Structure-Reactivity Studies of 2-Sulfonylpyrimidines Allow Selective Protein Arylation.

Protein arylation has attracted much attention for developing new classes of bioconjugates with improved properties. Here, we have evaluated 2-sulfonylpyrimidines as covalent warheads for the mild, chemoselective, and metal free cysteine S-arylation. 2-Sulfonylpyrimidines react rapidly with cysteine, resulting in stable S-heteroarylated adducts at neutral pH. Fine tuning the heterocyclic core and exocyclic leaving group allowed predictable SNAr reactivity in vitro, covering >9 orders of magnitude. Finally, we achieved fast chemo- and regiospecific arylation of a mutant p53 protein and confirmed arylation sites by protein X-ray crystallography. Hence, we report the first example of a protein site specifically S-arylated with iodo-aromatic motifs. Overall, this study provides the most comprehensive structure-reactivity relationship to date on heteroaryl sulfones and highlights 2-sulfonylpyrimidine as a synthetically tractable and protein compatible covalent motif for targeting reactive cysteines, expanding the arsenal of tunable warheads for modern covalent ligand discovery.

Double Click: Unexpected 1:2 Stoichiometry in a Norbornene-Tetrazine Reaction.

We report a new reactivity for the inverse electron demand Diels-Alder (iEDDA) reaction between norbornene and tetrazine. Instead of simple 1:1 condensation between norbornene- and tetrazine-conjugated biomolecules, we observed that dimeric products were preferentially formed. As such, an olefinic intermediate formed after the addition of the first tetrazine unit to norbornene rapidly undergoes a consecutive cycloaddition reaction with a second tetrazine unit to result in a conjugate with a 1:2 stoichiometric ratio. This unexpected dimer formation was consistently observed in the reactions of both small-molecule norbornenes and tetrazines, as well as oligonucleotide conjugates. When norbornene was replaced with bicyclononyne to bypass the formation of this olefinic reaction intermediate, the reactions resulted exclusively in rapid formation of the expected 1:1 stoichiometric conjugates.

A combined inelastic neutron scattering and simulation study of the 3He@C60 endofullerene.

The 3He@C60 endofullerene consists of a single 3He atom entrapped inside a C60 fullerene cage. The confining potential, arising from the non-covalent interaction between the enclosed He atom and the C atoms of the cage, is investigated by inelastic neutron scattering. These measurements allow us to obtain information in both energy (ω) and momentum (Q) transfers in the form of the dynamical structure factor S (Q, ω). Simulations of the S (Q, ω) maps are performed for a spherical anharmonic oscillator model. Good agreement between the experimental and simulated data sets is achieved.

Correction: Terahertz spectroscopy of the helium endofullerene He@C60.

Correction for 'Terahertz spectroscopy of the helium endofullerene He@C60' by Tanzeeha Jafari et al., Phys. Chem. Chem. Phys., 2022, 24, 9943-9952, https://doi.org/10.1039/D2CP00515H.

Ne, Ar, and Kr oscillators in the molecular cavity of fullerene C60.

We used THz (terahertz) and INS (inelastic neutron scattering) spectroscopies to study the interaction between an endohedral noble gas atom and the C60 molecular cage. The THz absorption spectra of powdered A@C60 samples (A = Ar, Ne, Kr) were measured in the energy range from 0.6 to 75 meV for a series of temperatures between 5 and 300 K. The INS measurements were carried out at liquid helium temperature in the energy transfer range from 0.78 to 54.6 meV. The THz spectra are dominated by one line, between 7 and 12 meV, at low temperatures for three noble gas atoms studied. The line shifts to higher energy and broadens as the temperature is increased. Using a spherical oscillator model, with a temperature-independent parameterized potential function and an atom-displacement-induced dipole moment, we show that the change of the THz spectrum shape with temperature is caused by the anharmonicity of the potential function. We find good agreement between experimentally determined potential energy functions and functions calculated with Lennard-Jones additive pair-wise potentials with parameters taken from the work of Pang and Brisse, J. Chem. Phys. 97, 8562 (1993).

Terahertz spectroscopy of the helium endofullerene He@C60.

We studied the quantized translational motion of single He atoms encapsulated in molecular cages by terahertz absorption. The temperature dependence of the THz absorption spectra of 3He@C60 and 4He@C60 crystal powder samples was measured between 5 and 220 K. At 5 K there is an absorption line at 96.8 cm-1 (2.90 THz) in 3He@C60 and at 81.4 cm (2.44 THz) in 4He@C60, while additional absorption lines appear at higher temperature. An anharmonic spherical oscillator model with a displacement-induced dipole moment was used to model the absorption spectra. Potential energy terms with powers of two, four and six and induced dipole moment terms with powers one and three in the helium atom displacement from the fullerene cage center were sufficient to describe the experimental results. Excellent agreement is found between potential energy functions derived from measurements on the 3He and 4He isotopes. One absorption line corresponds to a three-quantum transition in 4He@C60, allowed by the anharmonicity of the potential function and by the non-linearity of the dipole moment in He atom displacement. The potential energy function of icosahedral symmetry does not explain the fine structure observed in the low temperature spectra.

