Partially bridge-fluorinated dimethyl bicyclo[1.1.1]pentane-1,3-dicarboxylates: preparation and NMR spectra

A Practical and Scalable Approach to Fluoro-Substituted Bicyclo[1.1.1]pentanes

After more than 20 years of trials, a practical scalable approach to fluoro-substituted bicyclo[1.1.1]pentanes (F-BCPs) has been developed. The physicochemical properties of the F-BCPs have been studied, and the core was incorporated into the structure of the anti-inflammatory drug Flurbiprofen in place of the fluorophenyl ring.

Bridge Functionalisation of Bicyclo[1.1.1]pentane Derivatives

"Escaping from flatland", by increasing the saturation level and three-dimensionality of drug-like compounds, can enhance their potency, selectivity and pharmacokinetic profile. One approach that has attracted considerable recent attention is the bioisosteric replacement of aromatic rings, internal alkynes and tert-butyl groups with bicyclo[1.1.1]pentane (BCP) units. While functionalisation of the tertiary bridgehead positions of BCP derivatives is well-documented, functionalisation of the three concyclic secondary bridge positions remains an emerging field. The unique properties of the BCP core present considerable synthetic challenges to the development of such transformations. However, the bridge positions provide novel vectors for drug discovery and applications in materials science, providing entry to novel chemical and intellectual property space. This Minireview aims to consolidate the major advances in the field, serving as a useful reference to guide further work that is expected in the coming years.

Polyhalogenated Bicyclo[1.1.1]pentane-1,3-dicarboxylic Acids

Herein we report the highly selective radical chlorination of 2,2-difluorobicyclo[1.1.1]pentane-1,3-dicarboxylic acid. Together with radical hydrodechlorination by TMS₃SiH, four new bicyclo[1.1.1]pentane cages carrying two fluorine and one to three chlorine atoms in bridge positions have been obtained. The exact positions of all halogen atoms have been confirmed by X-ray diffraction. The acidity constants (pK_a) for all new derivatives have been determined by capillary electrophoresis, and these experimental values show excellent agreement with pK_as predicted by DFT methods. Extensive DFT calculations have been used to rationalize the selective formation of four out of nine possible F₂Cl_1-4 isomers of bridge-halogenated bicyclo[1.1.1]pentanes and to obtain relative strain energies for all possible isomers.

Improving Nonspecific Binding and Solubility: Bicycloalkyl Groups and Cubanes as para-Phenyl Bioisosteres

Bicycloalkyl groups have been previously described as phenyl group bioisosteres. This article describes the synthesis of new building blocks allowing their introduction into complex molecules, and explores their use as a means to modify the physicochemical properties of drug candidates and improve the quality of imaging agents. In particular, the replacement of an aromatic ring with a bicyclo[1.1.1]pentane-1,3-diyl (BCP) group improves aqueous solubility by at least 50-fold, and markedly decreases nonspecific binding (NSB) as measured by CHI(IAM), the chromatographic hydrophobicity index on immobilized artificial membranes. Structural variations with the bicyclo[2.2.2]octane-1,4-diyl group led to more lipophilic molecules and did not show the same benefits regarding NSB or solubility, whereas substitutions with cubane-1,4-diyl showed improvements for both parameters. These results confirm the potential advantages of both BCP and cubane motifs as bioisosteric replacements for optimizing para-phenyl-substituted molecules.

Organic chemistry. Strain-release amination

To optimize drug candidates, modern medicinal chemists are increasingly turning to an unconventional structural motif: small, strained ring systems. However, the difficulty of introducing substituents such as bicyclo[1.1.1]pentanes, azetidines, or cyclobutanes often outweighs the challenge of synthesizing the parent scaffold itself. Thus, there is an urgent need for general methods to rapidly and directly append such groups onto core scaffolds. Here we report a general strategy to harness the embedded potential energy of effectively spring-loaded C-C and C-N bonds with the most oft-encountered nucleophiles in pharmaceutical chemistry, amines. Strain-release amination can diversify a range of substrates with a multitude of desirable bioisosteres at both the early and late stages of a synthesis. The technique has also been applied to peptide labeling and bioconjugation.

