H-benzimidazole (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-15
    Description: This paper reports on the polymorphism of 2-propyl-1H-benzimidazole (2PrBzIm) induced by temperature change. Upon heating, an irreversible reconstructive-type phase transition at T = 384 K from the ordered form I (P212121) to a new polymorph, form IIHT (Pcam), was observed. The structural transformation between forms I and II involves significant changes in the crystal packing, as well as a key conformational variation around the propyl chain of the molecule. After the first irreversible phase transition, the IIHT form undergoes two further (reversible) phase transitions upon cooling at 361 K (IIRT) and 181 K (IILT). All three phases (forms IIHT, IIRT and IILT) have almost identical crystal packing and, given the reversibility of the conversions as a function of temperature, they are referred to as form II temperature phases. They differ, however, with respect to conformational variations around the propyl chain of 2PrBzIm. Energy calculations of the gas-phase conformational energy landscape of this compound about its flexible bonds allowed us to classify the observed conformational variations of all forms into changes and adjustments of conformers. This reveals that forms I and II are related by conformational change, and that two of the form II phases (HT and RT) are related by conformational adjustment, whilst the other two (RT and LT) are related by conformational change. We introduce the term `conformational phases' for different crystal phases with almost identical packing but showing changes in conformation.
    Keywords: molecular crystalspolymorphismphase transitionsconformational changesenergy minimization
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Signal-to-noise, spatial resolution and information capacity of coherent diffraction imaging (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-09-15
    Description: It is shown that the average signal-to-noise ratio (SNR) in the three-dimensional electron-density distribution of a sample reconstructed by coherent diffractive imaging cannot exceed twice the square root of the ratio of the mean total number of scattered photons detected during the scan and the number of spatially resolved voxels in the reconstructed volume. This result leads to an upper bound on Shannon's information capacity of this imaging method by specifying the maximum number of distinguishable density distributions within the reconstructed volume when the radiation dose delivered to the sample and the spatial resolution are both fixed. If the spatially averaged SNR in the reconstructed electron density is fixed instead, the radiation dose is shown to be proportional to the third or fourth power of the spatial resolution, depending on the sampling of the three-dimensional diffraction space and the scattering power of the sample.
    Keywords: coherent diffractive imagingsignal-to-noise ratiospatial resolutioninformation capacity
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
    Published by International Union of Crystallography (IUCr)
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    Three-beam convergent-beam electron diffraction for measuring crystallographic phases (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-10-09
    Description: Under almost all circumstances, electron diffraction patterns contain information about the phases of structure factors, a consequence of the short wavelength of an electron and its strong Coulombic interaction with matter. However, extracting this information remains a challenge and no generic method exists. In this work, a set of simple analytical expressions is derived for the intensity distribution in convergent-beam electron diffraction (CBED) patterns recorded under three-beam conditions. It is shown that these expressions can be used to identify features in three-beam CBED patterns from which three-phase invariants can be extracted directly, without any iterative refinement processes. The octant, in which the three-phase invariant lies, can be determined simply by inspection of the indexed CBED patterns (i.e. the uncertainty of the phase measurement is ±22.5°). This approach is demonstrated with the experimental measurement of three-phase invariants in two simple test cases: centrosymmetric Si and non-centrosymmetric GaAs. This method may complement existing structure determination methods by providing direct measurements of three-phase invariants to replace `guessed' invariants in ab initio phasing methods and hence provide more stringent constraints to the structure solution.
    Keywords: crystallographic phase problemthree-phase invariantsconvergent-beam electron diffractionstructure determinationenantiomorph ambiguitynanocrystalsdynamical studiesmultiple scattering
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Unwarping GISAXS data (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-10-09
    Description: Grazing-incidence small-angle X-ray scattering (GISAXS) is a powerful technique for measuring the nanostructure of coatings and thin films. However, GISAXS data are plagued by distortions that complicate data analysis. The detector image is a warped representation of reciprocal space because of refraction, and overlapping scattering patterns appear because of reflection. A method is presented to unwarp GISAXS data, recovering an estimate of the true undistorted scattering pattern. The method consists of first generating a guess for the structure of the reciprocal-space scattering by solving for a mutually consistent prediction from the transmission and reflection sub-components. This initial guess is then iteratively refined by fitting experimental GISAXS images at multiple incident angles, using the distorted-wave Born approximation (DWBA) to convert between reciprocal space and detector space. This method converges to a high-quality reconstruction for the undistorted scattering, as validated by comparing with grazing-transmission scattering data. This new method for unwarping GISAXS images will broaden the applicability of grazing-incidence techniques, allowing experimenters to inspect undistorted visualizations of their data and allowing a broader range of analysis methods to be applied to GI data.
    Keywords: X-ray scatteringGISAXSGTSAXSimage healingreconstructiondistorted-wave Born approximation
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Deformation pathway and defect generation in crystals: a combined group theory and graph theory description (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-12-19
    Description: The generation and motion of crystalline defects during plastic deformation are critical processes that determine the mechanical properties of a crystal. The types of defect generated are not only related to the symmetry of a crystal but also associated with the symmetry-breaking process during deformation. Proposed here is a new mathematical framework to capture the intrinsic coupling between crystal symmetry and deformation-induced symmetry breaking. Using a combination of group theory and graph theory, a general approach is demonstrated for the systematic determination of the types of crystalline defect induced by plastic deformation, through the construction of a crystal deformation group and a deformation pathway graph. The types of defect generated in the deformation of a face-centered cubic crystal are analyzed through the deformation pathway graph and compared with experimental observations.
    Keywords: crystal deformationcrystalline defectsgroup theoryCayley graph
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Incommensurate structures of the [CH3NH3][Co(COOH)3] compound (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-12-19
    Description: The present article is devoted to the characterization of the structural phase transitions of the [CH3NH3][Co(COOH)3] (1) perovskite-like metal–organic compound through variable-temperature single-crystal neutron diffraction. At room temperature, compound 1 crystallizes in the orthorhombic space group Pnma (phase I). A decrease in temperature gives rise to a first phase transition from the space group Pnma to an incommensurate phase (phase II) at approximately 128 K. At about 96 K, this incommensurate phase evolves into a second phase with a sharp change in the modulation vector (phase III). At lower temperatures (ca 78 K), the crystal structure again becomes commensurate and can be described in the monoclinic space group P21/n (phase IV). Although phases I and IV have been reported previously [Boča et al. (2004). Acta Cryst. C60, m631–m633; Gómez-Aguirre et al. (2016). J. Am. Chem. Soc. 138, 1122–1125; Mazzuca et al. (2018). Chem. Eur. J. 24, 388–399], phases III and IV corresponding to the Pnma(00γ)0s0 space group have not yet been described. These phase transitions involve not only the occurrence of small distortions in the three-dimensional anionic [Co(HCOO)3]− framework, but also the reorganization of the [CH3NH3]+ counter-ions in the cavities of the structure, which gives rise to an alteration of the hydrogen-bonded network, modifying the electrical properties of compound 1.
    Keywords: phase transitionsincommensurate structuresformate ligandmultiferroic materialsaperiodic structuresmaterials scienceinorganic chemistryphase transitionsMOFs
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Structure model of γ-Al2O3 based on planar defects (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-12-19
    Description: The defect structure of γ-Al2O3 derived from boehmite was investigated using a combination of selected-area electron diffraction (SAED) and powder X-ray diffraction (XRD). Both methods confirmed a strong dependence of the diffraction line broadening on the diffraction indices known from literature. The analysis of the SAED patterns revealed that the dominant structure defects in the spinel-type γ-Al2O3 are antiphase boundaries located on the lattice planes (00l), which produce the sublattice shifts {{1}\over{4}}\langle 10{\overline 1}\rangle. Quantitative information about the defect structure of γ-Al2O3 was obtained from the powder XRD patterns. This includes mainly the size of γ-Al2O3 crystallites and the density of planar defects. The correlation between the density of the planar defects and the presence of structural vacancies, which maintain the stoichiometry of the spinel-type γ-Al2O3, is discussed. A computer routine running on a fast graphical processing unit was written for simulation of the XRD patterns. This routine calculates the atomic positions for a given kind and density of planar defect, and simulates the diffracted intensities with the aid of the Debye scattering equation.
