Crystal structure refinement with SHELXL

Synthesis, crystal structure, spectroscopic properties and potential biological activities of salicylate‒neocuproine ternary copper(II) complexes

Mixed ligand copper(II) complexes containing derivatives of salicylic acid and heterocyclic ligands with nitrogen donor atoms have been the subject of various studies and reviews. In this paper, synthesis and characterization of the ternary copper(II) complexes of neocuproine (2,9-dimethyl-1,10-phenanthroline, Neo) and salicylate ligands (Sal) are reported. In addition, the crystal structures of ([Cu(H2O)(5-Cl-Sal)(Neo)] (1), [Cu(μ-Sal)(Neo)]2 (2), Cu2(μ-5-Cl-Sal)(5-Cl-HSal)2(Neo)2]·EtOH (3)) were determined. In order to compare structural and biological properties of the prepared complexes, spectroscopic and biological studies were performed. Results of X-ray diffraction show that prepared complexes form three types of crystal structures in a given system: monomeric, dimeric and dinuclear complex. The preliminary study on the DNA cleavage activity has shown that the complexes under study behave as the chemical nucleases in the presence of added hydrogen peroxide with slight differences in the activity (1 > 2 > 3). The complexes 1 and 2 exhibited nuclease activity itself indicating the interaction of complexes with the DNA. It has been proposed that the enhanced destructive effect of the complexes 1 and 2 on the DNA is a result of two possible mechanisms of action: (i) the conversion of closed circular DNA (form I) to the nicked DNA (form II) caused by the copper complex itself and (ii) damage of DNA by Reactive Oxygen Species (ROS)-products of the interaction of copper with hydrogen peroxide by means of Fenton reaction (hydroxyl radicals). Thus the biological activity of the prepared Cu(II) complexes containing derivatives of salicylic acid and phenanthroline molecules is substantiated by two independent mechanisms. While derivatives of salicylic acids in the coordination sphere of copper complexes are responsible for radical-scavenging activity (predominantly towards superoxide radical anion), the presence of chelating ligand 2,9-dimethyl-1,10-phenanthroline significantly enhances capability of Cu(II) complexes binding to DNA via intercalation.

The first polymorph in the family of nucleobases: a second form of cytosine

A new polymorph of cytosine, C4H5N3O, is reported half a century after the report of its first known crystal structure [Barker & Marsh (1964).Acta Cryst.17, 1581–1587]. Cytosine thus provides the first polymorphic example in the category of parent nucleobases. The new form, denoted (Ib), was observed unexpectedly during an attempt to cocrystallize cytosine with catechol. Form (Ib) crystallizes in the orthorhombic centrosymmetric space groupPccnwith two molecules in the asymmetric unit. The previously known form, denoted (Ia), crystallizes in the orthorhombic noncentrosymmetric space groupP212121. The cytosine molecule is planar in both forms. Hydrogen-bonding interactions are also similar for both forms. Infinite one-dimensional ribbons composed of cytosine base-pair dimers inR22(8) arrangements are observed in both (Ia) and (Ib). However, the way that the ribbons are packed differs in (Ia) and (Ib). This appears to guide the centrosymmetricversusnoncentrosymmetric space-group selection through the formation of an inversion-related motif in polymorph (Ib) and a helical propagation in polymorph (Ia). A few selected polymorphic systems have been gathered from the Cambridge Structural Database to understand possible structural features responsible for achiral molecules adopting centro- and noncentrosymmetric space groups.

The three-component cocrystal 1,3,5-trifluoro-2,4,6-triiodobenzene–pyridineN-oxide–water (1/2/1) built up by halogen bonds, hydrogen bonds and π–π interactions

The title three-component cocrystal, C6F3I3·2C5H5NO·H2O, has been prepared as a strong candidate for multiple I...O interactions. Its crystal structure is compared with its 1:1 close relative, C6F3I3·C5H5NO [Aakeröyet al.(2014a).CrystEngComm,16, 28–31]. The 1,3,5-trifluoro-2,4,6-triiodobenzene and water species both have crystallographic twofold axial symmetry. The main synthon in both structures is the π–π stacking of benzene rings, complemented by a number of O—H...O, C—F...π and, fundamentally, C—I...O interactions. As expected, the latter are among the strongest and more directional interactions of the sort reported in the literature, confirming that pyridineN-oxide is an eager acceptor. On the other hand, the structure presents only two of these contacts per 1,3,5-trifluoro-2,4,6-triiodobenzene molecule instead of the expected three. Possible reasons for this limitation are analyzed.

