Bioactivity-driven fungal metabologenomics identifies antiproliferative stemphone analogs and their biosynthetic gene cluster.

INTRODUCTION: Fungi biosynthesize chemically diverse secondary metabolites with a wide range of biological activities. Natural product scientists have increasingly turned towards bioinformatics approaches, combining metabolomics and genomics to target secondary metabolites and their biosynthetic machinery. We recently applied an integrated metabologenomics workflow to 110 fungi and identified more than 230 high-confidence linkages between metabolites and their biosynthetic pathways. OBJECTIVES: To prioritize the discovery of bioactive natural products and their biosynthetic pathways from these hundreds of high-confidence linkages, we developed a bioactivity-driven metabologenomics workflow combining quantitative chemical information, antiproliferative bioactivity data, and genome sequences. METHODS: The 110 fungi from our metabologenomics study were tested against multiple cancer cell lines to identify which strains produced antiproliferative natural products. Three strains were selected for further study, fractionated using flash chromatography, and subjected to an additional round of bioactivity testing and mass spectral analysis. Data were overlaid using biochemometrics analysis to predict active constituents early in the fractionation process following which their biosynthetic pathways were identified using metabologenomics. RESULTS: We isolated three new-to-nature stemphone analogs, 19-acetylstemphones G (1), B (2) and E (3), that demonstrated antiproliferative activity ranging from 3 to 5 µM against human melanoma (MDA-MB-435) and ovarian cancer (OVACR3) cells. We proposed a rational biosynthetic pathway for these compounds, highlighting the potential of using bioactivity as a filter for the analysis of integrated-Omics datasets. CONCLUSIONS: This work demonstrates how the incorporation of biochemometrics as a third dimension into the metabologenomics workflow can identify bioactive metabolites and link them to their biosynthetic machinery.

Wheldone Revisited: Structure Revision Via DFT-GIAO Chemical Shift Calculations, 1,1-HD-ADEQUATE NMR Spectroscopy, and X-ray Crystallography Studies.

Wheldone is a fungal metabolite isolated from the coculture of Aspergillus fischeri and Xylaria flabelliformis, displaying cytotoxic activity against breast, melanoma, and ovarian cancer cell lines. Initially, its structure was characterized as an unusual 5-methyl-bicyclo[5.4.0]undeca-3,5-diene scaffold with a 2-hydroxy-1-propanone side chain and a 3-(2-(1-hydroxyethyl)-2-methyl-2,5-dihydrofuran-3-yl)acrylic acid moiety. Upon further examination, minor inconsistencies in the data suggested the need for the structure to be revisited. Thus, the structure of wheldone has been revised using an orthogonal experimental-computational approach, which combines 1,1-HD-ADEQUATE NMR experiments, DFT-GIAO chemical shift calculations, and single-crystal X-ray diffraction (SCXRD) analysis of a semisynthetic p-bromobenzylamide derivative, formed via a Steglich-type reaction. The summation of these data now permits the unequivocal assignment of both the structure and absolute configuration of the natural product.

Soft Hydrogen-Bonded Organic Frameworks Constructed Using a Flexible Organic Cage Hinge.

Soft porous crystals combine flexibility and porosity, allowing them to respond structurally to external physical and chemical environments. However, striking the right balance between flexibility and sufficient rigidity for porosity is challenging, particularly for molecular crystals formed by using weak intermolecular interactions. Here, we report a flexible oxygen-bridged prismatic organic cage molecule, Cage-6-COOH, which has three pillars that exhibit "hinge-like" rotational motion in the solid state. Cage-6-COOH can form a range of hydrogen-bonded organic frameworks (HOFs) where the "hinge" can accommodate a remarkable 67° dihedral angle range between neighboring units. This stems both from flexibility in the noncovalent hydrogen-bonding motifs in the HOFs and the molecular flexibility in the oxygen-linked cage hinge itself. The range of structures for Cage-6-COOH includes two topologically complex interpenetrated HOFs, CageHOF-2α and CageHOF-2ß. CageHOF-2α is nonporous, while CageHOF-2ß has permanent porosity and a surface area of 458 m2 g-1. The flexibility of Cage-6-COOH allows this molecule to rapidly transform from a low-crystallinity solid into the two crystalline interpenetrated HOFs, CageHOF-2α and CageHOF-2ß, under mild conditions simply by using acetonitrile or ethanol vapor, respectively. This self-healing behavior was selective, with the CageHOF-2ß structure exhibiting structural memory behavior.

Reversible Pressure-Magnetic Modulation in a Tetrathiafulvalene-Based Dyad Piezochromic Dysprosium Single-Molecule Magnet.

