X-ray Crystallographic Analysis Research Articles

Structural and Computational Insights into Dynamics and Intermediate States of Orexin 2 Receptor Signaling.

Orexin 2 receptor (OX2R) is a G protein-coupled receptor (GPCR) whose activation is crucial to regulation of the sleep-wake cycle. Recently, inactive and active state structures were determined from X-ray crystallography and cryo-electron microscopy single particle analysis, and the activation mechanisms have been discussed based on these static data. GPCRs have multiscale intermediate states during activation, and insights into these dynamics and intermediate states may aid the precise control of intracellular signaling by ligands in drug discovery. Molecular dynamics (MD) simulations are used to investigate dynamics induced in response to thermal perturbations, such as structural fluctuations of main and side chains. In this study, we proposed collective motions of the TM domain during activation by performing 30 independent microsecond-scale MD simulations for various OX2R systems and applying relaxation mode analysis. The analysis results suggested that TM3 had a vertical structural movement relative to the membrane surface during activation. In addition, we extracted three characteristic amino acid residues on TM3, i.e., Q1343.32, V1423.40, and R1523.50, which exhibited large conformational fluctuations. We quantitatively evaluated the changes in their equilibrium during activation in relation to the movement of TM3. We also discuss the regulation of ligand binding recognition and intracellular signal selectivity by changes in the equilibrium of Q1343.32 and R1523.50, respectively, according to MD simulations and GPCR database. Additionally, the OX2R-Gi signaling complex is stabilized in the conformation resembling a non-canonical (NC) state, which was previously proposed as an intermediate state during activation of neurotensin 1 receptor. Insights into the dynamics and intermediate states during activation gained from this study may be useful for developing biased agonists for OX2R.

Synthesis and characterization of Cu(II) complexes supported by a pyridylamide ligand

In our effort to understand the impact of ligand platforms on the structure diversity and chemical properties of copper clusters, a tripod pyridylamide ligand H3tpmbc was used in this work. Two one-dimensional polymeric Cu(II) complexes [Cu(H3tpmbc)Cl2]n (1) and [Cu2(H3tpmbc)Cl4]n (2) were isolated and characterized. X-ray crystallography analysis showed that both structures have a similar one-dimensional backbone. The main structure difference of the two complexes is the presence of a second Cu(II) site in complex 2. Hirshfeld analysis revealed the presence of interesting C–H⋅⋅⋅π and π⋅⋅⋅π interaction networks in both complexes. Spectroscopic characterization of both complexes and [CuPyCl2] suggests the source of the color difference between the two polymers at the solid state. Computational studies based on the X-ray crystal structures were performed and the results provided a deeper understanding of the electronic structures of the Cu(II) site(s) in both complexes. Thermal gravimetric analysis (TGA) demonstrated that the two complexes have the similar thermal behavior, and this could be attributed to the similar one-dimensional backbone structure.

Cu(II) complexes of 5-sulfamoylbenzoic acid derivatives: Synthesis and characterization

Novel three Cu(II) complexes {[Cu2(MeOsba)4(H2O)2] (1, HMeOsba = 2-methoxy-5-sulfamoylbenzoic acid), [Cu(MeOsba)2(2a5mp)2].3H2O (2, 2a5mp = 2-amino-5-methylpyridine) and [Cu(Clsba)2(2amp)2].2H2O (3, 2amp = 2-picolylamine, HClsba = 2,4-dichloro-5-sulfamoylbenzoic acid)} were synthesized. The structure of 1–3 characterized by FT-IR, AAS, X-ray crystallographic analysis, UV, molar conductivity and magnetic moment. All complexes (1–3) formed crystals in the P-1 space group and the triclinic crystal system. The symmetric units of complexes (1–3) contains two Cu(II) cations, four MeOsba anions as bridges and two aqua ligands for 1, one Cu(II) cations, two MeOsba anions, two 2a5mp and three uncoordinated water molecules for 2 and one Cu(II) cations, two Clsba anions, two 2amp and three uncoordinated water molecules for 3. The structure of 1–3 have a crystallographic inversion centre.

