Crystal Structure Determination Research Articles

N-Alkylisoquinolinium bromides and α,ω-alkanediols: Eutectic systems with co-crystal formation

This research focuses on ionic liquids (ILs), specifically N-alkylisoquinolinium bromides with various chain lengths: octyl, decyl, dodecyl, and hexadecyl. The study covers the synthesis and thermophysical characterisation of these compounds, as well as crystal structure determination for all excluding N-decylisoquinolinium bromide ([i-QuinC10][Br]). The obtained thermophysical parameters were compared with the literature data and also within the extended homologous series.The solid–liquid phase equilibria (SLE) in mixtures of ILs with certain α,ω-alkanediols (1,6-hexanediol, 1,8-octanediol, 1,10-decanediol, 1,12-dodecanediol) were investigated. As a result of SLE studies, eutectic mixtures capable of acting as eutectic phase-change materials - ePCMs - were determined. Additionally, a self-organization phenomenon was observed between specific pairs, leading to the formation of co-crystals (solid-complex phase). All binary mixtures with [i-QuinC8][Br] formed a simple eutectic system, while in the case of [i-QuinC10][Br], the formation of a non-congruent melting compound was observed in the systems with 1,8-octanediol and 1,10-decanediol. Among the systems with [i-QuinC12][Br], congruent melting compounds were observed for mixtures with 1,8-octanediol, 1,10-decanediol and 1,12-dodecanediol, while a simple eutectic was recorded for 1,6-hexanediol. IL [i-QuinC16][Br] co-crystalised only with 1,12-dodecanediol, while with other diols formed simple eutectic systems. Calorimetric analysis (DSC) and crystal structure determination (X-ray diffraction) were used to characterize the obtained supramolecular compounds.As a result, a series of ePCMs with melting points ranging from 295 K to 343 K are presented, with the {[i-QuinC12][Br] + 1,10-decanediol} system showing the highest enthalpy of melting (173.5 J·g−1). The found features and correlations between structure and properties imply the necessity for additional investigation, indicating the potential for a new generation of compounds with customizable physicochemical properties.

On: X-ray diffraction from the electron gas in monatomic metallic hydrogen

Solid hydrogen is expected to become a monatomic metal under sufficiently high compression. With hydrogen having only a single valence electron and no ion core, the nature of x-ray diffraction patterns from the electron gas of monatomic metallic hydrogen is uncertain, and it is unclear whether they may yield enough information for a crystal structure determination. With emphasis on the Cs-IV-type ( I41/amd ) structure predicted for hydrogen at ∼500 GPa, the electron density distributions, zero-point and thermal atomic motion, and x-ray diffraction intensities are determined from first-principles calculations for several candidate phases of metallic hydrogen. It is shown that the electron distribution is much more structured than might be expected from the commonly employed free-electron-gas picture, and in fact more modulated than what is obtained from the superposition of free-atom charge densities. We demonstrate that an identification of the crystal structure of monatomic metallic hydrogen from x-ray diffraction is fundamentally possible and discuss the possibility of single-crystal diffraction from metallic hydrogen. An atomic scattering factor for the hydrogen atom in monatomic metallic hydrogen is constructed to aid the quantitative analysis of diffraction intensities from future x-ray diffraction experiments.

Chlorido-pentamethylcyclopentadienyl-[2-(2-pyridyl-кN)-ferrocenyl-кC]-iridium(III)

Treatment of 2-pyridyl-ferrocene wit [Cp*IrCl2]2 in the presence of NaOAc produces the title compound Cp*ClIr[(C5H3C5H4N-кN,кC)Fe(C5H5)] (2) in low yield. A crystal structure determination shows the (SpSIr/RpRIr)-2 enantiomeric pair of diastereomers.

