X-ray Crystallography Research Articles

Impact of Intracellular Proteins on μ-Opioid Receptor Structure and Ligand Binding.

Chronic pain is a prevalent problem affecting approximately one out of every five adults in the U.S. The most effective way to treat chronic pain is with opioids, but they cause dangerous side effects such as tolerance, addiction, and respiratory depression, which makes them quite deadly. Opioids, such as fentanyl, target the μ-opioid receptor (MOR), which can then bind to the intracellular Gi protein or the β-arrestin protein. The Gi pathway is primarily responsible for pain relief and potential side effects, but the β-arrestin pathway is chiefly responsible for the unwanted side effects. Ideally, an effective pain medication without side effects would bind to MOR, which would bias signaling solely through the Gi pathway. We used the Bio3D library to conduct principal component analysis to compare the cryo-electron microscopy MOR structures in complex with the Gi versus an X-ray crystallography MOR structure with a nanobody acting as a Gi mimic. Our results agree with a previous study by Munro, which concluded that nanobody-bound MOR is structurally different than Gi-bound MOR. Furthermore, we investigated the structural diversity of opioids that can bind to MOR. Quantum mechanical calculations show that the low energy solution structures of fentanyl differ from the one bound to MOR in the experimental structure, and pKa calculations reveal that fentanyl is protonated in aqueous solution. Glide docking studies show that higher energy structures of fentanyl in solution form favorable docking complexes with MOR. Our calculations show the relative abundance of each fentanyl conformation in solution as well as the energetic barriers that need to be overcome to bind to MOR. Docking studies confirm that multiple fentanyl conformations can bind to the receptor. Perhaps a variety of conformations of fentanyl can stabilize multiple conformations of the MOR, which can explain why fentanyl can induce different intracellular signaling and multiple physiological effects.

Substituent Effects on Cooperativity in Three-Component H-Bond Networks Involving Phenol-Phenol Interactions.

Cooperativity between H-bonding interactions in networks is a fundamental aspect of solvation and self-assembly in molecular systems. The interaction of a series of bisphenols, which make an intramolecular H-bond between the two hydroxyl groups, and quinuclidine was used to quantify cooperativity in three-component networks. The presence of the intramolecular H-bond in the bisphenols was established by using 1H NMR spectroscopy in solution and X-ray crystallography in the solid state. The interactions with quinuclidine were investigated using UV-vis and 1H NMR titrations, which show that the intramolecular hydrogen bonds persist in the 1:1 complexes. By varying substituents on one of the phenol groups, it was possible to measure the effect of changing the strength of the intramolecular H-bond between the hydroxyl groups on the strength of the intermolecular H-bond with quinuclidine. Strong positive cooperativity was observed between the two interactions, with increases in binding free energy of up to 16 kJ mol-1. By varying substituents on the other phenol group, which makes both an intramolecular H-bond and an intermolecular H-bond in the complex, it was possible to measure how the properties of this central hydroxyl group modulate cooperativity between the interactions with the other two functional groups. Changing the polarity of this phenol had no effect on the measured cooperativity. The results indicate that cooperativity in H-bond networks can be understood as a polar interaction between two remote functional groups that is damped by a central functional group. The extent of damping is quantified by cooperativity parameter κ, which is 0.33 for the hydroxyl group and appears to be an intrinsic property of the geometry or polarizability of the functional group rather than polarity.

Synthesis and Characterization of Novel Co(III)/Ru(II) Heterobimetallic Complexes as Hypoxia-Activated Iron-Sequestering Anticancer Prodrugs