The extreme sensitivity of trivalent lanthanide ions to crystal field variations led to the emergence of single-molecule magnetic switching under various stimuli. The use of pressure as an external stimulus instead of classic light irradiation, oxidation or any chemical reactions allows a fine tuning of the magnetic modulation. Here the well-known pure isotopically enriched [162 Dy(tta)3 (L)]⋅C6 H14 (162 Dy) Single-Molecule Magnet (SMM) (tta- =2-2-thenoyltrifluoroacetonate and L=4,5-bis(propylthio)-tetrathiafulvalene-2-(2-pyridyl)benzimidazole-methyl-2-pyridine) was experimentally investigated by single-crystal diffraction and squid magnetometry under high applied pressures. Both reversible piezochromic properties and pressure modulation of the slow magnetic relaxation behavior were demonstrated and supported by ab initio calculations. The magnetic study of the diluted sample [162 Dy0.05 Y0.95 (tta)3 (L)]⋅C6 H14 (162 Dy@Y) indicated that variations in the electronic structure have mainly intermolecular origin with weak intramolecular contribution. Quantitative magnetic interpretation concludes to a deterioration of the Orbach process for the benefit of both Raman and QTM mechanisms under applied pressure.

Differentiable Formation of Chiroptical Lanthanide Heterometallic Lnn Ln'4-n (L6 ) (n=0-4) Tetrahedra with C2 -Symmetrical Bis(tridentate) Ligands.

Construction of lanthanide heterometallic complex is important for engineering multifunction molecular containers. However, it remains a challenge because of the similar ionic radii of lanthanides. Herein we attempt to prepare chiral lanthanide heterometallic tetrahedra. Upon crystallization with a mixture of [Eu2 L3 ] and [Ln2 L3 ] (Ln=Gd, Tb and Dy) helicates, a mixture of heterometallic Eun Ln'4-n (L6 ) (n=0-4) tetrahedra was prepared. Selective formation of heterometallic tetrahedron was observed as MS deconvolution results deviated from statistical results. The formation of heterometallic tetrahedron was found to be sensitive to ionic radii as well as the ratio of the two helicates used in the crystallization.

Structural Diversity of Perylenequinones Is Driven by Their Redox Behavior.

Hypocrellins and hypomycins are two subclasses of fungal perylenequinones with unique structural, biological, and photochemical properties. With the growing interest in these naturally occurring photosensitizers, more studies were warranted to better understand the structural relationships between these two subclasses of perylenequinones. In this study, the long-postulated biosynthetic precursor (7) of class B fungal perylenequinones was isolated and characterized from a Shiraia-like sp. (strain MSX60519). Furthermore, the electrochemical and chemical redox behaviors of hypocrellins and hypomycins were investigated under aerobic and anaerobic conditions. These studies served to define the structural relationship within hypocrellins (1-3), which was further supported by X-ray crystallography, and between hypocrellins and hypomycins (4-6). Chemical reductions of hypocrellins under anaerobic conditions identified the origin of hypomycin A (4), hypomycin C (5), and hypomycin E (6), which in turn served to confirm 4 and revise the absolute configurations of 5 and 6. Hypocrellins were shown to undergo reversible reduction and reoxidation under aerobic conditions, while in an anaerobic environment and longer time scale, the fully reduced form can, to some extent, undergo an intramolecular ring closing metathesis. This may impart a means of reductive pathway for self-protection against these phototoxins and explain the chemical diversity observed in the fungal metabolites.

The Role of the Fused Ring in Bicyclic Triazolium Organocatalysts: Kinetic, X-ray, and DFT Insights.

Bicyclic triazolium scaffolds are widely employed in N-heterocyclic carbene (NHC) organocatalysis. While the incorporation of a fused ring was initially for synthetic utility in accessing chiral, modular triazolyl scaffolds, recent results highlight the potential for impact upon reaction outcome with the underpinning origins unclear. The common first step to all triazolium-catalyzed transformations is C(3)-H deprotonation to form the triazolylidene NHC. Herein, we report an analysis of the impact of size of the fused (5-, 6-, and 7-membered, n = 1, 2, and 3, respectively) ring on the C(3) proton transfer reactions of a series of bicyclic triazolium salts. Rate constants for the deuteroxide-catalyzed C(3)-H/D-exchange of triazolium salts, kDO, were significantly influenced by the size of the adjacent fused ring, with the kinetic acidity trend, or protofugalities, following the order kDO (n = 1) > kDO (n = 2) ≈ kDO (n = 3). Detailed analyses of X-ray diffraction (XRD) data for 20 triazolium salts (including 16 new structures) and of computational data for the corresponding triazolylidene NHCs provide insight on structural effects of alteration of fused ring size. In particular, changes in internal triazolyl NCN angle and positioning of the most proximal CH2 with variation in fused ring size are proposed to influence the experimental protofugality order.