    Keywords: γ-aluminamicrostructure defectsantiphase boundariesrotational boundariesselected-area electron diffractionpowder X-ray diffractionDebye equationanisotropic broadening
    Electronic ISSN: 2052-2525
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  • 43
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    Tailoring structural and magnetic properties of Mn3−xFexGa alloys towards multifunctional applications (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-18
    Description: This study investigated the structural and magnetic properties of Mn3−xFexGa alloys (x = 0, 0.2, 0.4, 0.6, 0.8, 1) under different heat-treatment conditions. A tetragonal structure was observed in samples that were heat treated at 623 K for three days followed by quenching in ice water. These tetragonal alloys present large coercive fields in the range 0.8–5 kOe and low saturation magnetization, and have great potential for application in spin-transfer torque-based devices. A hexagonal structure was observed in samples subjected to heat treatment at 883 K for three days following quenching in ice water. A moderate decrease in the coercive field has been observed for the hexagonal alloys compared with those with a tetragonal structure. However, the Mn3−xFexGa alloys with a hexagonal structure exhibit other attractive magnetic properties, including collinear and non-collinear magnetic properties, holding high promise for technological applications. A face-centred-cubic (f.c.c.) structure was observed when subjected to annealing at 1073 K for three days followed by quenching in ice water. In contrast to the tetragonal and hexagonal structures, all f.c.c. alloys exhibit antiferromagnetic behaviour. This versatile material can display a wide range of multi-functionalities attributed to its tuneable crystal structure. This investigation will guide the design of multiple structures of these materials in order to utilise the wide functionalities for practical applications.
    Keywords: Mn–Fe–Ga alloystetragonal Heusler alloysmultiple structural materials
    Electronic ISSN: 2052-2525
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    Structure-based mechanism of action of a viral poly(ADP-ribose) polymerase 1-interacting protein facilitating virus replication (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-01
    Description: Poly(ADP-ribose) polymerase 1 (PARP-1), an enzyme that modifies nuclear proteins by poly(ADP-ribosyl)ation, regulates various cellular activities and restricts the lytic replication of oncogenic gammaherpesviruses by inhibiting the function of replication and transcription activator (RTA), a key switch molecule of the viral life cycle. A viral PARP-1-interacting protein (vPIP) encoded by murine gammaherpesvirus 68 (MHV-68) orf49 facilitates lytic replication by disrupting interactions between PARP-1 and RTA. Here, the structure of MHV-68 vPIP was determined at 2.2 Å resolution. The structure consists of 12 α-helices with characteristic N-terminal β-strands (Nβ) and forms a V-shaped-twist dimer in the asymmetric unit. Structure-based mutagenesis revealed that Nβ and the α1 helix (residues 2–26) are essential for the nuclear localization and function of vPIP; three residues were then identified (Phe5, Ser12 and Thr16) that were critical for the function of vPIP and its interaction with PARP-1. A recombinant MHV-68 harboring mutations of these three residues showed severely attenuated viral replication both in vitro and in vivo. Moreover, ORF49 of Kaposi's sarcoma-associated herpesvirus also directly interacted with PARP-1, indicating a conserved mechanism of action of vPIPs. The results elucidate the novel molecular mechanisms by which oncogenic gammaherpesviruses overcome repression by PARP-1 using vPIPs.
    Keywords: viral PARP-1-interacting proteinopen reading frame 49poly(ADP-ribose) polymerase 1murine gammaherpesvirus 68Kaposi's sarcoma-associated herpesvirusstructure determinationX-ray crystallography
    Electronic ISSN: 2052-2525
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  • 45
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    A corrective prescription for GISAXS (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-01
    Keywords: X-ray scatteringGISAXSimage healingreconstructiondistorted-wave Born approximation
    Electronic ISSN: 2052-2525
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  • 46
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    K-paracelsian (KAlSi3O8·H2O) and identification of a simple building scheme of dense double-crankshaft zeolite topologies (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-12-05
    Description: During screening of the phase space using KOH and 1-methyl-4-aza-1-azoniabicyclo[2.2.2]octane hydroxide (1-methyl-DABCO) under hydrothermal zeolite synthesis conditions, K-paracelsian was synthesized. Scanning electron microscopy, energy dispersive X-ray spectroscopy and ex situ powder X-ray diffraction analysis revealed a material that is compositionally closely related to the mineral microcline and structurally closely related to the mineral paracelsian, both of which are feldspars. In contrast to the feldspars, K-paracelsian contains intrazeolitic water corresponding to one molecule per cage. In the case of K-paracelsian it might be useful to consider it a link between feldspars and zeolites. It was also shown that K-paracelsian can be described as the simplest endmember of a family of dense double-crankshaft zeolite topologies. By applying the identified building principle, a number of known zeolite topologies can be constructed. Furthermore, it facilitates the construction of a range of hypothetical small-pore structures that are crystallo-chemically healthy, but which have not yet been realized experimentally.
    Keywords: K-paracelsiandense double-crankshaft zeolite topologiesstructure refinementcrystal engineeringinorganic porous solidsmicroporous materials
    Electronic ISSN: 2052-2525
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    Determination of chemical ordering in the complex perovskite Pb(Cd1/3Nb2/3)O3 (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-25
    Description: Pure-phase Pb(Cd1/3Nb2/3)O3 (PCN) single crystals and ceramics with a complex perovskite structure are synthesized for the first time. The local chemical ordering in PCN has been investigated by X-ray diffraction (including diffuse scattering) and Cs-corrected transmission electron microscopy experiments. It is concluded that the PCN samples have large coherent chemical ordering regions that even extend to the long range, and the ordering model is consistent with β-type chemical ordered regions. The antiphase domain boundaries were also observed. Two dielectric anomaly peaks were found in these two types of samples, one of which indicates possible relaxor behaviour. The novel structure of the completely ordered regions and its relationship with the electrical properties make PCN a unique material for the fundamental understanding of chemically substituted perovskites.
    Keywords: chemical orderingdiffuse scatteringelectron microscopyatomic resolution EDSperovskitesdielectric permittivityrelaxors
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    Crystal engineering, crystals and crystallography (2018)
    International Union of Crystallography (IUCr)
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    Publication Date: 2018-10-30
    Keywords: crystal engineeringcrystalscrystallography
    Electronic ISSN: 2052-2525
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  • 49
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    Committee machine that votes for similarity between materials (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-30
    Description: A method has been developed to measure the similarity between materials, focusing on specific physical properties. The information obtained can be utilized to understand the underlying mechanisms and support the prediction of the physical properties of materials. The method consists of three steps: variable evaluation based on nonlinear regression, regression-based clustering, and similarity measurement with a committee machine constructed from the clustering results. Three data sets of well characterized crystalline materials represented by critical atomic predicting variables are used as test beds. Herein, the focus is on the formation energy, lattice parameter and Curie temperature of the examined materials. Based on the information obtained on the similarities between the materials, a hierarchical clustering technique is applied to learn the cluster structures of the materials that facilitate interpretation of the mechanism, and an improvement in the regression models is introduced to predict the physical properties of the materials. The experiments show that rational and meaningful group structures can be obtained and that the prediction accuracy of the materials' physical properties can be significantly increased, confirming the rationality of the proposed similarity measure.
    Keywords: data miningmaterials informaticsfirst-principles calculationsphysical properties of materialsmachine learningsimilarity
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  • 50
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    Self-adapted clustering of solute atoms into a confined two-dimensional prismatic platelet with an ellipse-like quasi-unit cell (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-30
    Description: This paper reports a new structured prismatic platelet, self-assembled by an ellipse-like quasi-unit cell, precipitated in Mg–In–Yb and Mg–In–Ca ternary alloys and aged isothermally at 200°C using aberration-corrected high-angle annular dark-field scanning transmission electron microscopy combined with density functional theory computations. The ordered stacking of solute atoms along the [0001]α direction based on elliptically shaped self-adapted clustering leads to the generation of the quasi-unit cell. The bonding of these ellipse-like quasi-unit-cell rods by the Mg atomic columns along the 〈11{\overline 2}0〉α directions formed a two-dimensional planar structure, which has three variants with a {10{\overline 1}0}α habit plane and full coherence with the α-Mg matrix. This finding is important for understanding the clustering and stacking behaviors of solute atoms in condensed matter, and is expected to guide the future design of novel high-strength Mg alloys strengthened by such high-density prismatic platelets.
