Differentiation of volatile aromatic isomers and structural elucidation of volatile compounds in essential oils by combination of HPLC separation and crystalline sponge method

Atomic-resolution structure analysis inside an adaptable porous framework

We introduce a versatile metal-organic framework (MOF) for encapsulation and immobilization of various guests using highly ordered internal water network. The unique water-mediated entrapment mechanism is applied for structural elucidation of 14 bioactive compounds, including 3 natural product intermediates whose 3D structures are clarified. The single-crystal X-ray diffraction analysis reveals that incorporated guests are surrounded by hydrogen-bonded water networks inside the pores, which uniquely adapt to each molecule, providing clearly defined crystallographic sites. The calculations of host-solvent-guest structures show that the guests are primarily interacting with the MOF through weak dispersion forces. In contrast, the coordination and hydrogen bonds contribute less to the total stabilization energy, however, they provide highly directional point interactions, which help align the guests inside the pore.

Recent advances in analytical strategies for coffee volatile studies: Opportunities and challenges

Coffee has attracted significant research interest owing to its complex volatile composition and aroma, which imparts a pleasant sensorial experience that remains challenging to analyse and interpret. This review summarises analytical challenges associated with coffee's volatile and matrix complexity, and recent developments in instrumental techniques to resolve them. The benefits of state-of-the-art analytical techniques applied to coffee volatile analysis from experimental design to sample preparation, separation, detection, and data analysis are evaluated. Complementary method selection coupled with progressive experimental design and data analysis are vital to unravel the increasing comprehensiveness of coffee volatile datasets. Considering this, analytical workflows for conventional, targeted, and untargeted coffee volatile analyses are thus proposed considering the trends towards sorptive extraction, multidimensional gas chromatography, and high-resolution mass spectrometry. In conclusion, no single analytical method addresses coffee's complexity in its entirely, and volatile analysis must be tailored to the key objectives and concerns of the analyst.

Conjugation of triphenylantimony(V) with carvacrol against human breast cancer cells

The organoantimony derivative of formula trans-O,O-[Ph₃Sb^V(Carv)₂] (TPAC) (CarvH = carvacrol) is obtained by the oxidation of triphenylstibine (Ph₃Sb^III) with hydrogen peroxide in the presence of carvacrol (CarvH). Physical methods such as X-ray Fluorescence (XRF) spectroscopy, single crystal and powder X-ray diffraction analysis (XRD and PXRD), Attenuated Total Reflection Fourier Transform Infra-red (ATR-FTIR) spectroscopy, Thermogravimetric Differential Thermal Analysis (TG-DTA) and Differential Scanning Calorimetry (DTG/DSC), confirm the retention of the formula of TPAC throughout the sample mass in solid state, while UV-Vis spectroscopy in the solution. TPAC is the first example of carvacrol (the main ingredient of oregano) covalently bonded to any metal ion. Only the trans-O,O-[Ph₃Sb(Carv)₂] isomer was isolated suggesting stereo-selectivity of the preparation route. TPAC inhibits in vitro both human breast adenocarcinoma cell lines: MCF-7 (positive to hormones receptor (HR +)), MDA-MB-231 (negative to hormones receptor (HR-)) stronger than normal human fetal lung fibroblast cells (MRC-5). The MCF-7 cells morphology, DNA fragmentation, Acridine Orange/Ethidium Bromide (AO/EB) Staining, cell cycle arrest and mitochondrial membrane permeabilization tests suggest an apoptotic pathway for cell death, especially, through the mitochondrion damage. The binding type of TPAC toward the calf thymus CT-DNA was initially deduced ex vivo from the differentiation of the DNA solution viscosity. Fluorescence spectroscopy confirms the interaction mode suggested. Spectroscopic evidence (FTIR, UV-Vis) suggest that glutathione (GSH) (a tripeptide over-expressed in tumor cells) induces conversion of non-active pentavalent antimony, which is contained in TPAC, to active trivalent one, providing a new strategy for the development of targeted chemotherapeutics.

Crystalline sponge X-ray analysis coupled with supercritical fluid chromatography: a novel analytical platform for the rapid separation, isolation, and characterization of analytes

Crystalline sponge (CS) based X-ray diffraction (XRD) analysis allows for the observation of the structure of an analyte, including its absolute configuration. Herein we report a powerful analytical platform for the separation, isolation, and structural elucidation of a target analyte in a seamless way by coupling supercritical fluid chromatography (SFC) with CS-based XRD analysis (SFC-CSXRD). The efficacy of this methodology is demonstrated by the rapid characterization of regio- and stereoisomers using three types of CSs with differing tolerances to the solvents used in SFC and guest-soaking.