Heterobimetallic complexes of an ambidentate deferiprone derivative, 3-hydroxy-2-methyl-1-(3-((pyridin-2-ylmethyl)amino)propyl)pyridin-4(1H)-one (PyPropHpH), incorporating an octahedral [Co(4N)]3+ (4N = tris(2-aminoethyl)amine (tren) or tris(2-pyridylmethyl)amine (tpa)) and a half-sandwich type [(η6-p-cym)Ru]2+ (p-cym = p-cymene) entity have been synthesized and characterized by various analytical techniques. The reaction between PyPropHpH and [Co(4N)Cl]Cl2 resulted in the exclusive (O,O) coordination of the ligand to Co(III) yielding [Co(tren)PyPropHp](PF6)2 (1) and [Co(tpa)PyPropHp](PF6)2 (2). This binding mode was further supported by the molecular structure of [Co(tpa)PyPropHp]2(ClO4)3(OH)·6H2O (5) and [Co(tren)PyPropHpH]Cl(PF6)2·2H2O·C2H5OH (6), respectively, obtained via the slow evaporation of the appropriate reaction mixtures and analyzed using X-ray crystallography. Subsequent treatment of 1 or 2 with [Ru(η6-p-cym)Cl2]2 in a one-pot reaction afforded the corresponding heterobimetallic complexes, [Co(tren)PyPropHp(η6-p-cym)RuCl](PF6)3 (3) and [Co(tpa)PyPropHp(η6-p-cym)RuCl](PF6)3 (4), in which the piano-stool Ru core is coordinated by the (N,N) chelating set of the ligand. Cyclic voltammetric measurements revealed that the tpa complexes can be reduced at less negative potentials, suggesting their capability to be bioreductively activated under hypoxia (1% O2). Hypoxia activation of 2 and 4 was demonstrated by cytotoxicity studies on the MCF-7 human breast cancer cell line. PyPropHpH was shown to be a typical iron-chelating anticancer agent, raising the mRNA levels of TfR1, Ndrg1 and p21. Further qRT-PCR studies provided unambiguous evidence for the bioreduction of 2 after 72 h incubation under hypoxia, in which the characteristic gene induction profile caused by the liberated iron-sequestering PyPropHpH was observed.

X-ray pulse compressors in Laue diffraction geometry

We theoretically investigate the impact of nonlinear dispersion of crystals and multilayers used in Laue-type pulse compressors (LPCs) on chirped x-ray pulse compression, as well as the optimization method for the configuration of LPCs. We also study the application of LPCs to compress chirped x-ray free-electron laser pulses based on the parameters of LCLS-II-HE. The results show that the optimal thickness is half of the Pendellosung period, yielding the best compressor performance with minimal impact from the nonlinear dispersion. This work also provides a new idea for generating ultra-short two-color or multi-color x-ray pulses by considering deviations from the optimized thickness.

Inorganic-organic hybrids of stannic-containing polyoxometalate and 2-aminopyridine: synthesis, characterization, and catalytic applications

A new inorganic-organic hybrid of 2-aminopyridine/[P2W18O68(HOSnIVOH)3]12− (1) has been synthesized via an aqueous solution reaction of [P2W18O68(HOSnIVOH)3]12− (P2W18Sn3) and 2-aminopyridine. The inorganic-organic hybrid has been characterized using elemental analysis, FE-SEM, EDX, TG analysis, FT-IR, powder X-ray diffraction, and single-crystal X-ray crystallography. The results show that the sandwich structure of P2W18Sn3 polyoxometalate remains intact in the inorganic-organic hybrid but a structure rearrangement of the nanoparticle composed of the Keggin structure (1a) was observed by calcination at higher than 300 °C. The single crystal analysis confirms the anchoring of 2-aminopyridine on the P2W18Sn3 polyanion via the formation of a Sn–O–C bond. The catalytic activity of 1 has been evaluated through the oxidation of sulfides to sulfone with H2O2 and that of (1a) in the synthesis of tetrazoles in water and mild reaction conditions.

Manganese(II) Complexes with Non-Steroidal Anti-Inflammatory Drugs: Structure and Biological Activity

Nine manganese(II) complexes with a series of non-steroidal anti-inflammatory drugs (namely sodium diclofenac, diflunisal, flufenamic acid, sodium meclofenamate, mefenamic acid, and tolfenamic acid) were prepared in the presence of diverse nitrogen donors, i.e., pyridine, 1,10–phenanthroline, 2,2′–bipyridine and neocuproine, as co-ligands and were characterized with spectroscopic techniques and single-crystal X-ray crystallography. The biological profile of the resultant complexes was investigated regarding their antioxidant potency and their interaction with DNA and serum albumins. The complexes interact with calf–thymus DNA in an intercalative mode and bind tightly and reversibly to human and bovine serum albumins studied. In order to assess the antioxidant activity of the Mn(II) complexes, their ability to scavenge 2,2′–azinobis(3–ethylbenzothiazoline–6–sulfonic acid) free radicals was monitored.