    Keywords: magnesium alloysprecipitationprismatic plateletsquasi-unit-cellsDFTHAADF-STEM
    Electronic ISSN: 2052-2525
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    Crystal structure, interaction energies and experimental electron density of the popular drug ketoprophen (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-30
    Description: The crystal and molecular structure of the pure (S)-enantiomer of the popular analgesic and anti-inflammatory drug ketoprophen (α-ket) is reported. A detailed aspherical charge-density model based on high-resolution X-ray diffraction data has been refined, yielding a high-precision geometric description and classification of the O—H...O interactions as medium strength hydrogen bonds. The crystal structure of the racemic form of ketoprophen (β-ket) was also redetermined at 100 K, at 0.5 Å resolution. A previously unreported disorder (10% occupancy) was discovered. In contrast to the racemic β-ket case, the (S)-enantiomer crystallizes with two independent molecules in the asymmetric unit with two distinct conformations. The major difference between the β-ket and α-ket crystal forms lies in the formation of distinct hydrogen-bonded motifs: a closed ring motif in β-ket versus infinite chains of hydrogen bonds in the chiral α-ket structure. However, the overall crystal packing of both forms is surprisingly similar, with close-packed layers of antiparallel-oriented benzophenone moieties bound by C—H...π interactions. Notably, the most important stabilizing term in the total lattice energies in both instances proved to be the dispersion related to these interactions. Both forms of the title compound (α- and β-ket) were additionally characterized by differential scanning calorimetry and thermogravimetric analysis.
    Keywords: ketoprophencharge densitycrystal structurespharmaceuticalsbioinversion
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    Deep Consensus, a deep learning-based approach for particle pruning in cryo-electron microscopy (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-30
    Description: Single-particle cryo-electron microscopy (cryo-EM) has recently become a mainstream technique for the structural determination of macromolecules. Typical cryo-EM workflows collect hundreds of thousands of single-particle projections from thousands of micrographs using particle-picking algorithms. However, the number of false positives selected by these algorithms is large, so that a number of different `cleaning steps' are necessary to decrease the false-positive ratio. Most commonly employed techniques for the pruning of false-positive particles are time-consuming and require user intervention. In order to overcome these limitations, a deep learning-based algorithm named Deep Consensus is presented in this work. Deep Consensus works by computing a smart consensus over the output of different particle-picking algorithms, resulting in a set of particles with a lower false-positive ratio than the initial set obtained by the pickers. Deep Consensus is based on a deep convolutional neural network that is trained on a semi-automatically generated data set. The performance of Deep Consensus has been assessed on two well known experimental data sets, virtually eliminating user intervention for pruning, and enhances the reproducibility and objectivity of the whole process while achieving precision and recall figures above 90%.
    Keywords: cryo-EMdeep learningimage processingparticle pruningthree-dimensional reconstruction
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    Thresholding of cryo-EM density maps by false discovery rate control (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-09
    Description: Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values. It is demonstrated that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures owing to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and is particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions in the structure.
    Keywords: electron cryo-microscopysignal detectionfalse discovery ratecryo-EM densitysubtomogram averaginglocal resolutionligand binding
    Electronic ISSN: 2052-2525
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    A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-09
    Description: A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. Since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. Finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative B factors to that damage in a robust way. The method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. The new method has been implemented as Bayesian polishing in RELION-3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.
    Keywords: Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy
    Electronic ISSN: 2052-2525
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    Homology-based loop modeling yields more complete crystallographic protein structures (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-08-09
    Description: Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and `graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.
    Keywords: loop buildingstructural re-buildingPDB-REDOmodel completioncrystallography
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    Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-08-30
    Description: Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.
    Keywords: phytochromesphotoreceptorsphotosynthetic bacteriamyxobacteriaabsorption spectra
    Electronic ISSN: 2052-2525
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    Bond orders for intermolecular interactions in crystals: charge transfer, ionicity and the effect on intramolecular bonds (2018)
    International Union of Crystallography (IUCr)
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    Publication Date: 2018-08-30
    Description: The question of whether intermolecular interactions in crystals originate from localized atom...atom interactions or as a result of holistic molecule...molecule close packing is a matter of continuing debate. In this context, the newly introduced Roby–Gould bond indices are reported for intermolecular `σ-hole' interactions, such as halogen bonding and chalcogen bonding, and compared with those for hydrogen bonds. A series of 97 crystal systems exhibiting these interaction motifs obtained from the Cambridge Structural Database (CSD) has been analysed. In contrast with conventional bond-order estimations, the new method separately estimates the ionic and covalent bond indices for atom...atom and molecule...molecule bond orders, which shed light on the nature of these interactions. A consistent trend in charge transfer from halogen/chalcogen bond-acceptor to bond-donor groups has been found in these intermolecular interaction regions via Hirshfeld atomic partitioning of the electron populations. These results, along with the `conservation of bond orders' tested in the interaction regions, establish the significant role of localized atom...atom interactions in the formation of these intermolecular binding motifs.
    Keywords: intermolecular interactionsbond orderionicityhydrogen bondinghalogen bondingcrystal engineeringcomputational modellingmolecular crystals
    Electronic ISSN: 2052-2525
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    Atomic level three-dimensional structure of individual particles with XFELs (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-09-06
    Keywords: single-particle three-dimensional imagingX-ray free electron lasersimaging virus particlesimage analysisthree-dimensional reconstructionatomic scale structure
    Electronic ISSN: 2052-2525
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    Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging (2018)
    International Union of Crystallography (IUCr)
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    Publication Date: 2018-09-06
    Description: Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.
    Keywords: XFELsMelbourneviruscoherent diffractive imagingLCLSimage reconstruction
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    Exploring the simultaneous σ-hole/π-hole bonding characteristics of a Br...π interaction in an ebselen derivative via experimental and theoretical electron-density analysis (2018)
    International Union of Crystallography (IUCr)
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    Publication Date: 2018-09-06
    Description: In this study, the nature and characteristics of a short Br...π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[d][1,2]selenazol-3(2H)-one, has been explored. The electronic nature of this Br...π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br...π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs).
    Keywords: σ-hole bondingπ-hole bondingebselenelectron densitymolecular electrostatic potentialscrystal engineeringcharge, spin and momentum densitiescomputational modellingmolecular crystals
    Electronic ISSN: 2052-2525
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    Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams (2018)
    International Union of Crystallography (IUCr)
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    Publication Date: 2018-09-12
    Description: Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70–2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector. This technique was used to characterize the `Uppsala injector', which is a pioneering and frequently used aerosol sample injector for XFEL single-particle imaging. The particle-beam focus, particle velocities, particle density and injection yield were measured at different operating conditions. It is also shown how high particle densities and good injection yields can be reached for large particles (100–500 nm). It is found that with decreasing particle size, particle densities and injection yields deteriorate, indicating the need for different injection strategies to extend XFEL imaging to smaller targets, such as single proteins. This work demonstrates the power of Rayleigh-scattering microscopy for studying focused aerosol beams quantitatively. It lays the foundation for lab-based injector development and online injection diagnostics for XFEL research. In the future, the technique may also find application in other fields that employ focused aerosol beams, such as mass spectrometry, particle deposition, fuel injection and three-dimensional printing techniques.
    Keywords: Rayleigh scatteringXFELsaerosol injectionUppsala injectorsnanoparticles
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    Photocage-initiated time-resolved solution X-ray scattering investigation of protein dimerization (2018)
    International Union of Crystallography (IUCr)
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    Publication Date: 2018-09-13
    Description: This work demonstrates a new method for investigating time-resolved structural changes in protein conformation and oligomerization via photocage-initiated time-resolved X-ray solution scattering by observing the ATP-driven dimerization of the MsbA nucleotide-binding domain. Photocaged small molecules allow the observation of single-turnover reactions of non-naturally photoactivatable proteins. The kinetics of the reaction can be derived from changes in X-ray scattering associated with ATP-binding and subsequent dimerization. This method can be expanded to any small-molecule-driven protein reaction with conformational changes traceable by X-ray scattering where the small molecule can be photocaged.
