Aspherical scattering factors for SHELXL - model, implementation and application

Advancing nonlinear optics: discovery and characterization of new non-centrosymmetric phenazine-based halides

Organic-inorganic metal halides (OIMHs) have drawn considerable attention due to their remarkable optoelectronic properties and substantial promise for nonlinear optical applications. In this research, phenazine has been selected as the organic cation because of its π-conjugated feature. Three compounds, (C12H9N2)PbCl3, (C12H9N2)SbCl4, and (C12H9N2)2InBr4·Br, were synthesized. Initial space group assignments were centrosymmetric for (C12H9N2)PbCl3 and (C12H9N2)SbCl4. However, under 1550 nm laser excitation, (C12H9N2)PbCl3 and (C12H9N2)SbCl4 exhibited second harmonic generation intensities ∼1.7 times greater than that of the benchmark KH2PO4. Structural reevaluation ultimately confirmed non-centrosymmetric P1 and P21 space groups for (C12H9N2)PbCl3 and (C12H9N2)SbCl4, respectively. Upon excitation at 335 nm and 470 nm, (C12H9N2)PbCl3, (C12H9N2)SbCl4, and (C12H9N2)2InBr4·Br emit fluorescence at room temperature. (C12H9N2)2InBr4·Br exhibits reversible phase transitions, showing potential for phase change energy storage. Our research underscores the critical role of comprehensive experimental validation in determining the precise crystallographic space groups and reveals the extensive potential of OIMHs as versatile candidates for advanced optoelectronic applications.

Hydrogen atoms in supramolecular chemistry: a structural perspective. Where are they, and why does it matter?

Hydrogen bonding interactions are ubiquitous across the biochemical and chemical sciences, and are of particular interest to supramolecular chemists. They have been used to assemble hydrogen bonded polymers, cages and frameworks, and are the functional motif in many host-guest systems. Single crystal X-ray diffraction studies are often used as a key support for proposed structures, although this presents challenges as hydrogen atoms interact only weakly with X-rays. In this Tutorial Review, we discuss the information that can be gleaned about hydrogen bonding interactions through crystallographic experiments, key limitations of the data, and emerging techniques to overcome these limitations.

Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time-accuracy trade-off

Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal-organic compounds and network structures such as covalent organic frameworks and metal-organic frameworks is now possible in a hybrid mode such as IAM-TAAM or HAR-TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement.

Crystal Structure Analysis of 4-Oxo, 4-hydroxy- and 4-alkyl-7-bromopyrazolo[5,1-c][1,2,4]triazines

The crystal structures of 8-R1-7-bromo-3-tert-butyl-1-R2-pyrazolo[5,1-c][1,2,4]triazin-4(1H)-ones 1a-c, 2a,c (R1 = CN, CO2Et, NO2, R2 = H, 1:1 and 3:1 solvates with DMSO; R1 = CN, CO2Et, R2 = CH2Boc), 8-R1-7-bromo-3-tert-butyl-1-R2-1,4-dihydropyrazolo[5,1-c][1,2,4]triazin-4-ols 3a,b (R1 = CN, R2 = n-Bu; R1 = Br, R2 = CH2Boc), 1,4-dihydro- and aromatic 7-R3-3-tert-butyl-4-R4-8-methylpyrazolo[5,1-c][1,2,4]triazines 5a,b, 6 (R3 = H, R4 = n-Pr; R3 = Br, R4 = n-Bu) were investigated by X-ray diffraction analysis. The structural preferences and different packing modes based on the intermolecular interactions were analyzed by the Hirshfeld surface and energy framework analysis.

Graphical Abstract

The crystal structures of ten 3-tert-butyl-4-oxo, 4-hydroxy- and 4-alkyl-7-bromopyrazolo[5,1-c][1,2,4]triazines including non-solvated, 1:1 and 3:1 solvates with DMSO were investigated by single crystal X-ray diffraction, Hirshfeld surface and energy framework analyses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10870-022-00973-x.

Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB

A fast and accurate operational model of electron density is crucial in many scientific disciplines including crystallography, molecular biology, pharmaceutical, and structural chemistry. In quantum crystallography, the aspherical refinement of crystal structures is becoming increasingly popular because of its accurate description in terms of physically meaningful properties. The transferable aspherical atom model (TAAM) is quick and precise, though it requires a robust algorithm for atom typing and coverage of the most popular atom types present in small organic molecules. Thus, the University at Buffalo Databank (UBDB) has been renamed to the Multipolar Atom Types from Theory and Statistical clustering (MATTS) data bank, broadened, restructured, and implemented into the software DiSCaMB with 651 atom types obtained from 2316 small-molecule crystal structures containing C, H, N, O, P, S, F, Cl, and Br atoms. MATTS2021 data bank now covers most of the small molecules, peptides, RNA, DNA, and some frequently occurring cations and anions in biological, pharmaceutical, and organic materials, including the majority of known crystal structures composed of the above elements. The multipole model parameters (P_val, κ, κ′, P_lm) obtained for different atom types were greatly influenced by neighboring atom types, hybridization, geometrical strain in the ring system, and charges on the molecule. Contrary to previous findings, the atoms showing variable oxidation states and ions deviate from the linear dependence of monopole-derived charges on the expansion–contraction κ parameter.

A novel symmetric pyrazine (pyz)-bridged uranyl dimer [UO2Cl3(H2O)(Pyz)0.5]22-: synthesis, structure and computational analysis

Herein we report on the synthesis of (HPyz⁺)₂[UO₂Cl₃(H₂O)(Pyz)_0.5]₂·2H₂O which features a novel pyrazine-bridged uranyl dimer, [UO₂Cl₃(H₂O)(Pyz)_0.5]₂^2-. A rigorous computational and experimental analysis of this compound was performed to fully explore the influence of coordination on the electronic structure and potential charge-transfer characteristics of this dimer, revealing a delocalized π-system across the bridging pyrazine and the axial components of both uranyl centers. Electrostatic surface potentials, used to rationalize the observed assembly, indicate a decreased basicity of the uranyl oxo versus [UO₂Cl₄]^2-, and signify a lessened capacity for the terminal -yl oxos of the [UO₂Cl₃(H₂O)(Pyz)_0.5]₂^2- dimer to participate in supramolecular assembly. A combined density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) analysis further evidenced an increase in UO bond strengths within the dimer, which is supported by a blue shift in the characteristic Raman-active uranyl symmetric stretch (ν₁) with respect to the more typically observed [UO₂Cl₄]^2-.

Organopnictogen(III) bis(arylthiolates) containing NCN-aryl pincer ligands: from synthesis and characterization to reactivity

Salt elimination reactions between organopnictogen(III) dichlorides, RPnCl₂ [R¹ = 2,6-(Me₂NCH₂)₂C₆H₃, Pn = Sb (1), Bi (2); R² = 2,6-{MeN(CH₂CH₂)₂NCH₂}₂C₆H₃, Pn = Sb (3), Bi (4); R³ = 2,6-{O(CH₂CH₂)₂NCH₂}₂C₆H₃, Pn = Sb (5), Bi (6)] and 2 equivalents of KSC₆H₃Me₂-2,6 afforded the isolation of a series of new NCN-chelated monoorganopnictogen(III) bis(arylthiolates), RPn(SC₆H₃Me₂-2,6)₂ [R¹, Pn = Sb (7), Bi (8); R², Pn = Sb (9), Bi (10); R³, Pn = Sb (11), Bi (12)]. Compounds 7 and 8 are unstable upon exposure to a dry O₂ atmosphere and their aerobic decomposition yields the monoorganopnictogen(III) oxides, cyclo-[2,6-(Me₂NCH₂)₂C₆H₃Pn(μ-O)]₂ [Pn = Sb (13), Bi (14)] with concomitant formation of the corresponding disulfide, ArS-SAr (Ar = C₆H₃Me₂-2,6). The oxidative addition of elemental sulfur or selenium to 7 undergoes a similar reaction path and gives stable heterocyclic species cyclo-[2,6-(Me₂NCH₂)₂C₆H₃Sb(μ-E)]₂ [E = S (15), Se (16)]. The reaction of 12 with I₂ (1 : 1 molar ratio) gives the diiodide [2,6-{O(CH₂CH₂)₂NCH₂}₂C₆H₃]BiI₂ (17), along with the S-S oxidative coupling by-product, ArS-SAr. The use of an excess of iodine affords the crystallization of a 2 : 1 iodine adduct of 17 (17·0.5I₂), built through halogen bonding. All new compounds were characterized by multinuclear NMR spectroscopy and ESI-MS as well as single crystal X-ray diffraction (except compounds 9 and 10).