Antifungal Pseuboyenes A-J, Bergamotene-Derived Sesquiterpenoids from a Cold-Seep-Derived Pseudallescheria boydii.

A chemical investigation of a cold-seep-sediment-derived fungus, Pseudallescheria boydii CS-793, resulted in characterization of 10 novel bergamotene-derived sesquiterpenoids, pseuboyenes A-J (1-10). Their structures were elucidated by spectroscopic and X-ray crystallographic analyses as well as using the modified Mosher's method. Compound 1 represents the first example of a β-bergamotene containing a 6-oxobicyclo[3.2.1]octane nucleus adducted with a methyl lactate unit, while 8-10 involve a skeletal rearrangement from bergamotene. Compounds 2-5 showed significant antifungal activities against Colletotrichum gloeosporioides Penz. and Fusarium oxysporum with MICs ranging from 0.5 to 8 μg/mL. Compound 4 exhibited an in vitro anti-F. proliferatum effect with an EC50 value of 1.0 μg/mL.

Lanthanide complexes of monosubstituted Calix[4]arene-ligands: Synthesis, structures, and magnetic properties of [Ln2(L)2(MeOH)4] (Ln = La, Gd, Tb, Tm) (H3L = mono-O-propargyl-calix[4]arene)

The ability of the propargylated calix[4]arene ligand H3L (= 25-(2-propynyloxy)-26,27,28-trihydroxy-calix[4]arene) to bind lanthanide ions has been studied. The triply deprotonated ligand was found to support dinuclear neutral complexes of composition [Ln2L2(MeOH)4] (Ln= La (1), Gd (2), Tb (3), Tm (4)). Spectroscopic data for 1–4 as well as X-ray crystallographic analysis of single crystals of 1∙(MeOH)2 and 2∙(MeOH)2 reveal that two [LnL] entities dimerize via two phenolato groups to generate a centrosymmetric (MeOH)2O3Ln(μ-O)2LnO3(OHMe)2 core structure. The Ln3+ ions reside in a distorted mono-capped octahedral coordination environment. Squid magnetic measurements for the Gd3+ and Tb3+ complexes agree with the formulation as dinuclear compounds, and reveal the presence of very weak antiferromagnetic exchange interactions (J < 0.1 cm−1). The ability of the La3+ complex to react with azides in a click reaction is also demonstrated.

Efficient and Selective Construction of 41 2 Metalla-links Using Weak C-H⋅⋅⋅Halogen Interactions.

Through a coordination-driven self-assembly method, four metalla-links and one tetranuclear monocycle were constructed with high selectivity and yield by adjusting the substituent species of the building blocks, as evidenced using X-ray crystallographic analysis, electrospray ionization-time-of-flight/mass spectrometry (ESI-TOF/MS), elemental analysis and detailed solution-state nuclear magnetic resonance (NMR) spectroscopy. Based on X-ray crystallographic analysis and independent gradient model analysis, a significant factor leading to the formation of metalla-links was the introduction of F, Cl, Br and I atoms, which generated additional weak C-H⋅⋅⋅X (X=F, Cl, Br and I) interactions. Furthermore, the dynamic conversion of metalla-links to monocyclic rings in methanol solution was systematically investigated using quantitative 1H NMR techniques.

Stereoselective Preparation of the Tricyclic Hexasubstituted Spirocyclopropane Core of Cyclohelminthol X.

This study focused on synthesizing the tricyclic hexasubstituted spirocyclopropane-core framework 2 of cyclohelminthol X (1), an antifungal cytotoxin isolated from Helminthosporium velutinum yone96 in a stereoselective manner. The synthesis features an SN2-type cyclopropanation of the quaternary chloride 23 generated via a retro-Michael-type ring-opening reaction of an 8-azatricyclo[4.3.0.12,5]deca-3,7,9-trione derivative 22. The successful synthesis confirmed the structure of 1, resolving the ambiguity from the absence of X-ray crystallographic analysis. The prepared models exhibited potent cytotoxicity.