A New Synthesis of Enantiopure Amine Fragment: An Important Intermediate to the Anti-HIV Drug Lenacapavir.

Herein, we describe a new seven-step approach to prepare (S)-1-(3,6-dibromopyridin-2-yl)-2-(3,5-difluorophenyl)ethan-1-amine ((S)-4) from the inexpensive 2-(3,5-difluorophenyl)acetic acid. The key steps in the sequence include (1) the Weinreb amide-based ketone synthesis to provide an entry point to the core structure; (2) simple functional group transformations to afford the racemic amine 4-rac; and (3) dynamic kinetic resolution (DKR) to access the chiral amine (S)-4. This seven-step process delivered the enantiopure amine (S)-4 in an overall isolated yield of approximately 15%. The process was demonstrated on a decagram scale, and the process requires no chromatographic purifications. Single-crystal X-ray crystallography measurements verified the chiral amine structure and absolute configuration.

Isolation and Biomimetic Semisynthesis of Hyperzrones A and B, Two Nor-Polycyclic Polyprenylated Acylphloroglucinols with a Characteristic Cyclobutane Moiety, from Hypericum beanii.

Hyperzrones A (1) and B (2), two unprecedented nor-polycyclic polyprenylated acylphloroglucinols with a characteristic cyclobutane moiety, were discovered from Hypericum beanii. Their structures were determined by extensive spectroscopic analysis, X-ray crystallography, and quantum chemical calculation methods. A bioinspired semisynthesis of 1 and 2 was achieved from the natural precursor hypercalin B (3), featuring a Favorskii-type rearrangement and a visible-light-mediated [2 + 2] photocycloaddition. Several diverse derivatives were also obtained, providing a compound library for biological studies.

Iridium Complexes of a Bis(N-pyrrolyl)boryl/Bis(phosphine) PBP Pincer Ligand.

This work reports the synthesis of a bis(pyrrolylphosphino)phenyl borane (PBP)Ph (2) and its incorporation of Ir by metal insertion into B-Ph to afford the dipyrrolylboryl/bis(phosphine) pincer complex (PBP)Ir(Ph)Cl (3). Hydrogenolysis of 3 afforded (PBP)Ir(H)Cl (4). Compound 4 was converted into (PBP)IrCl2 (5a) via reaction with N-chlorosuccinimide, and exposure of 5a to CO produced (PBP)IrCl2(CO) (6a). Compounds 5a and 6a were converted into their analogs (PBP)IrI2 (5b) and (PBP)IrI2(CO) (6b) via metathesis with Me3SiI, respectively. Treatment of either 3 or 4 with Li[HAl(OtBu)3] under H2 resulted in the formation of (PBP)IrH4 (7), with traces of 4 as a persistent impurity. Attempts to access 7 via the reaction of 4 with NaBH4 in isopropanol led to the loss of boron from the pincer and isolation of L2IrH5 (8, L = 2-diisopropylphosphinopyrrole). Compounds 4, 7, and 8 were examined as catalysts for alkane transfer dehydrogenation but displayed only the modest activity. Solid-state structures of 6b and 7 were established by X-ray crystallography.