Experimental determination of the interaction potential between a helium atom and the interior surface of a C60 fullerene molecule.

The interactions between atoms and molecules may be described by a potential energy function of the nuclear coordinates. Nonbonded interactions between neutral atoms or molecules are dominated by repulsive forces at a short range and attractive dispersion forces at a medium range. Experimental data on the detailed interaction potentials for nonbonded interatomic and intermolecular forces are scarce. Here, we use terahertz spectroscopy and inelastic neutron scattering to determine the potential energy function for the nonbonded interaction between single He atoms and encapsulating C60 fullerene cages in the helium endofullerenes 3He@C60 and 4He@C60, synthesized by molecular surgery techniques. The experimentally derived potential is compared to estimates from quantum chemistry calculations and from sums of empirical two-body potentials.

A Solid-State Intramolecular Wittig Reaction Enables Efficient Synthesis of Endofullerenes Including Ne@C60 , 3 He@C60 , and HD@C60.

An open-cage fullerene incorporating phosphorous ylid and carbonyl group moieties on the rim of the orifice can be filled with gases (H2 , He, Ne) in the solid state, and the cage opening then contracted in situ by raising the temperature to complete an intramolecular Wittig reaction, trapping the atom or molecule inside. Known transformations complete conversion of the product fullerene to C60 containing the endohedral species. As well as providing an improved synthesis of large quantities of 4 He@C60 , H2 @C60 , and D2 @C60 , the method allows the efficient incorporation of expensive gases such as HD and 3 He, to prepare HD@C60 and 3 He@C60 . The method also enables the first synthesis of Ne@C60 by molecular surgery, and its characterization by crystallography and 13 C NMR spectroscopy.

An Internuclear J-Coupling of 3He Induced by Molecular Confinement.

The solution-state 13C NMR spectrum of the endofullerene 3He@C60 displays a doublet structure due to a J-coupling of magnitude 77.5 ± 0.2 mHz at 340 K between the 3He nucleus and a 13C nucleus of the enclosing carbon surface. The J-coupling increases in magnitude with increasing temperature. Quantum chemistry calculations successfully predict the approximate magnitude of the coupling. This observation shows that the mutual proximity of molecular or atomic species is sufficient to induce a finite scalar nuclear spin-spin coupling, providing that translational motion is restricted by confinement. The phenomenon may have applications to the study of surface interactions and to mechanically bound species.

Fine structure in the solution state 13C-NMR spectrum of C60 and its endofullerene derivatives.

The 13C NMR spectrum of fullerene C60 in solution displays two small "side peaks" on the shielding side of the main 13C peak, with integrated intensities of 1.63% and 0.81% of the main peak. The two side peaks are shifted by -12.6 ppb and -20.0 ppb with respect to the main peak. The side peaks are also observed in the 13C NMR spectra of endofullerenes, but with slightly different shifts relative to the main peak. We ascribe the small additional peaks to minor isotopomers of C60 containing two adjacent 13C nuclei. The shifts of the additional peaks are due to a secondary isotope shift of the 13C resonance caused by the substitution of a 12C neighbour by 13C. Two peaks are observed since the C60 structure contains two different classes of carbon-carbon bonds with different vibrational characteristics. The 2 : 1 ratio of the side peak intensities is consistent with the known structure of C60. The origin and intensities of the 13C side peaks are discussed, together with an analysis of the 13C solution NMR spectrum of a 13C-enriched sample of C60, which displays a relatively broad 13C NMR peak due to a statistical distribution of 13C isotopes. The spectrum of 13C-enriched C60 is analyzed by a Monte Carlo simulation technique, using a theorem for the second moment of the NMR spectrum generated by J-coupled spin clusters.

First Synthesis and Characterization of CH4 @C60.

The endohedral fullerene CH4 @C60 , in which each C60 fullerene cage encapsulates a single methane molecule, has been synthesized for the first time. Methane is the first organic molecule, as well as the largest, to have been encapsulated in C60 to date. The key orifice contraction step, a photochemical desulfinylation of an open fullerene, was completed, even though it is inhibited by the endohedral molecule. The crystal structure of the nickel(II) octaethylporphyrin/ benzene solvate shows no significant distortion of the carbon cage, relative to the C60 analogue, and shows the methane hydrogens as a shell of electron density around the central carbon, indicative of the quantum nature of the methane. The 1 H spin-lattice relaxation times (T1 ) for endohedral methane are similar to those observed in the gas phase, indicating that methane is freely rotating inside the C60 cage. The synthesis of CH4 @C60 opens a route to endofullerenes incorporating large guest molecules and atoms.