Remote Stereoelectronic Effects in Pyrrolidone- and Caprolactam-Substituted Phenols: Discrepancies in Antioxidant Properties Evaluated by Electrochemical Oxidation and H-Atom Transfer Reactivity

New antioxidants are commonly evaluated via two main approaches, i.e., the ability to donate an electron and the ability to intercept free radicals. We compared these approaches by evaluating the properties of 11 compounds containing both antioxidant moieties (mono- and polyphenols) and auxiliary pharmacophores (pyrrolidone and caprolactam). Several common antioxidants, such as butylated hydroxytoluene (BHT), 2,3,5-trimethylphenol (TMP), quercetin, and dihydroquercetin, were added for comparison. The antioxidant properties of these compounds were determined by their rates of reaction with 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and their oxidation potentials from cyclic voltammetry. Although these methods test different chemical properties, their results correlate reasonably well. However, several exceptions exist where the two methods give opposite predictions! One of them is the different behavior of mono- and polyphenols: polyphenols can react with DPPH more than an order of magnitude faster than monophenols of a similar oxidation potential. The second exception stems from the size of a "bystander" lactam ring at the benzylic position. Although the phenols with a seven-membered lactam ring are harder to oxidize, the sterically nonhindered compounds react with DPPH about 2× faster than the analogous five-membered lactams. The limitations of computational methods, especially those based on a single parameter, are also evaluated and discussed.

Type Strains of Entomopathogenic Nematode-Symbiotic Bacterium Species, Xenorhabdus szentirmaii (EMC) and X. budapestensis (EMA), Are Exceptional Sources of Non-Ribosomal Templated, Large-Target-Spectral, Thermotolerant-Antimicrobial Peptides (by Both), and Iodinin (by EMC)

Antimicrobial multidrug resistance (MDR) is a global challenge, not only for public health, but also for sustainable agriculture. Antibiotics used in humans should be ruled out for use in veterinary or agricultural settings. Applying antimicrobial peptide (AMP) molecules, produced by soil-born organisms for protecting (soil-born) plants, seems a preferable alternative. The natural role of peptide-antimicrobials, produced by the prokaryotic partner of entomopathogenic-nematode/bacterium (EPN/EPB) symbiotic associations, is to sustain monoxenic conditions for the EPB in the gut of the semi-anabiotic infective dauer juvenile (IJ) EPN. They keep pathobiome conditions balanced for the EPN/EPB complex in polyxenic (soil, vanquished insect cadaver) niches. Xenorhabdus szentirmaii DSM16338(T) (EMC), and X. budapestensis DSM16342(T) (EMA), are the respective natural symbionts of EPN species Steinernema rarum and S. bicornutum. We identified and characterized both of these 15 years ago. The functional annotation of the draft genome of EMC revealed 71 genes encoding non-ribosomal peptide synthases, and polyketide synthases. The large spatial Xenorhabdus AMP (fabclavine), was discovered in EMA, and its biosynthetic pathway in EMC. The AMPs produced by EMA and EMC are promising candidates for controlling MDR prokaryotic and eukaryotic pathogens (bacteria, oomycetes, fungi, protozoa). EMC releases large quantity of iodinin (1,6-dihydroxyphenazine 5,10-dioxide) in a water-soluble form into the media, where it condenses to form spectacular water-insoluble, macroscopic crystals. This review evaluates the scientific impact of international research on EMA and EMC.