Predisposition in Dynamic Covalent Chemistry: The Role of Non-Covalent Interactions in the Assembly of Tetrahedral Boronate Cages.

Directional bonding strategies guide the design of complex molecular architectures, yet challenges arise due to emergent behavior. Rigid structures face geometric constraints and sensitivity to mismatches, hindering the efficient assembly of molecular organic cages (MOCs). Harnessing intramolecular non-covalent interactions offers a promising solution, broadening geometrical possibilities and enhancing adaptability to boost assembly yields. However, identifying these interactions remains challenging, with their full potential sometimes latent until final assembly. This study explores these challenges by synthesizing boronic acid tripods with varied oxygen positions at the tripodal feet and investigating their role in assembling tetrahedral boronate MOCs. Our results reveal substantial differences in the assembly efficiency among tripods. While the building blocks with oxygen in the benzylic position relative to the central aromatic ring form the MOCs in high yields, those with the oxygen atom directly bound to the central aromatic ring, only yield traces. Through X-ray crystallography and DFT analyses, we elucidate how intramolecular interactions profoundly influence the geometry of the building blocks and cages in a relay-like fashion, highlighting the importance of considering intramolecular interactions in the rational design of (supra)molecular architectures.

Guest-Induced Reversible Single-Crystal-to-Single-Crystal Transformation Involving Displacement of 2D Layers and Spin Crossover Behavior Change in a Hofmann-Type Coordination Polymer.

A novel two-dimensional (2D) Hofmann-type coordination polymer, {FeII(PyHbim)2[Pd(CN)4]}·2CH3OH [1·2CH3OH, PyHbim = 2-(4-pyridyl)benzimidazole], has been synthesized, which can undergo a spontaneous guest exchange, transforming to 1·2H2O in a single-crystal-to-single-crystal (SCSC) manner, shifting from orthorhombic Cmmm to monoclinic C2/m involving the displacement of 2D layers. The solvent-induced SCSC transformation process was reversible and verified through powder X-ray diffraction (PXRD) and single-crystal X-ray crystallography analyses. Both 1·2CH3OH and 1·2H2O exhibit complete and abrupt spin crossover (SCO) behaviors in two steps, while their SCO temperature ranges drastically shift by ca.100 K, spanning room temperature, owing to different intermolecular interactions resulting from diverse interlayer packing manners and host-guest interactions. Besides, a structural phase transition is observed in 1·2CH3OH, contributing to the two-step spin transition.

Experimental and theoretical studies of trinuclear cadmium(II) complex containing pyridine ring: Synthesis, crystallographic, spectroscopic, TD/DFT calculations and Hirshfeld surface analysis

Two three-dimensional supramolecular structures of L and [Cd3L2(CH3OH)4Cl6] complex (L = 2-(6-bromopyridin-2-yl)-4-methyl-1,2-dihydroquinazoline-N3-oxide), were synthesized and characterized by X-ray crystallography and elemental analysis, as well as FT-IR, UV–Vis, and fluorescence spectroscopy. The photoluminescence behavior of the Cd(II) complex was also investigated in different solvents. X-ray diffraction analysis results revealed that the Cd(II) complex was a trinuclear hexa-coordinate structure and made up of two L, three Cd2+ metal central, four methanol and six chlorine ions. In the crystal structures, it was noteworthy that L formed an infinite 1-D chain-like, 2-D square structure, parallelogram 3-D supramolecular skeleton, whereas the Cd(II) complex formed an infinite 1-D chain-like, 2-D ladder-like configuration, and even expanding into 3-D grid-like supramolecular frameworks. Density functional theory (DFT) calculation was used to compute the optimization, molecular frontier orbital energies (HOMO and LUMO). Specifically, owing to the combination of metal orbitals and the ligand, the energy gap of the complex was less than L. Electrostatic potential (ESP) was used to analyze the reaction sites of two compounds. On the basis of optimized geometry, time-dependent DFT (TD-DFT) simulated the electronic transitions rationalized the UV–Vis spectra peaks of L and Cd(II) complex. In addition, some non-covalent interactions were quantified by Hirshfeld surface and analyzed by Interaction region indicator (IRI).

