X-ray Crystallography Research Articles

Synthesis and antitumor activity of gold(I) N-heterocyclic carbene with dithiocarbamate and alkynyl complexes

A series of new type gold(I) N-heterocyclic carbene (NHC) complexes bearing a paeonol ligand in the side chain of NHC and bearing dithiocarbamate or alkynyl groups as a second ligand have been synthesized and structurally characterized by spectroscopic methods. The structure of Pa-NHC-Au-Cl has been established by X-ray crystallography. Their antitumor activities in vitro were investigated by CCK8 assay against two tumor cell lines (A549 and Hela). The gold(I) NHC with dithiocarbamate (DTC) complexes showed good to excellent antiproliferative activity and strongly inhibited the selenoenzyme thioredoxin reductase (TrxR).

A Semiflexible Tetrahydrazone Macrocycle for Binding of Pyrophosphate and Smaller Anions.

Macrocyclization has proven to be a useful design strategy in the development of efficient anion receptors. In addition to the ring size, the overall preorganization due to structural rigidity is key. To explore this in the context of developing an efficient pyrophosphate receptor, three macrocycles featuring a 26-membered interior ring size and similar H-bonding motifs have been synthesized, and their anion binding ability has been investigated. Computational studies and nuclear magnetic resonance (NMR) data showed different degrees of preorganization as a result of differences in flexibility. The interaction of the three macrocycles with chloride, dihydrogen phosphate, and dihydrogen pyrophosphate was investigated in solution by NMR and ultraviolet-visible spectroscopy and in the solid state by X-ray crystallography. The tetrahydrazone-based macrocycle featuring intermediate flexibility exhibited the best affinity for all three anions investigated. Our results suggest that in addition to the proper preorganization of binding groups in a macrocycle a certain degree of flexibility is also required for an optimal affinity with the target guest.

Acyclic Cucurbit[n]uril Receptors Function as Solid State Sequestrants for Organic Micropollutants.

The accumulation of organic micropollutants (OMP) in aquatic systems is a major societal problem that can be addressed by approaches including nanofiltration, flocculation, reverse osmosis and adsorptive methods using insoluble materials (e.g. activated carbon, MOFs, nanocomposites). More recently, polymeric versions of supramolecular hosts (e.g. cyclodextrins, calixarenes, pillararenes) have been investigated as OMP sequestrants. Herein, we report our study of the use of water insoluble dimethylcatechol walled acyclic cucurbit[n]uril (CB[n]) hosts as solid state sequestrants for a panel of five OMPs. A series of hosts (H1 - H4) were synthesized by reaction of glycoluril oligomer (monomer - tetramer) with 3,6-dimethylcatechol and fully characterized by spectroscopic means and x-ray crystallography. The solid hosts sequester OMPs from water with removal efficiencies exceeding 90% in some cases. The removal efficiencies of the new hosts parallel the known molecular recognition properties of analogous water soluble acyclic CB[n]. OMP uptake by solid host occurs rapidly (≈120 seconds). Head-to-head comparison with CB[6] in batch-mode separation and DARCO activated carbon in flow-through separation mode show that tetramer derived host (H4) performs very well under identical conditions. The work establishes insoluble acyclic CB[n]-type receptors as a promising new platform for OMP sequestration.

KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography.

Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. The method is named KINNTREX (kinetics-informed NN for time-resolved X-ray crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels of complexity. For the simulations, time-resolved X-ray data were generated that mimic data collected from the photocycle of the photoactive yellow protein. KINNTREX only requires the number of intermediates and approximate relaxation times (both obtained from a singular valued decomposition) and does not require an assumption of a candidate mechanism. It successfully predicts a consistent chemical kinetic mechanism, together with difference electron-density maps of the intermediates that appear during the reaction. These features make KINNTREX attractive for tackling a wide range of biomolecular questions. In addition, the versatility of KINNTREX can inspire more NN-based applications to time-resolved data from biological macromolecules obtained by other methods.

Absolute Structures of a Mirror Pair of Infinite Na(H2O)4 + -Connected ε-Keggin-Al13 Species.