Dinucleating N‐donor Ligands with 1,2‐Diethynylbenzene Backbone for the Copper‐Mediated Monooxygenation of Phenols

AbstractNew dinucleating, tweezer‐like ligands with 1,2‐diethynyl‐benzene backbone containing three pyridines (Tw1), a combination of pyridine and pyrazole (Tw2) or pyridine and triazole (Tw3), respectively, have been synthesized and characterized spectroscopically and by single crystal structure determination. The ability of the derived copper(I) complexes CuTw1–3 to act as model systems for tyrosinase (Ty) was investigated by studying the reactivity toward monophenolic substrates. No dioxygen intermediate was detected at low temperatures, and CuTw1 was found to be inactive toward monoxygenation of phenolic substrate DTBP‐H. However, a crystal structure containing a μ‐hydroxo ligand, similar to the met‐form of Ty, underlines the ability of the complex to bind oxygen. In contrast, CuTw2 converts phenols to o‐quinones with moderate yield and this activity is even higher when using CuTw3. The observed differences in reactivity are discussed.

Discovery of a Biotin Synthase That Utilizes an Auxiliary 4Fe-5S Cluster for Sulfur Insertion.

Biotin synthase (BioB) is a member of the Radical SAM superfamily of enzymes that catalyzes the terminal step of biotin (vitamin B7) biosynthesis, in which it inserts a sulfur atom in desthiobiotin to form a thiolane ring. How BioB accomplishes this difficult reaction has been the subject of much controversy, mainly around the source of the sulfur atom. However, it is now widely accepted that the sulfur atom inserted to form biotin stems from the sacrifice of the auxiliary 2Fe-2S cluster of BioB. Here, we bioinformatically explore the diversity of BioBs available in sequence databases and find an unexpected variation in the coordination of the auxiliary iron-sulfur cluster. After in vitro characterization, including the determination of biotin formation and representative crystal structures, we report a new type of BioB utilized by virtually all obligate anaerobic organisms. Instead of a 2Fe-2S cluster, this novel type of BioB utilizes an auxiliary 4Fe-5S cluster. Interestingly, this auxiliary 4Fe-5S cluster contains a ligated sulfide that we propose is used for biotin formation. We have termed this novel type of BioB, Type II BioB, with the E. coli 2Fe-2S cluster sacrificial BioB representing Type I. This surprisingly ubiquitous Type II BioB has implications for our understanding of the function and evolution of Fe-S clusters in enzyme catalysis, highlighting the difference in strategies between the anaerobic and aerobic world.

Carolina MacGillavry and the Determination of Crystal Structures

Carolina MacGillavry and the Determination of Crystal Structures

Designed additive suppresses interpenetration in IRMOF-10.

IRMOF-10, derived from biphenyl-4,4'-dicarboxylic acid and zinc, is a prototype for an open cubic structure prone to interpenetration. Interpenetration can compromise MOF pore volume and surface area which drives the need to develop strategies to synthesize non-interpenetrated MOFs. In this work, an additive design strategy was employed to suppress interpenetration of IRMOF-10. The presence of the additive during traditional solvothermal synthesis yielded an activated material with the highest surface area reported to date and enabled the determination of the single crystal structure. In situ monitoring of the nucleation of crystals under polarized light provided insights into the mechanism behind interpenetration in the IRMOF-9/10 system. This work provides a roadmap to suppress interpenetration more generically in other MOFs and achieve improved surface areas and pore volumes for this prominent class of porous sorbents.

Synthesis of bismuthanyl-substituted monomeric triel hydrides.

The syntheses and characterizations of the first bismuthanylborane monomers stabilized only by a donor in D·BH2Bi(SiMe3)2 (D = DMAP 1a, IDipp 1b, IMe41c; DMAP = 4-dimethylaminopyridine, IDipp = 1,3-bis(2,6-diisopropylphenyl)-imidazolin-2-ylidene, IMe4 = 1,3,4,5-tetramethylimidazol-2-ylidene) are presented. All compounds were synthesized by salt metathesis reactions between D·BH2I and KBi(SiMe3)2(THF)0.3 and represent some of the extremely rare compounds featuring a 2c-2e B-Bi bond in a molecular compound. The products display high sensitivity towards air and light and slowly decompose in solution even at -80 °C. By the reaction of IDipp·GaH2(SO3CF3) with KBi(SiMe3)2(THF)0.3, the synthesis of the first bismuthanylgallane IDipp·GaH2Bi(SiMe3)2 (2) stabilized only by a 2-electron donor was possible, as evident from single crystal X-ray structure determination, NMR spectroscopy and mass spectrometry. Computational studies shed light on the stability of the products and the electronic nature of the compounds.

