New insights into the molecular mechanisms of glutaminase C inhibitors in cancer cells using serial room temperature crystallography.

Cancer cells frequently exhibit uncoupling of the glycolytic pathway from the TCA cycle (i.e., the "Warburg effect") and as a result, often become dependent on their ability to increase glutamine catabolism. The mitochondrial enzyme Glutaminase C (GAC) helps to satisfy this 'glutamine addiction' of cancer cells by catalyzing the hydrolysis of glutamine to glutamate, which is then converted to the TCA-cycle intermediate α-ketoglutarate. This makes GAC an intriguing drug target and spurred the molecules derived from bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide (the so-called BPTES class of allosteric GAC inhibitors), including CB-839, which is currently in clinical trials. However, none of the drugs targeting GAC are yet approved for cancer treatment and their mechanism of action is not well understood. Here, we shed new light on the underlying basis for the differential potencies exhibited by members of the BPTES/CB-839 family of compounds, which could not previously be explained with standard cryo-cooled X-ray crystal structures of GAC bound to CB-839 or its analogs. Using an emerging technique known as serial room temperature crystallography, we were able to observe clear differences between the binding conformations of inhibitors with significantly different potencies. We also developed a computational model to further elucidate the molecular basis of differential inhibitor potency. We then corroborated the results from our modeling efforts using recently established fluorescence assays that directly read out inhibitor binding to GAC. Together, these findings should aid in future design of more potent GAC inhibitors with better clinical outlook.

Crystal structure of the pheromone Er-13 from the ciliate Euplotes raikovi, with implications for a protein-protein association model in pheromone/receptor interactions.

In the ciliate Euplotes raikovi, water-borne protein pheromones promote the vegetative cell growth and mating by competitively binding as autocrine and heterologous signals to putative cell receptors represented by membrane-bound pheromone isoforms. A previously determined crystal structure of pheromone Er-1 supported a pheromone/receptor binding model in which strong protein-protein interactions result from the cooperative utilization of two distinct types of contact interfaces that arrange molecules into linear chains, and these into two-dimensional layers. We have now determined the crystal structure of a new pheromone, Er-13, isolated from cultures that are strongly mating reactive withculturessource of pheromone Er-1.The comparison between the Er-1 and Er-13 crystal structuresreinforces the fundamental of the cooperative model of pheromone/receptor binding, in that the molecules arrange into linear chains taking a rigorously alternate opposite orientation reflecting the presumed mutual orientation of pheromone and receptor molecules on the cell surface. In addition, the comparison provides two new lines of evidence for a univocal rationalization of observations on the differentbehaviourbetween the autocrine and heterologous pheromone/receptor complexes. (i) In the Er-13 crystal, chains do not form layers which thus appear to be an over-structureunique tothe Er-1 crystal, not essential for the pheromone signalling mechanisms. (ii) In both crystal structures, the intra-chain interfaces are equally derived from burying amino-acid side-chains mostly residing on helix-3 of the three-helical pheromonefold. This helix is thus identified as the key structural motif underlying the pheromone activity, in line with its tight intra- and interspecificstructuralconservation.

Charge-Transfer Salts of 6,6-Dicyanopentafulvenes: From Topology to Charge Separation in Solution.

6,6-Dicyanopentafulvene derivatives and metallocenes with redox potentials appropriate for forming their radical anions form highly persistent donor-acceptor salts. The charge-transfer salts of 2,3,4,5-tetraphenyl-6,6-dicyanofulvene with cobaltocene (1⋅Cp2 Co) and 2,3,4,5-tetrakis(triisopropylsilyl)-6,6-dicyanofulvene with decamethylferrocene (2⋅Fc*) have been prepared. The X-ray structures of the two salts, formed as black plates, were obtained and are discussed herein. Compared with neutral dicyanopentafulvenes, the chromophores in the metallocene salts show substantial changes in bond lengths and torsional angles in the solid state. EPR, NMR, and optical spectroscopy, as well as superconducting quantum interference device (SQUID) measurements, reveal that charge-separation in the crystalline states and in frozen and fluid solutions depends on subtle differences of redox potentials, geometry, and on ion pairing. Whereas 1⋅Cp2 Co reveals paramagnetic character in the crystalline state and in solution, compound 2⋅Fc* shows a delicate balance between para- and diamagnetism, depending on the temperature and solvent characteristics.

