X-ray Crystallography Research Articles

Synthesis, Stable Radical Anion and Energy Storage Performance of Pentacene Tetraimides.

Imide functionalization has been widely proved to be an effective approach to enrich optoelectronic properties of polycyclic aromatic hydrocarbons (PAHs). However, appending multiple imide groups onto linear acenes is still a synthetic challenge. Herein, we demonstrate that by taking advantage of a "breaking and mending" strategy, a linear pentacene tetraimides (PeTI) was synthesized through a three-step sequence started from the naphthalene diimides (NDI). Compared with the parent pentacene, PeTI shows a deeper-lying lowest unoccupied molecular orbital (LUMO) energy level, narrower bandgap and better stability. The redox behavior of PeTI was firstly evaluated by generating a stable radical anion specie with the assistance of cobaltocene (CoCp2), and the structure of the electron transfer (ET) complex was confirmed by the X-ray crystallography. Moreover, due to the presence of multiple redox-active sites, we are able to show that the state-of-the-art energy storage performance of the dealkylated PeTI (designated as PeTCTI) in organic potassium ion batteries (OPIBs) as an anode. Our results shed light on the application of multiple imides functionalized linear acenes, and the reported synthetic strategy provides an effective way to get access to longer nanoribbon imides with fascinating electronic properties.

Stabilization of dimeric PYR/PYL/RCAR family members relieves abscisic acid-induced inhibition of seed germination

Abscisic acid (ABA) is the primary preventing factor of seed germination, which is crucial to plant survival and propagation. ABA-induced seed germination inhibition is mainly mediated by the dimeric PYR/PYL/RCAR (PYLs) family members. However, little is known about the relevance between dimeric stability of PYLs and seed germination. Here, we reveal that stabilization of PYL dimer can relieve ABA-induced inhibition of seed germination using chemical genetic approaches. Di-nitrobensulfamide (DBSA), a computationally designed chemical probe, yields around ten-fold improvement in receptor affinity relative to ABA. DBSA reverses ABA-induced inhibition of seed germination mainly through dimeric receptors and recovers the expression of ABA-responsive genes. DBSA maintains PYR1 in dimeric state during protein oligomeric state experiment. X-ray crystallography shows that DBSA targets a pocket in PYL dimer interface and may stabilize PYL dimer by forming hydrogen networks. Our results illustrate the potential of PYL dimer stabilization in preventing ABA-induced seed germination inhibition.

Structural and Functional Characterization of a Novel Class A Flavin Monooxygenase from Bacillus niacini.

A gene cluster responsible for the degradation of nicotinic acid (NA) in Bacillus niacini has recently been identified, and the structures and functions of the resulting enzymes are currently being evaluated to establish pathway intermediates. One of the genes within this cluster encodes a flavin monooxygenase (BnFMO) that is hypothesized to catalyze a hydroxylation reaction. Kinetic analyses of the recombinantly purified BnFMO suggest that this enzyme catalyzes the hydroxylation of 2,6-dihydroxynicotinic acid (2,6-DHNA) or 2,6-dihydroxypyridine (2,6-DHP), which is formed spontaneously by the decarboxylation of 2,6-DHNA. To understand the details of this hydroxylation reaction, we determined the structure of BnFMO using a multimodel approach combining protein X-ray crystallography and cryo-electron microscopy (cryo-EM). A liganded BnFMO cryo-EM structure was obtained in the presence of 2,6-DHP, allowing us to make predictions about potential catalytic residues. The structural data demonstrate that BnFMO is trimeric, which is unusual for Class A flavin monooxygenases. In both the electron density and coulomb potential maps, a region at the trimeric interface was observed that was consistent with and modeled as lipid molecules. High-resolution mass spectral analysis suggests that there is a mixture of phosphatidylethanolamine and phosphatidylglycerol lipids present. Together, these data provide insights into the molecular details of the central hydroxylation reaction unique to the aerobic degradation of NA in Bacillus niacini.