Spontaneous Decomposition of an Extraordinarily Twisted and Trans-Bent Fully-Phosphanyl-Substituted Digermene to an Unusual GeI Cluster.

Ditetrelenes R2 E=ER2 (E=Si, Ge, Sn, Pb) substituted by multiple N/P/O/S-donor groups are extremely rare due to their propensity to disaggregate into their tetrylene monomers R2 E. We report the synthesis of the first fully phosphanyl-substituted digermene {(Mes)2 P}2 Ge=Ge{P(Mes)2 }2 (3, Mes=2,4,6-Me3 C6 H2 ), which adopts a highly unusual structure in the solid state, that is both strongly trans-bent and highly twisted. Variable-temperature 31 P{1 H} NMR spectroscopy suggests that 3 persists in solution, but is subject to a dynamic equilibrium between two conformations, which have different geometries about the Ge=Ge bond (twisted/non-twisted) due to a difference in the nature of their π-stacking interactions. Compound 3 undergoes unprecedented, spontaneous decomposition in solution to give a unique GeI cluster {(Mes)2 P}4 Ge4 ⋅5 CyMe (7).

Minimizing Polymorphic Risk through Cooperative Computational and Experimental Exploration.

We combine state-of-the-art computational crystal structure prediction (CSP) techniques with a wide range of experimental crystallization methods to understand and explore crystal structure in pharmaceuticals and minimize the risk of unanticipated late-appearing polymorphs. Initially, we demonstrate the power of CSP to rationalize the difficulty in obtaining polymorphs of the well-known pharmaceutical isoniazid and show that CSP provides the structure of the recently obtained, but unsolved, Form III of this drug despite there being only a single resolved form for almost 70 years. More dramatically, our blind CSP study predicts a significant risk of polymorphism for the related iproniazid. Employing a wide variety of experimental techniques, including high-pressure experiments, we experimentally obtained the first three known nonsolvated crystal forms of iproniazid, all of which were successfully predicted in the CSP procedure. We demonstrate the power of CSP methods and free energy calculations to rationalize the observed elusiveness of the third form of iproniazid, the success of high-pressure experiments in obtaining it, and the ability of our synergistic computational-experimental approach to "de-risk" solid form landscapes.

Trigonal to Pentagonal Bipyramidal Coordination Switching in a Co(II) Single-Ion Magnet.

In molecular magnetism and single-ion magnets in particular, the observation of slow relaxation of the magnetization is intimately linked to the coordination environment of the metal center. Such systems typically have blocking temperatures well below that of liquid nitrogen, and therefore detailed magnetic characterization is usually carried out at very low temperatures. Despite this, there has been little advantage taken of ultralow temperature single-crystal X-ray diffraction techniques that could provide a full understanding of the crystal structure in the same temperature regime where slow magnetic relaxation occurs. Here, we present a systematic variable temperature single crystal X-ray diffraction study of [CoII(NO3)3(H2O)(HDABCO)] (1) {DABCO = 1,4-diazabicyclo[2.2.2]octane} conducted between 295 to 4 K. A reversible and robust disorder-to-order, single-crystal to single-crystal phase transition was identified, which accompanied a switching of the coordination geometry around the central Co(II) from 5- to 7-coordinate below 140 K. The magnetic properties were investigated, revealing slow relaxation of the magnetization arising from a large easy-plane magnetic anisotropy (+D) in the Co(II) pentagonal bipyramidal environment observed at low temperatures. This study highlights the importance of conducting thorough low temperature crystallographic studies, particularly where magnetic characterization is carried out at such low temperatures.

Structural and Synthetic Insights into Pyridine Homocouplings Mediated by a ß-Diketiminato Magnesium Amide Complex.

The reaction of [(Dipp Nacnac)Mg(TMP)] (1) with 4-subtituted pyridines proceeds via sequential regioselective metallation and 1,2-addition to furnish a range of symmetric 4,4'-R2 -2,2'-bipyridines in good yield, representing a new entry into bipyridine synthesis. Interestingly, the reaction of 1 with 2-OMe-pyridine led to formation of asymmetric bipyridine 6, resulting from the C6-magnesiation of the heterocycle followed by a C-C coupling step by addition to the C2 position of a second, non-metallated molecule, and subsequent elimination of [Dipp NacnacMgOMe]2 (7). Synthesis combined with spectroscopic and structural analysis help rationalise the underlying processes resulting in the observed reactivity, and elucidate the key role that the sterically encumbered ß-diketiminate ligand plays in determining regioselectivity.