Architecture of the Sap S-layer of Bacillus anthracis revealed by integrative structural biology

Bacillus anthracis is a spore-forming gram-positive bacterium responsible for anthrax, an infectious disease with a high mortality rate and a target of concern due to bioterrorism and long-term site contamination. The entire surface of vegetative cells in exponential or stationary growth phase is covered in proteinaceous arrays called S-layers, composed of Sap or EA1 protein, respectively. The Sap S-layer represents an important virulence factor and cell envelope support structure whose paracrystalline nature is essential for its function. However, the spatial organization of Sap in its lattice state remains elusive. Here, we employed cryoelectron tomography and subtomogram averaging to obtain a map of the Sap S-layer from tubular polymers that revealed a conformational switch between the postassembly protomers and the previously available X-ray structure of the condensed monomers. To build and validate an atomic model of the lattice within this map, we used a combination of molecular dynamics simulations, X-ray crystallography, cross-linking mass spectrometry, and biophysics in an integrative structural biology approach. The Sap lattice model produced recapitulates a close-to-physiological arrangement, reveals high-resolution details of lattice contacts, and sheds light on the mechanisms underlying the stability of the Sap layer.

Dimeric Copper(I) Complex with a Disulfonamide-Bridged Core.

Pyridine-2-yl-sulfonyl-quinolin-8-yl-amide (psq) has produced the first sulfonamidato-bridged dicopper(I) complex, {Cu[κ4-(μ-κN:κN-psq)]}2 containing the rhombic Cu(I)2N2 core. The single crystal X-ray structure of this complex shows that two anionic psq ligands straddle the metal atoms via bridging sulfonamide N atoms to give a Cu···Cu distance of 2.9593(8) Å. When it is dissolved in chloroform [Cu(psq)]2 activates C-Cl bonds as demonstrated through the rapid formation of [CuCl(psq)]2. While the solid orange compound is stable for weeks under N2. Acetonitrile solutions of [Cu(psq)]2 are rapidly oxidized in air. A 1D-carbonato-bridged coordination polymer, {Cu2[κ4-(μ-κO:κN-psq)]2[μ3-CO3][H2O]}, and the bis-homoleptic complex [Cu(κ3-psq)(κ2-psq)] are concurrently isolated in high yield without evidence of ligand oxidation with H2O2 detected as a side product. This implicit O2 activation was harnessed in the oxidation of phenol substrates. 2,6-Di-tert-butylphenol is catalytically converted to the coupled dione product with 100% yield. If a para-blocked phenol is used, the reaction become stoichiometric and an O2-derived hydroperoxide group is installed into the ortho position. In contrast, nitrophenol is not oxidized and the result is metal-based oxidation and isolation of [Cu(OC6H4NO2)(psq)]2. This is rationalized by this more acidic phenol acting as a proton donor, rather than a H atom donor to a putative O2 adduct.

Synthesis and X-ray Structures of Polymeric Calcium Carboxylates

The reactions of calcium hydroxide with pivalic, 1-naphthoic, and 2-furancarboxylic acids afford the corresponding polymeric calcium carboxylates. Depending on the crystallization conditions, calcium pivalate is isolated as two different coordination polymers: [Ca3(Piv)6(DMF)2]n · 0.635nC6H6 · 0.365nDMF (I) and [Ca(Рiv)(H2O)2.333(DMF)0.666]n · nРiv·0.333H2O (II). The synthesized calcium 1-naphthoate contains coordinated water molecules [Сa(Naph)2(H2O)2]n (III), and calcium furoate [Ca(Fur)2]n (IV) contains no ancillary ligands. The structures of compounds I–IV are determined by X-ray diffraction (XRD) (CIF files CCDC nos. 2342790–2342793, respectively). The structures of compounds I–III are characterized by the 1D polymeric structure, and compound IV is the 3D polymer.

A Multifunctional Tb(III)-Based Metal-Organic Framework for Chemical Conversion of CO2, Fluorescence Sensing of Trace Water and Metamitron.