Synthesis, characterization, and biological activity of a fresh class of sonochemically synthesized Cu2+ complexes

The synthesis and characterization of metal complexes have garnered significant attention due to their versatile applications in scientific and biomedical fields. In this research, two novel copper (Cu) complexes, [Cu(L)(L′)(H2O)2] (1) and [Cu(L)(Im)H2O] (2), where L = pyridine-2,6-dicarboxylic acid, L′ = 2,4-diamino-6-hydroxypyrimidine, and Im = imidazole, were investigated concerning their sonochemical synthesis, spectroscopic analysis, and biological activity. The complexes’ structural characterization was achieved using analytical techniques, including single-crystal X-ray structure determination, FTIR, PXRD, TGA and DTA, SEM, TEM, and EDS. Complex (1) displayed a six-coordinated Cu2+ ion, while complex (2) exhibited a five-coordinated Cu2+ ion. The crystal structures revealed monoclinic (C2/c) and triclinic (P-1) space groups, respectively. Both complexes showcased zero-dimensional (0D) supramolecular networks, primarily driven by hydrogen bonding and π–π stacking interactions, which played pivotal roles in stabilizing the structures and shaping the unique supramolecular architecture. Both complexes demonstrated significant antioxidant activity, suggesting their capability to neutralize free radicals and mitigate oxidative stress-related diseases. Hemolysis percentages were less than 2%, per the ASTM F756-00 standard, indicating non-hemolytic behavior. Low cytotoxicity was observed against fibroblast and MCF-7 cell lines. They do not exhibit antibacterial activity against Escherichia coli and Staphylococcus aureus. These findings suggest that the synthesized Cu2+‒complexes hold considerable promise for applications in drug delivery and cancer treatment. This research contributes to the advancement of supramolecular chemistry and the development of multifunctional materials for diverse scientific and medical applications.

Sucurchalasins A and B, Sulfur-Containing Heterodimers of a Cytochalasan and a Macrolide from the Endophytic Fungus Aspergillus spelaeus GDGJ-286.

Two sulfur-containing heterodimers of a cytochalasan and a macrolide, sucurchalasins A and B (1 and 2), and four known cytochalasan monomers (3-6), as well as four known macrolide derivatives (7-10), were obtained from the endophytic fungus Aspergillus spelaeus GDGJ-286. Sucurchalasins A and B (1 and 2) are the first cytochalasan heterodimers formed via a thioether bridge between cytochalasan and curvularin macrolide units. Their structures were elucidated by detailed analysis of NMR, LC-MS/MS, and X-ray crystallography. In bioassays, 1 and 2 exhibited cytotoxic effects on A2780 cells, with IC50 values of 3.9 and 8.3 μM, respectively. They also showed antibacterial activities against E. faecalis and B. subtilis with MIC values of 3.1 and 6.3 μg/mL, respectively.

Prediction of Ca2+ Binding Site in Proteins With a Fast and Accurate Method Based on Statistical Mechanics and Analysis of Crystal Structures.

Predicting the precise locations of metal binding sites within metalloproteins is a crucial challenge in biophysics. A fast, accurate, and interpretable computational prediction method can complement the experimental studies. In the current work, we have developed a method to predict the location of Ca2+ ions in calcium-binding proteins using a physics-based method with an all-atom description of the proteins, which is substantially faster than the molecular dynamics simulation-based methods with accuracy as good as data-driven approaches. Our methodology uses the three-dimensional reference interaction site model (3D-RISM), a statistical mechanical theory, to calculate Ca2+ ion density around protein structures, and the locations of the Ca2+ ions are obtained from the density. We have taken previously used datasets to assess the efficacy of our method as compared to previous works. Our accuracy is 88%, comparable with the FEATURE program, one of the well-known data-driven methods. Moreover, our method is physical, and the reasons for failures can be ascertained in most cases. We have thoroughly examined the failed cases using different structural and crystallographic measures, such as B-factor, R-factor, electron density map, and geometry at the binding site. It has been found that x-ray structures have issues in many of the failed cases, such as geometric irregularities and dubious assignment of ion positions. Our algorithm, along with the checks for structural accuracy, is a major step in predicting calcium ion positions in metalloproteins.

Structural basis for inhibition of the SARS-CoV-2 nsp16 by substrate-based dual site inhibitors.