Exploring the coordination chemistry of ruthenium complexes with lysozymes: structural and in-solution studies.

This study presents a comprehensive structural analysis of the adducts formed upon the reaction of two Ru(III) complexes [HIsq][trans-RuIIICl4(dmso)(Isq)] (1) and [H2Ind][trans-RuIIICl4(dmso)(HInd)] (2) (where HInd-indazole, Isq-isoquinoline, analogs of NAMI-A) and two Ru(II) complexes, cis-[RuCl2(dmso)4] (c) and trans-[RuCl2(dmso)4] (t), with hen-egg white lysozyme (HEWL). Additionally, the crystal structure of an adduct of human lysozyme (HL) with ruthenium complex, [H2Ind][trans-RuCl4(dmso)(HInd)] was solved. X-ray crystallographic data analysis revealed that all studied Ru complexes, regardless of coordination surroundings and metal center charge, coordinate to the same amino acids (His15, Arg14, and Asp101) of HEWL, losing most of their original ligands. In the case of the 2-HL adduct, two distinct metalation sites: (i) Arg107, Arg113 and (ii) Gln127, Gln129, were identified. Crystallographic data were supported by studies of the interaction of 1 and 2 with HEWL in an aqueous solution. Hydrolytic stability studies revealed that both complexes 1 and 2 liberate the N-heterocyclic ligand under crystallization-like conditions (pH 4.5) as well as under physiological pH conditions, and this process is not significantly affected by the presence of HEWL. A comparative examination of nine crystal structures of Ru complexes with lysozyme, obtained through soaking and co-crystallization experiments, together with in-solution studies of the interaction between 1 and 2 with HEWL, indicates that the hydrolytic release of the N-heterocyclic ligand is one of the critical factors in the interaction between Ru complexes and lysozyme. This understanding is crucial in shedding light on the tendency of Ru complexes to target diverse metalation sites during the formation and in the final forms of the adducts with proteins.

Efficient Synthesis and Structural Analysis of Chiral 4,4'-Biazulene.

4,4'-Biazulene is a potentially attractive key component of an axially chiral biaryl compound, however, its structure and properties have not been clarified owing to the lack of its efficient synthesis. We report a breakthrough in the reliable synthesis of 4,4'-biazulene, which is achieved by the access to azulen-4-ylboronic acid pinacol ester and 4-iodoazulene as novel key synthetic intermediates for the Suzuki-Miyaura cross-coupling reaction. The X-ray crystallographic analysis of 4,4'-biazulene confirmed its axial chirality. The enantiomers of 4,4'-biazulene were successfully resolved by HPLC on the chiral stationary phase column. The kinetic experiments and DFT calculations indicate that the racemization energy barrier of 4,4'-biazulene is comparable to that of 1,1'-binaphthyl.

Studies of the Functionalized α-Hydroxy-p-Quinone Imine Derivatives Stabilized by Intramolecular Hydrogen Bond.