Ethyl (4-benzyloxyphenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carboxylate and a redetermination of ethyl (4RS)-4-(4-methoxyphenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carboxylate, as its 0.105-hydrate, both at 200 K: subtly different hydrogen-bonded ribbons

Two sulfanylidene-1,2,3,4-tetrahydropyrimidine derivatives have been synthesized using acid-catalysed cyclocondensation reactions between thiourea, ethyl 3-oxobutanoate and substituted benzaldehydes. In each of ethyl (4RS)-4-(4-benzyloxyphenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carboxylate, C21H22N2O3S, (I), where Z' = 2, and ethyl (4RS)-4-(4-methoxyphenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carboxylate 0.105-hydrate, C15H18N2O3S·0.105H2O, (II), the reduced pyrimidine ring adopts a conformation intermediate between the boat, screw-boat and twist-boat forms. In (I) and (II), a combination of N-H...O and N-H...S hydrogen bonds links the organic molecules into ribbons containing alternating R2(2)(8) and R4(4)(20) rings. In (I), the ribbon contains three types of ring, viz. two different R2(2)(8) rings which are both centrosymmetric and R4(4)(20) rings which are not centrosymmetric. In (II), the ribbon contains two types of ring, both of which are centrosymmetric. In compound (II), the ribbons enclose continuous channels which run along the twofold rotation axes in the space group C2/c, and the partial-occupancy water molecules lie within these channels. Structural comparisons are made with a number of related compounds.

Zn(ii) complex with 2-quinolinecarboxaldehyde selenosemicarbazone: synthesis, structure, interaction studies with DNA/HSA, molecular docking and caspase-8 and -9 independent apoptose induction

A new Zn(ii)-based complex shows a concentration-dependent apoptotic response in highly resistant pancreatic adenocarcinoma cells with extensive activation of caspase-8 and -9.

Coordination polymers from a highly flexible alkyldiamine-derived ligand: structure, magnetism and gas adsorption studies

Studies into a series of coordination polymers from a new diamine polycarboxylate ligand reveal an interplay between flexibility and material properties.

Sulfonated Schiff base copper(ii) complexes as efficient and selective catalysts in alcohol oxidation: syntheses and crystal structures

Alcohol oxidation properties of four copper complexes (2–5) derived from the sulfonated Schiff base H₂L·3H₂O (1) are described. A quantitative conversion of 1-phenylethanol was obtained with 4 within 20 min of low power MW irradiation.

Synthesis and structures of [S(H)P(μ-NR)]2, potential building blocks for inorganic phosphorus–sulfur macrocycles

Steric factors are the principle influence on the favourability of the cis and trans isomers of the novel dimers [S(H)P(μ-NR)]₂.

Cyclometalated Ir(iii) complexes of deprotonated N-methylbipyridinium ligands: effects of quaternised N centre position on luminescence

The optical emission behaviour of tricationic Ir^III complexes depends markedly on the position of the N-methyl unit in cyclometalating ligands.

Synthesis of substituted β-diketiminate gallium hydrides via oxidative addition of H–O bonds

Substituted β-diketiminate gallium hydrides of the general formulaLGa(H)X have been obtained from the oxidative addition reactions of compounds with OH groups intoLGa (L= HC[CMeNAr]₂⁻, Ar = 2,6-iPr₂C₆H₃).

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.

