Bicyclo Octane Research Articles

Exceptional reactivity of the bridgehead amine on bicyclo[1.1.1]pentane.

Bicyclo[1.1.1]pentane (BCP) has received substantial interest in the field of synthetic chemistry recently for its potential use as a benzene isostere in medicinal chemistry. Whereas bicyclo[2.2.2]octane (BCO) has also been used as a bioisostere of benzene, the condensation of BCP-amine with nadic anhydride is significantly easier than that of BCO-amine. Analyses of the geometries and the frontier molecular orbitals of these amines suggest that the low steric hindrance and high intrinsic nucleophilicity of BCP-amine together contribute to its exceptional reactivity.

Cage hydrocarbons as linkers in dimeric drug design: Case studies with trimethoprim and tedizolid

The looming threat of a “post-antibiotic era” has been caused by a rapid rise in antibacterial resistance and subsequent depletion of effective antibiotic agents in the clinic. An efficient strategy to address this shortfall lies in the reengineering of pre-existing and commercially available antibiotic drugs. This is exemplified by dimerization, a design concept in which two pharmacophores are covalently linked to form a new chemical entity. The cage hydrocarbons cubane (1), bicyclo[2.2.2]octane (BCO) (2), adamantane (3), and bicyclo[1.1.1]pentane (BCP) (4) present themselves as an attractive family of linkers in this regard. In this report, all four hydrocarbon cages were employed as linkers in a series of dimers based on the commercially available antibiotics trimethoprim and tedizolid. A detailed synthetic roadmap for the protection and deprotection of each pharmacophore is outlined. Several members of the trimethoprim series showed activity on par with that of their trimethoprim progenitor, although this was not the case for the tedizolid series. The design strategy outlined herein highlights the utility of the group as a platform for the rapid and modular construction of future novel antibiotics.

Advances in nonclassical phenyl bioisosteres for drugstructuraloptimization.

The phenyl group is the most prevalent ring system and plays an essential role as a pharmacophore or scaffold in marketed drugs. However, the indiscriminate employment of phenyl is also a major causeof poor physicochemical properties of active molecules. Nonclassical phenyl bioisosteres (NPBs) have emerged as effectivereplacements for phenyl in structural optimization due to their unique steric structures and physicochemical properties. Herein, the effects of widely reported NPBs on physicochemical properties and biological activities, including bicyclo[1.1.1]pentane (BCP), bicyclo[2.1.1]hexanes (BCH), bicyclo[2.2.2]octane (BCO), cubane (CUB) and closo-carboborane, are reviewed. Issues that require consideration while using NPBs andpractical solutions to problems frequently encountered in structural optimization using NPBsare also discussed.

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.

Most of the field/inductive substituent effect works through the bonds

An application of the quantum chemical modeling allowed to investigate the nature of the field/inductive substituent effect (SE). For this purpose, series of X-tert-butyl···tert-butane (TTX) complexes (where X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, NO) were studied. A starting distance between central carbon atoms in substituted and unsubstituted fragments of TTX, dC1–C4, was the same as the distance C1–C4 in X-substituted bicyclo[2.2.2]octane (BCO), where the SE acts both via bonds and via space. A strength of interaction between substituted and unsubstituted components of TTX was described by deformation and interaction energies. The substituent effect on electronic structure through the bonds and the space was characterized using charge of the substituent active region (cSAR) approach. The comparison of the SE characteristics obtained for alicyclic BCO and for TTX complexes document a significantly stronger field/inductive effect through bonds than through space.