Gearing motion in cogwheel pairs of molecular rotors: weak-coupling limit

Investigation of the rotor dynamics by X-ray diffraction, spin–lattice relaxation, and DFT modelling of the two rotational barriers in arrays of rod-like molecules with 1,3-bis(ethynyl)bicyclo[1.1.1]pentane rotators conclude to gearing motion between two rotors in a pair.

Expedient synthesis of 3-phenylbicyclo[1.1.1]pentan-1-amine via metal-free homolytic aromatic alkylation of benzene

The inquisitiveness on the use of the BCP motif as a modern lead optimization tactic entails reliable synthetic access. In that direction, we disclose a new and versatile approach to 3-phenylbicyclo[1.1.1]pentan-1-amine, via metal-free homolytic alkylation of benzene.

Unexpected geometrical effects on paramagnetic spin-orbit and spin-dipolar 2J(FF) couplings

The second-rank tensor character of the paramagnetic spin-orbit and spin-dipolar contributions to nuclear spin-spin coupling constants is usually ignored when NMR measurements are carried out in the isotropic phase. However, in this study it is shown that isotropic (2)J(FF) couplings strongly depend on the relative orientation of the C-F bonds containing the coupling nuclei and the eigenvectors of such tensors. Predictions about such effect are obtained using a qualitative approach based on the polarization propagator formalism at the RPA, and results are corroborated performing high-level ab initio spin-spin coupling calculations at the SOPPA(CCSD)/EPR-III//MP2/EPR-III level in a model system. It is highlighted that no calculations at the RPA level were carried out in this work. The quite promising results reported in this paper suggest that similar properties are expected to hold for the second-rank nuclear magnetic shielding tensor.

Theoretical studies on polynitrobicyclo[1.1.1]pentanes in search of novel high energy density materials

Bicyclo[1.1.1]pentane is a highly strained hydrocarbon system due to close proximity of nonbonded bridge head carbons. Based on fully optimized molecular geometries at the density functional theory using the B3LYP/6-31G* level, densities, detonation velocities, and pressures for a series of polynitrobicyclo[1.1.1]pentanes, as well as their thermal stabilities were investigated in search for high energy density materials (HEDMs). The designed compounds with more than two nitro groups are characterized by high heat of formation and magnitude correlative with the number and space distance of nitro groups. Density was calculated using the crystal packing calculations and an increase in the number of nitro groups increases the density. The increase in density shows a linear increase in the detonation characteristics. Bond dissociation energy was analyzed to determine thermal stability. Calculations of the bond length and bond dissociation energies of the C-NO2 bond indicate that this may be the possible trigger bond in the pyrolysis mechanism. 1,2,3-Trinitrobicyclo[1.1.1]pentane (S3), 1,2,3,4-tetranitrobicyclo[1.1.1]pentane (S4), and 1,2,3,4,5-pentanitrobicyclo[1.1.1]pentane (S5) have better energetic characteristics with better stability and insensitivity, and as such may be explored in defense applications as promising candidates of the HEDMs series.

cis-endo-Bicyclo[1.1.1]pentane-1,2,3,4- tetracarboxylic Acid and Its Derivatives

[reaction: see text] We report the synthesis of cis-endo-bicyclo[1.1.1]pentane-1,2,3,4-tetracarboxylic acid and several of its derivatives with differentiated bridgehead and bridge positions, starting with tetracyclo[3.2.0.0(1,6).0(2,6)]heptane.

