9-Azahomocubane

Homocubane, a highly strained cage hydrocarbon, contains two very different positions for the introduction of a nitrogen atom into the skeleton, e. g., a position 1 exchange results in a tertiary amine whereas position 9 yields a secondary amine. Herein reported is the synthesis of 9-azahomocubane along with associated structural characterization, physical property analysis and chemical reactivity. Not only is 9-azahomocubane readily synthesized, and found to be stable as predicted, the basicity of the secondary amine was observed to be significantly lower than the structurally related azabicyclo[2.2.1]heptane, although similar to 1-azahomocubane.

Chemical modifications for a next generation of nucleic acid aptamers

In the past three decades, in vitro systematic evolution of ligands by exponential enrichment (SELEX) has yielded many aptamers for translational applications in both research and clinical settings. Despite their promise as an alternative to antibodies, the low success rate of SELEX (~ 30%) has been a major bottleneck that hampers the further development of aptamers. One hurdle is the lack of chemical diversity in nucleic acids. To address this, the aptamer chemical repertoire has been extended by introducing exotic chemical groups, which provide novel binding functionalities. This review will focus on how modified aptamers can be selected and evolved, with illustration of some successful examples. In particular, unique chemistries are exemplified. Various strategies of incorporating modified building blocks into the standard SELEX protocol are highlighted, with a comparison of the differences between pre-SELEX and post-SELEX modifications. Nucleic acid aptamers with extended functionality evolved from non-natural chemistries will open up new vistas for function and application of nucleic acids.

Cubic Octa-Carbon: Quantum-Chemical Design of Molecular Structure and Potential Way of Its Synthesis from Cubane

Quantum-chemical calculation of most important parameters of molecular and electronic structures of octa-carbon C₈ having cubic form (bond lengths, bond and torsion angles) using CCSD(T)/QZVP and DFT B3PW91/QZVP methods, has been carried out. NBO analysis data and HOMO/LUMO images for this compound are presented, too. Good agreement was found between the structural data obtained using the above two quantum-chemical methods and, also, with corresponding experimental data. Also, the standard thermodynamic parameters of formation of cubic C₈ considered here, and namely standard enthalpy Δ_fH⁰(298K), entropy S_f⁰(298K) and Gibbs’ energy Δ_fG⁰(298K) of formation for this compound were calculated. By using this data, a theoretically possible variant of the synthesis of this compound by dehydrogenation of cubane C₈H₈ is considered, and the thermodynamic characteristics of each of the four stages of this process have been calculated. It is noted that each of the four stages of this process is characterized by a very high (about 500 kJ/mol) enthalpy of activation, as a result of that, for their realization within a sufficiently short time, the use of appropriate catalysts is necessary.

Cubane, Bicyclo[1.1.1]pentane and Bicyclo[2.2.2]octane: Impact and Thermal Sensitiveness of Carboxyl-, Hydroxymethyl- and Iodo-substituents

With the burgeoning interest in cage motifs for bioactive molecule discovery, and the recent disclosure of 1,4-cubane-dicarboxylic acid impact sensitivity, more research into the safety profiles of cage scaffolds is required. Therefore, the impact sensitivity and thermal decomposition behavior of judiciously selected starting materials and synthetic intermediates of cubane, bicyclo[1.1.1]pentane (BCP), and bicyclo[2.2.2]octane (BCO) were evaluated via hammer test and sealed cell differential scanning calorimetry, respectively. Iodo-substituted systems were found to be more impact sensitive, whereas hydroxymethyl substitution led to more rapid thermodecomposition. Cubane was more likely to be impact sensitive with these substituents, followed by BCP, whereas all BCOs were unresponsive. The majority of derivatives were placed substantially above Yoshida thresholds-a computational indicator of sensitivity.

Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker

Nucleic acid aptamers selected through systematic evolution of ligands by exponential enrichment (SELEX) fold into exquisite globular structures in complex with protein targets with diverse translational applications. Varying the chemistry of nucleotides allows evolution of nonnatural nucleic acids, but the extent to which exotic chemistries can be integrated into a SELEX selection to evolve nonnatural macromolecular binding interfaces is unclear. Here, we report the identification of a cubane-modified aptamer (cubamer) against the malaria biomarker Plasmodium vivax lactate dehydrogenase (PvLDH). The crystal structure of the complex reveals an unprecedented binding mechanism involving a multicubane cluster within a hydrophobic pocket. The binding interaction is further stabilized through hydrogen bonding via cubyl hydrogens, previously unobserved in macromolecular binding interfaces. This binding mechanism allows discriminatory recognition of P. vivax over Plasmodium falciparum lactate dehydrogenase, thereby distinguishing these highly conserved malaria biomarkers for diagnostic applications. Together, our data demonstrate that SELEX can be used to evolve exotic nucleic acids bearing chemical functional groups which enable remarkable binding mechanisms which have never been observed in biology. Extending to other exotic chemistries will open a myriad of possibilities for functional nucleic acids.