Complexation of drug amifampridine with Cu(II), Zn(II) and Cd(II) ions, and its dimerization with the magic of Mn(II) salts. Potential anti-COVID-19 and anticancer activities.

The different behaviors of the drug amifampridine (AMP) against Mn(II), Cu(II), Zn(II) and Cd(II) metal ions, in the presence and absence of tris(2-aminoethyl)amine (tren) was studied. The results showed that AMP successfully coordinates with Cu(II), Zn(II) and Cd(II) metal ions, but interestingly it undergoes an unexpected dimerization through a C-H activation in the presence of different Mn(II) salts. A four-coordinate complex of zinc(II), [Zn(AMP)2Cl2] (1), a binuclear complex of cadmium(II), [Cd2(AMP)2Cl4] (2), three five-coordinate tren-based metal complexes, [Cu(tren)(AMP)](ClO4)2 (8), [Zn(tren)(AMP)]Cl2 (9) and [Cd(tren)(AMP)](ClO4)2 (10), three pyridinium salts, [AmpDimer]X (X = Cl-, NO3-, ClO4-; (3, 4 & 5)), and also two four-coordinate metal complexes with this pyridinium cation, [Zn(AmpDimer)Cl3] (6) and [Cd(AmpDimer)Cl3] (7), were synthesized. All new compounds were characterized by elemental analysis and IR spectroscopy, and by 1H- and 13C-NMR spectroscopy (for 1, 2, 3, 6, 7, 9 & 10) and by X-ray crystal structure determinations (for 1, 3, 4, 5, 7, 8 & 10). Theoretical studies showed that the [M(tren)(AMP)]2+ cations act as pH-sensitive drug carriers of AMP and release it upon protonation. The molecular docking studies on the interaction of AMP and the above complexes/salts with DNA and the proteins of SARS-CoV-2 showed that the synthesized complexes/salts have greater anticancer and anti-covid-19 activities than AMP alone.

Synthesis of diaminoacetylene from cyanido ligands of the octacyanidotungstate complex

First metal-asisted diaminoacetylene molecule synthesis is achieved. Three salts of [W(CN)6(C2N2H4)]2− ion were isolated and characterized including single crystal structure determination. The formation of diaminoacetylene is described and discussed.

Light-induced spin-state switching in Fe(II) spin-crossover complexes with thiazole-based chelating ligands.

Homoleptic complexes [Fe(4bt)3](ClO4)2 (1), [Fe(2bt)3](ClO4)2 (2), and [Fe(3tpH)3](ClO4)2 (3) were obtained by a reaction between the Fe(II) precursor salt and the corresponding thiazole-based bidentate ligand (L = 4bt = 4,4'-bithiazole, 2bt = 2,2'-bithiazole, 3tpH = 3-(thiazol-2-yl)pyrazole). X-ray crystal structure determination revealed crystallization of solvent-free complex 1, a solvate 2·MeOH, and a co-crystal 3·2(3tpH). The crystal packing of all these complexes is dominated by one-dimensional interactions between the [Fe(L)3]2+ cations. These interactions are stronger in 2·MeOH and 3·2(3tpH), leading to cooperative and slightly hysteretic transitions between the high-spin and low-spin electronic configurations at ∼235 K and 159 K, respectively. In contrast, weaker intermolecular interactions in 1 result in a gradual spin crossover above 300 K, with the maximum fraction of the HS state ∼25% achieved at 400 K. Complexes 2 and 3·2(3tpH) exhibit light-induced excited spin state trapping (LIESST) under irradiation with white light or a 532 nm laser at 5 K. After the photoexcitation, the trapped metastable HS state relaxes to the ground LS state with the average relaxation temperature of 81 K and 68 K, respectively. Examination of the relaxation dynamics by optical absorption spectroscopy on a single crystal of 3·2(3tpH) revealed the sigmoidal shape of the relaxation curves at lower temperatures, attributed to cooperative effects, as well as a plateau at ∼10% of the HS fraction at intermediate temperatures, hinting at a more complex mechanism for the relaxation of the LIESST phase in this material.

