X-ray Crystallographic Analysis Research Articles

Thermal fluctuation-induced selective CO2 uptake of seemingly nonporous N,C-protected dipeptide crystals as elucidated by in situ X-ray crystallographic analysis

A novel N,C-protected dipeptide deposited nonporous but yet CO2-sorbing molecular crystals, of which the CO2 sorption state was disclosed.

Synthetic access to diverse thiazetidines via a one-pot microwave assisted telescopic approach and their interaction with biomolecules.

A one-pot microwave assisted telescopic approach is reported for the chemo-selective synthesis of substituted 1,3-thiazetidines using readily available 2-aminopyridines/pyrazines/pyrimidine, substituted isothiocyanates and 1,2-dihalomethanes. The procedure involves thiourea formation from 2-aminopyridines/pyrazines/pyrimidine with the substituted isothiocyanates followed by a base catalysed nucleophilic attack of the CS bond on the 1,2-dihalomethane. Subsequently, a cyclization reaction occurs to yield substituted 1,3-thiazetidines. These four membered strained ring systems are reported to possess broad substrate scope with high functional group tolerance. The above synthetic sequence for the formation of four membered heterocycles is proven to be a modular and straightforward approach. Further the mechanistic pathway for the formation of 1,3-thiazetidines was supported by computational evaluations and X-ray crystallography analyses. The relevance of these thiazetidines in biological applications is evaluated by studying their ability to bind bio-macromolecules like proteins and nucleic acids.

Steric and electronic influence on Cu-Cu short contacts in β-thioketiminato tricopper(I) clusters.

A series of β-thioketiminate copper(I) complex trimers [LCuI]3 were synthesized by modifying the ligand framework with electron-withdrawing groups (F and Cl) or electron-donating groups (iPr and Me) at the N-aryl ring as well as with CF3 groups on the chelating backbone. This ligand modification significantly impacts the enhancement of Cu⋯Cu short contacts, which can be rationalized by using steric and electronic factors of the chelated ligand. We observed that this intramolecular cuprophilicity among [LCuI]3 complexes is primarily governed by the size of N-aryl ortho-substituents. These findings were well supported by X-ray crystallography, Raman spectroscopy, and Mayer bond order analysis. The electronic effects induced by the ligand modification on the LCuI fragment were investigated using CO and 2,4,6-CNC6H2Me3 as probe molecules. Corroborated by the FTIR and CV measurements, our results reveal that the β-thioketiminate SN chelators induce more pronounced changes in the electronic character of the LCuI fragment due to the presence of CF3 groups on the chelating backbone in comparison with the F or Cl substituents on the N-aryl ring.

A one-pot reduction route to bimetallic manganese 1,8-naphthyridine complexes.

Reaction of the dinucleating ligand 2,7-bis(6-methyl-2-pyridyl)-1,8-naphthyridine (MeL) with the MnI and MnII precursors MnBr(CO)5 and MnCl2 resulted in the formation of the monometallic complexes [MnBr(CO)3(MeL)] (1) and [MnCl2(MeL)] (3). In both cases, formation of bimetallic manganese complexes could be achieved by reduction with KC8, yielding the carbonyl-bridged complex [Mn2(CO)6(MeL)] (2) and the helicate complex [Mn2(MeL)2] (4), respectively. EPR results demonstrate that 4 represents a novel, weakly antiferromagnetically coupled homovalent dimer (J = -0.85 cm-1). The two formally Mn0 ions are both high spin (S = 3/2) and exhibit a zero-field splitting of ≈1 cm-1, suggesting reduction of the complex is substantially ligand centered, and may be better described as a MnII complex coupled to two open shell singlet ligands [MnII2(MeL2-)2]. X-ray crystallography, UV-Vis spectroscopy and DFT analysis support this finding.

Tuning the redox profile of the 6,6'-biazulenic platform through functionalization along its molecular axis.

The E1/2 potential associated with reduction of the linearly-functionalized 6,6'-biazulenic scaffold is accurately correlated to the combined σp Hammett parameters of the substituents over >600 mV range. X-ray crystallographic analysis of the 2,2'-dichloro-substituted derivative revealed unexpectedly short C-Cl bond distances, along with other metric changes, suggesting a non-trivial cycloheptafulvalene-like structural contribution.

Intramolecular exciplex featuring a bis-sp3 C-locked acceptor-donor-acceptor sandwich.