Bridging and Conformational Control of Porphyrin Units through Non-Traditional Rigid Scaffolds

Connecting two porphyrin units in a rigid linear fashion, without any undesired electron delocalization or communication between the chromophores, remains a synthetic challenge. Herein, a broad library of functionally diverse multi-porphyrin arrays that incorporate the non-traditional rigid linker groups cubane and bicyclo[1.1.1]pentane (BCP) is described. A robust, reliable, and versatile synthetic procedure was employed to access porphyrin-cubane/BCP-porphyrin arrays, representing the largest non-polymeric structures available for cubane/BCP derivatives. These reactions demonstrate considerable substrate scope, from utilization of small phenyl moieties to large porphyrin rings, with varying lengths and different angles. To control conformational flexibility, amide bonds were introduced between the bridgehead carbon of BCP/cubane and the porphyrin rings. Through varying the orientation of the substituents around the amide bond of cubane/BCP, different intermolecular interactions were identified through single crystal X-ray analysis. These studies revealed non-covalent interactions that are the first-of-their-kind including a unique iodine-oxygen interaction between cubane units. These supramolecular architectures indicate the possibility to mimic a protein structure due to the sp3 rigid scaffolds (BCP or cubane) that exhibit the essential conformational space for protein function while simultaneously providing amide bonds for molecular recognition.

Thermal and Sensitiveness Determination of Cubanes: Towards Cubane-Based Fuels for Infrared Countermeasures

As infrared seeking technology evolves, threats are better able to distinguish defensive infrared (IR) flares from true targets. Spectrally matched flares, which generally employ carbon-based fuels, are better able to decoy some advanced missiles by more closely mimicking the IR emission of the target. Cubane is a high-energy carbon-based scaffold which may be suitable for use as a fuel in spectrally matched flares. The enthalpy of formation and strain energy of a series of cubanes was predicted in silico, and their thermal and impact stability examined. All were found to undergo highly exothermic decomposition in sealed cell differential scanning calorimetry, and two cubanes subsequently underwent quantitative sensitiveness testing. Despite their F of I values being in the secondary explosive range, cubane-1,4-dicarboxylic acid (F of I=70) and 4-carbamoylcubane-1-carboxylic acid (F of I=90) were identified as potentially useful fuels for pyrotechnic infrared countermeasure flare formulations.

Stabilization of reactive Co4O4 cubane oxygen-evolution catalysts within porous frameworks

A major challenge to the implementation of artificial photosynthesis (AP), in which fuels are produced from abundant materials (water and carbon dioxide) in an electrochemical cell through the action of sunlight, is the discovery of active, inexpensive, safe, and stable catalysts for the oxygen evolution reaction (OER). Multimetallic molecular catalysts, inspired by the natural photosynthetic enzyme, can provide important guidance for catalyst design, but the necessary mechanistic understanding has been elusive. In particular, fundamental transformations for reactive intermediates are difficult to observe, and well-defined molecular models of such species are highly prone to decomposition by intermolecular aggregation. Here, we present a general strategy for stabilization of the molecular cobalt-oxo cubane core (Co₄O₄) by immobilizing it as part of metal-organic frameworks, thus preventing intermolecular pathways of catalyst decomposition. These materials retain the OER activity and mechanism of the molecular Co₄O₄ analog yet demonstrate unprecedented long-term stability at pH 14. The organic linkers of the framework allow for chemical fine-tuning of activity and stability and, perhaps most importantly, provide "matrix isolation" that allows for observation and stabilization of intermediates in the water-splitting pathway.

Cubane-Type [Mo3 S4 M] Clusters with First-Row Groups 4-10 Transition-Metal Halides Supported by C5 Me5 Ligands on Molybdenum

A synthetic protocol was developed for a series of cubane-type [Mo₃ S₄ M] clusters that incorporate halides of first-row transition metals (M) from Groups 4-10. This protocol is based on the anionic cluster platform [Cp*₃ Mo₃ S₄ ]^- ([1]^- ; Cp*=η⁵ -C₅ Me₅ ), which crystallizes when K(18-crown-6) is used as the counter cation. Treatment of in situ-generated [1]^- with such transition-metal halides led to the formation of [Mo₃ S₄ M] clusters, in which the M/halide ratio gradually changes from 1:2 to 1:1.5 and to 1:1, when moving from early to late transition metals. This trend suggests a tendency for early transition metals to tolerate higher oxidation states and adopt larger ionic radii relative to late transition metals. The properties of the [Mo₃ S₄ Fe] cluster 6 a were investigated in detail by using ⁵⁷ Fe Mössbauer spectroscopy and computational methods.

Discovery of Open Cubane Core Structures for Biomimetic LnCo3 (OR)4 Water Oxidation Catalysts

Bio-mimetic catalysts such as LnCo₃ (OR)₄ (Ln=Er, Tm; OR=alkoxide) cubanes have recently been in the focus of research for artificial water oxidation processes. Previously, the remarkable adaptability with respect to ligand shell, nuclear structure as well as protonation and oxidation states of those catalysts has been shown to be beneficial for the water oxidation process. We further explored the structural flexibility of those catalysts and present here a series of novel structures in which one metal center is pulled out of the cubane cage. This leads to an open cubane core, which is to some extent reminiscent of observed open/closed cubane-core forms of the oxygen-evolving complex in nature's photosystem II. We investigate how those open cubane core models alter the thermodynamics of the water oxidation cycle and how different solvation approaches influence their stability.