Unconventional Synthesis of a CuI Rotaxane with a Superacceptor Stopper: Ultrafast Excited-State Dynamics and Near-Infrared Luminescence.

A CuI bis-phenanthroline rotaxane was prepared by using the [2+2] cycloaddition-retroelectrocyclization (CA-RE) reaction to graft a bulky dicyanoquinodimethane (DCNQ) stopper. The electronic properties were investigated with electrochemical and photophysical techniques, in parallel with three reference compounds, namely, the DCNQ derivative alone, the DCNQ-based phenanthroline ligand, and an analogue CuI complex lacking the DCNQ moiety. In all the systems containing the DCNQ unit, the lowest electronic excited states are centered thereon, with the singlet level (S1 ) located at about 1.0 eV, as suggested by TDDFT calculations. Accordingly, in the DCNQ-equipped rotaxane, the typical metal-to-ligand charge-transfer luminescence of the CuI center is totally quenched. Ultrafast transient absorption and emission studies show that, in the rotaxane, the final sink of photoinduced processes is the lowest singlet state of the DCNQ moiety (S1 ), which exhibits strong charge-transfer character and a lifetime of 0.4 ps. Its deactivation leads to population of another excited state with a lifetime of 1.3 ps, which can be the related triplet state (T1 ) or a vibrationally hot level (hot-S0 ). Notably, S1 also shows stimulated fluorescence in the near-infrared (NIR) region between 1100 and 1500 nm, corroborating the TDDFT prediction. This unusual finding opens up the study of ultrashort-lived NIR luminescence in organic donor-acceptor systems.

Tridecacyclene: A Cyclic Tetramer of Acenaphthylene.

In this manuscript, we describe the single-step preparation of a cyclic tetramer of acenaphthylene through a Lewis acid-catalyzed aldol cyclization of 1-acenaphthenone. The previously unexplored cyclic tetramer material differs from the better-known cyclic trimer, decacyclene, due to the presence of a central eight-membered ring. This ring not only forces the molecule to distort significantly from planarity, but is also responsible for its unique electronic properties, including a decrease in the reduction potential (by about 0.4 eV) and optical gap (by about 0.73 eV), compared to the more planar decacyclene. The synthesized compound crystallizes into a unique packing structure with significant π-stacking observed between adjacent molecules. Furthermore, due to its saddle-like shape, the cyclic tetramer is able to form shape-complementary interactions between its concave surface and the convex outer surface of buckminsterfullerene to generate cocrystalline supramolecular assemblies.

Design and Synthesis of Aviram-Ratner-Type Dyads and Rectification Studies in Langmuir-Blodgett (LB) Films.

The design and synthesis of Aviram-Ratner-type molecular rectifiers, featuring an anilino-substituted extended tetracyanoquinodimethane (exTCNQ) acceptor, covalently linked by the σ-spacer bicyclo[2.2.2]octane (BCO) to a tetrathiafulvalene (TTF) donor moiety, are described. The rigid BCO spacer keeps the TTF donor and exTCNQ acceptor moieties apart, as demonstrated by X-ray analysis. The photophysical properties of the TTF-BCO-exTCNQ dyads were investigated by UV/Vis and EPR spectroscopy, electrochemical studies, and theoretical calculations. Langmuir-Blodgett films were prepared and used in the fabrication and electrical studies of junction devices. One dyad showed the asymmetric current-voltage (I-V) curve characteristic for rectification, unlike control compounds containing the TTF unit but not the exTCNQ moiety or comprising the exTCNQ acceptor moiety but lacking the donor TTF part, which both gave symmetric I-V curves. The direction of the observed rectification indicated that the preferred electron current flows from the exTCNQ acceptor to the TTF donor.