Effects of the Dzyaloshinskii–Moriya interaction in Cr3 triangular spin clusters detected by specific heat and multi-frequency electron spin resonance

An oxo-centered [Cr₃O(O₂C^tBu)₆(H₂O)₃](O₂C^tBu) HO₂C^tBu·2EtOH triangular cluster has been synthesized and its magnetic properties have been studied by means of complementary techniques.

5-(Fluorodinitromethyl)-2H-tetrazole and its tetrazolates – Preparation and Characterization of New High Energy Compounds

5-(Fluorodinitromethyl)-2H-tetrazole (HFDNTz) has been prepared by the cycloaddition reaction of HN₃ with F(NO₂)₂CCN, which in turn was prepared by aqueous fluorination of sodium dinitrocyanomethanide.

Assembly of photoluminescent [CunIn] (n = 4, 6 and 8) clusters by clickable hybrid [N,S] ligands

The controlled growth of luminescent copper(i)-iodide clusters has been achieved by tuning the structure of hybrid NS ligands using click chemistry.

Synergistic effect of sandwich polyoxometalates and copper–imidazole complexes for enhancing the peroxidase-like activity

Two inorganic–organic hybrids based on copper(ii)–imidazole complex modified sandwich-type tungstobismuthate or tungstoantimonite, have been synthesized, demonstrating higher peroxidase-like activity using TMB as a peroxidase substrate.

Preparation and characterization of 3,5-dinitro-1H-1,2,4-triazole

3,5-Dinitro-1H-1,2,4-triazole was isolated as an impact and friction sensitive solid, and fully characterized for the first time. The compound decomposes explosively upon heating to 170 °C. Impurities might lower the decomposition temperature and increase the sensitivity of the material.

A single-crystal to single-crystal phase transition in [Co(NH3)5NO2]Br2 at high pressure: a step towards understanding linkage photo-isomerisation

A single-crystal to single-crystal phase transition above 6.0 GPa is discussed in relation to the structural mechanism of homogeneous linkage photoisomerisation that is accompanied by photomechanical effects in the same compound.

Mono- and di-cationic hydrido boron compounds

Stable mono- and di-cationic hydrido boron compounds featuring CH₂BH₂(μ-H)BH₂CH₂ and CH₂BH(μ-H)₂BHCH₂ cores are readily accessible by dehydrogenative hydride abstractions. NBO calculations revealed the occurrence of two B–H–B 3c–2e bonds in the HB(μ-H)₂BH moiety of di-cations (7 and 8), where 43% is located at the H bridges and ∼28% at each boron atom.

Experimental observation and theoretical investigation of a novel Cd(ii) complex with π-hole interactions involving nitro groups

A cadmium(ii) complex, which represents a novel example of supramolecular system bearing a network of π-hole interactions, has been synthesized.

New Ni(ii) 1,2-bis(diphenylphosphino)ethane dithiolates: crystallographic, computational and Hirshfeld surface analyses

Three new Ni(ii) dppe dithiolates have been synthesized and the nature of weak interactions have been addressed using computational and Hirshfeld surface analyses.

Directed synthesis of {CuII2ZnII2} and {CuII8ZnII8} heterometallic complexes

The polydentate ligand Bis–tris propane is used to assemble two Cu/Zn heterometallic complexes: a tetramer which displays an unusually strong Cu(ii)⋯Cu(ii) exchange given the Cu⋯Cu separation or, in the presence of base, a hexadecanuclear complex with a remarkable double-concentric ring structure.

Gallium and indium complexes containing the bis(imino)phenoxide ligand: synthesis, structural characterization and polymerization studies

A series of gallium and indium complexes containing the bis(imino)phenolate ligand framework were synthesized and completely characterized with different spectroscopic techniques.

The selectivity of water-based pyrophosphate recognition is tuned by metal substitution in dimetallic receptors

Indicator displacement assays show that a digallium complex is selective for pyrophosphate even compared with higher concentrations of other common oxoanions like phosphate, ATP, arsenate, nitrate, perchlorate, sulfate, formate, carbonate and acetate.