Synthesis, Crystal Structure, and Magnetic Properties of a New Mixed Metal (Co(II), Ni(II)) Cubane

The mixed Co(II)/Ni(II) complex, [Co_2.67Ni_1.33L₄(CH₃COO)₂][BPh₄]₂·0.75H₂O where HL = 4-(salicylaldimine)antipyrine, was isolated as an orange solid from the reaction of 4-(salicylaldimine)antipyrine, with mixed cobalt(II) acetate and nickel(II) acetate in ethanol. The complex was characterized by Frustrated Total Internal Reflection (FTIR), UltraViolet Visible spectroscopy (UV-Vis), X-ray single crystal diffraction, and by elemental analysis. The complex is composed of two symmetry independent cationic units, A and B. The two units are essentially isostructural; nevertheless, small differences exist between them. The units contain four metal atoms, arranged at the corners of a distorted cubane-like core alternately with phenoxy oxygen of the Schiff base. The overall eight corners occupied by metal ions in the asymmetric unit are shared between cobalt and nickel in a 5.33:2.67 ratio. Each metal divalent cation binds three coordinated sites from the corresponding tridentate Schiff base ligand, the fourth one is bound by the acetate oxygen, the fifth and the sixth donor sites come from the phenolate oxygens of other Schiff base ligands. Intermolecular hydrogen bonds join the complexes to the water molecules present in the crystal packing. The magnetic characterization was carried out for this new complex and for its isostructural counterpart containing only cobalt ions. The magnetic measurements for the cobalt(II)/nickel(II) mixed compound indicate either antiferromagnetic interactions among the two cubanes or an anisotropic contribution, whereas a ferromagnetic interaction is observed within the cubane, for both the complexes, as expected by geometrical considerations. A comparison between the magnetic properties of the pure cobalt(II) derivative and similar systems discussed in literature, is presented.

Validating Eaton's Hypothesis: Cubane as a Benzene Bioisostere

Pharmaceutical and agrochemical discovery programs are under considerable pressure to meet increasing global demand and thus require constant innovation. Classical hydrocarbon scaffolds have long assisted in bringing new molecules to the market place, but an obvious omission is that of the Platonic solid cubane. Eaton, however, suggested that this molecule has the potential to act as a benzene bioisostere. Herein, we report the validation of Eaton's hypothesis with cubane derivatives of five molecules that are used clinically or as agrochemicals. Two cubane analogues showed increased bioactivity compared to their benzene counterparts whereas two further analogues displayed equal bioactivity, and the fifth one demonstrated only partial efficacy. Ramifications from this study are best realized by reflecting on the number of bioactive molecules that contain a benzene ring. Substitution with the cubane scaffold where possible could revitalize these systems, and thus expedite much needed lead candidate identification.

Molecular Cobalt Clusters as Precursors of Distinct Active Species in Electrochemical, Photochemical, and Photoelectrochemical Water Oxidation Reactions in Phosphate Electrolytes

Three cobalt model molecular compounds, Co-cubane ([Co4 (µ3 -O)4 (µ-OAc)4 py4 ]), Co-trimer ([Co3 (μ3 -O)(µ-OAc)6 py3 ]PF6 ), and Co-dimer ([Co2 (μ-OH)2 (µ-OAc)(OAc)2 py4 ]PF6 ), are investigated as water oxidation reaction (WOR) catalysts, using electrochemical, photochemical, and photoelectrochemical methodologies in phosphate electrolyte. The actual species contributing to the catalytic activity observed in the WOR are derived from the transformation of these cobalt compounds. The catalytic activity observed is highly dependent on the initial compound structure and on the particular WOR methodology used. Co-cubane shows no activity in the electrochemical WOR and negligible activity in the photochemical WOR, but is active in the photoelectrochemical WOR, in which it behaves as a precursor to catalytically active species. Co-dimer also shows no activity in the electrochemical WOR, but behaves as a precursor to catalytically active species in both the photochemical and photoelectrochemical WOR experiments. Co-trimer behaves as a precursor to catalytically active species in all three of the WOR methodologies.

Evaluation of a chiral cubane-based Schiff base ligand in asymmetric catalysis reactions

Recently, a novel chiral cubane-based Schiff base ligand was reported to yield modest enantioselectivity in the Henry reaction. To further explore the utility of this ligand in other asymmetric organic transformations, we evaluated its stereoselectivity in cyclopropanation and Michael addition reactions. Although there was no increase in stereocontrol, upon computational evaluation using both M06L and B3LYP calculations, it was revealed that a pseudo six-membered ring exists, through H-bonding of a cubyl hydrogen to the copper core. This decreases the steric bulk above the copper center and limits the asymmetric control with this ligand.