Dependence of the Substituent Effect on Solvent Properties

The influence of a solvent on the substituent effect (SE) in 1,4-disubstituted derivatives of benzene (BEN), cyclohexa-1,3-diene (CHD), and bicyclo[2.2.2]octane (BCO) is studied by the use of polarizable continuum model method. In all X-R-Y systems for the functional group Y (NO2, COOH, OH, and NH2), the following substituents X have been chosen: NO2, CHO, H, OH, and NH2. The substituent effect is characterized by the charge of the substituent active region (cSAR(X)), substituent effect stabilization energy (SESE), and substituent constants σ or F descriptors, the functional groups by cSAR(Y), whereas π-electron delocalization of transmitting moieties (BEN and CHD) is characterized by a geometry-based index, harmonic oscillator model of aromaticity. All computations were carried out by means of B3LYP/6-311++G(d,p) method. An application of quantum chemistry SE models (cSAR and SESE) allows to compare the SE in water solutions and in the gas phase. Results of performed analyses indicate an enhancement of the SE by water. The obtained Hammett-type relationships document different nature of interactions between Y and X in aromatic and olefinic systems (a coexistence of resonance and inductive effects) than in saturated ones (only the inductive effect). An increase of electric permittivity clearly enhances communications between X and Y for BEN and CHD systems.

Toward the Physical Interpretation of Inductive and Resonance Substituent Effects and Reexamination Based on Quantum Chemical Modeling.

An application of a charge of the substituent active region concept to 1-Y,4-X-disubstituted derivatives of bicyclo[2.2.2]octane (BCO) [where Y = NO2, COOH, OH, and NH2 and X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, and NO] provides a quantitative information on the inductive component of the substituent effect (SE). It is shown that the effect is highly additive but dependent on the kind of substituents. An application of the SE stabilization energy characteristics to 1,4-disubstituted derivatives of BCO and benzene allows the definition of inductive and resonance contributions to the overall SE. Good agreements with empirical approaches are found. All calculations have been carried out by means of the B3LYP/6-311++G(d,p) method.

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.

Asymmetric 1,4-bis(ethynyl)bicyclo[2.2.2]octane rotators via monocarbinol functionalization. Ready access to polyrotors.

Asymmetric rotators with a 1,4-bis(ethynyl)bicyclo[2.2.2]octane (BCO) core are needed for engineering crystalline arrays of functional molecular rotors. Their synthesis uses carbinol, 2-methyl-3-butyn-2-ol, as a protecting group because of its polar character and its ability to sustain orthogonal functionalization with the further advantage of being readily removed. The synthesis in good yields of unprecedented asymmetric rotors and polyrotors demonstrates the efficiency of this strategy.

Determining the Conformational Landscape of σ and π Coupling Using para-Phenylene and "Aviram-Ratner" Bridges.

The torsional dependence of donor-bridge-acceptor (D-B-A) electronic coupling matrix elements (H(DA), determined from the magnetic exchange coupling, J) involving a spin SD = 1/2 metal semiquinone (Zn-SQ) donor and a spin S(A) = 1/2 nitronylnitroxide (NN) acceptor mediated by the σ/π-systems of para-phenylene and methyl-substituted para-phenylene bridges and by the σ-system of a bicyclo[2.2.2]octane (BCO) bridge are presented and discussed. The positions of methyl group(s) on the phenylene bridge allow for an experimentally determined evaluation of conformationally dependent (π) and conformationally independent (σ) contributions to the electronic and magnetic exchange couplings in these D-B-A biradicals at parity of D and A. The trend in the experimental magnetic exchange couplings are well described by CASSCF calculations. The torsional dependence of the pairwise exchange interactions are further illuminated in three-dimensional, "Ramachandran-type" plots that relate D-B and B-A torsions to both electronic and exchange couplings. Analysis of the magnetic data shows large variations in magnetic exchange (J ≈ 1-175 cm(-1)) and electronic coupling (H(DA) ≈ 450-6000 cm(-1)) as a function of bridge conformation relative to the donor and acceptor. This has allowed for an experimental determination of both the σ- and π-orbital contributions to the exchange and electronic couplings.

Substituent effects in 1-nitro-4-substituted bicyclo[2.2.2]octane derivatives: inductive or field effects?