    Keywords: biophysicsX-ray solution scatteringphotocagingstructural biology
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Towards the theoretical limitations of X-ray nanocrystallography at high intensity: the validity of the effective-form-factor description (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-09-15
    Description: X-ray free-electron lasers (XFELs) broaden horizons in X-ray crystallography. Facilitated by the unprecedented high intensity and ultrashort duration of the XFEL pulses, they enable us to investigate the structure and dynamics of macromolecules with nano-sized crystals. A limitation is the extent of radiation damage in the nanocrystal target. A large degree of ionization initiated by the incident high-intensity XFEL pulse alters the scattering properties of the atoms leading to perturbed measured patterns. In this article, the effective-form-factor approximation applied to capture this phenomenon is discussed. Additionally, the importance of temporal configurational fluctuations at high intensities, shaping these quantities besides the average electron loss, is shown. An analysis regarding the applicability of the approach to targets consisting of several atomic species is made, both theoretically and via realistic radiation-damage simulations. It is concluded that, up to intensities relevant for XFEL-based nanocrystallography, the effective-form-factor description is sufficiently accurate. This work justifies treating measured scattering patterns using conventional structure-reconstruction algorithms.
    Keywords: XFELsX-ray nanocrystallographyeffective form factorionizationradiation damage
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 64
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    Single-particle imaging without symmetry constraints at an X-ray free-electron laser (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-09-19
    Description: The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.
    Keywords: single-particle imagingthree-dimensional virus reconstructionsXFELs
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Molecular dynamics study of tridymite (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-04-20
    Description: Structural changes in tridymite have been investigated by molecular dynamics simulation. Two thermal processes were carried out, one cooling from the high-temperature hexagonal structure of tridymite (HP-tridymite) and the other heating from the low-temperature monoclinic structure of tridymite (MX1-tridymite). The former process showed that HP, LHP (low-temperature hexagonal structure), OC (orthorhombic structure with C2221 symmetry) and OP (orthorhombic structure with P212121 symmetry)-like structures appeared in sequence. In contrast, the latter process showed that MX1, OP, OC, LHP and HP-like structures appeared in sequence. Detailed analysis of the calculated structures showed that the configuration underwent stepwise changes associated with several characteristic modes. First, the structure of HP-tridymite determined from diffraction experiments was identified as a time-averaged structure in a similar manner to β-cristobalite, thus indicating the important role of floppy modes of oxygen atoms at high temperature – one of the common features observed in silica crystals and glass. Secondly, the main structural changes were ascribed to a combination of distortion of the six-membered rings in the layers and misalignment between layers. We suggest that the slowing down of floppy oxygen movement invokes the multistage emergence of structures with lower symmetry on cooling. This study therefore not only reproduces the sequence of the main polymorphic transitions in tridymite, except for the appearance of the monoclinic phase, but also explains the microscopic dynamic structural changes in detail.
    Keywords: silicatridymitemolecular dynamicsstructurephase transitionspolymorphs
    Electronic ISSN: 2052-2525
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    Heterogeneous local order in self-assembled nanoparticle films revealed by X-ray cross-correlations (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-05-01
    Description: We report on the self-assembly of gold nanoparticles coated with a soft poly(ethylene glycol) shell studied by X-ray cross-correlation analysis. Depending on the initial concentration of gold nanoparticles used, structurally heterogeneous films were formed. The films feature hot spots of dominating four- and sixfold local order with patch sizes of a few micrometres, containing 104–105 particles. The amplitude of the order parameters suggested that a minimum sample amount was necessary to form well ordered local structures. Furthermore, the increasing variation in order parameters with sample thickness demonstrated a high degree of structural heterogeneity. This wealth of information cannot be obtained by the conventional microscopy techniques that are commonly used to study nanocrystal superstructures, as illustrated by complementary scanning electron microscopy measurements.
    Keywords: self-assembled nanoparticle filmsX-ray cross-correlationsXCCAgold nanoparticles
    Electronic ISSN: 2052-2525
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    Decoupling anion-ordering and spin-Peierls transitions in a strongly one-dimensional organic conductor with a chessboard structure, (o-Me2TTF)2NO3 (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-05-01
    Description: A mixed-valence conducting cation radical salt of the unsymmetrically substituted o-Me2TTF donor molecule (TTF is tetrathiafulvalene) was obtained upon electrocrystallization in the presence of the non-centrosymmetric NO3− anion. It crystallizes at room temperature in the monoclinic P21/c space group, with the anion disordered on an inversion centre. The donor molecules are stacked along the a axis. A 90° rotation of the longest molecular axis of o-Me2TTF generates a chessboard-like structure, preventing lateral S...S contacts between stacks and providing a strongly one-dimensional electronic system, as confirmed by overlap interaction energies and band structure calculations. A strong dimerization within the stacks explains the semiconducting behaviour of the salt, with σroom temp = 3–5 S cm−1 and Eactivated = 0.12–0.14 eV. An X-ray diffuse scattering survey of reciprocal space, combined with full structure resolutions at low temperatures (250, 85 and 20 K), evidenced the succession of two structural transitions: a ferroelastic one with an anion-ordering (AO) process and the establishment of a (0, ½, ½) superstructure below 124 (±3) K, also visible via resistivity thermal dependence, followed by a stack tetramerization with the establishment of a (½, ½, ½) superstructure below 90 (±5) K. The latter ground state is driven by a spin-Peierls (SP) instability, as demonstrated by the temperature dependence of the magnetic susceptibility. Surprisingly, these two kinds of instability appear to be fully decoupled here, at variance with other tetramethyltetrathiafulvalene (TMTTF) or tetramethyltetraselenafulvalene (TMTSF) salts with such non-centrosymmetric counter-ions.
    Keywords: anion-ordering transitionspin-Peierls transitionorganic conductorsmolecular crystalsphase transitions
    Electronic ISSN: 2052-2525
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    Direct shape determination of intermediates in evolving macromolecular solutions from small-angle scattering data (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-05-30
    Description: Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro. Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component. A method is presented to directly reconstruct the low-resolution shape of this transient component together with its volume fractions from multiple scattering patterns recorded from an evolving system. The method is implemented in the computer program DAMMIX freely available to academic users and its effectiveness is illustrated in several synthetic and experimental examples.
    Keywords: SAXSDAMMIXintermediatesmacromolecular solutionsbiological processes
    Electronic ISSN: 2052-2525
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    Symmetry breaking by enzyme-catalyzed epoxide hydrolysis (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-05-30
    Keywords: epoxide hydrolasestereoselectivitybiocatalysis
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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    Identification of ions in experimental electrostatic potential maps (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-06-02
    Description: Cryo-electron microscopy (cryo-EM) directly images the distribution of electrostatic potential (ESP) within macromolecules, and thus can provide much more information about atomic charge than X-ray crystallography. The electron-scattering length of an isolated ion is quite different from that of the corresponding neutral atom. The difference is very large at small scattering angles where the effects of electron distributions are largest, but becomes smaller at high scattering angles where nuclear charge determines outcomes. For this reason, in cryo-EM maps that have been solved at resolutions lower than ∼2.5 Å, peaks corresponding to anions will always be less prominent than those of cations, and may even be negative. Furthermore, if a map of this kind is smeared computationally after the fact, which reduces its effective resolution, anion peaks will diminish in size, cation peaks will grow and peaks that represent uncharged atoms will remain about the same. These effects can be used to determine the sign of the charges carried by the ions associated with a macromolecule and even estimate their magnitudes. The ESP value for a cation in a cation–anion pair is smaller than the value of the cation in isolation, but the ESP value for the anion in the ionic pair is greater than the value of the anion in isolation. The experimental range of ESP values for Mg2+ relative to that of the closest C1′ atom is found to be between 0.57 and 1.27.
    Keywords: cryo-EMelectron-scattering lengthtransition B factorMott equationribosome
    Electronic ISSN: 2052-2525
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    Model-free reconstruction of magnetic correlations in frustrated magnets (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-06-02
    Description: Frustrated magnetic systems exhibit extraordinary physical properties, but quantification of their magnetic correlations poses a serious challenge to experiment and theory. Current insight into frustrated magnetic correlations relies on modelling techniques such as reverse Monte-Carlo methods, which require knowledge about the exact ordered atomic structure. Here, we present a method for direct reconstruction of magnetic correlations in frustrated magnets by three-dimensional difference pair distribution function analysis of neutron total scattering data. The methodology is applied to the disordered frustrated magnet bixbyite, (Mn1−xFex)2O3, which reveals nearest-neighbor antiferromagnetic correlations for the metal sites up to a range of approximately 15 Å. Importantly, this technique allows for magnetic correlations to be determined directly from the experimental data without any assumption about the atomic structure.
