WinGX and ORTEP for Windows: an update
01 Aug 2012-Journal of Applied Crystallography (International Union of Crystallography)-Vol. 45, Iss: 4, pp 849-854
TL;DR: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF.
Abstract: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.
Citations
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TL;DR: In this paper, a large scale synthesis, crystal structure, and optical characterization of the 2D (CH3(CH2)3NH3)n−1PbnI3n+1 (n = 1, 2, 3, 4, ∞) perovskites is presented.
Abstract: The hybrid two-dimensional (2D) halide perovskites have recently drawn significant interest because they can serve as excellent photoabsorbers in perovskite solar cells. Here we present the large scale synthesis, crystal structure, and optical characterization of the 2D (CH3(CH2)3NH3)2(CH3NH3)n−1PbnI3n+1 (n = 1, 2, 3, 4, ∞) perovskites, a family of layered compounds with tunable semiconductor characteristics. These materials consist of well-defined inorganic perovskite layers intercalated with bulky butylammonium cations that act as spacers between these fragments, adopting the crystal structure of the Ruddlesden–Popper type. We find that the perovskite thickness (n) can be synthetically controlled by adjusting the ratio between the spacer cation and the small organic cation, thus allowing the isolation of compounds in pure form and large scale. The orthorhombic crystal structures of (CH3(CH2)3NH3)2(CH3NH3)Pb2I7 (n = 2, Cc2m; a = 8.9470(4), b = 39.347(2) A, c = 8.8589(6)), (CH3(CH2)3NH3)2(CH3NH3)2Pb3I10 (...
1,451 citations
TL;DR: In this paper, the authors examined the crystallographic and magnetic properties of single crystals of CrI3, an easily cleavable, layered and insulating ferromagnet with a Curie temperature of 61 K.
Abstract: We have examined the crystallographic and magnetic properties of single crystals of CrI3, an easily cleavable, layered and insulating ferromagnet with a Curie temperature of 61 K. Our X-ray diffraction studies reveal a first-order crystallographic phase transition occurring near 210–220 K upon warming, with significant thermal hysteresis. The low-temperature structure is rhombohedral (R3, BiI3-type) and the high-temperature structure is monoclinic (C2/m, AlCl3-type). We find evidence for coupling between the crystallographic and magnetic degrees of freedom in CrI3, observing an anomaly in the interlayer spacing at the Curie temperature and an anomaly in the magnetic susceptibility at the structural transition. First-principles calculations reveal the importance of proper treatment of the long-ranged interlayer forces, and van der Waals density functional theory does an excellent job of predicting the crystal structures and their relative stability. Calculations also suggest that the ferromagnetic order f...
781 citations
TL;DR: This paper provides additional background information on the checkCIF procedure and additional details for a number of ALERTS along with options for how to act on them.
Abstract: Authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of interest and their interpretation, but are also expected to archive in computer-readable CIF format the experimental data on which the crystal-structure analysis is based. Additionally, an IUCr/checkCIF validation report will be required for the review of a submitted paper. Such a validation report, automatically created from the deposited CIF file, lists as ALERTS not only potential errors or unusual findings, but also suggestions for improvement along with interesting information on the structure at hand. Major ALERTS for issues are expected to have been acted on already before the submission for publication or discussed in the associated paper and/or commented on in the CIF file. In addition, referees, readers and users of the data should be able to make their own judgment and interpretation of the underlying experimental data or perform their own calculations with the archived data. All the above is consistent with the FAIR (findable, accessible, interoperable, and reusable) initiative [Helliwell (2019). Struct. Dyn. 6, 05430]. Validation can also be helpful for less experienced authors in pointing to and avoiding of crystal-structure determination and interpretation pitfalls. The IUCr web-based checkCIF server provides such a validation report, based on data uploaded in CIF format. Alternatively, a locally installable checkCIF version is available to be used iteratively during the structure-determination process. ALERTS come mostly as short single-line messages. There is also a short explanation of the ALERTS available through the IUCr web server or with the locally installed PLATON/checkCIF version. This paper provides additional background information on the checkCIF procedure and additional details for a number of ALERTS along with options for how to act on them.
634 citations
Cites methods from "WinGX and ORTEP for Windows: an upd..."
...The CRYSTALS (Betteridge et al., 2003), JANA (Petricek & Dusek, 2000) and WinGX (Farrugia, 2012) refinement packages follow similar archival schemes....
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TL;DR: The second harmonic generation (SHG) properties of the hybrid organic/inorganic germanium perovskite compounds display remarkably strong, type I phase-matchable SHG response with high laser-induced damage thresholds (up to ∼3 GW/cm(2).
Abstract: The synthesis and properties of the hybrid organic/inorganic germanium perovskite compounds, AGeI3, are reported (A = Cs, organic cation). The systematic study of this reaction system led to the isolation of 6 new hybrid semiconductors. Using CsGeI3 (1) as the prototype compound, we have prepared methylammonium, CH3NH3GeI3 (2), formamidinium, HC(NH2)2GeI3 (3), acetamidinium, CH3C(NH2)2GeI3 (4), guanidinium, C(NH2)3GeI3 (5), trimethylammonium, (CH3)3NHGeI3 (6), and isopropylammonium, (CH3)2C(H)NH3GeI3 (7) analogues. The crystal structures of the compounds are classified based on their dimensionality with 1–4 forming 3D perovskite frameworks and 5–7 1D infinite chains. Compounds 1–7, with the exception of compounds 5 (centrosymmetric) and 7 (nonpolar acentric), crystallize in polar space groups. The 3D compounds have direct band gaps of 1.6 eV (1), 1.9 eV (2), 2.2 eV (3), and 2.5 eV (4), while the 1D compounds have indirect band gaps of 2.7 eV (5), 2.5 eV (6), and 2.8 eV (7). Herein, we report on the second...