Intramolecular exciplex systems featuring thermally activated delayed fluorescence (TADF) have garnered significant attention in the realm of organic light-emitting diodes (OLEDs). Nonetheless, the occurrence of organic sandwich intramolecular exciplexes remains rare due to structural limitations and synthetic challenges. Herein, we present a novel rigid acceptor-donor-acceptor (A-D-A) sandwich complex, dSFQP, characterized by two sp3 C-locking moieties. This compound exhibits TADF characteristics facilitated by a multiple through-space charge-transfer process. X-ray crystallographic analysis confirms the distinctive sandwich configuration. The parallel spatial arrangement and minimized A-D-A configuration enhance electronic interactions, resulting in a high photoluminescence quantum yield, rapid reverse intersystem crossing rate, and sluggish nonradiative decay rate. OLEDs employing dSFQP as the dopant achieve a maximum external quantum efficiency (EQE) of 28.5% with a low efficiency roll-off of merely 2.8% at 1000 cd m-2. Even at a high brightness of 10 000 cd m-2, the EQE remains notably high at 17.5%. Our current results provide an effective way to further innovate the design of new organic charge-transfer complexes.

In situ hydrolysis of a carbophosphazene ligand leads to one-dimensional lanthanide coordination polymers. Synthesis, structure and dynamic magnetic studies.

An in situ hydrolysis of the P-Cl bonds of the carbophosphazene [{NC(NMe2)}2{NPCl2}] (LPCl2) in the presence of hydrated lanthanide(III) nitrates in a dichloromethane and methanol (2 : 1) solvent mixture afforded a series of novel 1D coordination polymers: [{Ln(LHPO2)3(NO3)2(CH3OH)(H2O)} (Cl)]n {where Ln(III) = Gd (1), Tb (2), Dy (3), or Er (4) and LHPO2 is the hydrolyzed carbophosphazene (LPCl2) ligand}. X-ray crystallographic analysis revealed that complexes 1-4 are isostructural and crystallized in the monoclinic crystal system having P21/c space group. The coordination polymers are formed because of the involvement of the geminal P(O)(OH) moieties of the carbophosphazene ligand. Each lanthanide(III) ion is 9-coordinate (9O) in a distorted muffin geometry. Magnetic measurements revealed that both DyIII and ErIII analogues exhibit field-induced single-molecule magnet (SMM) behavior at 0.8 kOe and 2.2 k Oe, respectively. At such dc fields, the dynamic magnetic susceptibility displays complex behavior with a triple magnetic relaxation contribution for 3, while two contributions were identified for 4. The observed static and dynamic magnetic behavior for complexes 1-4 were further rationalized with the aid of BS-DFT and CASSCF/SO-RASSI/SINGLE_ANISO calculations.

STRUCTURAL INVESTIGATION AND HIRSHFELD SURFACE ANALYSIS OF TWO [ONO]-TYPE SCHIFF BASES

Two novel [ONO]-type tridentate Schiff base compounds namely (E)-2-(((2-hydroxyphenyl)imino)methyl)-4,5-dimethoxyphenol, C15H15NO4 (1), and (E)-2-(((5-chloro-2-hydroxyphenyl)imino)methyl)-4,5-dimethoxyphenol, C15H14ClNO4 (2) were synthesized. These compounds were characterized using various spectroscopic techniques, including single crystal X-ray diffraction (XRD), infrared (IR), proton nuclear magnetic resonance (1H NMR), carbon-13 nuclear magnetic resonance (13C NMR), and UV-Vis spectroscopy. The X-ray crystallographic analysis revealed that both compounds 1 and 2 contain two independent molecules within the asymmetric unit. Compound 1 crystallizes in the orthorhombic system with the Pna21 space group, while compound 2 crystallizes in the monoclinic system with the P21/c space group. An important feature observed in the crystal structure of compound 1 is the presence of O–H···N and O–H···O hydrogen bonds. In compound 2, the hydrogen bonding interactions involve C–H···O, O–H···O and O–H···N. Additionally, both compounds exhibit C–H···π interactions. To further understand the bonding interactions in compounds 1 and 2, Hirshfeld surface analyses and 2D fingerprint graphs were performed. The results indicate that the Hirshfeld surfaces are predominantly influenced by H⋯H, O⋯H, and C⋯H contacts.

Steric control of Mg-Mg bond formation vs. N2 activation in the reduction of bulky magnesium diamide complexes.