    Keywords: three-dimensional magnetic pair distribution functionmagnetic correlationsfrustrated magnetsmagnetic diffuse scattering
    Electronic ISSN: 2052-2525
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    Monoclinic distortion, polarization rotation and piezoelectricity in the ferroelectric Na0.5Bi0.5TiO3 (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-06-02
    Description: The relationship between crystal structure and physical properties in the ferroelectric Na0.5Bi0.5TiO3 (NBT) has been of interest for the last two decades. Originally, the average structure was held to be of rhombohedral (R3c) symmetry with a fixed polarization direction. This has undergone a series of revisions, however, based on high-resolution X-ray diffraction, total neutron scattering, and optical and electron microscopy. The recent experimental findings suggest that the true average symmetry is monoclinic (space group Cc), which allows for a rotatable spontaneous polarization. Neither polarization rotation nor its potentially important real role in enhanced piezoelectricity is well understood. The present work describes an in situ investigation of the average monoclinic distortion in NBT by time-resolved single-crystal X-ray diffraction under external electric fields. The study presents a high-resolution inspection of the characteristic diffraction features of the monoclinic distortion – splitting of specific Bragg reflections – and their changes under a cyclic electric field. The results favour a model in which there is direct coupling between the shear monoclinic strain and the polarization rotation. This suggests that the angle of polarization rotation under a sub-coercive electric field could be 30° or more.
    Keywords: ferroelectricspiezoelectricstime-resolved X-ray diffractionpolarization rotation
    Electronic ISSN: 2052-2525
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    Dynamics of soft nanoparticle suspensions at hard X-ray FEL sources below the radiation-damage threshold (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-20
    Description: The application of X-ray photon correlation spectroscopy (XPCS) at free-electron laser (FEL) facilities enables, for the first time, the study of dynamics on a (sub-)nanometre scale in an unreached time range between femtoseconds and seconds. For soft-matter materials, radiation damage is a major limitation when going beyond single-shot applications. Here, an XPCS study is presented at a hard X-ray FEL on radiation-sensitive polymeric poly(N-isopropylacrylamide) (PNIPAM) nanoparticles. The dynamics of aqueous suspensions of densely packed silica-PNIPAM core-shell particles and a PNIPAM nanogel below the radiation-damage threshold are determined. The XPCS data indicate non-diffusive behaviour, suggesting ballistic and stress-dominated heterogeneous particle motions. These results demonstrate the feasibility of XPCS experiments on radiation-sensitive soft-matter materials at FEL sources and pave the way for future applications at MHz repetition rates as well as ultrafast modes using split-pulse devices.
    Keywords: XPCSFELPNIPAM nanoparticlesSACLAradiation-damage thresholdsoft-matter materials
    Electronic ISSN: 2052-2525
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    Systematic synthesis of a 6-component organic-salt alloy of naftopidil, and pentanary, quaternary and ternary multicomponent crystals (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-10-25
    Description: The single-crystal X-ray structure of a 6-component organic-salt alloy (hexanary) of naftopidil (1) (an active pharmaceutical ingredient) with benzoic acid (2) and four different hydroxy-substituted benzoic acids, i.e. salicylic acid (3), 2,3-dihydroxybenzoic acid (4), 2,4-dihydroxybenzoic acid (5) and 2,6-dihydroxybenzoic acid (6), is reported. The hexanary assembly originates from the observation that the binary salts of naftopidil with the above acids are isostructural. In addition to the 6-component solid, we also describe five 5-component, ten 4-component, and ten 3-component organic-salt alloys of naftopidil (1) with carboxylic acids (2)–(6). These alloys were obtained from different combinations of the acids with the drug. The synthetic design of the multicomponent organic alloys is based on the rationale of geometrical factors (shape and size) and chemical interactions (hydrogen bonds). The common supramolecular synthon in all these crystal structures was the cyclic N+—H...O− and O—H...O hydrogen-bonded motif of R_2^2(9) graph set between the 2-hydroxyammonium group of naftopidil and the carboxylate anion. This ionic synthon is strong and robust, directing the isostructural assembly of naftopidil with up to five different carboxylic acids in the crystal structure together with the lower-level multicomponent adducts. Solution crystallization by slow evaporation provided the multicomponent organic salts and alloys which were characterized by a combination of single-crystal X-ray diffraction, powder X-ray diffraction, NMR and differential scanning calorimetry techniques.
    Keywords: active pharmaceutical ingredientscrystal engineeringnaftopidilmulticomponent solids6-component crystalsorganic-salt alloys
    Electronic ISSN: 2052-2525
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    Biological single-particle imaging using XFELs – towards the next resolution revolution (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-01
    Keywords: Rayleigh scatteringXFELsaerosol injectionsingle-particle imaging
    Electronic ISSN: 2052-2525
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    Structure-factor amplitude reconstruction from serial femtosecond crystallography of two-dimensional membrane-protein crystals (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-13
    Description: Serial femtosecond crystallography of two-dimensional membrane-protein crystals at X-ray free-electron lasers has the potential to address the dynamics of functionally relevant large-scale motions, which can be sterically hindered in three-dimensional crystals and suppressed in cryocooled samples. In previous work, diffraction data limited to a two-dimensional reciprocal-space slice were evaluated and it was demonstrated that the low intensity of the diffraction signal can be overcome by collecting highly redundant data, thus enhancing the achievable resolution. Here, the application of a newly developed method to analyze diffraction data covering three reciprocal-space dimensions, extracting the reciprocal-space map of the structure-factor amplitudes, is presented. Despite the low resolution and completeness of the data set, it is shown by molecular replacement that the reconstructed amplitudes carry meaningful structural information. Therefore, it appears that these intrinsic limitations in resolution and completeness from two-dimensional crystal diffraction may be overcome by collecting highly redundant data along the three reciprocal-space axes, thus allowing the measurement of large-scale dynamics in pump–probe experiments.
    Keywords: free-electron lasersserial femtosecond crystallographymembrane proteinstwo-dimensional crystals
    Electronic ISSN: 2052-2525
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    Computational design of symmetrical eight-bladed β-propeller proteins (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-19
    Description: β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles. By computationally reverse-engineering the duplication, fusion and diversification events in the evolutionary history of a WD40 protein, a perfectly symmetrical homologue called Tako8 was made. If two or four blades of Tako8 are expressed as single polypeptides, they do not self-assemble to complete the eight-bladed architecture, which may be owing to the closely spaced negative charges inside the ring. A different computational approach was employed to redesign Tako8 to create Ika8, a fourfold-symmetrical protein in which neighbouring blades carry compensating charges. Ika2 and Ika4, carrying two or four blades per subunit, respectively, were found to assemble spontaneously into a complete eight-bladed ring in solution. These artificial eight-bladed rings may find applications in bionanotechnology and as models to study the folding and evolution of WD40 proteins.
    Keywords: bioinformaticsprotein structurecomputational modellingmolecular simulationstructural biologyWD40 proteinsβ-propeller proteins
    Electronic ISSN: 2052-2525
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    Direct air capture of CO2 – topological analysis of the experimental electron density (QTAIM) of the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4 (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-11-30
    Description: Chemical bonding and all intermolecular interactions in the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4, recently employed in the direct air capture of CO2 via crystallization, have been analyzed within the framework of the quantum theory of atoms in molecules (QTAIM) based on the experimental electron density derived from X-ray diffraction data obtained at 20 K. Accurate hydrogen positions were included based on an analogous neutron diffraction study at 100 K. Topological features of the covalent bonds demonstrate the presence of multiple bonds of various orders within the PyBIGH22+ cation. Strong hydrogen bonds define ribbons comprising carbonate anions and water molecules. These ribbons are linked to stacks of essentially planar dications via hydrogen bonds from the guanidinium moieties and an additional one to the pyridine nitrogen. The linking hydrogen bonds are approximately perpendicular to the anion–water ribbons. The observation of these putative interactions provided motivation to characterize them by topological analysis of the total electron density. Thus, all hydrogen bonds have been characterized by the properties of their (3,−1) bond critical points. Weaker interactions between the PyBIGH22+ cations have similarly been characterized. Integrated atomic charges are also reported. A small amount of cocrystallized hydroxide ion (∼2%) was also detected in both the X-ray and neutron data, and included in the multipole model for the electron-density refinement. The small amount of additional H+ required for charge balance was not detected in either the X-ray or the neutron data. The results are discussed in the context of the unusually low aqueous solubility of (PyBIGH2)(CO3)(H2O)4 and its ability to sequester atmospheric CO2.