630 citations
TL;DR: A mononuclear Dy(iii) complex assembled just from five water molecules and two phosphonic diamide ligands combines the advantages of high anisotropy barrier, high blocking temperature and significant coercivity, apart from its remarkable air- and moisture-stability.
Abstract: Herein we report air-stable Dy(III) and Er(III) single-ion magnets (SIMs) with pseudo-D5h symmetry, synthesized from a sterically encumbered phosphonamide, tBuPO(NHiPr)2, where the Dy(III)-SIM exhibits a magnetization blocking (TB) up to 12 K, defined from the maxima of the zero-field cooled magnetization curve, with an anisotropy barrier (Ueff) as high as 735.4 K. The Dy(III)-SIM exhibits a magnetic hysteresis up to 12 K (30 K) with a large coercivity of ∼0.9 T (∼1.5 T) at a sweep rate of ∼0.0018 T s−1 (0.02 T s−1). These high values combined with persistent stability under ambient conditions, render this system as one of the best-characterized SIMs. Ab initio calculations have been used to establish the connection between the higher-order symmetry of the molecule and the quenching of quantum tunnelling of magnetization (QTM) effects. The relaxation of magnetization is observed via the second excited Kramers doublet owing to pseudo-high-order symmetry, which quenches the QTM. This study highlights fine-tuning of symmetry around the lanthanide ion to obtain new-generation SIMs and offers further scope for pushing the limits of Ueff and TB using this approach.
440 citations
References
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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.
81,116 citations
"WinGX and ORTEP for Windows: an upd..." refers background or methods in this paper
...…the RBLS least-squares refinement program from the GX suite, but with the release of the refinement program SHELXL93, and subsequently SHELXL97 (Sheldrick, 2008), which had a much more sophisticated implementation of constraints and restraints, it was decided to use the latter as the…...
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...The advent of general crystallographic codes such as XRAY72 (Stewart et al., 1972), the Oak Ridge program suite ORTEP (Johnson, 1965), ORFFE and ORFLS (Busing et al., 1962, 1964), and SHELX76 (Sheldrick, 2008) provided most of the necessary computational operations in a single program or suite of programs....
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...The philosophy of WinGX is to provide as many approaches as possible and it is considered worthwhile to continue supporting fairly old structuresolution programs, such as SHELXS86 (Sheldrick, 2008) and SIR92 (Altomare et al., 1993)....
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...The default refinement program for WinGX is currently SHELXL97 (Sheldrick, 2008)....
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...There are several ways to initiate a structural analysis in WinGX, including semi-automatic input from diffractometer data files (Nonius KappaCCD, Bruker SMART or SAINT, or Rigaku files) or from SHELX files (Sheldrick, 2008)....
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TL;DR: L Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
Abstract: Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and significant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. CrysL (1985). 18, 189190] and on the World Wide Web at http://www.iucr. ac. uk/journals/jac/software/. Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known. J. App/. CrysL (1997). 30, 565 ORTEP-3 for Windows a version of ORTEP-III with a Graphical User Interface (GUI)
19,468 citations
"WinGX and ORTEP for Windows: an upd..." refers background in this paper
...It now seems appropriate to describe some of the more modern features of these programs, which were not discussed in the original short computer program abstracts (Farrugia, 1997, 1999)....
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TL;DR: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones.
Abstract: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/. Lists of software presented and/or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
18,151 citations
"WinGX and ORTEP for Windows: an upd..." refers background or methods in this paper
...The GX code was first ported to the MS-DOS environment and then to the Windows environment, becoming the WinGX program (Farrugia, 1999)....
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...It was at this stage that WinGX was first publicly released on the internet in 1997 (Farrugia, 1999)....
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...It now seems appropriate to describe some of the more modern features of these programs, which were not discussed in the original short computer program abstracts (Farrugia, 1997, 1999)....
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TL;DR: SIR97 is the integration of two programs, SIR92 and CAOS, the first devoted to the solution of crystal structures by direct methods, the second to refinement via least-squares–Fourier procedures.
Abstract: SIR97 is the integration of two programs, SIR92 and CAOS, the first devoted to the solution of crystal structures by direct methods, the second to refinement via least-squares–Fourier procedures. Several new features have been introduced in SIR97 with respect to the previous version, SIR92: greater automatization, increased efficiency of the direct methods section, and a powerful graphics interface. The program also provides publication tables and CIF files.
8,807 citations
"WinGX and ORTEP for Windows: an upd..." refers background in this paper
...Similarly, if WinGX detects that the programs have been installed, it will also provide GUI menu items for SIR97 (Altomare et al., 1999), SIR2002 (Burla et al., 2003), SIR2004 (Burla et al., 2005), SIR2008 (Burla et al., 2007) and recently for SIR2011 (Burla et al., 2012)....
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