The absolute structures of a pair of infinite Na(H2O)4+-connected ε-Keggin-Al13 species (Na-ε-K-Al13) that were inversion structures and mirror images of each other were determined. Single crystals obtained by adding A2SO4 (A = Li, Na, K, Rb, or Cs) solution to NaOH-hydrolyzed AlCl3 solution were subjected to X-ray structure analyses. The statistical results for 36 single crystals showed that all the crystals had almost the same unit cell parameter, belonged to the same F4̅3m space group, and possessed the same structural formula [Na(H2O)4AlO4Al12(OH)24(H2O)12](SO4)4·10H2O. However, the crystals had two inverse absolute structures (denoted A and B), which had a crystallization ratio of 1:1. From Li+ to Cs+, with increasing volume of the cation coexisting in the mother solution, the degree of disorder of the four H2O molecules in the Na(H2O)4+ hydrated ion continuously decreased; they became ordered when the cation was Cs+. Absolute structures A and B are the first two infinite aluminum polycations connected by statistically occupied [(Na1/4)4(H2O)4]+ hydrated ions. The three-dimensional structure of the infinite Na-ε-K-Al13 species can be regarded as the assembly of finite ε-K-Al13 species linked by [(Na1/4)4(H2O)4]+ in a 1:1 ratio. In this assembly, each [(Na1/4)4(H2O)4]+ is connected to four ε-K-Al13 and each ε-K-Al13 is also connected to four [(Na1/4)4(H2O)4]+ in tetrahedral orientations to form a continuous rigid framework structure, which has an inverse spatial orientation between absolute structure A and B. This discovery clarifies that the ε-K-Al13 (or ε-K-GaAl12) species in Na[MO4Al12(OH)24(H2O)12](XO4)4·nH2O (M = Al, Ga; X = S, Se; n = 10-20) exists as discrete groups and deepens understanding of the formation and evolution process of polyaluminum species in forcibly hydrolyzed aluminum salt solution. The reason why Na+ statistically occupies the four sites was examined, and a formation and evolution mechanism of the infinite Na-ε-K-Al13 species was proposed.

5,6-Diphenyl-1,3,4,7-tetra-p-tolyl-1,3,3a,7a-tetrahydropentaleno[1,2-c]furan

The reaction of (Z)-5-phenyl-1,3-di-p-tolylpent-2-en-4-yn-1-ol (1) with trimethylsilyl chloride in dichloromethane at ambient temperature gave a dimeric ether compound 2 in 30% yield. Subsequently, heating 2 in toluene under refluxing temperature rendered the title compound quantitatively. The structure of this tricyclic-fused compound was characterized using NMR, mass spectroscopy, and X-ray crystallography. This unique linear tricyclic fused furan framework is reported for the first time.

Luminescent Pt(II) Complexes Using Unsymmetrical Bis(2-pyridylimino)isoindolate Analogues.

A series of ligands based upon a 1,3-diimino-isoindoline framework have been synthesized and investigated as pincer-type (N∧N∧N) chelates for Pt(II). The synthetic route allows different combinations of heterocyclic moieties (including pyridyl, thiazole, and isoquinoline) to yield new unsymmetrical ligands. Pt(L1-6)Cl complexes were obtained and characterized using a range of spectroscopic and analytical techniques: 1H and 13C NMR, IR, UV-vis and luminescence spectroscopies, elemental analyses, high-resolution mass spectrometry, electrochemistry, and one example via X-ray crystallography which showed a distorted square planar environment at Pt(II). Cyclic voltammetry on the complexes showed one irreversible oxidation between +0.75 and +1 V (attributed to Pt2+/3+ couple) and a number of ligand-based reductions; in four complexes, two fully reversible reductions were noted between -1.4 and -1.9 V. Photophysical studies showed that Pt(L1-6)Cl absorbs efficiently in the visible region through a combination of ligand-based bands and metal-to-ligand charge-transfer features at 400-550 nm, with assignments supported by DFT calculations. Excitation at 500 nm led to luminescence (studied in both solutions and solid state) in all cases with different combinations of the heterocyclic donors providing tuning of the emission wavelength around 550-678 nm.

Chaperone-mediated MHC-I peptide exchange in antigen presentation.

This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.

Daphmacrimines A−K, Daphniphyllum alkaloids from Daphniphyllum macropodum Miq

Daphmacrimines A–K (1–11) were isolated from the leaves and stems of Daphniphyllum macropodum Miq. Their structures and stereochemistries were determined by extensive techniques, including HRESIMS, NMR, ECD, IR, and single-crystal X-ray crystallography. Daphmacrimines A–D (1–4) are unprecedented Daphniphyllum alkaloids with a 2-oxazolidinone ring. Daphmacrimine I (9) contains a nitrile group, which is relatively rare in naturally occurring alkaloids. The abilities of daphmacrimines A–D and daphmacrimines G–K to enhance lysosomal biogenesis were evaluated through LysoTracker Red staining. Daphmacrimine K (11) can induce lysosomal biogenesis and promote autophagic flux.