Pentaindenocorannulene: Properties, Assemblies, and C60 Complex.

Pentaindenocorannulene (C50 H20 , 1), a deep bowl polynuclear aromatic hydrocarbon, accepts 4 electrons, crystallizes in columnar bowl-in-bowl assemblies and forms a nested C60 @12 complex. Spectra, structures and computations are presented.

Push-Pull Buta-1,2,3-trienes: exceptionally low rotational barriers of cumulenic C=C bonds and proacetylenic reactivity.

A variety of asymmetrically donor-acceptor-substituted [3]cumulenes (buta-1,2,3-trienes) were synthesized by developed procedures. The activation barriers to rotation ΔG(≠) were measured by variable temperature NMR spectroscopy and found to be as low as 11.8 kcal mol(-1) , in the range of the barriers for rotation around sterically hindered single bonds. The central C=C bond of the push-pull-substituted [3]cumulene moiety is shortened down to 1.22 Šas measured by X-ray crystallography, leading to a substantial bond length alternation (BLA) of up to 0.17 Å. All the experimental results are supported by DFT calculations. Zwitterionic transition states (TS) of bond rotation confirm the postulated proacetylenic character of donor-acceptor [3]cumulenes. Additional support for the proacetylenic character of these chromophores is provided by their reaction with tetracyanoethene (TCNE) in a cycloaddition-retroelectrocyclization (CA-RE) cascade characteristic of donor-polarized acetylenes.

The 6,6-dicyanopentafulvene core: a template for the design of electron-acceptor compounds.

The electron-accepting ability of 6,6-dicyanopentafulvenes (DCFs) can be varied extensively through substitution on the five-membered ring. The reduction potentials for a set of 2,3,4,5-tetraphenyl-substituted DCFs, with varying substituents at the para-position of the phenyl rings, strongly correlate with their Hammett σp-parameters. By combining cyclic voltammetry with DFT calculations ((U)B3LYP/6-311+G(d)), using the conductor-like polarizable continuum model (CPCM) for implicit solvation, the absolute reduction potentials of a set of twenty DCFs were reproduced with a mean absolute deviation of 0.10 eV and a maximum deviation of 0.19 eV. Our experimentally investigated DCFs have reduction potentials within 3.67-4.41 eV, however, the computations reveal that DCFs with experimental reduction potentials as high as 5.3 eV could be achieved, higher than that of F4-TCNQ (5.02 eV). Thus, the DCF core is a template that allows variation in the reduction potentials by about 1.6 eV.

6,6-Dicyanopentafulvenes: teaching an old dog new tricks.

6,6-Dicyanopentafulvene (DCF) is a fascinating molecular entity that consists of a cyclopentadiene ring conjugated to an exocyclic double bond bearing two cyano groups on its periphery. Herein, we give a brief history of the chemistry of DCFs prior to our arrival to the field in 2011, followed by a summary of our work. We show how substitution on the ring and the exocyclic bond affects the HOMO and LUMO energies of pentafulvenes and how the design of DCFs was exploited computationally for the first time. Shortly after the report of the first rational synthesis of DCFs, we discovered that DCFs had a vast and astonishing array of reactivities to form new molecular entities. Simple, catalyst-free reactions between DCF acceptors and electron-rich donors led to the formation of scaffolds of exceptional complexity. Furthermore, our discovery that DCFs are capable of undergoing mild pentafulvene-to-benzene rearrangements challenges previous conventions of fulvene chemistry.

Anilino-Substituted Multicyanobuta-1,3-diene Electron Acceptors: TICT Molecules with Accessible Conical Intersections.