Spin-Isomer Conversion of Water at Room Temperature and Quantum-Rotor-Induced Nuclear Polarization in the Water-Endofullerene H_{2}O@C_{60}.

Water exists in two forms, para and ortho, that have nuclear spin states with different symmetries. Here we report the conversion of fullerene-encapsulated para water to ortho water. The enrichment of para water at low temperatures is monitored via changes in the electrical polarizability of the material. Upon rapid dissolution of the material in toluene the excess para water converts to ortho water. In H_{2}^{16}O@C_{60} the conversion leads to a slow increase in the NMR signal. In H_{2}^{17}O@C_{60} the conversion gives rise to weak signal enhancements attributed to quantum-rotor-induced nuclear spin polarization. The time constants for the para-to-ortho conversion of fullerene-encapsulated water in ambient temperature solution are estimated as 30±4 s for the ^{16}O isotopolog of water, and 16±3 s for the ^{17}O isotopolog.

Synthesis and Properties of Open Fullerenes Encapsulating Ammonia and Methane.

We describe the synthesis and characterisation of open fullerene (1) and its reduced form (2) in which CH4 and NH3 are encapsulated, respectively. The 1 H NMR resonance of endohedral NH3 is broadened by scalar coupling to the quadrupolar 14 N nucleus, which relaxes rapidly. This broadening is absent for small satellite peaks, which are attributed to natural abundance 15 N. The influence of the scalar relaxation mechanism on the linewidth of the 1 H ammonia resonance is probed by variable temperature NMR. A rotational correlation time of τc =1.5 ps. is determined for endohedral NH3 , and of τc =57±5 ps. for the open fullerene, indicating free rotation of the encapsulated molecule. IR spectroscopy of NH3 @2 at 5 K identifies three vibrations of NH3 (ν1 , ν3 and ν4 ) redshifted in comparison with free NH3 , and temperature dependence of the IR peak intensity indicates the presence of a large number of excited translational/ rotational states. Variable temperature 1 H NMR spectra indicate that endohedral CH4 is also able to rotate freely at 223 K, on the NMR timescale. Inelastic neutron scattering (INS) spectra of CH4 @1 show both rotational and translational modes of CH4 . Energy of the first excited rotational state (J=1) of CH4 @1 is significantly lower than that of free CH4 .

Alignment of 17O-enriched water-endofullerene H2O@C60 in a liquid crystal matrix.

We present a 17O and 1H NMR study of molecular endofullerene H2O@C60 dissolved in the nematic liquid crystal N-(4-methoxybenzylidene)-4-butylaniline (MBBA). The 17O NMR peak is split into five components by the 17O residual quadrupolar coupling, each of which is split into a triplet by the 1H-17O residual dipolar coupling and scalar coupling. The splittings are analysed in terms of the partial alignment of the encapsulated water molecules. Order parameters describing the alignment are estimated. It is found that the preferential orientation of the endohedral water molecule has the molecular plane perpendicular to the liquid crystal director.

Structure and Dynamics of the Liver Receptor Homolog 1-PGC1α Complex.

Peroxisome proliferator-activated gamma coactivator 1-α (PGC1α) regulates energy metabolism by directly interacting with transcription factors to modulate gene expression. Among the PGC1α binding partners is liver receptor homolog 1 (LRH-1; NR5A2), an orphan nuclear hormone receptor that controls lipid and glucose homeostasis. Although PGC1α is known to bind and activate LRH-1, mechanisms through which PGC1α changes LRH-1 conformation to drive transcription are unknown. Here, we used biochemical and structural methods to interrogate the LRH-1-PGC1α complex. Purified, full-length LRH-1, as well as isolated ligand binding domain, bound to PGC1α with higher affinity than to the coactivator, nuclear receptor coactivator-2 (Tif2), in coregulator peptide recruitment assays. We present the first crystal structure of the LRH-1-PGC1α complex, which depicts several hydrophobic contacts and a strong charge clamp at the interface between these partners. In molecular dynamics simulations, PGC1α induced correlated atomic motion throughout the entire LRH-1 activation function surface, which was dependent on charge-clamp formation. In contrast, Tif2 induced weaker signaling at the activation function surface than PGC1α but promoted allosteric signaling from the helix 6/ß-sheet region of LRH-1 to the activation function surface. These studies are the first to probe mechanisms underlying the LRH-1-PGC1α interaction and may illuminate strategies for selective therapeutic targeting of PGC1α-dependent LRH-1 signaling pathways.

