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.
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TL;DR: Biological evaluation of a small library of N-palmitoyl-ethanolamine analogues or derivatives, characterized by a protected acid function, useful to decrease their hydrolysis rate in vitro and prolong their biological activity are reported.
Abstract: N-Palmitoyl-ethanolamine (PEA) is an anti-inflammatory component of egg yolk that is usually employed for the prevention of respiratory apparatus virus infection and then frequently used for its efficient anti-inflammatory and analgesic effects in experimental models of visceral, neuropathic, and inflammatory diseases. Nevertheless, data of its use in animal or human therapy are still scarce and further studies are needed. Herein, we report the biological evaluation of a small library of N-palmitoyl-ethanolamine analogues or derivatives, characterized by a protected acid function (either as palmitoyl amides or hexadecyl esters), useful to decrease their hydrolysis rate in vitro and prolong their biological activity. Two of these compounds—namely phenyl-carbamic acid hexadecyl ester (4) and 2-methyl-pentadecanoic acid (4-nitro-phenyl)-amide (5)—have shown good anti-inflammatory and antioxidant properties, without affecting the viability of J774A.1 macrophages. Finally, crystals suitable for X-ray analysis of compound 4 have been obtained, and its solved crystal structure is here reported. Our outcomes may be helpful for a rational drug design based on new PEA analogues/derivatives with improved biological properties.
482 citations
Cites methods from "Crystal structure refinement with S..."
...The structures were solved by direct methods (SIR97) [47] and refined by full-matrix least-squares on F2 (SHELXL-97 [48] and WINGX programs [49]) using anisotropic displacement parameters for all atoms except for hydrogens (ORTEP view of 4 is given in Figure 6)....
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...The structures were solved by direct methods (SIR97) [47] and refined by full-matrix leastsquares on F2 (SHELXL-97 [48] and WINGX programs [49]) using anisotropic displacement parameters for all atoms except for hydrogens (ORTEP view of 4 is given in Figure 6)....
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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
TL;DR: In this paper, the authors used graph theory to predict the self-assembly of even larger tetravalent Goldberg polyhedra, which should be more stable, enabling another member of this polyhedron family to be assembled from 144 components: 48 palladium ions and 96 bent ligands.
Abstract: Rational control of the self-assembly of large structures is one of the key challenges in chemistry, and is believed to become increasingly difficult and ultimately impossible as the number of components involved increases. So far, it has not been possible to design a self-assembled discrete molecule made up of more than 100 components. Such molecules-for example, spherical virus capsids-are prevalent in nature, which suggests that the difficulty in designing these very large self-assembled molecules is due to a lack of understanding of the underlying design principles. For example, the targeted assembly of a series of large spherical structures containing up to 30 palladium ions coordinated by up to 60 bent organic ligands was achieved by considering their topologies. Here we report the self-assembly of a spherical structure that also contains 30 palladium ions and 60 bent ligands, but belongs to a shape family that has not previously been observed experimentally. The new structure consists of a combination of 8 triangles and 24 squares, and has the symmetry of a tetravalent Goldberg polyhedron. Platonic and Archimedean solids have previously been prepared through self-assembly, as have trivalent Goldberg polyhedra, which occur naturally in the form of virus capsids and fullerenes. But tetravalent Goldberg polyhedra have not previously been reported at the molecular level, although their topologies have been predicted using graph theory. We use graph theory to predict the self-assembly of even larger tetravalent Goldberg polyhedra, which should be more stable, enabling another member of this polyhedron family to be assembled from 144 components: 48 palladium ions and 96 bent ligands.
429 citations
University of California, Santa Barbara1, Colorado School of Mines2, University of Illinois at Urbana–Champaign3, National Center for Supercomputing Applications4, Johns Hopkins University5, Gdańsk University of Technology6, Colorado State University7, University of Maryland, College Park8, National Institute of Standards and Technology9
TL;DR: In this paper, a new kagome prototype structure is presented, which is based on vanadium, with the Fermi level in close proximity to several Dirac points.
Abstract: In this work, we present our discovery and characterization of a new kagome prototype structure, ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. We also present the discovery of the isostructural compounds ${\mathrm{RbV}}_{3}{\mathrm{Sb}}_{5}$ and ${\mathrm{CsV}}_{3}{\mathrm{Sb}}_{5}$. All materials exhibit a structurally perfect two-dimensional kagome net of vanadium. Density-functional theory calculations indicate that the materials are metallic, with the Fermi level in close proximity to several Dirac points. Powder and single-crystal syntheses are presented, with postsynthetic treatments shown to deintercalate potassium from single crystals of ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. Considering the proximity to Dirac points, deintercalation provides a convenient means to tune the Fermi level. Magnetization measurements indicate that ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$ exhibits behavior consistent with a the Curie-Weiss model at high temperatures, although the effective moment is low $(0.22{\ensuremath{\mu}}_{\text{B}}$ per vanadium ion). An anomaly is observed in both magnetization and heat capacity measurements at 80 K, below which the moment is largely quenched. Elastic neutron scattering measurements find no obvious evidence of long-range or short-range magnetic ordering below 80 K. The possibility of an orbital-ordering event is considered. Single-crystal resistivity measurements show the effect of deintercalation on the electron transport and allow estimation of the Kadowaki-Woods ratio in ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. We find that $A/{\ensuremath{\gamma}}^{2}\ensuremath{\sim}61\phantom{\rule{4pt}{0ex}}\ensuremath{\mu}\mathrm{Ohm}$ cm ${\mathrm{mol}}_{\text{FU}}^{2}\phantom{\rule{4pt}{0ex}}{\mathrm{K}}^{2}\phantom{\rule{4pt}{0ex}}{\mathrm{J}}^{\ensuremath{-}2}$, suggesting that correlated electron transport may be possible. ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$ and its cogeners ${\mathrm{RbV}}_{3}{\mathrm{Sb}}_{5}$ and ${\mathrm{CsV}}_{3}{\mathrm{Sb}}_{5}$ represent a new family of kagome metals, and our results demonstrate that they deserve further study as potential model systems.
378 citations
TL;DR: Examination of the impact of organic cation and inorganic layer choice on the exciton absorption/emission properties, among the set of compounds considered, reveals that perovskite layer distortion has a more global effect on theexciton properties than octahedral distortion.
Abstract: A series of two-dimensional (2D) hybrid organic–inorganic perovskite (HOIP) crystals, based on acene alkylamine cations (i.e., phenylmethylammonium (PMA), 2-phenylethylammonium (PEA), 1-(2-naphthyl)methanammonium (NMA), and 2-(2-naphthyl)ethanammonium (NEA)) and lead(II) halide (i.e., PbX42–, X = Cl, Br, and I) frameworks, and their corresponding thin films were fabricated and examined for structure–property relationship. Several new or redetermined crystal structures are reported, including those for (NEA)2PbI4, (NEA)2PbBr4, (NMA)2PbBr4, (PMA)2PbBr4, and (PEA)2PbI4. Non-centrosymmetric structures from among these 2D HOIPs were confirmed by piezoresponse force microscopy—especially noteworthy is the structure of (PMA)2PbBr4, which was previously reported as centrosymmetric. Examination of the impact of organic cation and inorganic layer choice on the exciton absorption/emission properties, among the set of compounds considered, reveals that perovskite layer distortion (i.e., Pb–I–Pb bond angle between adj...
367 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
"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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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.
13,163 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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TL;DR: In this article, the behaviour of the Rogers's η parameter for enantiomorph-polarity estimation is examined theoretically and experimentally on simulated intensity data for seven well-assorted compounds.
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.
9,932 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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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.
9,865 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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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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