A theoretical investigation based on DFT, TD-DFT, and CASSCF/CASPT2 methods has been carried out to elucidate the photophysics of two anilino-substituted pentacyano- and tetracyanobuta-1,3-dienes (PCBD and TCBD, respectively). These molecules exhibit exceptional electron-accepting properties, but their effective use in multicomponent systems for photoinduced electron transfer is limited because they undergo ultrafast (∼1 ps) radiationless deactivation. We show that the lowest-energy excited states of these molecules have a twisted intramolecular charge-transfer character and deactivate to the ground state through energetically accessible conical intersections (CIs). The topology of the lowest-energy CI, analyzed with a linear interpolation of the two branching-space vectors (g and h), indicates it is a sloped CI, ultimately responsible for the ultrafast deactivation of this class of compounds.

Stabilizing Pentacene By Cyclopentannulation.

A new class of stabilized pentacene derivatives with externally fused five-membered rings are prepared by means of a key palladium-catalyzed cyclopentannulation step. The target compounds are synthesized by chemical manipulation of a partially saturated 6,13-dibromopentacene precursor that can be fully aromatized in a final step through a DDQ-mediated dehydrogenation reaction (DDQ=2,3-dichloro-5,6-dicyano-1,4-benzoquinone). The new 1,2,8,9-tetraaryldicyclopenta[fg,qr]pentacene derivatives have narrow energy gaps of circa 1.2 eV and behave as strong electron acceptors with lowest unoccupied molecular orbital energies between -3.81 and -3.90 eV. Photodegradation studies reveal the new compounds are more photostable than 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-pentacene).

All-optical switching with 1-ps response time in a DDMEBT enabled silicon grating coupler/resonator hybrid device.

An amorphous film of the third-order nonlinear optical material DDMEBT was spun onto silicon chips for the first time, filling 80 nm lithographic features. A 710 µm² device was designed, fabricated, and tested that acts both as a nonlinear resonator switch and as an input/output grating coupler to a perfectly vertical single mode fiber. Autocorrelation and spectral measurements indicate the device has <1 ps response time, 4 nm of switching bandwidth, and 4 dB of on/off contrast. With sufficient power, this all-optical device can potentially modulate a single optical carrier frequency in excess of 1 THz.

One-pot access to push-pull oligoenes by sequential [2 + 2] cycloaddition-retroelectrocyclization reactions.

The formal [2 + 2] cycloaddition-retroelectrocyclization reaction was employed as the key transformation to obtain donor-substituted, π-conjugated polycyanohexa-1,3,5-trienes (TCHTs and PCHTs) and polycyanoocta-1,3,5,7-tetraenes from donor-substituted tetracyanobuta-1,3-dienes (TCBDs) and electron-rich alkynes. These push-pull-substituted oligoene chromophores were also accessed in good yield from tetracyanoethylene and donor-substituted alkynes by using a one-pot protocol. All bis-(N,N-dialkylanilino) donor-substituted push-pull trienes and tetraenes showed better electron-accepting potency and lower HOMO-LUMO gaps than the corresponding TCBDs, as evidenced by optical and electrochemical studies.

Synthesis of cyano-substituted diaryltetracenes from tetraaryl[3]cumulenes.

A versatile, two-step synthesis of highly substituted, cyano-functionalized diaryltetracenes has been developed, starting from easily accessible tetraaryl[3]cumulenes. This unprecedented transformation is initiated by [2+2] cycloaddition of tetracyanoethylene (TCNE) to the proacetylenic central double bond of the cumulenes to give an intermediate zwitterion, which after an electrocyclization cascade and dehydrogenation yields 5,5,11,11-tetracyano-5,11-dihydrotetracenes in a one-pot procedure. A subsequent copper-assisted decyanation/aromatization provided the target 5,11-dicyano-6,12-diaryltetracene derivatives. All of the postulated structures were confirmed by X-ray crystallography. The new chromophores are thermally highly stable and feature promising fluorescence properties for potential use in optoelectronic devices. They are selective chemosensors for Cu(I) ions, which coordinate to one of the CN substituents and form a 1:1 complex with an association constant of Ka =1.5×10(5)  L mol(-1) at 298 K.

Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP.

Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.

Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase.

Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.

Electron acceptors based on functionalizable cyclopenta[hi]aceanthrylenes and dicyclopenta[de,mn]tetracenes.

We report the synthesis and selective functionalization of two externally fused cyclopenta-fused polycyclic aromatic hydrocarbons (CP-PAHs) and demonstrate their electron accepting behavior. 2,7-Bis(trimethylsilyl)cyclopenta[hi]aceanthrylene (1) and 2,8-bis(trimethylsilyl)dicyclopenta[de,mn]tetracene (4) were prepared in a one-pot, palladium-catalyzed cross-coupling of (trimethylsilyl)acetylene and either 9,10-dibromoanthracene or 5,11-dibromotetracene, respectively. The trimethylsilyl groups were selectively converted into bromides via substitution with N-bromosuccinimide to create universal partners (2 and 6) for metal-catalyzed cross-coupling reactions. To demonstrate the utility of the halogenated CP-PAHs, we successfully employed a Sonogashira cross-coupling between the CP-PAHs and a phenylacetylene derivative. The resulting compounds (3 and 7) were found to be highly conjugated between the CP-PAH core and the substituents, as demonstrated by large bathochromic shifts in the absorption spectra as well as density functional theory calculations. Ethynylated CP-PAHs 3 and 7 were found to possess low optical bandgaps (1.52 and 1.51 eV, respectively) and displayed two reversible reductions. We further demonstrated the fullerene-like electron-accepting behavior of 3 through solution-phase fluorescence quenching of the prototypical electron donor, poly(3-hexylthiophene).

6,6-Dicyanopentafulvenes: electronic structure and regioselectivity in [2 + 2] cycloaddition-retroelectrocyclization reactions.

We present an investigation of the electronic properties and reactivity behavior of electron-accepting 6,6-dicyanopentafulvenes (DCFs). The electron paramagnetic resonance (EPR) spectra of the radical anion of a tetrakis(silylalkynyl) DCF, generated by Na metal reduction, show delocalization of both the charge and unpaired electron to the nitrogens of the cyano moieties and also, notably, to the silicon atoms of the four alkynyl moieties. By contrast, in the radical anion of the previously reported tetraphenyl DCF, coupling to the four phenyl rings is strongly attenuated. The data provide physical evidence for the different conjugation between the DCF core and the substituents in both systems. We also report the preparation of new fulvene-based push-pull chromophores via formal [2 + 2] cycloaddition-retroelectrocyclization reaction of DCFs with electron-rich alkynes. Alkynylated and phenylated DCFs show opposite regioselectivity of the cycloaddition, which can be explained by the differences in electronic communication between substituents and the DCF core as revealed in the EPR spectra of the radical anions.

Engineering solid-state morphologies in carbazole-ethynylene macrocycles.

We present a crystallographic study that systematically investigates the effects of the n-alkyl side-chain length on the crystal packing in shape-persistent macrocycles. The solid-state packing of carbazole-ethynylene-containing macrocycles is sensitive to the alkyl-chain length. In macrocycles containing n-alkyl side chains up to nine carbons in length, face-on aromatic π interactions predominate, while the addition of one carbon leads to a completely different packing arrangement. Macrocycles with C(10) or C(11) chains exhibit a novel packing motif wherein the alkyl chains intercalate between macrocycles, leading in one case to continuous solvent-filled channels. When crystals of the C(10) macrocycle are bathed in solvent, the included molecules exchange with the external solvent, and the alkyl chain disorder changes in response to changes in the guest volume in order to retain crystallinity. Powder X-ray diffraction data indicate that alkyl-macrocycle interactions in the longer chains "emulate" the distances typical of face-to-face π interactions, leading to deceptive indicators of π stacking.