Coronaviruses, including SARS-CoV-2, possess an mRNA 5' capping apparatus capable of mimicking the natural eukaryotic capping signature. Two SAM-dependent methylating enzymes play important roles in this process: nsp14 methylates the N7 of the guanosine cap, and nsp16-nsp10 methylates the 2'-O- of subsequent nucleotides of viral mRNA. The 2'-O-methylation performed by nsp16-nsp10 is crucial for the escape of the viral RNA from innate immunity. Inhibition of this enzymatic activity has been proposed as a way to combat coronaviruses. In this study, we employed X-ray crystallography to analyze the binding of the SAM analogues to the active site of nsp16-nsp10. We obtained eleven 3D crystal structures of the nsp16-nsp10 complexes with SAM-derived inhibitors, demonstrated different conformations of the methionine substituting part of the molecules, and confirmed that simultaneous dual-site targeting of both SAM and RNA sites correlates with higher inhibitory potential.

Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes

Nucleoside diphosphate kinases (NDPKs) are encoded by nme genes and exist in various isoforms. Based on interactions with other proteins, they are involved in signal transduction, development and pathological processes such as tumorigenesis, metastasis and heart failure. In this study, we report a 1.25 Å resolution structure of human homohexameric NDPK-C bound to ADP and describe the yet unknown complexes formed with GDP, UDP and cAMP, all obtained at a high resolution via X-ray crystallography. Each nucleotide represents a distinct group of mono- or diphosphate purine or pyrimidine bases. We analyzed different NDPK-C nucleotide complexes in the presence and absence of Mg2+ and explain how this ion plays an essential role in NDPKs’ phosphotransferase activity. By analyzing a nucleotide-depleted NDPK-C structure, we detected conformational changes upon substrate binding and identify flexible regions in the substrate binding site. A comparison of NDPK-C with other human isoforms revealed a strong similarity in the overall composition with regard to the 3D structure, but significant differences in the charge and hydrophobicity of the isoforms’ surfaces. This may play a role in isoform-specific NDPK interactions with ligands and/or important complex partners like other NDPK isoforms, as well as monomeric and heterotrimeric G proteins. Considering the recently discovered role of NDPK-C in different pathologies, these high-resolution structures thus might provide a basis for interaction studies with other proteins or small ligands, like activators or inhibitors.

Synthesis and Structural Characterization of a Non-Heme Iron Hyponitrite Complex.

Flavodiiron NO reductases (FNORs) are important enzymes in microbial pathogenesis, as they equip microbes with resistance to the human immune defense agent nitric oxide (NO). Despite much efforts, intermediates that would provide insight into how the non-heme diiron active sites of FNORs reduce NO to N2O could not be identified. Computations predict that iron-hyponitrite complexes are the key species, leading from NO to N2O. However, the coordination chemistry of non-heme iron centers with hyponitrite is largely unknown. In this study, we report the reactivity of two non-heme iron complexes with preformed hyponitrite. In the case of [Fe(TPA)(CH3CN)2](OTf)2, cleavage of hyponitrite and formation of an Fe2(NO)2 diamond core is observed. With less Lewis-acidic [Fe2(BMPA-PhO)2(OTf)2] (2), reaction with Na2N2O2 in polar aprotic solvent leads to the formation of a red complex, 3. X-ray crystallography shows that 3 is a tetranuclear iron-hyponitrite complex, [{Fe2(BMPA-PhO)2}2(μ-N2O2)](OTf)2, with a unique hyponitrite binding mode. This species provided the unique opportunity to us to study the interaction of hyponitrite with non-heme iron centers and the reactivity of the bound hyponitrite ligand. Here, either protonation or oxidation of 3 is found to induce N2O formation, supporting the hypothesis that hyponitrite is a viable intermediate in NO reduction.

Biostructural, biochemical and biophysical studies of mutant IDH1

We report bio-structural, bio-chemical and bio-physical evidence demonstrating how small molecules can bind to both wild-type and mutant IDH1, but only inhibit the enzymatic activity of the mutant isoform. Enabled through x-ray crystallography, we characterized a series of small molecule inhibitors that bound to mutant IDH1 differently than the marketed inhibitor Ivosidenib, for which we have determined the x-ray crystal structure. Across the industry several mutant IDH1 inhibitor chemotypes bind to this allosteric IDH1 pocket and selectively inhibit the mutant enzyme. Detailed characterization by a variety of biophysical techniques and NMR studies led us to propose how compounds binding in the allosteric IDH1 R132H pocket inhibit the production of 2-Hydroxy glutarate.