A pyridine-N-oxide catenane for cation recognition.

The rapid preparation of a pyridine-N-oxide containing [2]catenane is described. The [2]catenane was characterized by NMR spectroscopy, mass spectrometry and X-ray single crystal structure determination. 1H NMR titration experiments reveal the [2]catenane may be reversibly protonated, as well as an ability to bind lithium cations more strongly than sodium cations.

Selenosalicylate; a little-studied heavy-element analogue of the versatile thiosalicylate ligand.

Selenosalicylic acid (ortho-HSeC6H4CO2H), the heavy element congener of the widely studied thiosalicylic acid, was prepared by reaction of 2-carboxybenzenediazonium chloride (HO2CC6H4N2+Cl-) with Na2Se2, followed by reduction of the resulting diselenide (SeC6H4CO2H)2 with zinc and acetic acid. The coordination chemistry of the selenosalicylate ligand towards a variety of platinum(ii), palladium(ii), nickel(ii), gold(iii), gold(i), rhodium(iii), iridium(iii) and ruthenium(ii) centres was explored. X-ray crystal structure determinations were carried out on the complexes [Pt(SeC6H4CO2)(PPh3)2], [{(p-cym)Ru(SeC6H4CO2)}2] (p-cym = η6-p-cymene, CH3C6H4CH(CH3)2), [{Cp*Rh(SeC6H4CO2)}2] (Cp* = η5-C5Me5) and [Cp*Ir(SeC6H4CO2)(PPh3)], and comparisons are made with corresponding thiosalicylate complexes. The complexes were characterised by NMR spectroscopy as well as ESI mass spectrometry, which indicated a greater propensity for fragmentation including by selenium loss, compared to the thiosalicylate analogues. Hirshfeld surface analysis to visualise and quantify intermolecular interactions revealed the dominance of H⋯H contacts in [{(p-cym)Ru(SeC6H4CO2)}2] and [Cp*Ir(SeC6H4CO2)(PPh3)].

Domain of unknown function (DUF) proteins in plants: function and perspective.

Domains of unknown function (DUFs), which are deposited in the protein family database (Pfam), are protein domains with conserved amino acid sequences and uncharacterized functions. Proteins with the same DUF were classified as DUF families. Although DUF families are generally not essential for the survival of plants, they play roles in plant development and adaptation. Characterizing the functions of DUFs is important for deciphering biological puzzles. DUFs were generally studied through forward and reverse genetics. Some novelty approaches, especially the determination of crystal structures and interaction partners of the DUFs, should attract more attention. This review described the identification of DUF genes by genome-wide and transcriptome-wide analyses, summarized the function of DUF-containing proteins, and addressed the prospects for future studies in DUFs in plants.

Structural consequences in differently substituted haloarylcarboxylates and non-covalent interactions on crystal packing and biological efficacy of copper(II) complexes with N,N,N′,N′-tetramethylethylenediamine N-donor ligand