Reduction of the magnesium(II) diamide [Mg(TripNON)] (TripNON = 4,5-bis(2,4,6-triisopropylanilido)-2,7-diethyl-9,9-dimethyl-xanthene) with 5% w/w K/KI leads to a good yield of a dianionic dimagnesium(I) species, as its potassium salt, [{K(TripNON)Mg}2]. An X-ray crystallographic analysis shows the molecule to contain a very long Mg-Mg bond (3.137(2) Å). The formation of [{K(TripNON)Mg}2] contrasts with a previously reported reduction of a magnesium(II) complex incorporating a bulkier diamide ligand, which instead afforded a magnesium-dinitrogen complex. In the current study, [{K(TripNON)Mg}2] has been shown to be a viable reagent for the reductive activation of CO, H2 and N2O.

Square-planar imido complexes of cobalt: synthesis, reactivity and computational study.

Treatment of [Co(N2)(tBuPNP)] (tBuPNP = anion of 2,5-bis(di-tert-butylphosphinomethyl)pyrrole) with one equivalent of an aryl azide generates the four-coordinate imido complexes [Co(NAr)(tBuPNP)] (Ar = mesityl, phenyl, or 4-tBu-phenyl). X-ray crystallographic analysis of the compounds shows an unusual square-planar geometry about cobalt with nearly linear imido units. In the presence of the hydrogen atom donor, TEMPOH, [Co(NPh)(tBuPNP)] undergoes addition of the H atom to the imido nitrogen to generate the corresponding amido complex, [Co(NHPh)(tBuPNP)], whose structure and composition were verified by independent synthesis. Despite the observation of H atom transfer reactivity with TEMPOH, the imido complexes do not show catalytic activity for C-H amination or aziridination for several substrates examined. In the case of [Co(NPh)(tBuPNP)], addition of excess azide produced the tetrazido complex, [Co(N4Ph2)(tBuPNP)], whose bond metrics were most consistent with an anionic Ph2N4 ligand. Density Functional Theory (DFT) investigations of the imido and tetrazido species suggest that they adopt a ground state best described as possessing a low-spin cobalt(II) ion ferromagnetically coupled to an iminyl radical.

Insight into ferromagnetic interactions in CuII-LnIII dimers with a compartmental ligand.

In the last two decades, efforts have been devoted to obtaining insight into the magnetic interactions between CuII and LnIII utilizing experimental and theoretical means. Experimentally, it has been observed that the exchange coupling (J) in CuII-LnIII systems is often found to be ferromagnetic for ≥4f7 metal ions. However, exchange interactions at sub-Kelvin temperatures between CuII and the anisotropic/isotropic LnIII ions are not often explored. In this report, we have synthesized a series of heterobimetallic [CuLn(HL)(μ-piv)(piv)2] complexes (LnIII = Gd (1), Tb (2), Dy (3) and Er (4)) from a new compartmental Schiff base ligand, N,N'-bis(3-methoxy-5-methylsalicylidene)-1,3-diamino-2-propanol (H3L). X-ray crystallographic analysis reveals that all four complexes are isostructural and isomorphous. Magnetic susceptibility measurements reveal a ferromagnetic coupling between the CuII ion and its respective LnIII ion for all the complexes, as often observed. Moreover, μ-SQUID studies, at sub-Kelvin temperatures, show S-shaped hysteresis loops indicating the presence of antiferromagnetic coupling in complexes 1-3. The antiferromagnetic interaction is explained by considering the shortest Cu⋯Cu distance in the crystal structure. The nearly closed loops for 1-3 highlight their fast relaxation characteristics, while the opened loops for 4 might arise from intermolecular ordering. CASSCF calculations allow the quantitative assessment of the interactions, which are further supported by BS-DFT calculations.

Synergistic meso-β regulation of porphyrins: squeezing the band gap into the near-infrared I/II region.

The development of novel near-infrared (NIR) materials with extremely small energy gaps and high stability is highly desirable in bioimaging and phototherapy. Here we report an effective strategy for narrowing the energy gaps of porphyrins by synergistic regulation of meso/β substituents. The novel NIR absorbing/emitting meso-alkynyl naphthoporphyrins (Zn-TNP and Pt-TNP) are synthesized via the retro-Diels-Alder reaction. X-ray crystallography analysis confirms the highly distorted structures of the complexes. Both compounds exhibit intense Q bands around 800 nm, while Zn-TNP shows deep NIR fluorescence at 847 nm. Pt-TNP displays NIR-II room temperature phosphorescence peaking at 1106 nm with an extremely large Stokes shift of 314 nm, which are the longest wavelengths observed among the reported platinum porphyrinoids. Furthermore, Pt-TNP shows remarkable photostability and a notable capacity for synchronous singlet oxygen and heat generation under NIR light irradiation, demonstrating potential in combined photodynamic/photothermal therapy. A theoretical analysis reveals the progressive lifting of the HOMO by the β-fused benzene ring, the decrease of the LUMO upon meso-alkynyl substitution, and energy-releasing pathways varying with metal ions. This dual regulation approach demonstrates great promise in designing innovative multifunctional NIR porphyrin materials.