Syntheses, Structural Analyses, and Properties of Condensed Arenes with Multihelicity.

A C1-symmetric hexapole helicene (HH) and a C3-symmetric dodecapole helicene (DH) were prepared, and their three-dimensional structures were verified by X-ray crystallography and density functional theory calculations. The molecular geometries and local helical configurations of their most stable diastereomers were correctly predicted by arranging suitable conformations of the peripheral aryl rings. Importantly, the outermost three [5]helicenes with a consistent configuration in DH were observed to increase the thermostability, enantiomerization barrier (ΔH⧧ = 40.5 kcal/mol), specific rotation ([α]24D = -4228°) and absorption dissymmetry factor (gabs = 1.35 × 10-3 at 453 nm).

Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.

Protein dynamics play a crucial role in biological function, encompassing motions ranging from atomic vibrations to large-scale conformational changes. Recent advancements in experimental techniques, computational methods, and artificial intelligence have revolutionized our understanding of protein dynamics. Nuclear magnetic resonance spectroscopy provides atomic-resolution insights, while molecular dynamics simulations offer detailed trajectories of protein motions. Computational methods applied to X-ray crystallography and cryo-electron microscopy (cryo-EM) have enabled the exploration of protein dynamics, capturing conformational ensembles that were previously unattainable. The integration of machine learning, exemplified by AlphaFold2, has accelerated structure prediction and dynamics analysis. These approaches have revealed the importance of protein dynamics in allosteric regulation, enzyme catalysis, and intrinsically disordered proteins. The shift towards ensemble representations of protein structures and the application of single-molecule techniques have further enhanced our ability to capture the dynamic nature of proteins. Understanding protein dynamics is essential for elucidating biological mechanisms, designing drugs, and developing novel biocatalysts, marking a significant paradigm shift in structural biology and drug discovery.

Unveiling the solution structure of a DNA duplex with continuous silver-modified Watson-Crick base pairs

The challenge of transforming organized DNA structures into their metallized counterparts persists in the scientific field. In this context, utilizing DNA molecules modified with 7-deazapurine, provides a transformative solution. In this study, we present the solution structure of a DNA duplex that can be transformed into its metallized equivalent while retaining the natural base pairing arrangement through the creation of silver-modified Watson-Crick base pairs. Unlike previously documented X-ray structures, our research demonstrates the feasibility of preserving the intrinsic DNA self-assembly while incorporating AgI into the double helix, illustrating that the binding of silver does not disrupt the canonical base-pairing organization. Moreover, in our case, the uninterrupted AgI chain deviates from forming conventional straight linear chains; instead, it adheres to a helical arrangement dictated by the underlying DNA structure. This research challenges conventional assumptions and opens the door to precisely design structures based on the organization of highly stable Ag-DNA assemblies.

Long-Chain Molecular Crystals Antimony(III) Alkanethiolates Sb(SCnH2n+1)3 (n ≥ 12): Synthesis, Crystal and Electronic Structures, and Supramolecular Self-Assembly via Secondary Interactions.

Currently, there is not much success in solving the molecular and crystal structures of long-chain metal alkanethiolate complexes [M(SCnH2n+1)m] at the atomic level. Taking Sb(SC16H33)3 (1) as an example, we herein disclose the structural characteristics of long-chain trivalent antimony(III) alkanethiolates Sb(SCnH2n+1)3 (n ≥ 12) by single-crystal X-ray crystallography. Specifically, the Sb atom is three-coordinated by alkanethiolate ligands and a slightly distorted triangular pyramid SbS3 core is formed owing to the unique intramolecular stereochemistry of three alkyl chains, namely, two of them almost parallel aligning and the third chain extending alone around the SbS3 core. We further determine the conformation, spatial orientation and packing density of alkyl chains in 1 along with a comparison to those in other long-chain crystalline systems, and reveal the roles of intermolecular van der Waals and Sb···S secondary interactions in molecular self-assembly, which enables 1 to be a layer-structured molecular crystal with a monoclinic P21/c unit cell. The band structures and the atomic orbital contributions to the valence band maximum and conduction band minimum for 1 have also been evaluated by DFT calculations and rationally correlated with its optical absorption property. This study will help understand and discover new structures and structure-property relations of long-chain chemical systems.

