checkCIF validation ALERTS: what they mean and how to respond

Authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of inter-est and their inter-pretation, 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 inter-esting 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 inter-pretation of the underlying experimental data or perform their own calculations with the archived data. All the above is consistent with the FAIR (findable, accessible, inter-operable, 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 inter-pretation 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.

Facial triad modelling using ferrous pyridinyl prolinate complexes: synthesis and catalytic applications

A series of new chiral pyridinyl prolinate (RPyProR) ligands and their corresponding Fe(II) triflate and chloride complexes are reported. The ligands possess an NN'O coordination motif, as found in the active site of non-heme iron enzymes with the so-called 2-His-1-carboxylate facial triad. The coordination behaviour of these ligands towards iron turned out to be dependent on the counter ion (chloride or triflate), the crystallization conditions (coordinating or non-coordinating solvents) and the presence of substituents on the ligand. In combination with Fe(II)(OTf)2, coordinatively saturated complexes of the type [Fe(L)2](OTf)2 are formed, in which the ligands adopt a meridional coordination mode. The use of FeCl2 in a non-coordinating solvent leads to 5-coordinated complexes [Fe(L)(Cl)2] with a meridional N,N',O ligand. Crystallization of these complexes from a coordinating solvent leads to 6-coordinated [Fe(L)(solv)(Cl)2] complexes (solv = methanol or acetonitrile), in which the N,N',O ligand is coordinated in a facial manner. For RPyProR ligands bearing a 6-Me substituent on the pyridine ring, solvent coordination and, accordingly, ligand rearrangement are prevented by steric constraints. The complexes were tested as oxidation catalysts in the epoxidation of alkene substrates in acetonitrile with hydrogen peroxide as the oxidant under oxidant limiting conditions. The complexes were shown to be especially active in the epoxidation of styrene type substrates (styrene and trans-beta-methylstyrene). In the best case, complex [Fe(6-Me-PyProNH2)Cl2] (15) allowed for 65% productive consumption of hydrogen peroxide toward epoxide and benzaldehyde products.

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

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.

Organometallic benzylidene anilines: donor–acceptor features in NCN-pincer Pt(ii) complexes with a 4-(E)-[(4-R-phenyl)imino]methyl substituent

Inductively the Pt-moiety in these organometallic benzylidene anilines is a very strong electron-withdrawing group, but mesomerically a very strong electron-donating group.

Directed ortho-lithiation: observation of an unexpected 1-lithio to 3-lithio conversion of 1-lithio-naphthyllithium compounds with an ortho-directing 2-(dimethylamino)methyl group

Regioselectivity is an important aspect in the design of organic protocols involving Directed ortho-Lithiation (DoL) of arenes, in particular with those arenes containing heteroatom substituents as directing groups. The DoL of 2-[(dimethylamino)methyl]naphthalene (dman) that proceeds with low regioselectivity was revisited by varying both the nature of the lithiating reagent (either n-BuLi or t-BuLi) and/or the solvent (pentane or diethyl ether); the 3-deuterated substrate, 3-Ddman, was also investigated as a substrate to compare to that of dman. The 3-lithio regioisomer exists as tetranuclear [2-(Me2NCH2)C10H6Li-3]4, 1, both in the solid state (X-ray) and in solution (NMR). The 1-lithio regioisomer, 2a, is insoluble; in the presence of additional coordinating solvents (Et2O) or ligands (dman), it exists as dinuclear [2-(Me2NCH2)C10H6Li-1]2·L (coordinated L = Et2O: 2b, dman: 2c) in apolar solvents. Heating solutions of 2c in toluene-d8 (to 90 °C) induced a surprisingly clean and quantitative 1-lithio to 3-lithio conversion of the 1-lithio-naphthalene isomer. This type of reaction is rare in organolithium chemistry and has obvious significant implications for the design of regioselective DoL protocols; this thus represents the synthetically useful protocol for the DoL of dman in a one-pot/two-step process in toluene solution. The results of the use of 3-Ddman in these reactions gives strong credence to a mechanism involving formation of the heteroleptic species [(2-(Me2NCH2)C10H6-1)(2-(Me2NCH2)C10H6-3)Li2]·[dman], A, as the key intermediate. Intramolecular trans-lithiation takes place with A; dman becomes selectively lithiated at its 3-position, while the formerly 1-lithio-naphthalene fragment, acting as a highly unusual ortho-lithiating reagent, is converted into the N-coordinated amine, dman. In this intramolecular DoL process, free dman can be considered to act as a catalyst.