Variation of M···H-C Interactions in Square-Planar Complexes of Nickel(II), Palladium(II), and Platinum(II) Probed by Luminescence Spectroscopy and X-ray Diffraction at Variable Pressure.

Luminescence spectra of isoelectronic square-planar d8 complexes with 3d, 4d, and 5d metal centers show d-d luminescence with an energetic order different from that of the spectrochemical series, indicating that additional structural effects, such as different ligand-metal-ligand angles, are important factors. Variable-pressure luminescence spectra of square-planar nickel(II), palladium(II), and platinum(II) complexes with dimethyldithiocarbamate ({CH3}2DTC) ligands and their deuterated analogues show unexpected variations of the shifts of their maxima. High-resolution crystal structures and crystal structures at variable pressure for [Pt{(CH3)2DTC}2] indicate that intermolecular M···H-C interactions are at the origin of these different shifts.

Utilising Sodium-Mediated Ferration for Regioselective Functionalisation of Fluoroarenes via C-H and C-F Bond Activations.

Pairing iron bis(amide) Fe(HMDS)2 with Na(HMDS) to form new sodium ferrate base [(dioxane)0.5 ⋅NaFe(HMDS)3 ] (1) enables regioselective mono and di-ferration (via direct Fe-H exchange) of a wide range of fluoroaromatic substrates under mild reaction conditions. Trapping of several ferrated intermediates has provided key insight into how synchronised Na/Fe cooperation operates in these transformations. Furthermore, using excess 1 at 80 °C switches on a remarkable cascade process inducing the collective twofold C-H/threefold C-F bond activations, where each C-H bond is transformed to a C-Fe bond whereas each C-F bond is transformed into a C-N bond.

Remote Substituent Effects on the Structures and Stabilities of P═E π-Stabilized Diphosphatetrylenes (R2P)2E (E = Ge, Sn).

A rare P-E π interaction between the lone pair of a planar P center and the vacant p orbital at the Ge or Sn center provides efficient stabilization for P-substituted tetrylenes (R2P)2E (E = Ge, Sn) and enables isolation of the first example of a compound with a crystallographically authenticated P═Sn bond. Subtle changes in the electronic properties of the bulky aryl substituents in these compounds change the preference for planar versus pyramidal P centers in the solid state; however, variable-temperature NMR spectroscopy indicates that in solution these species are subject to a dynamic equilibrium, which interconverts the planar and pyramidal P centers. Consistent with this, density functional theory studies suggest that there is only a small energy difference between the planar and pyramidal forms of these compounds and reveal a small singlet-triplet energy separation, suggesting potentially interesting reactivities.

Two-Dimensional Frameworks Based on Ag(I)-N Bond Formation: Single Crystal to Single Molecular Sheet Transformation.

A series of new two-dimensional coordination framework materials, based on Ag(I)-N bond formation, has been synthesized and structurally characterized by single crystal methods. Reactions between the poly-monodentate bridging ligand N,N'-((1r,4r)-cyclohexane-1,4-diyl)bis(1-(pyridin-3-yl)methanimine), L1, and silver salts yield compounds {[Ag(L1)(MeCN)](CF3SO3-)}n, 1, {[Ag(L1)(PF2O2-)]·H2O}n, 2, and {Ag2(L1)(tosylate)2}n, 3. The frameworks of these materials exhibit two distinct net topologies: 36.46.53 (1 and 2) and 44.62 (3). In all cases, L1 ligands are found to be fully saturated, in terms of metal ion binding, with both sets of pyridyl and imino N atoms involved, though in 1 and 2, crystallographically independent L1 moieties also display pyridyl-only binding. Either solvent (1) or the anion (2 and 3) acts as a terminal ligand to support interlayer interactions in the solid state. For 2 and 3 the molecular sheet orientation lies in the plane of the largest crystal face, indicating that crystal growth is preferentially driven by coordinate bond formation. Despite the relatively labile nature, typical of such Ag(I)-N bonds, solvent-based exfoliation of crystals of 3 was shown to provide dispersions of large, µm2, flakes which readily deposit on oxide surfaces as single-molecule sheets, as revealed by atomic force microscopy.

Structure of organic solids at low temperature and high pressure.

