X-ray Crystal Structure Analysis Research Articles

Synthesis of (Z)-Enediynes via Stereoinvertive Nucleophilic Substitution of (E)-Sulfonylethenes with Arylethynide, and Their Aggregation-Induced Optical Properties.

(Z)-Enediynes were successfully synthesized from a trio of terminal ethynes through consecutive three-step reactions: iodosulfonylation of ethyne with I2/PhSO2Na, followed by ethynylations of iodo and sulfonyl moieties of the resulting iodosulfonylethene via Sonogashira-Hagihara coupling and nucleophilic addition-elimination, respectively. The molecular structure of the obtained (Z)-enediyne was fully characterized by X-ray crystal structure analysis, revealing that the nucleophilic substitution of (E)-sulfonylethene with arylethynide underwent a selective stereoinversion. The (Z)-enediynes exhibited photoluminescence in both the solution and solid states (crystals and powders). Ph2N-substituted derivatives showed remarkable solvatofluorochromism, and upon replacing the solvent from toluene to acetonitrile, the emission color changed from blue to yellow.

Creation of Metal-Complex-Integrated Tensegrity Triangle DNA Crystals.

Structural DNA nanotechnology is an emerging field and is expected to be used for various applications in materials science. In this study, we designed a DNA tensegrity triangle to accommodate the bipyridine complexes with metal ions (Ni2+ and Fe2+) at the center of the space within the triangle. A metal-bipyridine-incorporated DNA tensegrity triangle was crystalized, and the presence of metals within it was confirmed through X-ray crystal structure analysis. A signal of the anomalous dispersion effect derived from metal was observed in the center of the DNA triangle.

Defining unique structural features in the MAFA and MAFB transcription factors that control Insulin gene activity

MAFA and MAFB are related basic-leucine-zipper domain-containing transcription factors which have important overlapping and distinct regulatory roles in a variety of cellular contexts, including hormone production in pancreatic islet cells. Here we first examined how mutating conserved MAF protein-DNA contact sites obtained from X-ray crystal structure analysis impacted their DNA-binding and Insulin enhancer-driven activity. While most of these interactions were essential and their disruption severely compromised activity, we identified that regions outside of these contact sites also contributed to transcriptional activity. AlphaFold 2, an artificial intelligence-based structural prediction program, was used to determine if there were also differences in the three-dimensional organization of the non-DNA binding/dimerization sequences of MAFA and MAFB. This analysis was conducted on the wildtype (WT) proteins as well as the pathogenic MAFASer64Phe and MAFBSer70Alatrans-activation domain mutants, with differences revealed between MAFAWT and MAFBWT as well as between MAFASer64Phe and MAFAWT, but not between MAFBSer70Ala and MAFBWT. Moreover, dissimilarities between these proteins were also observed in their ability to cooperatively stimulate Insulin enhancer-driven activity in the presence of other islet-enriched transcription factors. Analysis of MAFA and MAFB chimeras disclosed that these properties were influenced by their unique C-terminal region structural differences predicted by AlphaFold 2. Our findings have revealed key structural features of these closely related proteins that impact their ability to regulate gene expression.

New Tricyclic Aryl Quinazoline Derivatives by Suzuki-Miyaura Cross-Coupling.

A number of new deoxyvasicinone (2,3-dihydropyrrolo[2,1-b]quinazolin-9(1H)-one) and mackinazolinone (6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-one) derivatives with aryl substituents at C7/C8 and at C5 are reported. These compounds are rare representatives of their kind and were prepared in high yields by Suzuki-Miyaura cross-coupling reactions between 7-bromo-2,3-dihydro[2,1-b]quinazoline-9-(1H)-one, 5,7-dibromo-2,3-dihydro[2,1-b]quinazoline-9-(1H)-one or 8-bromomackinazolinone and respective arylboronic acids with palladium acetate as the catalyst. The products were characterized spectroscopically and, in addition, by X-ray crystal structure analyses in six cases.