Crystal Structures of the Nuclear Receptor, Liver Receptor Homolog 1, Bound to Synthetic Agonists.

Liver receptor homolog 1 (NR5A2, LRH-1) is an orphan nuclear hormone receptor that regulates diverse biological processes, including metabolism, proliferation, and the resolution of endoplasmic reticulum stress. Although preclinical and cellular studies demonstrate that LRH-1 has great potential as a therapeutic target for metabolic diseases and cancer, development of LRH-1 modulators has been difficult. Recently, systematic modifications to one of the few known chemical scaffolds capable of activating LRH-1 failed to improve efficacy substantially. Moreover, mechanisms through which LRH-1 is activated by synthetic ligands are entirely unknown. Here, we use x-ray crystallography and other structural methods to explore conformational changes and receptor-ligand interactions associated with LRH-1 activation by a set of related agonists. Unlike phospholipid LRH-1 ligands, these agonists bind deep in the pocket and do not interact with residues near the mouth nor do they expand the pocket like phospholipids. Unexpectedly, two closely related agonists with similar efficacies (GSK8470 and RJW100) exhibit completely different binding modes. The dramatic repositioning is influenced by a differential ability to establish stable face-to-face π-π-stacking with the LRH-1 residue His-390, as well as by a novel polar interaction mediated by the RJW100 hydroxyl group. The differing binding modes result in distinct mechanisms of action for the two agonists. Finally, we identify a network of conserved water molecules near the ligand-binding site that are important for activation by both agonists. This work reveals a previously unappreciated complexity associated with LRH-1 agonist development and offers insights into rational design strategies.

NMR of molecular endofullerenes dissolved in a nematic liquid crystal.

We report the NMR of the molecular endofullerenes H2@C60, H2O@C60 and HF@C60 dissolved in the nematic liquid crystal N-(4-methoxybenzylidene)-4-butylaniline (MBBA). The 1H NMR lines of H2 and H2O display a doublet splitting due to residual dipole-dipole coupling. The dipolar splitting depends on temperature in the nematic phase and vanishes above the nematic-isotropic phase transition. The 19F spectrum of HF@C60 dissolved in MBBA displays a doublet splitting in the nematic phase, with contributions from the 1H-19F dipole-dipole coupling and J-coupling. The phenomena are analyzed using a model in which the fullerene cages acquire a geometrical distortion, either through interaction with the liquid crystal environment, or through their interaction with the endohedral molecules. The distorted cages become partially oriented with respect to the liquid crystal director, and the endohedral molecules become partially oriented with respect to the distorted cages.

ChemTrove: enabling a generic ELN to support chemistry through the use of transferable plug-ins and online data sources.

In designing an Electronic Lab Notebook (ELN), there is a balance to be struck between keeping it as general and multidisciplinary as possible for simplicity of use and maintenance and introducing more domain-specific functionality to increase its appeal to target research areas. Here, we describe the results of a collaboration between the Royal Society of Chemistry (RSC) and the University of Southampton, guided by the aims of the Dial-a-Molecule Grand Challenge, intended to achieve the best of both worlds and augment a discipline-agnostic ELN, LabTrove, with chemistry-specific functionality and using data provided by the ChemSpider platform. This has been done using plug-in technology to ensure maximum transferability with minimal effort of the chemistry functionality to other ELNs and equally other subject-specific functionality to LabTrove. The resulting product, ChemTrove, has undergone a usability trial by selected academics, and the resulting feedback will guide the future development of the underlying ELN technology.

Generation and Trapping of Ketenes in Flow.

Ketenes were generated by the thermolysis of alkoxyalkynes under flow conditions, and then trapped with amines and alcohols to cleanly give amides and esters. For a 10 min reaction time, temperatures of 180, 160, and 140 °C were required for >95 % conversion of EtO, iPrO, and tBuO alkoxyalkynes, respectively. Variation of the temperature and flow rate with inline monitoring of the output by IR spectroscopy allowed the kinetic parameters for the conversion of 1-ethoxy-1-octyne to be easily estimated (Ea = 105.4 kJ/mol). Trapping of the in-situ-generated ketenes by alcohols to give esters required the addition of a tertiary amine catalyst to prevent competitive [2+2] addition of the ketene to the alkoxyalkyne precursor.

Exploring diradical chemistry: a carbon-centered radical may act as either an anion or electrophile through an orbital isomer.

Diradical intermediates, formed by thermolysis of alkynylcyclobutenones, can display radical, anion, or electrophilic character because of the existence of an orbital isomer with zwitterionic and cyclohexatrienone character. Our realization that water, alcohols, and certain substituents can induce the switch provides new opportunities in synthesis. For example, it can be used to shut down radical pathways and to give access to aryl carbonates and tetrasubstituted quinones.