The utilization of metal-organic frameworks (MOFs) as fluorescent sensors for the detection of environmental and chemical reagent pollutants as well as heterogeneous catalysis for CO2 conversion represents a crucial avenue of research with significant implications for the protection of human health. In this work, a Tb(III)-based three-dimensional metal-organic framework, [Tb(L)·4DMF]n (Tb-MOF) (H3L = 5'-(4-carboxy-3-hydroxyphenyl)-3,3″-dihydroxy-[1,1':3',1″-terphenyl]-4,4″-dicarboxylic acid), has been structurally conformed by single-crystal X-ray crystallography. It possesses a 1D rhombus channel along the [010] direction, featuring a pore size of 6.02 × 9.13 Å. Tb-MOF was proved to be a multifunctional material for a fluorescent sensor and CO2 cycloaddition heterogeneous catalyst material. Fluorescence sensing studies revealed that Tb-MOF demonstrates high sensitivity, selectivity, and favorable regeneration properties, making it an effective chemosensor for detecting the metamitron (MMT) pesticide and trace water in organic solvents. The mechanism of fluorescence quenching by MMT and water was elucidated by a combination of XRD, UV-vis absorption spectra, IR spectra, theoretical calculations, and fluorescence lifetimes. The material was also utilized for the sensing of MMT and water in paper strips. Additionally, the open Tb3+ site as Lewis acidic centers makes Tb-MOF achieve efficiently catalytic conversion for CO2 and epoxides to cyclic carbonates. Moreover, a possible catalytic mechanism for the conversion of carbon dioxide to cyclic carbonates was proposed by in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) experiments. It also exhibited recyclability for up to five cycles without noticing an appreciable loss in sensing or catalytic efficiency.

A personal account of the history of X-ray crystallography at the University of La Plata, Argentina.

Prompted by visionary political leaders and a flowering economy, the University of La Plata was founded in 1905, the third Argentinian university after the Universities of Cordoba (1613) and Buenos Aires (1821). Differing from the older universities, more prone to professional formation, the new university was oriented towards teaching and scientific research following western European academic tradition. Along with the university was created the Institute of Physics, the first of its kind in Latin America. To pursue the foundational plan, the university recruited distinguished German physicists, some of whom became the first directors. From the start, the institute became acquainted with Röntgen rays, their generation and use, initially for radiographic images and later in occasional diffraction studies. The first dedicated crystallographic X-ray diffraction laboratory was set up in the early 1970s, when it solved the first molecular structures. Soon the fascination brought about by a methodology that afforded the visualization of atoms, molecules and crystals lured the local and national physical chemistry communities. In close partnership with an equally oriented laboratory at the University of Sao Paulo, Brazil, and in collaboration with several physical chemistry laboratories from Argentina and the Latin American region, and also from Europe, we undertook studies on the crystal structures and physicochemical and spectroscopic properties of a wide range of materials, including inorganic, organic, bioinorganic, metal-organic, organic-metal, supramolecular, pharmaceutical, organic minerals and liquid crystals. The present essay is a personal account of the origin and development of structural X-ray crystallography at the University of La Plata and its impact on the scientific research of Argentina and Latin America.

Synthesis and Characterisation of Phosphino-Aryloxide Rare Earth Complexes.

A series of homoleptic rare earth (RE) complexes bearing phosphino-aryloxide ligands (1-RE, 2-La) has been prepared. The complexes have been characterised using multinuclear NMR and IR spectroscopy, X-ray crystallography and elemental analysis. Structural characterisation highlighted the different RE-P interactions as a result of differing Lewis acidity and ionic size across the series, hinting at the possibility of FLP-type activity. The potential reactivity of these complexes has been tested by reacting them with small molecules (H2, CO, CO2). A series of side-products (3-RE) has also been observed, isolated and characterised, featuring the incorporation of a phosphonium-aryloxide ligand.

Organometallic Half-Sandwich Complexes of 8-Hydroxyquinoline-Derived Mannich Bases with Enhanced Solubility: Targeting Multidrug Resistant Cancer.