Design of non-fused ring electron acceptors with “embracing-type” side chains for organic solar cells

Backbone planarity is an inherent structural feature for fused ring electron acceptors and one of important prerequisites for their high photovoltaic performance. However, for non-fused ring electron acceptors (NFREAs), it is a challenging task to achieve it. In this work, two NFREAs (Ph2TIC and BT2TIC) containing thiophene-benzene-thiophene or thiophene-benzothiadiazole-thiophene three non-fused aromatic rings in central scaffold were designed with an attempt to use a pair of 2,4,6-triisopropylphenyl substituents (referred as “embracing”-type side chains) at 3,3′-positions of the two thiophene units to lock the backbone in a planar conformation. X-ray crystallography revealed that Ph2TIC has a quasi-planar backbone, whereas BT2TIC shows a twisted one, but both tend to form two-dimensional layered arrays through intermolecular π-π stacking involving terminal acceptor moieties. UV–vis light-absorption spectroscopy showed that both compounds have similar optoelectronic properties either in dilute solutions or in solid film state, thus confirming the conformation-lock function of the “embracing”-type side chains. While for photophysical properties, BT2TIC displays a red-shifted broader light absorption spectrum as compared to Ph2TIC due to the introduction of an additional acceptor moiety in the structure. Ph2TIC and BT2TIC were evaluated as the acceptor materials in organic solar cells in combination with PM6, a typical donor polymer, and delivered the optimized power conversion efficiencies of 4.31 % and 3.78 %, respectively. Although the photovoltaic performances are modest, the work provides a new thought for maintaining the backbone planarity in NFREAs and would be useful in their future design.

Expression, purification and preliminary crystallographic analysis of bacterial transmembrane protein EfeU for iron import

The bacterial Efe system functions as an importer of free Fe2+ into cells independently of iron-chelating compounds such as siderophores and consisted of iron-binding protein EfeO, peroxidase EfeB, and transmembrane permease EfeU. While we and other researchers reported crystal structures of EfeO and EfeB, that of EfeU remains undetermined. In this study, we constructed expression system of EfeU derived from Escherichia coli, selected E. coli Rosetta-gami 2 (DE3) as an expression host, and succeeded in purification of the proteins which were indicated to form an oligomer by blue native PAGE. We obtained preliminary data of the X-ray crystallography, suggesting that expression and purification methods we established in this study enable structural analysis of the bacterial Efe system.

Unusual Stabilisation of Remarkably Bent Tetra-Cationic Tetra-radical Intermolecular Fe(III) μ-Oxo Tetranuclear Complexes.

A hitherto unknown series of air stable, π-conjugated, remarkably bent tetra-cation tetra-radical intermolecular Fe(III) μ-oxo tetranuclear complex, isolated from the dication diradical diiron(III) porphyrin dimers, has been synthesised and spectroscopically characterised along with single crystal X-ray structure determination of two such molecules. These species facilitate long-range charge/radical delocalisation through the bridge across the entire tetranuclear unit manifesting an unusually intense NIR band. Assorted spin states of Fe(III) centres are stabilised within these unique tetranuclear frameworks: terminal six-coordinate iron centres stabilise the admixed intermediate spin states while the central five-coordinate iron centres stabilise the high-spin states. Variable temperature magnetic susceptibility measurements indicated strong antiferromagnetic coupling for the Fe(III)-O-Fe(III) unit while the exchange interactions between the Fe centres and the porphyrin π-cation radicals are weaker as supported both by magnetic data and DFT calculations. The nature of orbital overlap between the SOMOs of Fe(III) and π* orbital of the porphyrin was found to rationalise the observed exchange coupling, establishing such a complex magnetic exchange in this tetranuclear model with a significant bioinorganic relevance.

Diverse Reactivity of Amidinate-Supported Boron Centers with the Hypersilyl Anion and Access to a Monomeric Secondary Boron Hydride.

Diverse reactivity of the bulky tris(trimethylsilyl)silyl substituent [Si(SiMe3)3], also known as the hypersilyl group, was observed for amidinate-supported dichloro- and phenylchloroborane complexes. Treatment of the dichloroborane with potassium tris(trimethylsilyl)silyl led to the activation of the backbone β-carbon center and formation of saturated four-membered heterocyclic chloroboranes R'{Si(SiMe3)3}C(NR)2BCl [R' = Ph, R = Cy (3); R' = Ph, R = iPr (6); R' = tBu, R = Cy (8)], whereas the four-membered amidinate hypersilyl-substituted phenyl borane 4 {PhC(NCy)2B(Ph)[Si(SiMe3)3]} was observed for the case of an amidinate-supported phenylchloroborane. The highly deshielded 11B NMR spectroscopic resonance and the distinct difference in the 29Si NMR spectrum confirmed the presence of a σ-donating hypersilyl effect on compounds 3, 6, and 8. Reaction of 3 with the Lewis acid AlCl3 led to the formation of complex 11 in which an unusual cleavage of one of the C-N bonds of the amidinate backbone is observed. Nucleophilic substitution at the boron center of saturated chloroborane 3 with phenyllithium generated the phenylborane derivative 12, whereas the secondary monomeric boron hydride 13 was observed after treatment with alane (AlH3). All compounds (2-13) have been fully characterized by NMR spectroscopy and single-crystal X-ray structure determination studies.