In this work, we reported four new copper(II) halo-benzoate complexes (2-chloro-4-nitrobenzoate (2-Cl-4-NO2-BZ), 3,5-DICBZ, 2-chloro-5-nitrobenzoate (2-Cl-5-NO2-BZ), 3,5-difluoro benzoate (3,5-DIFBZ), and 3,5-dichlorobenzene (3,5-DICBZ) respectively in complexes 1–4) with N,N,N’,N’- tetramethylethylene diamine (temed) N-donor ligand in order to study the interesting coordination features and biological evaluation of such complexes under ambient reaction conditions. All the complexes 1–4 were characterized by elemental analyses, and spectroscopic techniques, including FT-IR, UV–vis, and EPR etc. Single crystal X-ray structure determination (SCXRD) of complexes revealed the distorted octahedral geometry in all complexes. Notably, the halobenzoate ligands exhibited a bidentate chelation mode in complexes 1 and 2, while they showed a monodentate mode in complex 3. In complex 4, the carboxylate ligand exhibited both monodentate as well as bidentate coordination. Furthermore, detailed packing analyses of complexes 1–4 highlighted the significance of halogen bonding in lattice stabilization besides hydrogen bonding and π∙∙∙π interactions as evidenced by Hirshfeld surface analyses and crystal analysis. Moreover, packing analyses displayed that complex 1 exhibited a layered or wave-like arrangement, while complex 2 featured a helical arrangement supported by a supramolecular halogen-bonded network guided by Cl∙∙∙O interactions. Complex 3 displayed a zig-zag layered arrangement with a stacking topology, and Complex 4 showcased a ribbon-like arrangement stabilized by F∙∙∙F and Cl∙∙∙Cl halogen bonding interactions. Furthermore, sigma hole on halogen atoms has also been examined (which play an important role in halogen bonding) by electrostatic-potential isosurfaces. In order to exploit the biological efficacy of complexes 1–4 owing to the inherent biological activity of copper metal, molecular docking analyses against gram +ve bacteria i.e. S. epidermidis (PDB ID; 8DO6), B. subtilis (1QD9), as well as two gram -ve bacteria, namely, P. aeruginosa (5WZE) and S. dysenteriae (1DM0), have also been carried out. Interestingly, values of docking scores and inhibition constant of all complexes 1–4 (with a maximum binding score (inhibition constant) of -9.8 kcal/mol (0.063 µMol) in 1 against 8DO6 and 1DM0) revealed higher biological efficacy than that of standard drugs.

Experimental Determination of Phase Equilibria in the Mn-Zn Binary System

Phase equilibria in the Mn-Zn binary system were experimentally determined by chemical composition examination, crystal structure determination, and thermal analysis. Major changes were detected for the β, ε, and δ phases. The β-B2 single-phase region could not be confirmed in the studied system because a disordered body-centered cubic structure, which is identical to the δMn phase, was confirmed in a quenched sample from the previously proposed region of β phase. The ε phase has been controversial whether the phase is separated into ε, ε1, and ε2 phases or not. By studying a diffusion couple and several alloy compositions, it was established that the ε, ε1, and ε2 phases are not separate and comprise a single ε phase. Furthermore, the δ phase is not present in the Zn-rich region of the system because the corresponding invariant reactions were not detected via thermal analysis.

Pressure-Assisted Synthesis of Highly Crystalline 1T''-Lix MoS2.

Lix MoS2 is not only a lithium battery material, but is also an important precursor for the synthesis of MoS2 nanomaterials. Current syntheses of MoS2 , such as in n-butyllithium/LiBH4 or electrochemically, are not satisfying in terms of defined stoichiometry and crystallinity, so an accurate experimental crystal structure determination of this important and widely used material has been long awaited. A high-pressure/high-temperature synthesis yielded highly crystalline 1T''-Lix MoS2 (x=1, 1.333). 1T''-LiMoS2 crystallizes in the space group P with a=6.2482(3) Å, b=6.6336(3) Å, c=6.7480(3) Å, α=119.321(2)°, β=90.010(2)° and γ=90.077(2)°. The arrangement of Mo atoms within the b-c-plane confirmed a predicted Peierls distortion. A similar atom distribution pattern to that of Mo is also observed for the lithium atoms. Calculation of bond valence site energies gave an activation barrier of 1.244 eV for 2D lithium-ion migration. For x=1.333, a phase-pure synthesis was achieved.

First Gallium and Indium Crystal Structures of Curcuminoid Homoleptic Complexes: All-Different Ligand Stereochemistry and Cytotoxic Potential.