    Keywords: carbon captureguanidineX-ray diffractionneutron diffractioncharge densitytopological analysiscrystal engineeringintermolecular interactionshydrogen bondingenvironmental chemistry
    Electronic ISSN: 2052-2525
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    Solving protein structure from sparse serial microcrystal diffraction data at a storage-ring synchrotron source (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-07-21
    Description: In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand–maximize–compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.
    Keywords: X-ray serial microcrystallographysparse dataEMC algorithmprotein microcrystallographystorage-ring synchrotron sources
    Electronic ISSN: 2052-2525
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    Towards a practical implementation of X-ray ghost imaging with synchrotron light (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-06-07
    Description: An experimental procedure for transmission X-ray ghost imaging using synchrotron light is presented. Hard X-rays from an undulator were divided by a beamsplitter to produce two copies of a speckled incident beam. Both beams were simultaneously measured on an indirect pixellated detector and the intensity correlation between the two copies was used to retrieve the ghost image of samples placed in one of the two beams, without measuring the samples directly. Aiming at future practical uses of X-ray ghost imaging, the authors discuss details regarding data acquisition, image reconstruction strategies and measure the point-spread function of the ghost-imaging system. This approach may become relevant for applications of ghost imaging with X-ray sources such as undulators in storage rings, free-electron lasers and lower-coherence laboratory facilities.
    Keywords: X-ray imagingX-ray ghost imagingX-ray specklecoherencecomputational X-ray imaginghard X-rayspoint-spread function
    Electronic ISSN: 2052-2525
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    Chlamydia protein Pgp3 studied at high resolution in a new crystal form (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-06-07
    Description: The protein Pgp3 is implicated in the sexually transmitted disease chlamydia and comprises an extended complex arrangement of a C-terminal domain (CTD) and an N-terminal domain (NTD) linked by a triple-helix coiled coil (THCC). Here, the X-ray crystal structure of Pgp3 from an LGV1 strain is reported at the highest X-ray diffraction resolution obtained to date for the full protein. The protein was crystallized using a high concentration of potassium bromide, which resulted in a new crystal form with relatively low solvent content that diffracted to a resolution of 1.98 Å. The three-dimensional structure of this new crystal form is described and compared with those of other crystal forms, and the potassium bromide binding sites and the relevance to chlamydia isolates from around the globe are described. The crystal packing is apparently driven by the CTDs. Since the threefold axes of the THCC and NTD are not collinear with the threefold axis of a CTD, this naturally leads to disorder in the THCC and the portion of the NTD that does not directly interact with the CTD via crystal packing. The key avenue to resolving these oddities in the crystal structure analysis was a complete new analysis in space group P1 and determining the space group as P212121. This space-group assignment was that originally determined from the diffraction pattern but was perhaps complicated by translational noncrystallographic symmetry. This crystal structure of a three-domain multi-macromolecular complex with two misaligned threefold axes was a unique challenge and has not been encountered before. It is suggested that a specific intermolecular interaction, possibly of functional significance in receptor binding in chlamydia, might allow the design of a new chemotherapeutic agent against chlamydia.
    Keywords: chlamydia proteinPgp3crystallizationcrystal formprotein structureX-ray crystallographystructural biologysexually transmitted diseases
    Electronic ISSN: 2052-2525
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    Identification of a tyrosine switch in copper-haem nitrite reductases (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-06-26
    Description: There are few cases where tyrosine has been shown to be involved in catalysis or the control of catalysis despite its ability to carry out chemistry at much higher potentials (1 V versus NHE). Here, it is shown that a tyrosine that blocks the hydrophobic substrate-entry channel in copper-haem nitrite reductases can be activated like a switch by the treatment of crystals of Ralstonia pickettii nitrite reductase (RpNiR) with nitric oxide (NO) (−0.8 ± 0.2 V). Treatment with NO results in an opening of the channel originating from the rotation of Tyr323 away from AspCAT97. Remarkably, the structure of a catalytic copper-deficient enzyme also shows Tyr323 in the closed position despite the absence of type 2 copper (T2Cu), clearly demonstrating that the status of Tyr323 is not controlled by T2Cu or its redox chemistry. It is also shown that the activation by NO is not through binding to haem. It is proposed that activation of the Tyr323 switch is controlled by NO through proton abstraction from tyrosine and the formation of HNO. The insight gained here for the use of tyrosine as a switch in catalysis has wider implications for catalysis in biology.
    Keywords: catalysisredox biologystructural biologyenzyme mechanismdenitrificationnitrogen cyclecopper-haem nitrite reductasesRalstonia pickettii
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 83
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    Structural flexibility of halogen bonds showed in a single-crystal-to-single-crystal [2+2] photodimerization (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-06-26
    Description: Halogen bonds have emerged as noncovalent forces that govern the assembly of molecules in organic solids with a degree of reliability akin to hydrogen bonds. Although the structure-directing roles of halogen bonds are often compared to hydrogen bonds, general knowledge concerning the fundamental structural behavior of halogen bonds has had limited opportunity to develop. Following an investigation of solid-state reactions involving organic syntheses and the development of photoresponsive materials, this work demonstrates the ability of the components of intermolecular N...I halogen bonding – a `workhorse' interaction for the crystal engineer – to support a single-crystal-to-single-crystal [2+2] photodimerization. A comparison is provided of the geometric changes experienced by the halogen-bonded components in the single-crystal reaction to the current crystal landscape of N...I halogen bonds, as derived from the Cambridge Structural Database. Specifically, a linear-to-bent type of deformation of the halogen-bonded components was observed, which is expected to support the development of functional halogen-bonded materials containing molecules that can undergo movements in close-packed crystal environments.
    Keywords: solid-state reactivityhalogen bondsphotodimerizationsupramolecular chemistrysingle-crystal-to-single-crystal reactioncrystal engineeringco-crystalsorganic solid-state reactionsframework-structured solids and amorphous materialsmolecular crystals
    Electronic ISSN: 2052-2525
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  • 84
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    X-ray lasers for structure and dynamics in biology (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-04-20
    Keywords: X-ray lasersXFELsprotein dynamicsstructural biology
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 85
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    Using cryo-electron microscopy maps for X-ray structure determination (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-05-12
    Description: X-ray crystallography and cryo-electron microscopy (cryo-EM) are complementary techniques for structure determination. Crystallography usually reveals more detailed information, while cryo-EM is an extremely useful technique for studying large-sized macromolecules. As the gap between the resolution of crystallography and cryo-EM data narrows, the cryo-EM map of a macromolecule could serve as an initial model to solve the phase problem of crystal diffraction for high-resolution structure determination. FSEARCH is a procedure to utilize the low-resolution molecular shape for crystallographic phasing. The IPCAS (Iterative Protein Crystal structure Automatic Solution) pipeline is an automatic direct-methods-aided dual-space iterative phasing and model-building procedure. When only an electron-density map is available as the starting point, IPCAS is capable of generating a completed model from the phases of the input map automatically, without the requirement of an initial model. In this study, a hybrid method integrating X-ray crystallography with cryo-EM to help with structure determination is presented. With a cryo-EM map as the starting point, the workflow of the method involves three steps. (1) Cryo-EM map replacement: FSEARCH is utilized to find the correct translation and orientation of the cryo-EM map in the crystallographic unit cell and generates the initial low-resolution map. (2) Phase extension: the phases calculated from the correctly placed cryo-EM map are extended to high-resolution X-ray data by non-crystallographic symmetry averaging with phenix.resolve. (3) Model building: IPCAS is used to generate an initial model using the phase-extended map and perform model completion by iteration. Four cases (the lowest cryo-EM map resolution being 6.9 Å) have been tested for the general applicability of the hybrid method, and almost complete models have been generated for all test cases with reasonable Rwork/Rfree. The hybrid method therefore provides an automated tool for X-ray structure determination using a cryo-EM map as the starting point.