Crystalline Sponge Method: X-ray Structure Analysis of Small Molecules by Post-Orientation within Porous Crystals-Principle and Proof-of-Concept Studies

This Review discusses, along with the historical background, the principles as well as proof-of-concept studies of the crystalline sponge (CS) method, a new single-crystal X-ray diffraction (SCXRD) method for the analysis of the structures of small molecules without sample crystallization. The method uses single-crystalline porous coordination networks (crystalline sponges) that can absorb small guest molecules within their pores. The absorbed guest molecules are ordered in the pores through molecular recognition and become observable by conventional SCXRD analysis. The complex {[(ZnI₂ )₃ (tpt)₂ ]⋅x(solvent)}_n (tpt=tris(4-pyridyl)-1,3,5-triazine) was first proposed as a crystalline sponge and has been most generally used. Crystalline sponges developed later are also discussed here. The principle of the CS method can be described as "post-crystallization" of the absorbed guest, whose ordering is templated by the pre-latticed cavities. The method has been widely applied to synthetic chemistry as well as natural product studies, for which proof-of-concept examples will be shown here.

Applying the Crystalline Sponge Method to Agrochemicals: Obtaining X-ray Structures of the Fungicide Metalaxyl-M and Herbicide S-Metolachlor

The crystalline sponge method is a technique that provides the ability to elucidate the absolute structure of noncrystalline or hard to crystallize compounds through single-crystal X-ray diffraction by removing the need to obtain crystals of the target compound. In this study the crystalline sponges {[(ZnX₂)₃(2,4,6-tris(4-pyridyl)-1,3,5-trazine)₂].x(solvent)} _n (X = I, Br) were used to obtain X-ray structures of the agrochemical active ingredients metalaxyl-M and S-metolachlor. The effect of the temperature used during guest uptake and the influence of changing the host framework ZnX₂ nodes on guest encapsulation were investigated. Additionally, three compounds containing chemical fragments similar to those of metalaxyl-M and S-metolachlor (phenylacetaldehyde, N-ethyl-o-toluidine, and methyl phenylacetate) were also encapsulated. This allowed for the effect of guest size on the position that guests occupy within the host frameworks to be examined. The disorder experienced by the guest compounds was documented, and an analysis of the intermolecular host-guest interactions (CH···π and π ···π) used for guest ordering within the host frameworks was also undertaken in this study.

Application of Crystalline Matrices for the Structural Determination of Organic Molecules

While single-crystal X-ray diffraction (SC-XRD) is one of the most powerful structural determination techniques for organic molecules, the requirement of obtaining a suitable crystal for analysis limits its applicability, particularly for liquids and amorphous solids. The emergent use of preformed porous crystalline matrices that can absorb organic compounds and stabilize them via host-guest interactions for observation via SC-XRD offers a way to overcome this hindrance. A topical and current discussion of SC-XRD in organic chemistry and the use of preformed matrices for the in crystallo analysis of organic compounds, with a particular focus on the absolute structure determination of chiral molecules, is presented. Preformed crystalline matrices that are covered include metal-organic frameworks (MOFs) as used in the crystalline sponge method, metal-organic polyhedra (MOPs, coordination cages), porous organic materials (POMs)/porous organic molecular crystals (POMCs), and biological scaffolds. An outlook and perspective on the current technology and on its future directions is provided.

Stepwise Evolution of Molecular Nanoaggregates Inside the Pores of a Highly Flexible Metal-Organic Framework

The crystalline sponge method (CSM) is primarily used for structural determination by single-crystal X-ray diffraction of a single analyte encapsulated inside a porous MOF. As the host-guest systems often show severe disorder, reliable crystallographic determination is demanding; thus the dynamics of the guest entering and the formation of nanoconfined molecular aggregates has not been in the spotlight. Now, the concept is investigated of the CSM for monitoring the structural evolution of nanoconfined supramolecular aggregates of eugenol guests with displacement of DMF inside the cavities of the flexible MOF, PUM168. The interpretation of the electron density provides a series of unique detailed snapshots depicting the supramolecular guest aggregation, thus showing the tight interplay between the host flexible skeleton and the molecular guests through the DMF-to-eugenol exchange process.

Crystallography of encapsulated molecules

The crystallography of supramolecular host-guest complexes is reviewed and discussed as a part of small molecule crystallography. In these complexes, the host binds the guests through weak supramolecular interactions, such as hydrogen and halogen bonding, cation-π, anion-π, C-H-π, π-π, C-H-anion interactions and the hydrophobic effect. As the guest often shows severe disorder, large thermal motion and low occupancies, the reliable crystallographic determination of the guest can be very demanding. The analysis of host-guest interactions using tools such as Hirshfeld and cavity volume surface analysis will help to look closely at the most important host-guest interactions. The jewel in the crown of utilizing host-guest interactions in the solid-state is the recently developed Crystalline Sponge Method (CSM) by Makoto Fujita. This method, when successful, gives an accurate and unambiguous 3-D structure of the structurally unknown guest molecule from only micro- or nanogram amounts of the guest molecule. In the case of an optically pure enantiomer, its absolute configuration can be determined.

Confinement effects of a crystalline sponge on ferrocene and ferrocene carboxaldehyde

The pivotal role of ππ interactions in the inclusion behaviour of a series of organometallic sandwich compounds is studied through single-crystal X-ray diffraction. The confinement effects of a crystalline sponge host are investigated where, notably, we observe an enhanced rotation of the ligand ring once encapsulated by the nanoporous framework, as evidenced by SSNMR experiments.