A Urease-Catalyzed Three-Component Reaction for the Efficient and Sustainable Synthesis of Highly Substituted 4H-Pyrans in Water as the Solvent

AbstractAn efficient urease-catalyzed approach for the synthesis of highly substituted 6-amino-4H-pyran-3-carbonitriles based on the formation of three bonds in one step is developed. This unprecedented three-component reaction between one molecule of an aromatic aldehyde and two molecules of an aroylacetonitrile proceeds by employing commercially available urease from jack bean (Canavalia ensiformis) as the catalyst in water at 65 °C to deliver the desired 4H-pyrans in yields of up to 92%. The transformation is proposed to occur via a domino Knoevenagel condensation/1,4-addition/O-cyclization/tautomerization sequence, providing a practical and sustainable approach to 6-amino-4H-pyran-3-carbonitriles from commercially available substrates. Full and unambiguous structural elucidation of all the products is achieved by means of NMR spectroscopy and X-ray crystal structure analysis.

Titanium (IV) μ-Oxo Complex Supported by Phenoxyimine Ligand: Synthesis, Crystal Structure Characterisation, DFT and Molecular Docking Studies

Background: Most of the transition elements in the 3d series (first row transition metals) have been discovered to be extremely significant and practical in biological systems. Naturally, many of the enzymes that are present in the human body system act as catalysts for biological processes and are made of coordination compounds or complexes. Objective: The complex has been characterised by various spectroscopic and analytic techniques. A suitable crystal analysed by X-ray diffraction establishes the formation of a stable binuclear µ-oxo-complex with a hexacoordinate titanium centre. Methods: A new crystalline complex [Ti{La}] has been synthesised in the reaction of titanium butoxide with a phenoxyimine ligand in a 1:1 stoichiometry in toluene at room temperature under a nitrogen atmosphere. The newly synthesised Ti complex has undergone density functional theory and docking study. Results: The crystal shows a monoclinic system with space group C 1 2/c 1. X-ray crystal structure analysis reveals that this complex has a rhomboidal Ti-O-Ti core and exhibits a C2 symmetric conformation with distorted octahedral geometry. Density Functional Theory (DFT) calculations giving insights into the frontier orbitals and mulliken charge analysis, which showed good correlation with the experimental findings. Additionally, in silico molecular docking of ligand and complex was carried out against the HER2 inhibitor kinase. Conclusion: This complex exhibits a higher binding energy of ΔGb = -19.7 kcal/mol with the active pocket of HER2 (PDB:7JXH) than the ligand ΔGb = -8.5 kcal/mol.

Design and synthesis of two new thiosemicarbazide based Schiff base metal complexes of nickel (II): DNA binding study and cytotoxicity profile analysis

Two new nickel (II) substituted thiosemicarbazone Schiff base complexes [Ni(meph)2] (1) [where H2meph = (2E)-N-methyl-2-[1-(pyridin-2-yl)ethylidene]hydrazine-1-carbothioamide] and [Ni(hmm)2](NO3)2·2H2O (2) [where H2hmm = (2E)-2-[(2-hydroxyphenyl)methylidene]-N-methylhydrazine-1-carbothioamide] have been designed and synthesized by the condensation of 4-methyl-3-thiosemicarbazide with 2-acetylpyridine and salicylaldehyde respectively. Both the metal complexes 1 and 2 are characterized using different available spectroscopic techniques like FT-IR, UV–Vis spectroscopy, elemental analysis, and single crystal X-ray structure analysis. X-ray crystal structure analysis reveal that complex 1 and 2 are octahedral Ni(II) complexes. The calf-thymus CT-DNA-binding property of 1 and 2 has been evaluated by employing UV–Vis and fluorescence spectral titration. All the results show that CT-DNA binds with both nickel(II) complexes 1 and 2. In vitro cytotoxicity activity of complexes 1 and 2 toward A375 and MDA-MB-231 was evaluated using MTT assay and other methods which confirm that both complexes 1 and 2 behave as promising anti-cancer agents.