Structure and magnetic properties of the AB(HCO2)3 (A = Rb+ or Cs+, B = Mn2+, Co2+ or Ni2+) frameworks: probing the effect of size on the phase evolution of the ternary formates

The AB(HCO₂)₃ (A = Rb⁺ or Cs⁺ & B = Mn²⁺, Co²⁺ and Ni²⁺) frameworks adopt either a perovskite-like or chiral hexagonal structure with dominantly antiferromagnetic interactions. This clarifies the phase evolution of the ternary formates with cation size.

Crystal growth and characterization of solvated organic charge-transfer complexes built on TTF and 9-dicyanomethylenefluorene derivatives

A series of solvated donor–acceptor organic complexes were shown to slowly release the lattice solvent while the degree of charge transfer decreases steadily. This behavior is not observed in the case of a hydrate.

Anisotropic displacement parameters from dispersion-corrected DFT methods and their experimental validation by temperature-dependent X-ray diffraction

How reliably can anisotropic displacement parameters be derived from theory? Experiments and computations on pentachloropyridine shed new light on this question.

Ca3ZnGeO2[Ge4O12]: a Ca-Zn germanate related to the mineral taikanite

The title compound, Ca3ZnGeO2[Ge4O12] (tricalcium zinc germanium dioxide dodecaoxidotetragermanate), adopts a taikanite-type structure. The tetrahedral [Ge4O12] chain geometry is very similar to that of the silicate chain of taikanite, i.e. BaSr2Mn(3+)2O2[Si4O12], while the major difference is found parallel to the c axis. In taikanite, Mn(3+) octahedra form an infinite zigzag chain, whereas the title compound has a chain of distorted ZnO6 octahedra, which alternates with distorted GeO4 tetrahedra connected to each other via two common edges. Eightfold-coordinated Ca(2+) polyhedra and ZnO6 octahedra form a slab parallel to (001) which alternates with another slab containing the tetrahedrally coordinated Ge sites along the c axis.

Tetraphenolate niobium and tantalum complexes for the ring opening polymerization of ε-caprolactone

Reaction of the pro-ligands α,α,α′,α′-tetra(3,5-di-tert-butyl-2-hydroxyphenyl-p-(or -m-)xylene-para-(or -meta-)tetraphenol with [MCl₅] (M = Nb, Ta) or [Nb(O)Cl₃(NCMe)₂] afforded complexes capable of the ROP of e-caprolactone at high temperature.

The first example of erbium triple-stranded helicates displaying SMM behaviour

Subcomponent self-assembly gives a new family of the triple-stranded helicates of the {LnIII2O₃}³⁻ core (Ln = Tb, Dy, Ho, Er, Tm and Yb) yielding an erbium congener revealing field-induced SMM characteristics.

Isolation and structural determination of non-racemic tertiary cathinone derivatives

In this paper the dynamic resolution of racemic tertiary cathinones is demonstrated through co-crystallization with enantiopure aromatic tartaric acids.

Heterometallic complexes with cube-type [MTi3N4] cores containing Group 10 metals in a variety of oxidation states

The metalloligand [{Ti(η⁵-C₅Me₅)(μ-NH)}₃(μ₃-N)] is capable of stabilizing Group 10 metals in the oxidation states 0,iioriv.

Energetic derivatives of 5-(5-amino-2H-1,2,3-triazol-4-yl)-1H-tetrazole

This study presents the preparation of the novel nitrogen-rich compound 5-(5-amino-2H-1,2,3-triazol-4-yl)-1H-tetrazole (5) in a five step synthesis, and additionally its more energetic derivatives with azido (6) and nitro (7) groups, as well as a diazene bridge (8).

SHELXT - integrated space-group and crystal-structure determination

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.

Copper pyromellitates: a complex story

Copper pyromellitate complexes range from unusual discrete molecular ions to 2- and 3-dimensional polymeric networks with considerable ligand structural versatility.

Transition from isolated to interacting copper(ii) pairs in extended lattices evaluated by single crystal EPR spectroscopy

Single crystal EPR experiments in copper-doped dimeric Zn(tda)(phen) allowed determination of Cu(ii) g- and A-matrices and ZFS parameters, which are used to evaluate the interdimeric exchange interaction in pure Cu(tda)(phen).