Structure-Property Relationships for Potential Inversion From Electron Acceptors Based on Thiophene-Fused Triptycene Quinones, 1,4-Diketones and Their Malononitrile Adducts.

The synthesis and properties of a series of 11,11,12,12-tetracyano-9,10-anthraquinodimethane (TCAQ) inspired electron acceptors based on thiophene-fused quinone and triptycene motifs is presented. This has yielded insights into structure-property relationships for establishing and modulating simultaneous two-electron reduction processes in TCAQ analogues. These new compounds were synthesised using a Friedel-Crafts acylation between triptycene and thiophene-3,4-dicarbonyl chloride. Isomeric para-quinones featuring a [c]-fused thiophene on one side and a β,β- or α,β-fused triptycene on the other were isolated alongside a thiophene-3,4-diketone which bears two triptycene fragments. Knoevenagel condensation of these products with malononitrile produced a quinoidal bis(dicyanomethylene), an oxo-dicyanomethylene and an acyclic bis(dicyanomethylene). This series of new electron accepting molecules has been studied using X-ray crystallography and the implications of their 3D structures on NMR and UV/vis absorbance spectroscopy and cyclic voltammetry results have been ascertained with conclusions underpinned by computational methods.

High Pressure Promotes Binding of the Allosteric Inhibitor Zn2+-Cyclen in Crystals of Activated H-Ras.

In this work, we experimentally investigate the potency of high pressure to drive a protein toward an excited state where an inhibitor targeted for this state can bind. Ras proteins are small GTPases cycling between active GTP-bound and inactive GDP-bound states. Various states of GTP-bound Ras in active conformation coexist in solution, amongst them, state 2 which binds to effectors, and state 1, weakly populated at ambient conditions, which has a low affinity for effectors. Zn2+-cyclen is an allosteric inhibitor of Ras protein, designed to bind specifically to the state 1. In H-Ras(wt).Mg2+.GppNHp crystals soaked with Zn2+-cyclen, no binding could be observed, as expected in the state 2 conformation which is the dominant state at ambient pressure. Interestingly, Zn2+-cyclen binding is observed at 500 MPa pressure, close to the nucleotide, in Ras protein that is driven by pressure to a state 1 conformer. The unknown binding mode of Zn2+-cyclen to H-Ras can thus be fully characterized in atomic details. As a more general conjunction from our study, high pressure x-ray crystallography turns out to be a powerful method to induce transitions allowing drug binding in proteins that are in low-populated conformations at ambient conditions, enabling the design of specific inhibitors.

Supramolecular clumps of μ2-1,3-acetate bridges of Cd(II)-Salen complex: Synthesis, spectroscopic characterization, crystal structure, DFT quantization's, and antifungal photodynamic therapy

The article divulges the crystal growth, synthesis, and X-ray structure characterization of one centrosymmetric cadmium complex, [Cd{CdL(μ2-1,3-acetate)}2] using Salen ligand (SL). The complex is further characterized using spectroscopic and analytical techniques, including DRS, SEM-EDX, PXRD, and ICP-MS. The crystallographic study showed that the complex has a monoclinic space P21/c. Addison parameters (Ʈ) show the hexagonal geometry of the central Cd(II) metal ion. Hirshfeld surface and 2-D fingerprint confirm supramolecular contacts despite weak C–H⋯O and C–H···π interactions. Energy frameworks, FMOs, global reactivity parameters, MEP, and energy bandgap explain the complex reactivity outlook. The complex inter- and intramolecular bonding interactions were explored through natural bond orbital (NBO), QTAIM, NCI-RDG, Electron Location Function (ELF), and Localized Orbital Locator (LOL) quantization methods. In addition, the complex and its synthetic components in vitro antibacterial efficacy were investigated using Gram-positive and Gram-negative microbial strains. SAR (structure-activity relationship) correlates with biological potency. Molecular docking assessed antimicrobial potency with proteins S. aureus (PDB ID: 1JIJ), C. albicans (PDB ID: 1M7A), E. coli (PDB ID: 1T9U), P. aeruginosa (PDB ID: 2UV0), and A. Niger (PDB ID: 3K4P). The findings are backed by the Protein-Ligand Interaction Profiler (PLIP). The antifungal potency and cell viability test of C. albicans were conducted using photodynamic therapy (APDT).