This tutorial review looks at structural and supramolecular chemistry of molecular solids under extreme conditions, and introduces the instrumentation and facilities that enable single crystal diffraction studies on molecular crystals at both high pressure and low temperature. The equipment used for crystallography under extreme conditions is explored, particularly pressure cells such as the diamond anvil cell, and their mechanism of action, as well as the cryogenic apparatus which allows materials to be cooled to significantly low temperatures. The review also covers recent advances in the structural chemistry of molecular solids under extreme conditions with an emphasis on the use of single crystal crystallography in high pressure and low temperature environments to probe polymorphism and supramolecular interactions.

Locating Gases in Porous Materials: Cryogenic Loading of Fuel-Related Gases Into a Sc-based Metal-Organic Framework under Extreme Pressures.

An alternative approach to loading metal organic frameworks with gas molecules at high (kbar) pressures is reported. The technique, which uses liquefied gases as pressure transmitting media within a diamond anvil cell along with a single-crystal of a porous metal-organic framework, is demonstrated to have considerable advantages over other gas-loading methods when investigating host-guest interactions. Specifically, loading the metal-organic framework Sc2BDC3 with liquefied CO2 at 2 kbar reveals the presence of three adsorption sites, one previously unreported, and resolves previous inconsistencies between structural data and adsorption isotherms. A further study with supercritical CH4 at 3-25 kbar demonstrates hyperfilling of the Sc2 BDC3 and two high-pressure displacive and reversible phase transitions are induced as the filled MOF adapts to reduce the volume of the system.

A magnetostructural investigation of an abrupt spin transition for 1-phenyl-3-trifluoromethyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl.

1-Phenyl-3-trifluoromethyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl is the first example of a hydrazyl radical that shows a reversible sharp spin transition fully completed within 5(1) K. The nominally first-order transition takes place at ca. 58(2) K and proceeds via subtle changes of intra- and interstack interactions between two similar structural phases. The low-temperature phase (5-60 K) is diamagnetic and has a singlet ground state (2Jexp = -166.8 cm(-1), gsolid = 2.0042, ρ = 0.2%) stemming from a multicenter two-electron interaction. The high-temperature phase (60-300 K) is paramagnetic as a result of noninteracting S = 1/2 spins arising from weakly bound dimers.

A State of Independents: Rationalizing the High Z' Crystal Structures of Shikimate Esters.

Z' is a parameter used to denote the number of symmetry-independent molecules in the asymmetric unit of a crystal structure. High Z' (>1) crystal structures are relatively uncommon and are thought to arise through competition between intermolecular interactions of similar strength. As such high Z' crystal structures are challenging to predict and new examples are valuable in improving understanding in the field. Herein, we report the X-ray crystal structures of a series of shikimate esters, the asymmetric units of which exhibit high Z' values. Of special interest is the crystal structure of methyl shikimate, the asymmetric unit of which comprises 12 independent molecules; Z' = 12. This uncommonly large Z' value arises through a combination of factors, including the intrinsic homochirality of the molecule, the conformational inflexibility of the cyclohexene ring, the presence of multiple hydrogen bonding motifs, and both the cis- and trans-conformers of the ester moiety. Comparison of the X-ray crystal structures of shikimic acid, methyl shikimate, ethyl shikimate, and iso-propyl shikimate suggests that instances of high Z' in this series correlate with specific hydrogen bonding motifs influenced by the steric bulk of the ester. The results of this study provide important insights into factors that influence the formation of organic crystal structures where the value of Z' is greater than 1.

High-throughput nanoscale crystallization of dihydropyridine active pharmaceutical ingredients.

Single-crystal X-ray diffraction analysis of small molecule active pharmaceutical ingredients is a key technique in the confirmation of molecular connectivity, including absolute stereochemistry, as well as the solid-state form. However, accessing single crystals suitable for X-ray diffraction analysis of an active pharmaceutical ingredient can be experimentally laborious, especially considering the potential for multiple solid-state forms (solvates, hydrates and polymorphs). In recent years, methods for the exploration of experimental crystallization space of small molecules have undergone a `step-change', resulting in new high-throughput techniques becoming available. Here, the application of high-throughput encapsulated nanodroplet crystallization to a series of six dihydropyridines, calcium channel blockers used in the treatment of hypertension related diseases, is described. This approach allowed 288 individual crystallization experiments to be performed in parallel on each molecule, resulting in rapid access to crystals and subsequent crystal structures for all six dihydropyridines, as well as revealing a new solvate polymorph of nifedipine (1,4-dioxane solvate) and the first known solvate of nimodipine (DMSO solvate). This work further demonstrates the power of modern high-throughput crystallization methods in the exploration of the solid-state landscape of active pharmaceutical ingredients to facilitate crystal form discovery and structural analysis by single-crystal X-ray diffraction.