Co-crystallization of organic chromophore roseolumiflavin and effect on its optical characteristics

Three roseolumiflavin co-crystals are designed to elucidate the accessibility of flavins for the targeted tuning of luminescence in the solid state.

The Aza-Prins Reaction of 1,2-Dicarbonyl Compounds with 3-Vinyltetrahydroquinolines: Application to the Synthesis of Polycyclic Spirooxindole Derivatives

The aza-Prins reaction of 6,7-dimethoxy-3-vinyl-1,2,3,4-tetrahydroquinoline (1) with 1,2-dicarbonyl compounds proceeded smoothly in the presence of HCl, and the corresponding tricyclic benzazocines were isolated in yields of 20-86%. The reaction proceeded in a stereoselective manner, and the formation of the 2,4-trans isomer was observed. The reaction of 1 with an enantiopure ketoester gave the corresponding tricyclic benzazocine as a mixture of diastereomers. The diastereomers were easily separated and converted to enantiopure tricyclic benzazocines. The synthesis of spirooxindole derivatives was achieved by the reaction of 1 with isatin derivatives.

Quassinoids from the Roots of Eurycoma longifolia and Their Anti-Proliferation Activities

A phytochemical investigation on the roots of medicinal plant Eurycoma longifolia resulted in the isolation of 10 new highly oxygenated C₂₀ quassinoids longifolactones G‒P (1–10), along with four known ones (11–14). Their chemical structures and absolute configurations were unambiguously elucidated on the basis of comprehensive spectroscopic analysis and X-ray crystallographic data. Notably, compound 1 is a rare pentacyclic C₂₀ quassinoid featuring a densely functionalized 2,5-dioxatricyclo[5.2.2.0^4,8]undecane core. Compound 4 represents the first example of quassinoids containing a 14,15-epoxy functionality, and 7 features an unusual α-oriented hydroxyl group at C-14. All isolated compounds were evaluated for their anti-proliferation activities on human leukemia cells. Among the isolates, compounds 5, 12, 13, and 14 potently inhibited the in vitro proliferation of K562 and HL-60 cells with IC₅₀ values ranging from 2.90 to 8.20 μM.

Bimetallic uranyl/cobalt(II) isothiocyanates: structure, property and spectroscopic analysis of homo- and heterometallic phases

We report the synthesis and characterization of a family of UO22+/Co2+ isothiocyanate materials containing [UO2(NCS)5]3- and/or [Co(NCS)4]2- building units charged balanced by tetramethylammonium cations and assembled via SS or SOyl non-covalent interactions (NCIs), namely (C4H12N)3[UO2(NCS)5], (C4H12N)2[Co(NCS)4], and (C4H12N)5[Co(NCS)4][UO2(NCS)5]. The homometallic uranyl phase preferentially assembles via SS interactions, whereas in the heterometallic phase SOyl interactions are predominant. The variation in assembly mode is explored using electrostatic surfaces potentials, revealing that the pendant -NCS ligands of the [Co(NCS)4]2- anion is capable of outcompeting those of the [UO2(NCS)5]3- anion. Notably, the heterometallic phase displays atypical blue shifting of the uranyl symmetric stretch in the Raman spectra, which is in contrast to many other compounds featuring non-covalent interactions at uranyl oxygen atoms. A combined experimental and computational (density functional theory and natural bond orbital analyses) approach revealed that coupling of the uranyl symmetric stretch with isothiocyanate modes of equatorial -NCS ligands was responsible for the atypical blue shift in the heterometallic phase.

