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Title: Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

Abstract

A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)

Authors:
;  [1];  [2];  [3];  [4];  [1];  [5];  [1];  [3];  [6];  [1];  [3];  [7];  [1];  [2];  [8]
  1. Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands)
  2. (C-CINA), Biozentrum, University of Basel, CH-4058 Basel (Switzerland)
  3. Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium)
  4. Department of Physics and Energy, Materials and Surface Science Institute (MSSI), University of Limerick, Limerick (Ireland)
  5. (Netherlands)
  6. (Spain)
  7. Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen (Switzerland)
  8. (PSI), 5232 Villigen (Switzerland)
Publication Date:
OSTI Identifier:
22535125
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section A, Foundations and Advances (Online); Journal Volume: 72; Journal Issue: Pt 2; Other Information: PMCID: PMC4770873; PMID: 26919375; PUBLISHER-ID: td5026; OAI: oai:pubmedcentral.nih.gov:4770873; Copyright (c) E. van Genderen et al. 2016; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United Kingdom
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; COMPUTER CODES; ELECTRON DIFFRACTION; MATHEMATICAL SOLUTIONS; NANOSTRUCTURES; RADIATION EFFECTS; SIGNAL-TO-NOISE RATIO; TEMPERATURE RANGE 0273-0400 K; THREE-DIMENSIONAL CALCULATIONS; TRANSMISSION ELECTRON MICROSCOPY; X RADIATION

Citation Formats

Genderen, E. van, Clabbers, M. T. B., Center for Cellular Imaging and NanoAnalytics, Das, P. P., Stewart, A., Nederlof, I., Amsterdam Scientific Instruments, Postbus 41882, 1009 DB Amsterdam, Barentsen, K. C., Portillo, Q., Centres Científics i Tecnològics de la Universitat de Barcelona, University of Barcelona, Carrer de Lluís Solé i Sabaris, 1-3, Barcelona, Pannu, N. S., Nicolopoulos, S., Gruene, T., E-mail: tim.gruene@psi.ch, Abrahams, J. P., E-mail: tim.gruene@psi.ch, Center for Cellular Imaging and NanoAnalytics, and Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. United Kingdom: N. p., 2016. Web. doi:10.1107/S2053273315022500.
Genderen, E. van, Clabbers, M. T. B., Center for Cellular Imaging and NanoAnalytics, Das, P. P., Stewart, A., Nederlof, I., Amsterdam Scientific Instruments, Postbus 41882, 1009 DB Amsterdam, Barentsen, K. C., Portillo, Q., Centres Científics i Tecnològics de la Universitat de Barcelona, University of Barcelona, Carrer de Lluís Solé i Sabaris, 1-3, Barcelona, Pannu, N. S., Nicolopoulos, S., Gruene, T., E-mail: tim.gruene@psi.ch, Abrahams, J. P., E-mail: tim.gruene@psi.ch, Center for Cellular Imaging and NanoAnalytics, & Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. United Kingdom. doi:10.1107/S2053273315022500.
Genderen, E. van, Clabbers, M. T. B., Center for Cellular Imaging and NanoAnalytics, Das, P. P., Stewart, A., Nederlof, I., Amsterdam Scientific Instruments, Postbus 41882, 1009 DB Amsterdam, Barentsen, K. C., Portillo, Q., Centres Científics i Tecnològics de la Universitat de Barcelona, University of Barcelona, Carrer de Lluís Solé i Sabaris, 1-3, Barcelona, Pannu, N. S., Nicolopoulos, S., Gruene, T., E-mail: tim.gruene@psi.ch, Abrahams, J. P., E-mail: tim.gruene@psi.ch, Center for Cellular Imaging and NanoAnalytics, and Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute. 2016. "Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector". United Kingdom. doi:10.1107/S2053273315022500.
@article{osti_22535125,
title = {Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector},
author = {Genderen, E. van and Clabbers, M. T. B. and Center for Cellular Imaging and NanoAnalytics and Das, P. P. and Stewart, A. and Nederlof, I. and Amsterdam Scientific Instruments, Postbus 41882, 1009 DB Amsterdam and Barentsen, K. C. and Portillo, Q. and Centres Científics i Tecnològics de la Universitat de Barcelona, University of Barcelona, Carrer de Lluís Solé i Sabaris, 1-3, Barcelona and Pannu, N. S. and Nicolopoulos, S. and Gruene, T., E-mail: tim.gruene@psi.ch and Abrahams, J. P., E-mail: tim.gruene@psi.ch and Center for Cellular Imaging and NanoAnalytics and Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute},
abstractNote = {A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)},
doi = {10.1107/S2053273315022500},
journal = {Acta Crystallographica. Section A, Foundations and Advances (Online)},
number = Pt 2,
volume = 72,
place = {United Kingdom},
year = 2016,
month = 2
}
  • No abstract prepared.
  • A method for the determination of the room-temperature fluorescence and room-temperature phosphorescence quantum yields for organic compounds adsorbed on different surfaces is described and evaluated. Quantum yield values were determined for compounds adsorbed on sodium acetate, a polyacrylic acid-NaBr mixture, and filter paper. The approach employs conventional instrumentation with various instrumental modifications for obtaining accurate and reproducible data. Quantum yield values at room temperature with and without nitrogen flowing over the solid surfaces are compared. The results show that the method is very reproducible and relatively low quantum yield values can be obtained. 17 references, 1 figure, 3 tables.
  • An ultrasensitive Medipix2 detector allowed the collection of rotation electron-diffraction data from single three-dimensional protein nanocrystals for the first time. The data could be analysed using the standard X-ray crystallography programs MOSFLM and SCALA. When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irrespective of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e{sup −} Å{sup −2}),more » a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resolution, indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that volumes of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-analysis software (MOSFLM and SCALA) from X-ray protein crystallography can be used in principle for analysing electron-diffraction data from three-dimensional nanocrystals of proteins.« less
  • A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for themore » SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.« less