Chalcogen Bonding in Selective Recognition and Liquid-Liquid Extraction of Perrhenate.

Efficient recognition and extraction of hazardous anionic pollutants from water medium is of great significance for environmental concerns, representing a challenging area of research in supramolecular chemistry. In this study, we present, for the first time, a comprehensive demonstration of the ability of chalcogen bonding (ChB) to recognize and remove the ReO4 - from 100 % water medium. The anion recognition ability is well elucidated through solution phase NMR and ITC studies, which clearly reveal the selective binding of ReO4 - over other oxo-anions. Moreover, the selenoimidazolium scaffold effectively engages in Se•••O ChB interaction with ReO4 - as confirmed by X-ray crystal structure and XPS analysis. More importantly, the binding of ReO4 - with different prolongations of the σ-holes, along with Se•••Se chalcogen bonding interactions, lead to the formation of a 1D supramolecular assembly. Eventually, ChB receptor Se4Me-Br exhibits ~62 % ReO4 - extraction efficiency through precipitation as the extraction method. Furthermore, in efforts to enhance efficiency, a hydrophobic ChB receptor Se4Do-PF6 has been prepared, achieving an efficiency of up to ~93 % at a very low concentration (~5 ppm) by liquid-liquid extraction.

Functionalization of Position 7 of Pyrazolo[1,5-a]pyrazines

AbstractWe report a straightforward formylation at position 7 of pyrazolo[1,5-a]pyrazine derivatives featuring substituents at the 2,3,4 positions. N,N,N′,1,1,1-Hexamethylsilanecarboximidamide exists in equilibrium with its carbene form due to 1,2-migration of the silyl group. The ensuing carbene can be inserted into the most acidic C–H group of the pyrazolo[1,5-a]pyrazines. The most acidic calculated pK a (DMSO) C–H group is at position 7 and does not depend significantly on the substituents. The reactions proceed in high yields affording aminals that can be hydrolyzed to the corresponding aldehydes. Methanolysis of the aminals affords the corresponding methylimines. The constitution of the aminals was unambiguously proved by X-ray crystal structure analysis of a set of derivatives. The method is simple, often does not require even solvents, and can be extended to other heterocyclic compounds.

A biologically inspired fluorescent probe with enhanced sensing performance for detection of Al3+ based on metal replacement strategy

Salicylaldehyde acyl-hydrazone derivatives have been widely applied to design fluorescent probe for Al3+ detection, but they are always restricted to detect Al3+ in water and actual samples by their poor solubility, low sensitivity, and long response time. Biologically inspired, four salicylaldehyde acyl-hydrazone compounds were designed and synthesized and H4L1 as one of them was selected for in-situ assembly of the ytterbium complex (FP-Al), which has been developed to be a new fluorescent probe for Al3+ detection by the central mental displacement process. The in-situ structure transformation from FP-Al to Al-L was fully characterized by X-ray crystal structure analysis, 1H NMR, FT-IR, and spectral analysis. The intrinsic driving force was explained and elaborated by theoretical calculation. FP-Al showed a significant visible fluorescence enhancement and near-infrared luminescence decreased upon the addition of Al3+. Compared with the ligand H4L1, FP-Al showed enhanced sensing performance during Al3+ detection, especially in improving water solubility and selectivity to Al3+, promoting response speed, reducing background fluorescence and increase cell-membrane permeability. The application of spontaneous metal replacement reaction might be able to provide a new strategy to develop high-performance optical chemo-sensors.

Structural Studies of a Complex of a CAG/CTG Repeat Sequence-Specific Binding Molecule and A-A-Mismatch-Containing DNA.