Methods in molecular photocrystallography.

Over the last three decades, the technology that makes it possible to follow chemical processes in the solid state in real time has grown enormously. These studies have important implications for the design of new functional materials for applications in optoelectronics and sensors. Light-matter interactions are of particular importance, and photocrystallography has proved to be an important tool for studying these interactions. In this technique, the three-dimensional structures of light-activated molecules, in their excited states, are determined using single-crystal X-ray crystallography. With advances in the design of high-power lasers, pulsed LEDs and time-gated X-ray detectors, the increased availability of synchrotron facilities, and most recently, the development of XFELs, it is now possible to determine the structures of molecules with lifetimes ranging from minutes down to picoseconds, within a single crystal, using the photocrystallographic technique. This review discusses the procedures for conducting successful photocrystallographic studies and outlines the different methodologies that have been developed to study structures with specific lifetime ranges. The complexity of the methods required increases considerably as the lifetime of the excited state shortens. The discussion is supported by examples of successful photocrystallographic studies across a range of timescales and emphasises the importance of the use of complementary analytical techniques in order to understand the solid-state processes fully.

Self-Assembled Nanostructure of Ionic Sn(IV)porphyrin Complex Based on Multivalent Interactions for Photocatalytic Degradation of Water Contaminants.

[Sn(H2PO4)2(TPyHP)](H2PO4)4∙6H2O (2), an ionic tin porphyrin complex, was synthesized from the reaction of [Sn(OH)2TPyP] (1) with a dilute aqueous solution of a polyprotic acid (H3PO4). Complex 2 was fully characterized using various spectroscopic methods, such as X-ray single-crystal crystallography, 1H NMR spectroscopy, elemental analysis, FTIR spectroscopy, UV-vis spectroscopy, emission spectroscopy, EIS mass spectrometry, PXRD, and TGA analysis. The crystal structure of 2 reveals that the intermolecular hydrogen bonds between the peripheral pyridinium groups and the axially coordinated dihydrogen phosphate ligands are the main driving force for the supramolecular assembly. Simultaneously, the overall association of these chains in 2 leads to an open framework with porous channels. The photocatalytic degradation efficiency of methyl orange dye and tetracycline antibiotic by 2 was 83% within 75 min (rate constant = 0.023 min-1) and 75% within 60 min (rate constant = 0.018 min-1), respectively. The self-assembly of 2 resulted in a nanostructure with a huge surface area, elevated thermodynamic stability, interesting surface morphology, and excellent catalytic photodegradation performance for water pollutants, making these porphyrin-based photocatalytic systems promising for wastewater treatment.

Re-examination of the Claimed Isolation of Stable Noncyclic 1,2-Disulfoxides.

Re-examination of the claimed isolation and X-ray characterization of di-p-tolyl and dimesityl 1,2-disulfoxides from thermolysis of the corresponding aryl sulfinimines and thiosulfinates showed that the isolated disulfide dioxides are instead the well-known isomeric thiosulfonates, as confirmed by XAS, DART-MS, X-ray, IR and NMR methods. Concerns with the original X-ray structures are addressed. Our results agree with the DFT prediction of very weak diaryl 1,2-disulfoxide S-S bond dissociation enthalpies. For now, room-temperature-stable noncyclic 1,2-disulfoxides remain unknown.

Isolation and Diverse Reactivity of an Unsymmetrical 1,2-Bis(silylene)-Stabilized Pentacarbonyl Chromium(0) Species.