Interactions between the NO2 group and 13 different substituents (BF2, BH2, CF3, CH3, CHO, CN, F, NH2, NMe2, NO2, NO, OH, OMe) were investigated computationally for bicyclo[2.2.2]octane (BCO) and benzene substituted at 1,4 and 1,3 positions in the ring. Three methods were employed to estimate the character and strength of the substituent effect: substituent effect stabilization energy (SESE), sigma/pi electron donor acceptor index (sEDA/pEDA) and substituent active region (cSAR) parameter. For the first time the sEDA/pEDA parameters were calculated not for the ring but for the NO2 group. All calculations were performed at the B3LYP/6-31G(d,p) level of theory. For 1,4 derivatives, a direct comparison of slopes of linear regressions between BCO and benzene reveals a much better transmission of the substituent effect in the latter. The ratio of slopes (benzene over BCO) is always larger than 4. It follows that the resonance effects, which are absent in the BCO, dominate in this case. For 1,3 derivatives, because of much lower correlation coefficients, estimated standard deviations (ESD) were used to calculate the ratio instead of the slopes. For these systems the ratio is much closer to the unity, which indicates that only the sigma/through space effects are present and they are of similar magnitude in benzene and BCO. It follows from natural population analysis (NPA) charges that the substituent effect in the studied systems is due mainly to through-space interactions.

Amphidynamic crystals of a steroidal bicyclo[2.2.2]octane rotor: a high symmetry group that rotates faster than smaller methyl and methoxy groups.

The synthesis, crystallization, single crystal X-ray structure, and solid state dynamics of molecular rotor 3 provided with a high symmetry order and relatively cylindrical bicyclo[2.2.2]octane (BCO) rotator linked to mestranol fragments were investigated in this work. By use of solid state (13)C NMR, three rotating fragments were identified within the molecule: the BCO, the C19 methoxy and the C18 methyl groups. To determine the dynamics of the BCO group in crystals of 3 by variable temperature (1)H spin-lattice relaxation (VT (1)H T1), we determined the (1)H T1 contributions from the methoxy group C19 by carrying out measurements with the methoxy-deuterated isotopologue rotor 3-d6. The contributions from the quaternary methyl group C18 were estimated by considering the differences between the VT (1)H T1 of mestranol 8 and methoxy-deuterated mestranol 8-d3. From these studies it was determined that the BCO rotator in 3 has an activation energy of only 1.15 kcal mol(-1), with a barrier for site exchange that is smaller than those of methyl (E(a) = 1.35 kcal mol(-1)) and methoxy groups (E(a) = 1.92 kcal mol(-1)), despite their smaller moments of inertia and surface areas.

Crystalline Arrays of Pairs of Molecular Rotors: Correlated Motion, Rotational Barriers, and Space-Inversion Symmetry Breaking Due to Conformational Mutations

The rod-like molecule bis((4-(4-pyridyl)ethynyl)bicyclo[2.2.2]oct-1-yl)buta-1,3-diyne, 1, contains two 1,4-bis(ethynyl)bicyclo[2.2.2]octane (BCO) chiral rotators linked by a diyne fragment and self-assembles in a one-dimensional, monoclinic C2/c centrosymmetric structure where two equilibrium positions with large occupancy imbalance (88% versus 12%) are identified on a single rotor site. Combining variable-temperature (70-300 K) proton spin-lattice relaxation, (1)H T1(-1), at two different (1)H Larmor frequencies (55 and 210 MHz) and DFT calculations of rotational barriers, we were able to assign two types of Brownian rotators with different activation energies, 1.85 and 6.1 kcal mol(-1), to the two (1)H spin-lattice relaxation processes on the single rotor site. On the basis of DFT calculations, the low-energy process has been assigned to adjacent rotors in a well-correlated synchronous motion, whereas the high-energy process is the manifestation of an abrupt change in their kinematics once two blades of adjacent rotors are seen to rub together. Although crystals of 1 should be second harmonic inactive, a large second-order optical response is recorded when the electric field oscillates in a direction parallel to the unique rotor axle director. We conclude that conformational mutations by torsional interconversion of the three blades of the BCO units break space-inversion symmetry in sequences of mutamers in dynamic equilibrium in the crystal in domains at a mesoscopic scale comparable with the wavelength of light used. A control experiment was performed with a crystalline film of a similar tetrayne molecule, 1,4-bis(3-((trimethylsilyl)ethynyl)bicyclo[1.1.1]pent-1-yl)buta-1,3-diyne, whose bicyclopentane units can rotate but are achiral and produce no second-order optical response.

