Crystal structure refinement with SHELXL

George M. Sheldrick

doi:10.1107/S2053229614024218

Journal Article•DOI•

Crystal structure refinement with SHELXL

01 Jan 2015-Acta Crystallographica Section C-crystal Structure Communications (International Union of Crystallography)-Vol. 71, Iss: 1, pp 3-8

TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.

Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

Topics: Crystallographic Information File (51%)

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Journal Article•DOI•

SHELXT - Integrated space-group and crystal- structure determination

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George M. Sheldrick¹•Institutions (1)

01 Jan 2015-Acta Crystallographica Section A

TL;DR: This work automates routine small-molecule structure determination starting from single-crystal reflection data, the Laue group and a reasonable guess as to which elements might be present.

Abstract: The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.

11,698 citations

Cites background or methods from "Crystal structure refinement with S..."

...This structure was published by Barkley et al. (2011) in the noncentrosymmetric space group P62c, but there are two warning signs: checkCIF (Spek, 2009) detects an inversion centre (a B alert) and the Flack parameter is dubious: the current SHELXL (Sheldrick, 2015) gives a value of 0.46 (11)....
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...This is similar to the CGLS refinement in SHELXL (Sheldrick, 2008, 2015) and is performed in parallel....
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Journal Article•DOI•

J. Appl. Cryst.の発刊に際して

[...]

良二上田

10 Mar 1970-

8,159 citations

Journal Article•DOI•

The Cambridge Structural Database

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Colin R. Groom¹, Ian J. Bruno¹, Matthew P. Lightfoot¹, Suzanna C. Ward¹•Institutions (1)

01 Apr 2016-Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry

TL;DR: The creation, maintenance, information content and availability of the Cambridge Structural Database (CSD), the world’s repository of small molecule crystal structures, are described.

Abstract: The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

4,784 citations

Cites methods from "Crystal structure refinement with S..."

...The embedding of reflection data into the CIF by structure refinement programs such as SHELXL (Sheldrick, 2015) greatly simplifies this process....
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Journal Article•DOI•

PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors

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Anthony L. Spek¹•Institutions (1)

01 Jan 2015-Acta Crystallographica Section C-crystal Structure Communications

TL;DR: The SQUEEZE method is documents as an alternative means of addressing the solvent disorder issue and conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL, and many twinned structures containing disordered solvents are now also treatable by SQUEEze.

Abstract: The completion of a crystal structure determination is often hampered by the presence of embedded solvent molecules or ions that are seriously disordered. Their contribution to the calculated structure factors in the least-squares refinement of a crystal structure has to be included in some way. Traditionally, an atomistic solvent disorder model is attempted. Such an approach is generally to be preferred, but it does not always lead to a satisfactory result and may even be impossible in cases where channels in the structure are filled with continuous electron density. This paper documents the SQUEEZE method as an alternative means of addressing the solvent disorder issue. It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015). Acta Cryst. C71. In the press] and other refinement programs that accept externally provided fixed contributions to the calculated structure factors. The PLATON SQUEEZE tool calculates the solvent contribution to the structure factors by back-Fourier transformation of the electron density found in the solvent-accessible region of a phase-optimized difference electron-density map. The actual least-squares structure refinement is delegated to, for example, SHELXL. The current versions of PLATON SQUEEZE and SHELXL now address several of the unnecessary complications with the earlier implementation of the SQUEEZE procedure that were a necessity because least-squares refinement with the now superseded SHELXL97 program did not allow for the input of fixed externally provided contributions to the structure-factor calculation. It is no longer necessary to subtract the solvent contribution temporarily from the observed intensities to be able to use SHELXL for the least-squares refinement, since that program now accepts the solvent contribution from an external file (.fab file) if the ABIN instruction is used. In addition, many twinned structures containing disordered solvents are now also treatable by SQUEEZE. The details of a SQUEEZE calculation are now automatically included in the CIF archive file, along with the unmerged reflection data. The current implementation of the SQUEEZE procedure is described, and discussed and illustrated with three examples. Two of them are based on the reflection data of published structures and one on synthetic reflection data generated for a published structure.

2,100 citations

Cites background or methods from "Crystal structure refinement with S..."