The construction of the unsymmetrical 1,2-bis(silylene) pentacarbonyl chromium(0) complex 1 was achieved through the reaction of chlorosilylene with half an equivalent of K2Cr(CO)5. X-ray diffraction analysis of 1 confirms the formation of the Si-Si bond and the coordination of one of the silicon atoms to the Cr center. Density functional theory (DFT) calculations disclose that highest occupied molecular orbital (HOMO) mainly corresponds to the lone pair of electrons on the silicon atom and the σ-bonding interaction between two Si atoms. Based on its unique electronic structure, its diverse reactivity toward the transition metal compounds and small molecules was investigated in detail. The reactions of 1 with Fe2(CO)9 or CuCl yielded the 1,2-bis(silylene)-stabilized heterobimetallic complex 2 or oxidized product 3, respectively. Additionally, treatments of 1 with selenium, CO2, or Me3SiN3 led to the formation of the corresponding selenium-, oxo-, and nitrogen-bridged complexes 4-7. All compounds were characterized by multinuclear NMR spectroscopy and X-ray crystallography.

Structure-Based Design and Development of Phosphine Oxides as a Novel Chemotype for Antibiotics that Dysregulate Bacterial ClpP Proteases.

A series of arylsulfones and heteroarylsulfones have previously been demonstrated to dysregulate the conserved bacterial ClpP protease, causing the unspecific degradation of essential cellular housekeeping proteins and ultimately resulting in cell death. A cocrystal structure of a 2-β-sulfonylamide analog, ACP1-06, with Escherichia coli ClpP showed that its 2-pyridyl sulfonyl substituent adopts two orientations in the binding site related through a sulfone bond rotation. From this, a new bis-aryl phosphine oxide scaffold, designated as ACP6, was designed based on a "conformation merging" approach of the dual orientation of the ACP1-06 sulfone. One analog, ACP6-12, exhibited over a 10-fold increase in activity over the parent ACP1-06 compound, and a cocrystal X-ray structure with ClpP confirmed its predicted binding conformation. This allowed for a comparative analysis of how different ligand classes bind to the hydrophobic binding site. The study highlights the successful application of structure-based rational design of novel phosphine oxide-based antibiotics.

Aqua-complexes of pyrimidine-4,6-dicarboxylic acid and its monoester with organometallic fac-[M(CO)3]+ (M = Re and 99mTc) core as radiopharmaceutical probes: synthesis and characterization

The current study highlights on the synthesis and characterization of aqua-complexes of the fac-[M(CO)3]+ (M = Re and 99mTc) core with pyrimidine-4,6-dicarboxylic acid (H2pmdc) and its monoester 6-(ethoxycarbonyl)pyrimidine-4-carboxylic acid (Hetpmdc), which are the model for future design of imaging and therapeutic radiopharmaceuticals. Complexes [M(CO)3(OH2)(Hpmdc)] (M = Re (1) and 99mTc (2)) were formed from the reaction of H2pmdc with [Re(CO)5Br] in water and aqueous solution of [99mTc(CO)3(OH2)3]+ respectively. The reaction of [Re(CO)5Br] with H2pmdc in ethanol (EtOH) has also studied and led to the complex [Re(CO)3(OH2)(etpmdc)] (3), where etpmdc− is 6-(ethoxycarbonyl)pyrimidine-4-carboxylate anion which was formed from the mono-esterification of H2pmdc in parallel with its coordination to the fac-[Re(CO)3]+ unit. The complex [99mTc(CO)3(OH2)(etpmdc)] (4) was formed in parallel with 2 by reacting H2pmdc with aqueous solution of [99mTc(CO)3(OH2)3]+ and ethanol. The chemical identification of 1 and 3 was achieved by using 1H NMR, 13C NMR, IR, ESI-MS and elemental analysis. Complex 3 was furtherly identified by using single crystal X-ray crystallography. The structural similarities of 1 and 2 was assessed by coinjection of both complexes in the HPLC with UV/Vis detection coupled with a γ-detector followed by comparison of retention times of the γ-peak of 2 and the UV-peak of 1 which allowed unambiguous identification of 2. Similarly, the formation of complex [99mTc(CO)3(OH2)(etpmdc)] (4) in parallel with 2 was assessed by coinjection of complexes 1 and 3 with the product from the reaction of H2pmdc with aqueous solution of [99mTc(CO)3(OH2)3]+ and ethanol in the same HPLC as one used for the structural identification of 2 followed by comparison of retention times of the γ-peaks of 2 and 4 and the UV-peaks of 1 and 3.