ChemInform Abstract: New Approach to the Preparation of Bicyclo Octane Derivatives via the Enantioselective Cascade Reaction Catalyzed by Chiral Diamine‐Ni(OAc)2 Complex.

AbstractA simple and highly efficient reaction of various 1,2‐diones with substituted nitroalkenes is reported.

New approach to the preparation of bicyclo octane derivatives via the enantioselective cascade reaction catalyzed by chiral diamine-Ni(OAc)2 complex

A highly efficient catalyst system assembled from enantiomerically pure diaminocyclohexane and Ni(OAc)(2) is, for the first time, used to catalyze the cascade Michael-Henry reaction of various diones and substituted nitroalkenes. A series of polyfunctionalized bicyclo[3.2.1]octane derivatives containing four stereogenic centers are prepared with excellent enantioselectivities (up to >99% ee) and diastereoselectivities (up to 50 : 1 dr) with high yields. In addition, via this chiral diamine-Ni(OAc)(2) catalyst system, the base-induced epimerization leading to the decrease of stereoselectivity can be prevented.

Crystal and molecular structure studies of 1′-Benzyl-8-(4-fluorobenzyl)-8-azaspiro[bicyclo-[3.2.1]octane-3,4′-imidazolidine]-2′,5′-dione

The title compound 1′-Benzyl-8-(4-fluorobenzyl)-8-azaspiro[bicyclo[3.2.1] octane-3,4′-imidazolidine]-2′,5′-dione, C23H23FN3O2 is synthesized and the structure is investigated by X-ray diffraction studies. The compound crystallizes in the triclinic crystal class in the P1 space group. The hydantoin ring adopts a planar conformation and is affected by the π conjugation. The pyrrolidine and piperidine rings in the bicyclo octane moiety adopt envelope and chair conformations respectively. The structure exhibits both inter- and intramolecular hydrogen bonds of the type N-H...O, C-H...O, and C-H...N. The oxygen atom in the hydantoin ring simultaneously accepts two hydrogen bonds to form a three-centered hydrogen bonding pattern.

Crystal and Molecular Structure Studies of 1′-Benzyl-8-(4-fluorobenzyl)-8-azaspiro[bicyclo-[3.2.1]octane-3,4′-imidazolodine]-2′,5′-dione

The title compound 1′-Benzyl-8-(4-fluorobenzyl)-8-azaspiro[bicyclo[3.2.1] octane-3,4′-imidazolidine]-2′,5′-dione, C23H23FN3O2 is synthesized and the structure is investigated by X-ray diffraction studies. The compound crystallizes in the triclinic crystal class in the P1 space group. The hydantoin ring adopts a planar conformation and is affected by the π conjugation. The pyrrolidine and piperidine rings in the bicyclo octane moiety adopt envelope and chair conformations respectively. The structure exhibits both inter- and intramolecular hydrogen bonds of the type N-H...O, C-H...O, and C-H...N. The oxygen atom in the hydantoin ring simultaneously accepts two hydrogen bonds to form a three-centered hydrogen bonding pattern.

Solid state coordination chemistry of the oxovanadium-diphosphonate system: Structural consequences of aryl tethers on materials of the type cation/V xO y/diphos, where cation = organoammonium and diphos = 1,4-phenyldiphosphonic acid