...…parameter values, the geometric parameter values themselves and the confidence factors R[F 2 > 2 (F 2)], wR(F 2) and S. Programs such as SHELXL (Sheldrick, 2008, 2015), CRYSTALS (Betteridge et al., 2003), JANA (Petřı́ček et al., 2014) and OLEX2 (Dolomanov et al., 2009) offer elaborate…...
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...It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015)....
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...The SQUEEZE procedure can be carried out using as input either name.cif and name.fcf data files or name.ins and name.hkl data files, where name is the chosen name for the data set [these are the usual files, respectively generated by, or used as input to, the SHELXL program (Sheldrick, 2015)]....
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...This paper describes the current SQUEEZE implementation that is based on new functionality included in the 2014 version of SHELXL (Sheldrick, 2015)....
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Journal Article•DOI•

Magnetic hysteresis up to 80 kelvin in a dysprosium metallocene single-molecule magnet

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Fu-Sheng Guo¹, Benjamin M. Day¹, Benjamin M. Day², Yan-Cong Chen³ +3 more•Institutions (4)

21 Dec 2018-Science

TL;DR: A dysprosium compound is reported that manifests magnetic hysteresis at temperatures up to 80 kelvin, which overcomes an essential barrier toward the development of nanomagnet devices that function at practical temperatures.

Abstract: Single-molecule magnets (SMMs) containing only one metal center may represent the lower size limit for molecule-based magnetic information storage materials. Their current drawback is that all SMMs require liquid-helium cooling to show magnetic memory effects. We now report a chemical strategy to access the dysprosium metallocene cation [(CpiPr5)Dy(Cp*)]+ (CpiPr5 = penta-iso-propylcyclopentadienyl, Cp* = pentamethylcyclopentadienyl), which displays magnetic hysteresis above liquid-nitrogen temperatures. An effective energy barrier to reversal of the magnetization of Ueff = 1,541 cm–1 is also measured. The magnetic blocking temperature of TB = 80 K for this cation overcomes an essential barrier towards the development of nanomagnet devices that function at practical temperatures.

785 citations

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Journal Article•DOI•

A short history of SHELX

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George M. Sheldrick¹•Institutions (1)

01 Jan 2008-Acta Crystallographica Section A

TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

Abstract: An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

77,177 citations

"Crystal structure refinement with S..." refers background in this paper

...ABIN takes two free variable numbers (Sheldrick, 2008) n1 and n2 as parameters....
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...Readers not familiar with SHELX may find it useful to look at Sheldrick (2008) before reading this paper....
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...The early history has been described by Sheldrick (2008)....
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Journal Article•DOI•

Structure validation in chemical crystallography

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Anthony L. Spek¹•Institutions (1)

01 Feb 2009-Acta Crystallographica Section D-biological Crystallography

TL;DR: This paper reports on the current status of structure validation in chemical crystallography and describes the current state of research in this area.

Abstract: Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.

12,245 citations

"Crystal structure refinement with S..." refers methods in this paper

...This option is essential for applying the SQUEEZE option in PLATON to twinned structures, but also has other uses....
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...For twinned structures, it is necessary first to use the new LIST 8 instruction (see below) to generate detwinned data for input to PLATON....
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...PLATON calculates the partial structure factors corresponding to a blob of unmodelled difference density and writes them to the .fab file....
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...The new ABIN instruction was primarily designed to facilitate the use of the SQUEEZE facility (Spek, 2015) in the program PLATON (Spek, 2009), but it can also be used to input a bulk solvent model for a macromolecule....
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Journal Article•DOI•

On enantiomorph‐polarity estimation

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H. D. Flack

01 Nov 1983-Acta Crystallographica Section A

Abstract: The behaviour of Rogers's η parameter for enantiomorph-polarity estimation is examined theoretically and experimentally on simulated intensity data for seven well-assorted compounds. An alternative parameter x, based on incoherent scattering from twin components related by a centre of symmetry, is also considered. It is found that both parameters are very well adapted to implementation in a least-squares program and converge well. The η parameter can give false and over-precise indications of chirality-polarity for structures which are nearly centrosymmetric, whereas the x parameter does not have this fault and converges more rapidly than η.

9,824 citations

"Crystal structure refinement with S..." refers methods in this paper

...When the 2008 SHELX paper was written, the method of choice to determine the absolute structure was to refine the Flack parameter (Flack, 1983) as one of the parameters in a full-matrix refinement....
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Journal Article•DOI•

The Cambridge Structural Database: a quarter of a million crystal structures and rising

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Frank H. Allen¹•Institutions (1)

01 Jun 2002-Acta Crystallographica Section B-structural Science

TL;DR: The Cambridge Structural Database now contains data for more than a quarter of a million small-molecule crystal structures, and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.

Abstract: The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.

9,664 citations

"Crystal structure refinement with S..." refers background in this paper

...…to understand why several leading chemical journals still only require the deposition of the atom coordinates, etc., but not the reflection data, especially now that the Cambridge Structural Database (CSD; Allen, 2002) accepts the new CIFs and strongly encourages deposition of the reflection data....
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Journal Article•DOI•

J. Appl. Cryst.の発刊に際して

[...]

良二上田

10 Mar 1970-

8,159 citations

"Crystal structure refinement with S..." refers methods in this paper

...Multithreading is achieved using OpenMP along the lines suggested by Diederichs (2000), and the program is particularly suitable for multiple-core processors....
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