Synthesis, structural characterization and antimycobacterial evaluation of several halogenated non-nitro benzothiazinones

8-Nitro-1,3-benzothiazin-4-ones (BTZs), with BTZ043 and PBTZ169 as the most advanced compounds, represent a new class of potent antitubercular agents, which irreversibly inhibit decaprenylphosphoryl-β-d-ribose-2'-epimerase (DprE1), an enzyme crucial for cell wall synthesis in the pathogen Mycobacterium tuberculosis. Synthesis, structural characterization and in vitro testing against Mycobacterium aurum DSM 43999 and M. tuberculosis H₃₇Rv of halogenated 2-(4-ethoxycarbonylpiperazin-1-yl)-1,3-benzothiazin-4-ones lacking a nitro group are reported. X-ray crystallography reveals that the structure of the BTZ scaffold can significantly deviate from planarity. In contrast to recent reports, the results of the present study indicate that further investigation of halogenated non-nitro BTZs for antitubercular activity is less than a promising approach.

On modelling disordered crystal structures through restraints from molecule-in-cluster computations, and distinguishing static and dynamic disorder

Distinguishing disorder into static and dynamic based on multi-temperature X-ray or neutron diffraction experiments is the current state of the art, but is only descriptive, not predictive. Here, several disordered structures are revisited from the Cambridge Crystallographic Data Center 'drug subset', the Cambridge Structural Database and own earlier work, where experimental intensities of Bragg diffraction data were available. Using the molecule-in-cluster approach, structures with distinguishable conformations were optimized separately, as extracted from available or generated disorder models of the respective disordered crystal structures. Re-combining these 'archetype structures' by restraining positional and constraining displacement parameters for conventional least-squares refinement, based on the optimized geometries, then often achieves a superior fit to the experimental diffraction data compared with relying on experimental information alone. It also simplifies and standardizes disorder refinement. Ten example structures were analysed. It is observed that energy differences between separate disorder conformations are usually within a small energy window of RT (T = crystallization temperature). Further computations classify disorder into static or dynamic, using single experiments performed at one single temperature, and this was achieved for propionamide.

Accurate crystal structures and chemical properties from NoSpherA2

The relationship between the structure and the properties of a drug or material is a key concept of chemistry. Knowledge of the three-dimensional structure is considered to be of such importance that almost every report of a new chemical compound is accompanied by an X-ray crystal structure – at least since the 1970s when diffraction equipment became widely available. Crystallographic software of that time was restricted to very limited computing power, and therefore drastic simplifications had to be made. It is these simplifications that make the determination of the correct structure, especially when it comes to hydrogen atoms, virtually impossible. We have devised a robust and fast system where modern chemical structure models replace the old assumptions, leading to correct structures from the model refinement against standard in-house diffraction data using no more than widely available software and desktop computing power. We call this system NoSpherA2 (Non-Spherical Atoms in Olex2). We explain the theoretical background of this technique and demonstrate the far-reaching effects that the improved structure quality that is now routinely available can have on the interpretation of chemical problems exemplified by five selected examples.

NoSpherA2 brings quantum crystallography to routine structure determination and to the analysis of chemical properties for any class of materials.

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d_min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

Syntheses and structures of two novel fluorescent metal-organic frameworks generated from a tridentate donor-acceptor motif ligand

The tridentate organic ligand 4,4',4''-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6,10-triyl)tribenzoic acid (H₃L) has been synthesized (as the methanol 1.25-solvate, C₄₈H₃₉NO₆·1.25CH₃OH). As a donor-acceptor motif molecule, H₃L possess strong intramolecular charge transfer (ICT) fluorescence. Through hydrogen bonds, H₃L molecules construct a two-dimensional (2D) network, which pack together into three-dimensional (3D) networks with an ABC stacking pattern in the crystalline state. Based on H₃L and M(NO₃)₂ salts (M = Cd and Zn) under solvothermal conditions, two metal-organic frameworks (MOFs), namely, catena-poly[[triaquacadmium(II)]-μ-10-(4-carboxyphenyl)-4,4'-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6-diyl)dibenzoato], [Cd(C₄₈H₃₇NO₆)(H₂O)₃]_n, I, and poly[[μ₃-4,4',4''-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6,10-triyl)tribenzoato](μ₃-hydroxido)zinc(II)], [Zn₂(C₄₈H₃₆NO₆)(OH)]_n, II, were synthesized. Single-crystal analysis revealed that both MOFs adopt a 3D structure. In I, partly deprotonated HL^2- behaves as a bidentate ligand to link a Cd^II ion to form a one-dimensional chain. In the solid state of I, the existence of weak interactions, such as O-H...O hydrogen bonds and π-π interactions, plays an essential role in aligning 2D nets and 3D networks with AB packing patterns for I. The deprotonated ligand L^3- in II is utilized as a tridentate building block to bind Zn^II ions to construct 3D networks, where unusual Zn₄O₁₄ clusters act as connection nodes. As a donor-acceptor molecule, H₃L exhibits fluorescence with a photoluminescence quantum yield (PLQY) of 70% in the solid state. In comparison, the PL of both MOFs is red-shifted with even higher PLQYs of 79 and 85% for I and II, respectively.