    Keywords: FSEARCHIPCASiterative phasingcryo-EMmodel buildingstructure determinationcryo-electron microscopyX-ray crystallographyphase problem
    Electronic ISSN: 2052-2525
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  • 86
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    Multiple-scale structures: from Faraday waves to soft-matter quasicrystals (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-03-28
    Description: For many years, quasicrystals were observed only as solid-state metallic alloys, yet current research is now actively exploring their formation in a variety of soft materials, including systems of macromolecules, nanoparticles and colloids. Much effort is being invested in understanding the thermodynamic properties of these soft-matter quasicrystals in order to predict and possibly control the structures that form, and hopefully to shed light on the broader yet unresolved general questions of quasicrystal formation and stability. Moreover, the ability to control the self-assembly of soft quasicrystals may contribute to the development of novel photonics or other applications based on self-assembled metamaterials. Here a path is followed, leading to quantitative stability predictions, that starts with a model developed two decades ago to treat the formation of multiple-scale quasiperiodic Faraday waves (standing wave patterns in vibrating fluid surfaces) and which was later mapped onto systems of soft particles, interacting via multiple-scale pair potentials. The article reviews, and substantially expands, the quantitative predictions of these models, while correcting a few discrepancies in earlier calculations, and presents new analytical methods for treating the models. In so doing, a number of new stable quasicrystalline structures are found with octagonal, octadecagonal and higher-order symmetries, some of which may, it is hoped, be observed in future experiments.
    Keywords: quasicrystalssoft matterpattern formation
    Electronic ISSN: 2052-2525
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  • 87
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    Polymorphism of terthiophene with surface confinement (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-03-30
    Description: The origin of unknown polymorphic phases within thin films is still not well understood. This work reports on crystals of the molecule terthiophene which were grown by thermal gradient crystallization using glass-plate substrates. The crystalline domains displayed a plate-like morphology with an extended lateral size of about 100 µm, but a thickness of only a few µm. Specular X-ray diffraction patterns confirmed the presence of a new polymorph of terthiophene. Crystal structure solution from a single crystal peeled from the film revealed a structure with an extremely large unit-cell volume containing 42 independent molecules. In contrast to the previously determined crystal structure of terthiophene, a herringbone packing motif was observed where the terminal ends of the molecules are arranged within one plane (i.e. the molecular packing conforms to the flat substrate surface). This type of molecular packing is obtained by 180° flipped molecules combined with partially random (disordered) occupation. A densely packed interface between terthiophene crystallites and the substrate surface is obtained, this confirms that the new packing motif has adapted to the flat substrate surface.
    Keywords: molecular crystalssurface-mediated polymorphismthermal gradient crystallizationsingle-crystalline filmsspecular X-ray diffraction
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 88
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    Structural studies of crystalline forms of triamterene with carboxylic acid, GRAS and API molecules (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-04-07
    Description: Pharmaceutical salt solvates (dimethyl sulfoxide, DMSO) of the drug triamterene with the coformers acetic, succinic, adipic, pimelic, azelaic and nicotinic acid and ibuprofen are prepared by liquid-assisted grinding and solvent-evaporative crystallization. The modified ΔpKa rule as proposed by Cruz-Cabeza [(2012). CrystEngComm, 14, 6362–6365] is in close agreement with the results of this study. All adducts were characterized by X-ray diffraction and thermal analytical techniques, including single-crystal X-ray diffraction, powder X-ray diffraction, differential scanning calorimetry and thermal gravimetric analysis. Hydrogen-bonded motifs combined to form a variety of extended tapes and sheets. Analysis of the crystal structures showed that all adducts existed as salt solvates and contained the aminopyridinium–carboxylate heterodimer, except for the solvate containing triamterene, ibuprofen and DMSO, as a result of the presence of a strong and stable hemitriamterenium duplex. A search of the Cambridge Structural Database (CSD 5.36, Version 1.18) to determine the frequency of occurrence of the putative supramolecular synthons found in this study showed good agreement with previous work.
    Keywords: triamterenepKa analysiscrystal engineeringliquid-assisted grindingpharmaceutical salt solvateshydrogen bondingmotif analysisstable duplex structures
    Electronic ISSN: 2052-2525
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  • 89
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    Sample manipulation and data assembly for robust microcrystal synchrotron crystallography (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-04-20
    Description: With the recent developments in microcrystal handling, synchrotron microdiffraction beamline instrumentation and data analysis, microcrystal crystallography with crystal sizes of less than 10 µm is appealing at synchrotrons. However, challenges remain in sample manipulation and data assembly for robust microcrystal synchrotron crystallography. Here, the development of micro-sized polyimide well-mounts for the manipulation of microcrystals of a few micrometres in size and the implementation of a robust data-analysis method for the assembly of rotational microdiffraction data sets from many microcrystals are described. The method demonstrates that microcrystals may be routinely utilized for the acquisition and assembly of complete data sets from synchrotron microdiffraction beamlines.
    Keywords: microcrystalsmicrodiffractionradiation damagedata analysismultiple crystalsX-ray crystallographystructural biology
    Electronic ISSN: 2052-2525
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  • 90
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    π–π-Induced aggregation and single-crystal fluorescence anisotropy of 5,6,10b-triazaacephenanthrylene (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-04-20
    Description: The structural origin of absorption and fluorescence anisotropy of the single crystal of the π-conjugated heterocyclic system 5,6,10b-triazaacephenanthrylene, TAAP, is presented in this study. X-ray analysis shows that the crystal framework in the space group P\overline{1} is formed by centrosymmetric dimers of face-to-face mutually oriented TAAP molecules joined by π–π non-covalent interactions. The conformation of the TAAP molecule is stabilized by intramolecular C—H...N(sp2), N(sp2)H...π(CN), and C—H...O(sp2) hydrogen bonds. The presence of weak π–π interactions is confirmed by quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analysis. The analysis of the optical spectra of TAAP in solution and in the solid state does not allow the specification of the aggregation type. DFT calculations for the dimer in the gas phase indicate that the lowest singlet excitation is forbidden by symmetry, suggesting H-type aggregation, even though the overall absorption spectrum is bathochromically shifted as for the J-type. The experimental determination of the permanent dipole moment of a TAAP molecule in 1,4-dioxane solution indicates the presence of the monomer form. The calculated absorption and emission spectra of the crystal in a simple approximation are consistent with the experimentally determined orientation of the absorption and emission transition dipole moments in TAAP single crystals. The electrostatic interaction between monomers with a permanent dipole moment (ca 4 D each) could result in the unusual spectroscopic JH-aggregate behaviour of the TAAP dimer.
    Keywords: optical materialsfluorescenceanisotropyJH aggregatestriazaacephenanthrylene (TAAP)hydrogen bondingπ–π interactionstransition dipole moments
    Electronic ISSN: 2052-2525
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  • 91
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    Ionic scattering factors of atoms that compose biological molecules (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-05-01
    Description: Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac–Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O−. Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology. The calculated X-ray and electron scattering factors have then been parameterized for the major scattering curve models used in X-ray and electron protein crystallography and single-particle cryo-EM. The X-ray and electron scattering factors and the fitting parameters are presented for future reference.
    Keywords: form factorselectron crystallographysingle-particle cryo-EMstructure refinementX-ray crystallographyimagingstructure determination
    Electronic ISSN: 2052-2525
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  • 92
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    Dummy-atom modelling of stacked and helical nanostructures from solution scattering data (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-05-12
    Description: The availability of dummy-atom modelling programs to determine the shape of monodisperse globular particles from small-angle solution scattering data has led to outstanding scientific advances. However, there is no equivalent procedure that allows modelling of stacked, seemingly endless structures, such as helical systems. This work presents a bead-modelling algorithm that reconstructs the structural motif of helical and rod-like systems. The algorithm is based on a `projection scheme': by exploiting the recurrent nature of stacked systems, such as helices, the full structure is reduced to a single building-block motif. This building block is fitted by allowing random dummy-atom movements without an underlying grid. The proposed method is verified using a variety of analytical models, and examples are presented of successful shape reconstruction from experimental data sets. To make the algorithm available to the scientific community, it is implemented in a graphical computer program that encourages user interaction during the fitting process and also includes an option for shape reconstruction of globular particles.