Triplet repeat diseases are caused by the abnormal elongation of repeated sequences comprising three bases. In particular, the elongation of CAG/CTG repeat sequences is thought to result in conditions such as Huntington's disease and myotonic dystrophy type 1. Although the causes of these diseases are known, fundamental treatments have not been established, and specific drugs are expected to be developed. Pyrrole imidazole polyamide (PIP) is a class of molecules that binds to the minor groove of the DNA duplex in a sequence-specific manner; because of this property, it shows promise in drug discovery applications. Earlier, it was reported that PIP designed to bind CAG/CTG repeat sequences suppresses the genes that cause triplet repeat diseases. In this study, we performed an X-ray crystal structure analysis of a complex of double-stranded DNA containing A-A mismatched base pairs and a cyclic-PIP that binds specifically to CAG/CTG sequences. Furthermore, the validity and characteristics of this structure were analyzed using in silico molecular modeling, ab initio energy calculations, gel electrophoresis, and surface plasmon resonance. With our direct observation using atomic force microscopy and DNA origami, we revealed that the PIP caused structural changes in the DNA strands carrying the expanded CAG/CTG repeat. Overall, our study provides new insight into PIP from a structural perspective.

3-Allyl-2-(allylthio)-5,5-diphenyl-3,5-dihydro-4H-imidazol-4-one: Synthesis, spectroscopic characterization, crystal structure, computational investigations, antibacterial activity and ADMET studies

In this investigation, we successfully synthesized a novel thiohydantoin derivative, 3-allyl-2-(allylthio)-5,5-diphenyl-3,5-dihydro-4H-imidazol-4-one (AM1). The compound underwent comprehensive characterization using various analytical techniques, including FT-IR, 1H NMR, 13C NMR, HRMS-ESI and X-ray crystal structure analysis. In the crystal, the 5-membered ring is planar with the allylthio group largely coplanar with it and the other allyl group rotated well out of the plane. Quantum computational methods were used to further information on the structure of the compound. The density functional theory was applied to optimize the structure. Using the optimized structure, vibration frequencies and global index parameters were computed, UV–Vis spectrum was simulated, and NBO analysis was carried out. Furthermore, we conducted an evaluation of its antibacterial activity against three different strains. The alkylation of thiohydantoin (AM0) resulted in a heightened antibacterial activity, leading to an increase in the inhibition zone from 13.25 ± 0.35 to 14.25±0.35 mm against Rhodococcus sp GK3. Similarly, an elevation from 12.75±0.35 to 14.15±0.35 mm was noted against Rhodococcus sp GK1. Additionally, ADMET studies were conducted to explore the potential of the title compound for use as an antibacterial drug. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the title compound which expressed good drug-like behavior and a non-toxic nature.

Unveiling a Novel Solvatomorphism of Anti-inflammatory Flufenamic Acid: X-ray Structure, Quantum Chemical, and In Silico Studies.

This paper delves into the polymorphism of 2-[3-(trifluoromethyl)anilino]benzoic acid, commonly referred to as flufenamic acid (FA), a pharmaceutical agent employed in treating inflammatory conditions. The central focus of the study is on a newly unearthed solvatomorphic structure of FA in methanol (FAM), and a thorough comparison is conducted with the commercially available standard structure. Employing a comprehensive approach, including X-ray crystallography, Hirshfeld surface analysis, density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulations, the research aims to unravel the structural and functional implications of solvatomorphism. The X-ray crystal structure analysis brings to light notable differences between the standard FA and solvatomorphic FAM, showcasing variations in intermolecular interactions and crystal packing. Key features such as hydrogen bonding, π···π stacking, and C-H···π interactions are identified as influential factors shaping the stability and conformation of the compounds. Hirshfeld surface analysis further quantifies the nature and contribution of intermolecular interactions, providing a comprehensive perspective on molecular stability. Density functional theory offers valuable electronic structure insights, highlighting disparities in frontier molecular orbitals between FA and FAM. Molecular docking studies against prostaglandin D2 11-ketoreductase explore potential drug interactions, unveiling distinct binding modes and hydrogen bonding patterns that shed light on how the solvatomorphic structure may impact drug-target interactions. In-depth molecular dynamics simulations over 100 ns investigate the stability of the protein-ligand complex, with root mean square deviation and root mean square fluctuation analyses revealing minimal deviations and affirming the stability of FAM within the active site of the target protein.