Parameter-free structure-property correlation via progressive reaction posets for substituted benzenes

Progressive reaction networks as frequently arise in chemistry are naturally identifiable as "partially ordered sets" (or posets). Here the direction of the reaction identifies the partial ordering of the set of molecular species. The possibility that different properties are similarly ordered is a further natural consideration and is here investigated for a suite of over 30 properties for (methyl and chloro) substituted benzenes. Such a posetic correlation is favorably demonstrated for these substituted benzenes, and it is illustrated how suitable properties may be simply predicted in an interpolative parameter-free (albeit not model-free) fashion through the use of the reaction poset. Some numerical model-quality indicators are identified, and the simple approach is deemed quite reasonable.

Substituent effects on scalar J(13C, 13C) couplings in pyrimidines. An experimental and DFT study

One- two- and three 13C, 13C (n = 1, 2, 3) scalar couplings, (n)J(C,C) in a set of pyrimidine derivatives were studied both experimentally at natural abundance and theoretically by their DFT calculation of all four contributions. Trends of non-contact terms are discussed and substituent effects are rationalized, comparing some of them with the corresponding values in benzene and pyridine. Although substituent effects on non-contact terms are relatively important, the whole trend is dominated by the Fermi contact term. According to the current literature, substituent effects on 1J(C,C) couplings in benzene derivatives are dominated by the inductive effect, which, apparently, is also the case in nitrogen heteroaromatic compounds. However, some differences observed in this work for substituent effects on 1J(C,C) couplings in pyrimidine derivatives suggest that in the latter type of compounds substituent effects can be affected by the orientation of the ring nitrogen lone pairs.

DFT-GIAO calculations of19F NMR chemical shifts for perfluoro compounds

The (19)F NMR shieldings for 53 kinds of perfluoro compounds were calculated by the B3LYP-GIAO method using the 6-31G(d), 6-31+G(d), 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311++G(d,p), 6-311G(2d,2p), 6-311++G(2d,2p), 6-311++G(2df,2p), 6-311++G(3d,2p), and 6-311++G(3df,2p) basis sets. The diffuse functions markedly reduce the difference between the calculated and experimental chemical shifts. The calculations using the 6-31++G(d,p) basis set give the chemical shifts within 10 ppm deviations from experimental values except for the fluorine nuclei attached to an oxygen atom, a four- and a six-coordinated sulfur atom, and FC(CF(3))(2) attached to a sulfur atom.

On the capriciousness of the FCCF Karplus curve

Numerous well-behaved Karplus curves correlating dihedral angle (phi) and NMR coupling constants (3JXY) exist for X-C-Z-Y fragments with X or Y = H, C, F, and P. Absent is the enigmatic F-C-C-F moiety. By calculating the four Ramsey contributions to 3JFF for F-CH2-CH2-F, a pleasing phi/3JFF curve with both positive and negative regions arises. Unlike the H-C-C-H curve, F-C-C-F is PSO vs FC dominated. The latter and the F lone electron pairs cause both the negative J values and the substituent-induced J-leveling effect.

Synthesis and structure of trigonal and tetragonal connectors for a "Tinkertoy" construction set

We describe a convergent synthesis of eight 1,3,5- and 1,2,4,5-substituted benzene derivatives with long rigid arms containing 4-pyridyl, 2,2'-bipyridyl, and 2,2'-bipyrimidyl termini, meant to be used as trigonal or tetragonal connectors for the construction of large molecular structures. The synthesis involved copper-free Pd-mediated coupling of terminal acetylenes to aryl halides. First, one of the termini of 1,3-diethynylbicyclo[1.1.1]pentane was coupled with a brominated aza heterocycle, and second, 3 equiv of the resulting extended arm were coupled with 1,3,5-triiodobenzene or 4 with 1,2,4,5-tetraiodobenzene. An improved large-scale synthesis for 1,3-diethynylbicyclo[1.1.1]pentane is described. The structures of two of the arms were determined by single-crystal X-ray analysis. Several long molecular rods with 4-pyridyl termini were obtained as byproducts, and a single-crystal X-ray structure is reported for the shortest of these.