    Keywords: SAXSstacked structureshelical structuresshape retrievalSasHelstructure determinationsolution scatteringcomputational modellingstructural biologynanoscience
    Electronic ISSN: 2052-2525
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  • 93
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    Response to comment on `Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase' (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-05-12
    Keywords: protein crystalscrystal lattices
    Electronic ISSN: 2052-2525
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  • 94
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    Comment on the article `Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase' (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-05-12
    Keywords: protein crystalscrystal lattices
    Electronic ISSN: 2052-2525
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  • 95
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    Exploitation of knowledge databases in the synthesis of zinc(II) malonates with photo-sensitive and photo-insensitive N,N′-containing linkers (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
    Details
    Publication Date: 2018-03-28
    Description: Photoinitiated solid-state reactions are known to affect the physical properties of coordination polymers, such as fluorescence and sorption behaviour, and also afford extraordinary architectures (e.g. three-periodic structures with polyorganic ligands). However, the construction of novel photo-sensitive coordination polymers requires an understanding of the factors which govern the mutual disposition of reactive fragments. A series of zinc(II) malonate complexes with 1,2-bis(pyridin-4-yl)ethylene and its photo-insensitive analogues has been synthesized for the purpose of systematic analysis of their underlying nets and mutual disposition of N-donor ligands. The application of a big data-set analysis for the prediction of a variety of possible complex compositions, coordination environments and networks for a four-component system has been demonstrated for the first time. Seven of the nine compounds possess one of the highly probable topologies for their underlying nets; in addition, two novel closely related four-coordinated networks were obtained. Complexes containing 1,2-bis(pyridin-4-yl)ethylene and 1,2-bis(pyridin-4-yl)ethane form isoreticular compounds more readily than those with 4,4′-bipyridine and 1,2-bis(pyridin-4-yl)ethylene. The effects of the precursor, either zinc(II) nitrate or zinc(II) acetate, on the composition and dimensionality of the resulting architecture are discussed. For three of the four novel complexes containing 1,2-bis(pyridin-4-yl)ethylene, the single-crystal-to-single-crystal [2 + 2] cycloaddition reactions were carried out. UV irradiation of these crystals afforded either the 0D→1D or the 3D→3D transformations, with and without network changes. One of the two 3D→3D transformations was accompanied by solvent (H2O) cleavage.
    Keywords: crystal engineeringcrystal structure predictionscoordination polymersorganic solid-state reactionscycloaddition reactionssingle-crystal-to-single-crystal transformationsphoto-sensitive ligands
    Electronic ISSN: 2052-2525
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    Sr2Pt8−xAs: a layered incommensurately modulated metal with saturated resistivity (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-06-09
    Description: The high-pressure synthesis and incommensurately modulated structure are reported for the new compound Sr2Pt8−xAs, with x = 0.715 (5). The structure consists of Sr2Pt3As layers alternating with Pt-only corrugated grids. Ab initio calculations predict a metallic character with a dominant role of the Pt d electrons. The electrical resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly, ρ showed a near-flat temperature dependence. This observation fits the description of the Mooij correlation for electrical resistivity in disordered metals, originally developed for statistically distributed point defects. The discussed material has a long-range crystallographic order, but the high concentration of Pt vacancies, incommensurately ordered, strongly influences the electronic conduction properties. This result extends the range of validity of the Mooij correlation to long-range ordered incommensurately modulated vacancies. Motivated by the layered structure, the resistivity anisotropy was measured in a focused-ion-beam micro-fabricated well oriented single crystal. A low resistivity anisotropy indicates that the layers are electrically coupled and conduction channels along different directions are intermixed.
    Keywords: platinum-based metallic compoundsincommensurately modulated structurevacanciesMooij correlationcomposite materialsinorganic materialsdensity functional theory
    Electronic ISSN: 2052-2525
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    Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-06-09
    Description: This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium–cytosinium trans sugar/sugar edge pair and an adeninium–adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation–cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.
    Keywords: charge densitymultipole refinementquantum crystallographyelectrostatic potentialelectrostatic interaction energylike-charged ionsnucleobasescytosineadenineguaninebase pairsintermolecular interactionsspin densitymomentum densityhydrogen bondingpharmaceutical solidsnucleic acid structures
    Electronic ISSN: 2052-2525
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    Double role of metalloporphyrins in catalytic bioinspired supramolecular metal–organic frameworks (SMOFs) (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-07-21
    Description: Heterogeneous catalysts are of great interest in many industrial processes for environmental reasons and, during recent years, a great effort has been devoted to obtain metal–organic frameworks (MOFs) with improved catalytic behaviour. Few supramolecular metal–organic frameworks (SMOFs) are stable under ambient conditions and those with anchored catalysts exhibit favourable properties. However, this paper presents an innovative approach that consists of using metal nodes as both structural synthons and catalysts. Regarding the latter, metalloporphyrins are suitable candidates to play both roles simultaneously. In fact, there are a number of papers that report coordination compounds based on metalloporphyrins exhibiting these features. Thus, the aim of this bioinspired work was to obtain stable SMOFs (at room temperature) based on metalloporphyrins and explore their catalytic activity. This work reports the environmentally friendly microwave-assisted synthesis and characterization of the compound [H(bipy)]2[(MnTPPS)(H2O)2]·2bipy·14H2O (TPPS = meso-tetraphenylporphine-4,4′,4′′,4′′′-tetrasulfonic acid and bipy = 4,4′-bipyridine). This compound is the first example of an MnTPPS-based SMOF, as far as we are aware, and has been structurally and thermally characterized through single-crystal X-ray diffraction, IR spectroscopy, thermogravimetry and transmission electron microscopy. Additionally, this work explores not only the catalytic activity of this compound but also of the compounds μ-O-[FeTCPP]2·16DMF and [CoTPPS0.5(bipy)(H2O)2]·6H2O. The structural features of these supramolecular materials, with accessible networks and high thermal stability, are responsible for their excellent behaviour as heterogeneous catalysts for different oxidation, condensation (aldol and Knoevenagel) and one-pot cascade reactions.
    Keywords: metalloporphyrinssupramolecular MOFsheterogeneous catalystsKnoevenagel condensationsaldol condensationsone-pot cascade reactions
    Electronic ISSN: 2052-2525
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  • 99
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    Do the basic crystal chemistry principles agree with a plethora of recent quantum chemistry data? (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-07-21
    Description: The main descriptors of chemical bonding such as bond order (BO) and electron density at the bond critical point, ρc, are customarily used to understand the crystal and electronic structure of materials, as well as to predict their reactivity and stability. They can be obtained in the framework of crystal chemistry and quantum chemistry approaches, which are mostly applied as alternatives to each other. This paper verifies the convergence of the two approaches by analyzing a plethora of quantum chemistry data available in the literature. The exponential correlation between the electron descriptors [BOij and ρc(ij)] and the length of chemical bonds, Rij, which is basic in crystal chemistry, was confirmed for 72 atom pairs, regardless of the nature of their interactions (ionic/covalent, metal–metal, etc.). The difference between the BOij (Rij) correlations obtained in this work and those accepted in crystal chemistry for the same atomic pairs does not exceed the dispersion of quantum chemistry data, confirming the qualitative validity of the BO conservation principle. Various examples are presented to show that knowledge of the exponential parameters ensures a surprisingly simple determination of two basic electron descriptors in any complex compound with known interatomic distances. In particular, the BO analysis for 20 Re6-cluster complexes illustrates the BO conservation for systems with delocalized electrons. Despite the significant transfer of electron density from the Re–Re to the Re–ligand bonds, the total number of Re valence electrons used in bonding remains close to the formal value of seven electrons.
    Keywords: chemical bondingbond orderbond lengthsbond critical pointelectron densityconservation principles
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    Rapid sample delivery for megahertz serial crystallography at X-ray FELs (2018)
    International Union of Crystallography (IUCr)
    In: IUCrJ
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    Publication Date: 2018-07-28
    Description: Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s−1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.
    Keywords: X-ray free-electron lasersFELsX-ray FEL pulse trainsmegahertz repetition rates
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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