Drug resistance is a major obstacle in cancer treatment. Herein, four novel organometallic complexes, with the general formula [Ru(η6-p-cymene)(HL)Cl]Cl and [Rh(η5-C5Me5)(HL)Cl]Cl, were developed to target multidrug-resistant (MDR) cancer cells, where HL denotes 8-hydroxyquinoline-derived Mannich bases (HQCl-pyr and HQCl-pip). The aim of the complexation was to obtain compounds with improved drug-like properties. The complexes were comprehensively characterized by various spectroscopic methods in terms of their structure, solution speciation and interaction with human serum albumin. The structure of [Rh(η5-C5Me5)(HQCl-pip)Cl]Cl was analyzed by X-ray crystallography. The complexes were found to be highly stable in solution and in various biological matrices, showing enhanced solubility compared with the ligands and significant binding ability to albumin via coordination. The Rh(η5-C5Me5) complexes exhibited strong cytotoxicity against MDR MES-SA/Dx5 cell lines (IC50 = 0.19 and 0.22 μM), demonstrating high MDR-selectivity. Ganglioside-functionalized nanoparticles with the most promising ligand HQCl-pip and its Rh(η5-C5Me5) complex were prepared to enhance the bioavailability. The nanocarriers showed faster drug release at acidic pH than at pH 7.4, and could retain the cytotoxicity and selectivity of the loaded compounds. The encapsulated Rh(η5-C5Me5) complex of HQCl-pip has been identified as an optimal candidate for the pharmacological development of MDR-selective compounds.

Mercury (II) compound with a quaternary phosphonium: X-ray structure, Hirshfeld surface analysis, optical band gap, and dielectric properties

Mercury (II) compound with a quaternary phosphonium: X-ray structure, Hirshfeld surface analysis, optical band gap, and dielectric properties

3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase

Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we show that 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) identifies a functional role for the Arg-142 side chain and test this hypothesis experimentally by characterizing the R142I variant in which Arg-142 is replaced by isoleucine. Support for Arg-142 playing a role in the intramolecular translocation of ammonia between the active site of the enzyme is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS, and MD simulations provide a possible molecular mechanism for these findings. Combining 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes.

Chiral Pd2L4 Capsules from Readily Accessible Tröger's Base Ligands Inducing Circular Dichroism on Fullerenes C60 and C70.

The induction of chirality on pristine fullerenes through non-covalent embedding in an asymmetric nano-confinement has only been rarely reported. Bringing molecules with such a unique electronic structure and broad application range into a chiral environment is particularly appealing for the development of chiroptical materials, enantioselective photoredox catalysts and systems showing chirality-induced spin selectivity (CISS). In this study, we report the formation of a chiral, configurationally stable Pd2L4capsule assembled from aC2-symmetric, 'ribbon-shaped' ligand with a Tröger's base naphthalimide (TbNaps) backbone, easily synthesized in three steps from commercially available compounds. Embedding chirality directly into the ligand backbone ensures a relatively lightweight receptor design whose aromatic panels create a strongly shielded inner cavity of about 700 Å3volume. Fullerenes C60and C70, as well as a pair of corannulenes, can be bound in acetonitrile (where unsubstituted fullerenes are insoluble) and X-ray structures of host-guest complexes were obtained. Tight interactions between the chiral host and the fullerene guests leads to the induction of a circular dichroism (CD) on the characteristic absorption bands of the forbidden π-π* transitions of the fullerenes, backed up by sTDA TD-DFT calculations and detailed investigation of the electronic excited states.

Using a New Pt(II) Source to Make Pt(II) Lantern-Shaped Cages, Including Low-Symmetry, Heteroleptic, and Multicavity Examples.

Current synthetic methods towards Pt(II) lantern-shaped cages involve the use of dry solvent, inert atmosphere, lengthy reaction times, and highly variable yields if isolated. Starting materials such as [Pt(CH3CN)4](BF4)2 suffer from a poor shelf-life, reducing the synthetic accessibility of various Pt(II) architectures. A new Pt(II) source (with varied counterions), [Pt(3-ClPy)4](X)2 (3-ClPy=3-chloropyridine, X=BF4 -, OTf-, NO3 -), is developed and characterised, showing greatly enhanced shelf-life characteristics under ambient atmospheric conditions. Using this starting material, the assembly of Pt(II) lantern-shaped cages was completed in as little as 1.5 hours with wet solvent and ambient atmosphere. The first examples of low-symmetry, heteroleptic and multicavity Pt(II) lantern-shaped cages are reported using this approach. Attempts towards an M6L8 octahedron using a tritopic ligand instead generate an interesting M2L4 cage with unbound pyridyl arms. Ligands and cages are characterised by NMR spectroscopy, IR spectroscopy, mass spectrometry, and X-ray crystallography in some cases.