Pal power: Demonstration of the functional association of the Helicobacter pylori flagellar motor with peptidoglycan-associated lipoprotein (Pal) and its preliminary crystallographic analysis.

The bacterial flagellar motor is a molecular nanomachine, the assembly and regulation of which requires many accessory proteins. Their identity, structure and function are often discovered through characterisation of mutants with impaired motility. Here, we demonstrate the functional association of the Helicobacter pylori peptidoglycan-associated lipoprotein (HpPal) with the flagellar motor by analysing the motility phenotype of the ∆pal mutant, and present the results of the preliminary X-ray crystallographic analysis of its globular C-terminal domain HpPal-C. Purified HpPal-C behaved as a dimer in solution. Crystals of HpPal-C were grown by the hanging drop vapour diffusion method using medium molecular weight polyethylene glycol (PEG) Smear as the precipitating agent. The crystals belong to the primitive orthorhombic space group P1 with unit cell parameters a = 50.7, b = 63.0, c = 75.1 Å. X-ray diffraction data were collected to 1.8 Å resolution on the Australian Synchrotron beamline MX2. Calculation of the Matthews coefficient (VM=2.24 Å3/Da) and molecular replacement showed that the asymmetric unit contains two protein subunits. This study is an important step towards elucidation of the non-canonical role of H. pylori Pal in the regulation, or function of, the flagellar motor.

Identification of New Diterpenoids from the Pulp of Coffea arabica and Their α-Glucosidase Inhibition Activity.

Six new (1, 2, 3, 5, 6, and 8) and seven known (4, 7, 9, 10, 11, 12, and 13) diterpenoids have been identified in the pulp of Coffea arabica. The structures of new diterpenoids were elucidated by extensive spectroscopic analysis, including 1D, 2D NMR (HSQC, HMBC, 1H-1H COSY, and ROESY), HRESIMS, IR, DP4+, electronic circular dichroism, and X-ray crystallography analysis. Compound 1 is ent-labdane-type diterpenoid, whereas compounds (2-13) are ent-kaurane diterpenoids. The result of α-glucosidase inhibitory assay demonstrated that compounds (1, 3, 5, 7, and 10) have moderate inhibitory activity with IC50 values of 55.23 ± 0.84, 74.02 ± 0.89, 66.46 ± 1.05, 49.70 ± 1.02, and 76.34 ± 0.46 μM, respectively, compared to the positive control (acarbose, 51.62 ± 0.21 μM). Furthermore, molecular docking analysis has been conducted to investigate the interaction between the compounds and the receptors of α-glucosidase to interpret their mechanism of activity. This study is the first investigation that successfully discovered the presence of diterpenoids within the coffee pulp.

Synthesis of two air- and moisture-stable copper (II)-N-heterocyclic carbene complexes

N-heterocyclic carbenes (NHCs) are a versatile class of ligands that have been widely applied in transition metal catalysis. However, NHCs are soft bases, and as such, complexes of NHCs with hard acids—such as many first-row transition metals—are typically sensitive to air and moisture, hence requiring multistep preparations. In this work, two examples of rare copper (II)-NHC complexes were prepared directly from 1,3-bis(pyridylmethyl)imidazolium chloride and 1,3-bis(2-pyridylmethyl)benzimidazolium chloride in protic conditions with no effort to exclude air or moisture. X-ray crystallographic analysis showed that both species display distorted square pyramidal geometry. A probe reaction demonstrated both complexes displayed poor catalytic activity for Chan–Evans–Lam coupling reactions.

The Synthesis and Properties of Ladder-Type π-Conjugated Compounds with Pyrrole and Phosphole Rings.

The phosphole ring is known as a useful building block for constructing π-conjugated organic materials. Here, we report ladder-type benzophospholo[3,2-b]indole (BPI) derivatives where the phosphole and the pyrrole rings are directly fused. Compounds 8a-8d with different aryl groups on the phosphorous center were successfully synthesized, and the solid-state structure of 8a was confirmed using X-ray crystallographic analysis. The BPIs exhibit relatively high fluorescence quantum yield (Φ 0.50-0.72) and demonstrate a larger Stokes shift compared with a series of benzophospholo[3,2-b]benzoheteroles. The benzophospholo[3,2-b]carbazole derivative 9, which possesses a benzene ring between the phosphole and the pyrrole rings of the BPI, was also synthesized, and its solid-state structure was confirmed using X-ray crystallographic analysis. Compound 9 was found to show a smaller Stokes shift compared with the BPI.