Regulating the bioactivity of non-glycosylated recombinant human bone morphogenetic protein-2 to enhance bone regeneration

Recombinant human bone morphogenetic protein-2 (rhBMP-2) is the predominant growth factor that effectively induces osteogenic differentiation in orthopedic procedures. However, the bioactivity and stability of rhBMP-2 are intrinsically associated with its sequence, structure, and storage conditions. In this study, we successfully determined the amino acid sequence and protein secondary structure model of non-glycosylated rhBMP-2 expressed by an E. coli expression system through X-ray crystal structure analysis. Furthermore, we observed that acidic storage conditions enhanced the proliferative and osteoinductive activity of rhBMP-2. Although the osteogenic activity of non-glycosylated rhBMP-2 is relatively weaker compared to glycosylated rhBMP-2; however, this discrepancy can be mitigated by incorporating exogenous chaperone molecules. Overall, such information is crucial for rationalizing the design of stabilization methods and enhancing the bioactivity of rhBMP-2, which may also be applicable to other growth factors.

Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma.

Transthyretin amyloidosis is a fatal disorder caused by transthyretin amyloid aggregation. Stabilizing the native structure of transthyretin is an effective approach to inhibit amyloid aggregation. To develop kinetic stabilizers of transthyretin, it is crucial to explore compounds that selectively bind to transthyretin in plasma. Our recent findings demonstrated that the uricosuric agent benziodarone selectively binds to transthyretin in plasma. Here, we report the development of benziodarone analogues with enhanced potency for selective binding to transthyretin in plasma compared to benziodarone. These analogues featured substituents of chlorine, bromine, iodine, a methyl group, or a trifluoromethyl group, at the 4-position of the benzofuran ring. X-ray crystal structure analysis revealed that CH···O hydrogen bonds and a halogen bond are important for the binding of the compounds to the thyroxine-binding sites. The bioavailability of benziodarone analogues with 4-Br, 4-Cl, or 4-CH3 was comparable to that of tafamidis, a current therapeutic agent for transthyretin amyloidosis.

Molecular basis for pH sensing in the KDEL trafficking receptor

Trafficking receptors control protein localization through the recognition of specific signal sequences that specify unique cellular locations. Differences in luminal pH are important for the vectorial trafficking of cargo receptors. The KDEL receptor is responsible for maintaining the integrity of the ER by retrieving luminally localized folding chaperones in a pH-dependent mechanism. Structural studies have revealed the end states of KDEL receptor activation and the mechanism of selective cargo binding. However, precisely how the KDEL receptor responds to changes in luminal pH remains unclear. To explain the mechanism of pH sensing, we combine analysis of X-ray crystal structures of the KDEL receptor at neutral and acidic pH with advanced computational methods and cell-based assays. We show a critical role for ordered water molecules that allows us to infer a direct connection between protonation in different cellular compartments and the consequent changes in the affinity of the receptor for cargo.

A macrocycle-based “Russian doll”: The smallest cucurbit[4]uril in cucurbit[10]uril

Host-guest recognition-based macrocycle in macrocycle to form “Russian doll” assemblies remains an interesting topic in supramolecular chemistry. Herein, a macrocycle-in-macrocycle assembly was studied using cucurbit[10]uril (Q[10]) and the smallest cucurbituril-like macrocycle (TD[4]). X-ray crystal structure analysis revealed that TD[4] was encapsulated in the cavity of Q[10] to form a 1:1 complex. Importantly, competitive guest studies suggested that TD[4] had the highest binding constant with the Q[10] host among the guests used, including Q[5], Me8TD[4], and amantadine molecules in water. Our results provided a new cucurbituril-based Russian-doll structure containing both the largest and smallest cavities of the cucurbiturils, which expanded the family of molecular Russian dolls.