New eremophilane-type sesquiterpenes from Synotis solidaginea

Eleven new highly oxygenated eremophilane-type sesquiterpenoids were isolated from the whole plant of Synotis solidaginea, including two pairs of C-8 S/R epimers. The structures of the new compounds were elucidated on the basis of detailed spectroscopic analysis and the absolute configurations of 1 and 9 were confirmed by single-crystal X-ray crystallography using Cu Kα radiation. All the isolates were tested for the inhibition of LPS-stimulated NO production in macrophage-like mouse monocytic leukemia RAW264.7 cells. Compound 1 exhibited weak inhibitory effects with an IC50 of 71.2 μM.

Schiff baseAlkyne precursor for1,2,3-Triazole functionalized organosiliconas a PotentialSensor for Zn(II)andAntioxidantActivity

Schiff base linked1,2,3-triazole silane5has been synthesized through the Schiff base terminated alkyne with azido via click chemistry,the compound4 structure elucidated through X-ray crystallography, and the compound5 is well characterized through different techniques such asFT-IR, 1H and 13C NMR and Mass spectrometry. UV–visible sensing studies of synthesized compounds4 and5 have been performed, and both are efficient in detectingZn(II) ion, but compound 5 has imparted a higher mode of attraction to Zn(II) with limit of detection (LOD) value (1.4 x 10-6M) wherethe compound 4 is calculated to be (1.25 x 10-5M). By Job's method, the stoichiometric ratio of compound5 and Zn(II) iscalculated to bea 1:1 ratio. The complex of compound 5 with Zn(II) was prepared. A radical and oxidative species are responsible for the deteriorating of stabilized molecules. The synthesized compound 5hasantioxidant propertiesthat can potentially scavenge 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals. Further to verify the mode of binding interaction between compound 5andZn(II), computational Density functional theory (DFT) study was evaluated.

Cytotoxic and Antibacterial Meroterpenoids Isolated from the Marine-Derived Fungus Talaromyces sp. M27416.

Three novel meroterpenoids, taladrimanins B-D (1-3), were isolated from the marine-derived fungus Talaromyces sp. M27416, alongside three biogenetically related compounds (4-6). We delineated taladrimanin B's (1) structure using HRESIMS and NMR, confirmed its configuration via quantum chemical NMR analysis and DP4+ methodology, and verified it through X-ray crystallography. ECD calculations determined the absolute configuration of compound 1, while comparative NMR and ECD analyses elucidated the absolute configurations of 2 and 3. These compounds are drimane-type meroterpenoids with a C10 polyketide unit (8R-configuration). We proposed a biosynthetic pathway and noted that compound 1 showed cytotoxic activity against MKN-45 and 5637 cell lines and selective antibacterial effects against Staphylococcus aureus CICC 10384.

1H, 13C, and 15N backbone and methyl group resonance assignments of ricin toxin A subunit

Ricin is a potent plant toxin that targets the eukaryotic ribosome by depurinating an adenine from the sarcin-ricin loop (SRL), a highly conserved stem-loop of the rRNA. As a category-B agent for bioterrorism it is a prime target for therapeutic intervention with antibodies and enzyme blocking inhibitors since no effective therapy exists for ricin. Ricin toxin A subunit (RTA) depurinates the SRL by binding to the P-stalk proteins at a remote site. Stimulation of the N-glycosidase activity of RTA by the P-stalk proteins has been studied extensively by biochemical methods and by X-ray crystallography. The current understanding of RTA’s depurination mechanism relies exclusively on X-ray structures of the enzyme in the free state and complexed with transition state analogues. To date we have sparse evidence of conformational dynamics and allosteric regulation of RTA activity that can be exploited in the rational design of inhibitors. Thus, our primary goal here is to apply solution NMR techniques to probe the residue specific structural and dynamic coupling active in RTA as a prerequisite to understand the functional implications of an allosteric network. In this report we present de novo sequence specific amide and sidechain methyl chemical shift assignments of the 267 residue RTA in the free state and in complex with an 11-residue peptide (P11) representing the identical C-terminal sequence of the ribosomal P-stalk proteins. These assignments will facilitate future studies detailing the propagation of binding induced conformational changes in RTA complexed with inhibitors, antibodies, and biologically relevant targets.