Triphenylsilanol–4,4′-bipyridyl (4/1): theZ′ = 4 polymorph revisited

A fully ordered structure is reported for the polymorph of triphenylsilanol–4,4′-bipyridyl (4/1), 4C18H16OSi·C10H8N2, havingZ′ = 4. The asymmetric unit contains four similar but distinct five-molecule aggregates, in which the central bipyridyl unit is linked to two molecules of triphenylsilanolviaO—H...N hydrogen bonds, with a further pair of triphenylsilanol molecules linked to the first pairviaO—H...O hydrogen bonds. An extensive series of C—H...π(arene) hydrogen bonds links these aggregates into complex sheets. This structure is compared with a previously reported structure [Bowes, Ferguson, Lough & Glidewell (2003).Acta Cryst.B59, 277–286], which was based on an erroneous disordered structural model arising from a false direct-methods solution with reference to a strong pseudo-inversion centre.

Mono- and dinuclear iron complexes of bis(1-methylimidazol-2-yl)ketone (bik): structure, magnetic properties, and catalytic oxidation studies

The newly synthesized dinuclear complex [Fe(III)(2)(μ-OH)(2)(bik)(4)](NO(3))(4) (1) (bik, bis(1-methylimidazol-2-yl)ketone) shows rather short Fe···Fe (3.0723(6) Å) and Fe-O distances (1.941(2)/1.949(2) Å) compared to other unsupported Fe(III)(2)(μ-OH)(2) complexes. The bridging hydroxide groups of 1 are strongly hydrogen-bonded to a nitrate anion. The (57)Fe isomer shift (δ = 0.45 mm s(-1)) and quadrupole splitting (ΔE(Q) = 0.26 mm s(-1)) obtained from Mössbauer spectroscopy are consistent with the presence of two identical high-spin iron(III) sites. Variable-temperature magnetic susceptibility studies revealed antiferromagnetic exchange (J = 35.9 cm(-1) and H = JS(1)·S(2)) of the metal ions. The optimized DFT geometry of the cation of 1 in the gas phase agrees well with the crystal structure, but both the Fe···Fe and Fe-OH distances are overestimated (3.281 and 2.034 Å, respectively). The agreement in these parameters improves dramatically (3.074 and 1.966 Å) when the hydrogen-bonded nitrate groups are included, reducing the value calculated for J by 35%. Spontaneous reduction of 1 was observed in methanol, yielding a blue [Fe(II)(bik)(3)](2+) species. Variable-temperature magnetic susceptibility measurements of [Fe(II)(bik)(3)](OTf)(2) (2) revealed spin-crossover behavior. Thermal hysteresis was observed with 2, due to a loss of cocrystallized solvent molecules, as monitored by thermogravimetric analysis. The hysteresis disappears once the solvent is fully depleted by thermal cycling. [Fe(II)(bik)(3)](OTf)(2) (2) catalyzes the oxidation of alkanes with t-BuOOH. High selectivity for tertiary C-H bond oxidation was observed with adamantane (3°/2° value of 29.6); low alcohol/ketone ratios in cyclohexane and ethylbenzene oxidation, a strong dependence of total turnover number on the presence of O(2), and a low retention of configuration in cis-1,2-dimethylcyclohexane oxidation were observed. Stereoselective oxidation of olefins with dihydrogen peroxide yielding epoxides was observed under both limiting oxidant and substrate conditions.