Structure and Photophysics of N-Tolanyl-phenochalcogenazines and their Radical Cations.

The study focuses on the structural and photophysical characteristics of neutral and oxidized forms of N-tolanyl-phenochalcogenazines PZX-tolan with X=O, S, Se, and Te. X-ray crystal structure analyses show a pseudo-equatorial (pe) structure of the tolan substituent in the O, S, and Se dyads, while the Te dyad possesses a pseudo-axial (pa) structure. DFT calculations suggest the pe structure for O and S, and the pa structure for Se and Te as stable forms. Steady-state and femtosecond-time resolved optical spectroscopy in toluene solution indicate that the O and S dyads emit from a CT state, whereas the Se and Te dyads emit from a tolan-localized state. The T1 state is tolan-localized in all cases, showing phosphorescence at 77 K. The heavy atom effect of chalcogens induces intersystem crossing from S1 to Tx, resulting in a decreasing S1 lifetime from 2.1 ns to 0.42 ps. The T1 states possess potential for singlet oxygen sensitization with a high quantum yield (ca. 40 %) for the O, S, and Se dyads. Radical cations exhibit spin density primarily localized at the heterocycle. EPR measurements and quasirelativistic DFT calculations reveal a very strong g-tensor anisotropy, supporting the pe structure for the S and Se derivatives.

Synthesis of bimetallic palladacycles via C[sbnd]H bond activation: Crystal structure, DNA binding and in vitro cytotoxicity study

Herein, we report the synthesis, characterization and in vitro anticancer activity of two μ-Cl and μ-O bridged dimeric cyclometalated palladium(II) complexes having general formula [Pd2(L1)Cl2] (1) and [Pd2(L2)Cl2] (2). The complexes are synthesized via palladium assisted aromatic CH bond activation of coordinating ligands (HL1/HL2) and thoroughly characterized by spectroscopic techniques. X-ray crystal structure analysis has confirmed the square planar geometry of the complexes. DFT and TDDFT results have interpreted the electronic structure and solution spectra of the complexes. Cytotoxicity of the complexes was studied by in vitro model with human gastric cancer cell lines (AGS). Cytotoxicity investigation reveals that the complexes have promising anti-cancer activity, with IC50 values of 13.03 µM and 17.86 µM for 1 and 2, respectively. UV–vis and fluorescence techniques are used to examine how the complexes interact with CT DNA. Fluorescence-based competitive binding analysis with ethidium bromide (EB) indicates that the complexes effectively displace EB from the EB-DNA complex.

Photo-oxidative aromatization and photo-rearrangement of 2, 4-diaryl-5-oxohexahydroquinolines

Various 2,4-bisaryl substituted 5-oxohexahydroquinolines were synthesized and the electronic effects of 2- and 4-substitutions on the photochemical behaviors of these compounds were investigated. UV light irradiation of these compounds resulted in the occurrence of two types of photoreactions; oxidative normal photo-oxidation and photo-rearranged reactions. In both reactions, the aromatization of the heterocyclic 1,4-dihydropyridine ring to the pyridine ring was observed. The photochemical results indicated the involvement of the radical intermediate, responsible for the aryl ring migration and the occurrence of the photo-rearrangement reaction. The partial synergistic effect of the capto-dative radical stabilization of the involved radical intermediate was supported by the results of the experimental works and the DFT-computational studies. X-ray crystal structure analysis of two of 5-oxohexahydroquinoline compounds indicated that i). The C4-aryl ring occupies the pseudo-axial position of the twisted-boat conformation of the heterocyclic dihydropyridine ring and, ii). Owing to the steric ortho-repulsion, the C2-aryl ring has a non-planar orientation concerning the attached CC double bond of the heterocyclic ring. These observations were in good agreement with the data of the DFT-computational studies and the X-ray crystal structure analysis.