The crystal structure determination of metal complexes of curcuminoids is a relevant topic to assess their unequivocal molecular structure. We report herein the first two X-ray crystal structures of homoleptic metal complexes of a curcuminoid, namely Dimethoxycurcumin (DiMeOC), with gallium and indium. Such successful achievement can be attributed to the suppression of interactions from the phenolic groups, which favor an appropriate molecular setup, rendering Dimethoxycurcumin gallium ((DiMeOC)2-Ga) and Dimethoxycurcumin indium ((DiMeOC)3-In) crystals. Surprisingly, the conformation of ligands in the crystal structures shows differences in each metal complex. Thus, the ligands in the (DiMeOC)2-Ga complex show two different conformers in the two molecules of the asymmetric unit. However, the ligands in the (DiMeOC)3-In complex exhibit three different conformations within the same molecule of the asymmetric unit, constituting the first such case described for an ML3 complex. The cytotoxic activity of the (DiMeOC)2-Ga complex is 4-fold higher than cisplatin against the K562 cell line and has comparable activity towards U251 and PC-3 cell lines. Interestingly, this complex exhibit three times lesser toxicity than cisplatin and even slightly lesser cytotoxicity than curcumin itself.

Formation, Characterization, and Bonding of cis- and trans-[PtCl2{Te(CH2)6}2], cis-trans-[Pt3Cl6{Te(CH2)6}4], and cis-trans-[Pt4Cl8{Te(CH2)6}4]: Experimental and DFT Study.

[PtCl2{Te(CH2)6}2] (1) was synthesized from the cyclic telluroether Te(CH2)6 and cis-[PtCl2(NCPh)2] in dichloromethane at room temperature under the exclusion of light. The crystal structure determination showed that in the solid state, 1 crystallizes as yellow plate-like crystals of the cis-isomer 1cis and the orange-red interwoven needles of 1trans. The crystals could be separated under the microscope. NMR experiments showed that upon dissolution of the crystals of 1cis in CDCl3, it isomerizes and forms a dynamic equilibrium with the trans-isomer 1trans that becomes the predominant species. Small amounts of cis-trans-[Pt3Cl6{Te(CH2)6}4] (2) and cis-trans-[Pt4Cl8{Te(CH2)6}4] (3) were also formed and structurally characterized. Both compounds show rare bridging telluroether ligands and two different platinum coordination environments, one exhibiting a cis-Cl/cis-Te(CH2)6 arrangement and the other a trans-Cl/trans-Te(CH2)6 arrangement. Complex 2 has an open structure with two terminal and two bridging telluroether ligands, whereas complex 3 has a cyclic structure with four Te(CH2)6 bridging ligands. The bonding and formation of the complexes have been discussed through the use of DFT calculations combined with QTAIM analysis. The recrystallization of the mixture of the 1:1 reaction from d6-DMSO afforded [PtCl2{S(O)(CD3)2}{Te(CH2)6}] (4) that could also be characterized both structurally and spectroscopically.

Novel Schiff Base Derived from Amino Pyrene: Synthesis, Characterization, Crystal Structure Determination, and Anticancer Applications of the Ligand and Its Metal Complexes.

In this study, we report the cytotoxicity of a newly synthesized Schiff base HL ((E)-2-ethoxy-6((pyren-1-ylimino)methyl)phenol) and its derived metal complexes (Zn(II), Cu(II), Co(II), Cr(III), and Fe(III)) along with their structural characterizations by means of elemental analysis, magnetic moment, molar conductance, IR, UV-Vis, ESR, and mass spectrometry. The single X-ray diffraction of the HL shows that it exists in the phenol-imine form in its solid state. The NMR and IR data indicate that the bidentate binding of the Schiff base ligand with the metal center occurs during complexation through the azomethine nitrogen atom and the hydroxyl group oxygen atom of the 3-ethoxy salicylaldehyde. The electronic spectra and magnetic measurements indicate that the Co(II) complex has a tetrahedral geometry and that the Cr(III) and Fe(III) complexes have a distorted octahedral geometry. The ESR and electronic spectra suggest that the Cu(II) complex has a distorted tetrahedral geometry. The cytotoxic effects of the HL and all of the metal complexes were studied using human breast cancer (MCF-7) cells. The Cu(II) and Zn(II) complexes exhibited the highest activity against the tested cell line, with IC50 values of 5.66 and 12.74 μg/mL, respectively, and their activity was higher than that of the fluorouracil cancer drug against the MCF-7 cells (18.05 μg/mL).