Synthesis and Systematic Structural Analysis of Cationic Half-Sandwich Ruthenium Chalcogenocarbonyl Complexes

Although the chemistry of transition-metal complexes with carbonyl (CO) and thiocarbonyl (CS) ligands has been well developed, their heavier analogues, namely selenocarbonyl (CSe) and tellurocarbonyl (CTe) complexes remain scarce. The limited availability of such CSe and CTe complexes has so far hampered our understanding of the differences between such chalcogenocarbonyl (CE: E=O, S, Se, Te) ligands. Herein, we report the synthesis and properties of a series of cationic half-sandwich ruthenium CE complexes of the type [CpRu(CE)(H₂ IMes)(CNCH₂ Ts)][BAr^F ₄ ] (Cp=η⁵ -C₅ H₅ ^- ; H₂ IMes=1,3-dimesitylimidazolin-2-ylidene; Ar^F =3,5-(CF₃ )₂ C₆ H₃ ). A combination of X-ray diffraction analyses, NMR spectroscopic analyses, and DFT calculations revealed an increasing π-accepting ability of the CE ligands in the order O<S<Se<Te. A variable-temperature NMR analysis of the thus obtained chiral-at-metal CE complexes indicated high stereochemical stability.

Synthesis and properties of anionic ruthenium thionitrosyl and selenonitrosyl complexes that contain tetraanionic 2-hydroxybenzamidobenzene ligands

Although transition-metal complexes that contain thiocarbonyl (CS) and selenocarbonyl (CSe) ligands have been well studied, only three neutral or cationic selenonitrosyl (NSe) complexes have been reported, while anionic NSe complexes remain elusive. Herein, we report the first examples of anionic NSe-ligated ruthenium complexes, which were obtained from the reaction of anionic ruthenium nitrido complexes, elemental selenium, and 4-(N,N-dimethylamino)pyridine (DMAP). The structures of one of these ruthenium NSe complexes, as well as of the corresponding thionitrosyl (NS) and nitrosyl (NO) complexes, were systematically examined by X-ray diffraction analyses and theoretical calculations. In contrast to previous reportes, the NSe ligand in these complexes is a better π-acceptor than the NO and NS ligands and exhibits a stronger trans influence.

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.

Fast energy minimization of the CCDC drug-subset structures by molecule-in-cluster computations allows independent structure validation and model completion

Optimizing structures with computations on clusters of molecules permits generation of structure-specific restraints for refinement and structure validation.

Disappearing disorder

Disorder in crystal structures can disappear, depending on the circumstances, as shown by multi-temperature measurements, aspherical-atom refinement and computational analyses.

The upcoming subatomic resolution revolution

Subatomic resolution macromolecular crystallography has been revealing the most fascinating details of macromolecular structures for many years. This most extreme form of macromolecular crystallography is going through rapid changes. A new generation of superbrilliant X-ray sources and detectors is facilitating the rapid acquisition of high-quality datasets. Equally important, a new breed of methods and highly integrated advanced computational tools for structure refinement and analysis is poised to change the way we use subatomic resolution data and reposition high-resolution macromolecular crystallography in medicinal chemistry studies. Subatomic resolution macromolecular crystallography may soon be a routine source of detailed molecular information besides precise geometries, including binding energies and other chemical descriptors, opening new possibilities of application.