In this work, reactions between 6,7-dichloropyrido[1,2-a]benzimidazole-8,9-diones with different benzohydrazides were studied. Nucleophilic substitution at C(6) was followed by isomerization and led to α-hydroxy-p-quinone imine derivatives. Synthesized compounds represent a combination of several structural motifs: a benzimidazole core fused with α-hydroxy-p-quinone imine, which contains a benzamide fragment. X-ray crystallography analysis revealed the formation of dimers linked through OH···O interactions and stabilization of the imine form by strong intramolecular NH···N hydrogen bonds. The protonation/deprotonation processes were investigated in a solution using UV-Vis spectroscopy and a 1H NMR titration experiment. Additionally, the electrochemical properties of 6,7-dichloropyrido[1,2-a]benzimidazole-8,9-dione and its α-hydroxy-p-quinone imine derivative as cathode materials were investigated in acidic and neutral environments using cyclic voltammetry measurements. Cathode material based on 6,7-dichloropyrido[1,2-a]benzimidazole-8,9-dione could act as a potentially effective active electrode in aqueous electrolyte batteries; however, further optimization is required.

Toonanoronoids A-E, five new limonoids from Toona ciliata var. yunnanensis

Five new B-seco-limonoids, namely toonanoronoids A-E (1–5), in conjunction with three previously reported compounds, were isolated from the EtOAc extract of the twigs and leaves of Toona ciliata var. yunnanensis. Their structures were elucidated through comprehensive spectroscopic and X-ray crystallographic analysis. The cytotoxic activities of new compounds against five human tumor cell lines (HL-60, SMMC-7721, A549, MCF-7, and SW480) were screened, Compounds 4 and 5 exerted inhibition toward two tumor cell lines (HL-60, SW-480) with IC50 values between 1.7 and 5.9 μM.

Synthesis of fused oligosiloles by rhodium-catalyzed stitching reaction and subsequent remote conjugate dehydration

Abstract A new synthetic method for π-conjugated fused oligosiloles has been developed by combining a rhodium-catalyzed stitching reaction and subsequent remote conjugate elimination. Aromatization-driven 1,8-, 1,10-, or 1,12-dehydration was successfully utilized and up to 3 silole units were consecutively fused in a π-conjugated manner. The structural change upon conjugate elimination was confirmed by using X-ray crystallographic analysis, and the optical and electrochemical properties of a series of newly synthesized fused oligosiloles were also examined.

Lemneolemnanes A-D, Four Uncommon Sesquiterpenoids from the Soft Coral Lemnalia sp.

Four undescribed sesquiterpenoids, lemneolemnanes A-D (1-4), have been isolated from the marine soft coral Lemnalia sp. The absolute configurations of the stereogenic carbons of 1-4 were determined by single-crystal X-ray crystallographic analysis. Compounds 1 and 2 are epimers at C-3 and have an unusual skeleton with a formyl group on C-6. Compound 3 possesses an uncommonly rearranged carbon skeleton, while 4 has a 6/5/5 tricyclic system. Compound 1 showed significant anti-Alzheimer's disease (AD) activity in a humanized Caenorhabditis elegans AD pathological model.

Structural Characterization of 4-(4-Nitrophenyl)thiomorpholine, a Precursor in Medicinal Chemistry

4-(4-nitrophenyl)thiomorpholine, the title compound, has been used as a precursor for the corresponding 4-thiomorpholinoaniline, which is a useful building block in medicinal chemistry. The crystal and molecular structures of the title compound, however, have not been described thus far. We synthesized the title compound by means of a nucleophilic aromatic substitution reaction of 4-fluoronitrobenzene and thiomorpholine and structurally characterized it by X-ray crystallography, DFT calculations, and Hirshfeld surface analysis. In the crystal, the molecule exhibits an approximately CS-symmetric structure, with the nitrogen-bound 4-nitrophenyl group in a quasi axial position on the six-membered thiomorpholine ring in a low-energy chair conformation. The solid-state structure of the title compound is markedly different from that of its morpholine analogue. This can be ascribed to the formation of centrosymmetric dimers through intermolecular C–H···O weak hydrogen bonds involving the methylene groups adjacent to the sulfur atom and face-to-face aromatic stacking.

A Metallocene Bis(phosphoranocarbene) of Uranium and a Probe of Its Reactivity with Alcohols.