Divergent syntheses of (−)-carvone-derived dimers

A series of diterpene-type compounds were synthesized starting from commercially available (−)-carvone. The Michael reaction of (−)-carvone itself delivered four diastereomeric dimers divergently. Following in parallel transformations of reduction, condensation and reductive amination, the corresponding alcohol, oxime and amine were obtained respectively. Particularly, several cage-like structures were obtained via late-stage olefin functionalization. The absolute configurations of the aforementioned compounds were unambiguously determined by NMR spectral, X-ray crystallographic and conformational analysis. Finally, the in-vitro anti-cancer and anti-inflammatory activities of these dimers were tested preliminarily.

Synthesis, crystal structure and antitumor activity of trialkyltin (IV) 9,10-anthraquinone-2-carboxylate

Two new anthraquinone-organotin complexes [Ph3Sn(O2CC14H7O2)·MeOH]·MeOH (AQS01) and Cy3Sn(O2CC14H7O2) (AQS02) were synthesized and characterized by elemental analysis, IR, 1H NMR, 13C NMR, 119 Sn NMR, X-ray crystallography and thermo-gravimetric analysis. Incorporation of 9,10-anthraquinone with organotin successfully enhanced its anticancer activity. Interestingly, the anti-proliferative activity of AQS01 against CAL-27 cells in vitro was almost 10-fold that of mitoxantrone and 40-fold that of cisplatin. Flow cytometry showed that AQS01 could induce apoptosis and arrest cell cycle in S phase. UV–visible absorption spectrometry and molecular docking showed that AQS01 can be well embedded in the double helix of DNA. Moreover, AQS01 induced cell death by upregulating the expression level of the DNA damage protein γ-H2AX and activating the mitochondrial apoptotic signaling pathway (Bax/Bcl-2). Therefore, AQS01 can be used as a potential anticancer drug and has potential for further research.

A Conformationally Stable π-Expanded X-Type Double Helicene Comprising Dihydropyracylene Units with Multistage Redox Behavior.

A π-expanded X-type double [5]helicene comprising dihydropyracylene moieties was synthesized from commercially available acenaphthene. X-ray crystallographic analysis revealed the unique highly twisted structure of the compound resulting in the occurrence of two enantiomers which were separated by chiral HPLC, owing to their high conformational stability. The compound shows strongly bathochromically shifted UV/vis absorption and emission bands with small Stokes shift and considerable photoluminescence quantum yield and circular polarized luminescence response. The electrochemical studies revealed five facilitated reversible redox events, including three reductions and two oxidations, thus qualifying the compound as chiral multistage redox amphoter. The experimental findings are in line with the computational studies based on density functional theory pointing towards increased spatial extension of the frontier molecular orbitals over the polycyclic framework and a considerably narrowed HOMO-LUMO gap.

Dual-Ligand Strategy for the Design and Construction of a Cd-Zn Heterometallic Metal-Organic Framework by One-Pot Synthesis as a Heterogeneous Catalyst for the Epoxidation Reaction of Olefins.

The use of metal-organic frameworks (MOFs) as catalysts is reported in various industrial applications. In contrast to monometallic MOFs, heterometallic MOFs with mixed organic ligands showed enhanced catalytic properties. The catalytic properties of heterometallic MOFs can be enhanced by generating defects and the synergistic effect between the two heterometals at secondary building units. By using a solvothermal technique, a Cd-Zn heterometallic MOF with a new morphology, [Cd2Zn(DPTTZ)0.5(OBA)3(H2O)(HCOOH)] (IUST-4) [DPTTZ = 2,5-di(4-pyridyl)thiazolo[5,4-d]thiazole, OBA = 4,4'-oxybis(benzoic acid)], was synthesized via a mixed-ligand strategy and characterized by single-crystal and powder X-ray diffraction, Fourier transform infrared spectroscopy, elemental analysis, and thermogravimetric analysis. X-ray crystallographic analysis showed that IUST-4 is a neutral 3D metal-organic framework crystallized in the monoclinic system with space group C2/c. In this study, the catalytic properties of IUST-4 for the epoxidation of cyclooctene were investigated. IUST-4 was selected as the optimal catalyst for epoxy product production due to its high selectivity and yield. Moreover, the catalytic performance of IUST-4 was maintained despite five recycling cycles without significant degradation. The epoxidation of cyclooctene with IUST-4 has several advantages, including good selectivity, easy recovery, and short-time reaction.