Synthesis, structure, and magnetic properties of dicopper and tricobalt complexes based on N-(2-pyridylmethyl)iminodiethanol

A novel unsymmetrical dinuclear copper complex [Cu(H₂pmide)(NO₃)Cu(Hpmide)](NO₃)₂ (1) and a mixed-valence trinuclear cobalt compound [(pmide)₂Co₃(CH₃CO₂)₂(NCS)₂]·4CH₃OH (2) have been prepared and characterized using structure and molecular magnetism.

Solvent effects in solvo-hydrothermal synthesis of uranyl ion complexes with 1,3-adamantanediacetate

Uranyl ion complexes with 1,3-adamantanediacetate display different topologies arising from variations in coordination mode and the presence of additional ligands.

Crosslinking of the Pd(acacCN)2 building unit with Ag(i) salts: dynamic 1D polymers and an extended 3D network

Pd(acacCN)₂ and Ag(i) salts aggregate to a 3D network or 1D chains. The latter topology provides an example for a tunable phase transition.

Homo- and heteroalumoxane silicates

Homo- or hetero alumoxanesilicates or bridged M–OH–M hydroxidesilicates with unusual or unprecedented inorganic cores have been obtained in reactions between 1 and nBuLi, AlMe₃, GaMe₃ or ZnMe₂. The aluminum derivatives serve as models for MAO.

Covalent attachment of diphosphine ligands to glassy carbon electrodes via Cu-catalyzed alkyne-azide cycloaddition. Metallation with Ni(ii)

Covalent tethering of a P₂N₂ ligand to a planar, azide-terminated glassy carbon electrode surface was accomplished using a Cu^I-catalyzed “click” reaction, followed by metallation with Ni^II.

Dichlorodioxomolybdenum(vi) complexes bearing oxygen-donor ligands as olefin epoxidation catalysts

The complexes [MoO₂Cl₂(N,N-dimethylbenzamide)₂] and [MoO₂Cl₂(N,N′-diethyloxamide)] are active olefin epoxidation catalysts and can be easily recycled when using ionic liquid solvents.

Hydrotelluration of acetylenic esters: structural characterization of stereoisomers of methyl/ethyl β-(aryltelluro)acrylates

Synthesis of tellurated acrylates, ArTeCHCHCOOR and their solid state structures have been explored. The ¹²⁵Te chemical shift and ²J(¹H–¹²⁵Te) are useful indicators of their geometry in solution.

Five Cu(i) and Zn(ii) clusters and coordination polymers of 2-pyridyl-1,2,3-triazoles: synthesis, structures and luminescence properties

2-Pyridyl-1,2,3-triazoles with flexible substituents demonstrate rare coordination modes and support new luminescent clusters and coordination polymers.

Interplay of ligand chirality and metal configuration in mononuclear complexes and in a coordination polymer of Cr(iii)

Chiral information may be transferred from a ligand to the coordinated chromium cation. The resulting complex can be crosslinked with a Ag(i) salt to a mixed-metal polymer with well-defined configuration at the Cr(iii).

Mechanism of proton transfer to coordinated thiolates: encapsulation of acid stabilizes precursor intermediate

Hydrogen bonded intermediate in protonation of [Ni(thiolate)(triphos)]⁺ by 2,6-lutidinium is stabilized by encapsulation of the acid by phenyl groups of triphos.

Syntheses, crystal structure, electrochemistry and luminescence properties of lanthano–germanotungstates

[Ln(α-GeW₁₁O₃₉)₂]¹³⁻ (Ln = La^III and Ce^III) and [{Ln(μ-CH₃COO)GeW₁₁O₃₉(H₂O)}₂]¹²⁻ (Ln = Pr^III, Nd^III and Sm^III) complexes were synthesized using a one-pot reaction. Similar complexes were isolated and their electrochemical and photochromic properties were studied.