The addition of 2 equiv of the phosphaylide H2C═PPh3 to the dimethyl uranium metallocene Cp*2UMe2 (Cp* = η5-C5Me5) in toluene with gentle heating at 40 °C generates the phosphorano-stabilized bis(carbene) Cp*2U[C(H)PPh3]2 (1) in good yield. Characterization of 1 by X-ray crystallographic analysis reveals two short uranium-carbon bonds, ranging from 2.301(5) to 2.322(5) Å, consistent with the presence of U═C carbene-type bonds. Monitoring the reaction by NMR spectroscopy suggests that it proceeds through the intermediate formation of the methyl carbene complex Cp*2U[C(H)PPh3](Me) (1Int); however, prolonged heating of these solutions leads to the ortho-cyclometalated carbene species Cp*2U{κ2-[C(H)PPh2(C6H4)]} (2) via intramolecular C-H activation. Rapid conversion from 1 to 2 occurs within hours upon heating its toluene solutions to 100 °C. Preliminary reactivity studies of 1 show that it readily reacts with alcohols, such as HODipp (Dipp = 2,6-diisopropylphenyl) and HOC(CF3)3, to give the mixed carbene alkoxide compounds Cp*2U[C(H)PPh3](OR) (R = Dipp (4Dipp), C(CF3)3 (5CF3)). In one case, the reaction of 1 with HODipp in the presence of adventitious water led to the formation of a few crystals of the terminal U(IV) oxo complex, [Ph3PCH3][Cp*2U(O)(ODipp)] (3oxo). The isolation of 1 marks the first instance of an unchelated, heteroatom-stabilized bis(carbene) complex of uranium that also provides an entryway to the synthesis of its monocarbene derivatives through protonolysis.

Experimental and theoretical studies for I⋯F, I⋯I and I⋯N intermolecular interactions Analysis in 5, 7-diiodoquinoline derivatives and their In-vitro DPP-4 inhibitory activity

5, 7-diiodoquinoline derivatives have been synthesized and characterized to study quantitative intermolecular noncovalent interactions through theoretical and experimental investigations, particularly for interactions involving electronegative atoms like I⋯F, I⋯I, and I⋯N. X-ray crystallography and Hirshfeld surface analysis have been used to perform the quantitative assessments of non-covalent interactions. Using Crystal Explorer 17, the calculations for intermolecular interactions were completed. Further, antidiabetic in-silico and in-vitro DPP-4 inhibitory activity have been done. The silicon studies have been carried out by Schrodinger on 2OLE pdb id. The in-vitro inhibitory DPP- 4 activity was determined by observing the rate of hydrolysis of a substrate Gly-pro-p-nitroanilide taking sitagliptin as a standard drug. The molecular docking and in-vitro studies revealed that all molecules had shown significant DPP-4 inhibitory activity compared to standard drugs sitagliptin.

Variation in biosynthesis and metal-binding properties of isonitrile-containing peptides produced by Mycobacteria versus Streptomyces.

A number of bacteria are known to produce isonitrile-containing peptides (INPs) that facilitate metal transport and are important for cell survival; however, considerable structural variation is observed among INPs depending on the producing organism. While non-heme iron 2-oxoglutarate dependent isonitrilases catalyze isonitrile formation, how the natural variation in INP structure is controlled and its implications for INP bioactivity remain open questions. Herein, total chemical synthesis is utilized with X-Ray crystallographic analysis of mycobacterial isonitrilases to provide a structural model of substrate specificity that explains the longer alkyl chains observed in mycobacterial versus Streptomyces INPs. Moreover, proton NMR titration experiments demonstrate that INPs regardless of alkyl chain length are specific for binding copper instead of zinc. These results suggest that isonitrilases may act as gatekeepers in modulating the observed biological distribution of INP structures and this distribution may be primarily related to differing metal transport requirements among the producing strains.