Hydrothermal reactions of V 2O 5, 1,4-phenyldiphosphonic acid and an appropriate organoamine, in the presence of HF as solubilizer, were exploited to prepare a series of materials of the general type [organoammonium cation] n [V x O y (H m O 3PC 6H 4PO 3H p ) 3]. Compound 1, [H 3N(CH 2) 4NH 3][V 2O 4(O 3PC 6H 4PO 3)], exhibits a one-dimensional V–P–O substructure, linked through the phenyl tethers of the ligand into a { V 2 O 4 ( O 3 PC 6 H 4 PO 3 ) } n 2 n - layer. Compound 1 is a unique example of a V(V)-diphosphonate phase. Compounds 2 and 3, [H 3N(CH 2) 2NH 3][V 2O 2(O 3PC 6H 4PO 3H) 2] and [H 2pip][V 2O 2(O 3PC 6H 4PO 3H) 2] (H 2pip = piperazinium), exhibit identical two dimensional { V 2 O 2 ( O 3 PC 6 H 4 PO 3 H ) 2 } n 2 n - substructures, constructed from { V 2 O 2 ( O 3 PR ) 2 ( HO 3 PR ) 2 } n 2 n - ribbons connected through the phenyl tethers of the ligands. The three-dimensional framework of [H 3N(CH 2) 7NH 3] 2[V 3O 4(O 3PC 6H 4PO 3) 2] ( 4) consists of V–P–O layers characterized by trinuclear V(IV)-oxide subunits and 9 and 12 polyhedral connect rings; the layers are buttressed by the phenyl spacers to provide the typical “pillared” layer structure common to metal diphosphonate materials. Compound 5, [H 2dabco][V 2F 3O 2(O 3PC 6H 4PO 3H)]·H 2O, is also three-dimensional with oxyfluoro-vanadium(IV) chains linked through the diphosphonate ligands into a framework structure with void spacers to accommodate the {H 2dabco} 2+ cations (dabco = diamino bicyclo octane). The magnetic properties of 2– 5 reflect the structural characteristics of the materials.

Differentiation of molecules in a mixed self-assembled monolayer of H-and Cl-terminatedbicyclo[2.2.2]octane derivatives

H- and Cl-terminal groups of bicyclo[2.2.2]octane (BCO) derivatives in a mixedself-assembled monolayer (SAM) on Au(111) were imaged using a modified Si tip with aCaF2 nanocluster to differentiate the two terminals, which have different electronegativities.In order to achieve this we fabricated a new sample holder, on which aCaF2 single crystal and the mixed SAM on Au(111) could be mounted side byside. We transferred the holder with the two samples into a ultrahighvacuum (UHV) atomic force microscopy (AFM) chamber. Upon cleaving theCaF2 single crystal underUHV, a fresh and clean CaF2(111) surface parallel with the SAM surface appeared within 2 mm of the separation. Themodified Si tip was prepared by repeatedly making contact between a Si tip and theCaF2(111) surface. The resulting modified tip could image the atomic periodicity of aCa2+ and anF− sublatticeon the CaF2(111) surface depending on the sign of the tip-terminating ion, i.e. anF− anda Ca2+ ion, respectively, as reported previously (Foster et al 2002 Phys. Rev. B 66235417). Using the modified Si tip with the known tip-terminating ion, weobserved the Cl-terminal in the surrounding H-terminals in the mixed SAM bynoncontact (NC) AFM. Here, the Cl-terminal is negatively charged due to itselectronegativity and thus the BCO moiety with the Cl-terminal is terminated by aCδ+–Clδ− permanent dipole, while the H-terminal is almost neutral. The Cl-terminal appearedbrighter (more attractive) and darker (more repulsive) than the surrounding H-terminalsin NC-AFM images depending on the sign of the tip-terminating ion, i.e. aCa2+ andan F− on the modified tip, respectively, although the relationship between the image contrast andthe sign of the tip-terminating ion was not always perfect because of the instability of thetip-terminating ion on the nanocluster. The present method can be used to distinguishterminal groups with different electronegativities.

A self-assembled monolayer of a disulfide with a pair of bicyclo[2.2.2]octane moieties on Au(1 1 1) investigated by non-contact atomic force microscopy

A self-assembled monolayer (SAM) of a disulfide with a pair of bicyclo[2.2.2]octane (BCO) moieties was prepared on Au(1 1 1). The resulting SAMs were separately imaged by scanning tunneling microscopy (STM) and non-contact atomic force microscopy (NC-AFM) under ultra-high vacuum at room temperature. The images of the BCO SAM by NC-AFM were similar to those by STM, in which adsorbed molecules were hexagonally packed with the spacing of ca. 6.2 nm.