Do intramolecular halogen bonds exist? Ab initio calculations and crystal structures’ evidences

Cl···O intramolecular contacts are analysed here. Hence the Cambridge Structural Database (CSD) search was performed to find five-membered Cl–C=C–C=O pseudo-rings closed through Cl···O intramolecular contacts. Such rings were analysed and it was found that some of Cl···O distances are smaller than the corresponding sum of van der Waals radii. Additionally ab initio MP2/6-311++G(d,p) calculations and AIM analyses were carried out here on 3-chloropropenal and its fluoro derivatives to deepen the nature of intramolecular Cl···O interactions, some of findings may indicate that they are attractive and stabilizing ones. This paper is dedicated to Prof. T. M. Krygowski on the occasion of his 70th birthday     

Is planarity of pyridin-2-yl- and pyrazin-2-yl-formamide thiosemicarbazones related to their tuberculostatic activity? X-ray structures of two pyrazine-2-carboxamide-N′-carbonothioyl-hydrazones

Crystal structures of two title compounds and several their relatives known earlier reveal conservative and characteristic features, which may be related to their tuberculostatic activity. The molecules are predominantly planar due to conjugation through five successive bonds in the zwitterionic fragment S⁻–C(sp²)–N–NH⁺–C(sp²)–NH₂ and intramolecular hydrogen bonds, which prevent rotation of the adjacent pyrazine (or pyridine) ring. It has been suggested that in spatial sense such planar molecules resemble acridines intercalating with nucleic acids and that similar process may be responsible for tuberculostatic activity of the title pyrazine-2-carboxamide-N′-carbonothioyl-hydrazones.     

Theoretical study on the intramolecular proton transfer reactions of 3-methyl-5-hydroxyisoxazole and its water complexes

The optimized structures and proton transfer reactions of 3-methyl-5-hydroxyisoxazole and its water complexes (3-M-5-HIO · (H₂O)_n · (n = 0–3)) were computed at B3LYP and MP2 theoretical level. The results indicates that 3-M-5-HIO has four isomers (Ecis, Etrans, K1 and K2), and the keto tautomer, and K2 is the most stable isomer in the gas phase. Hydrogen bonding between 3-M-5-HIO and the water molecules can dramatically lower the barrier by the concerted transfer mechanism. Ecis · (H₂O)₃ → K1 · (H₂O)₃ and Ecis · (H₂O)₂ → K2 · (H₂O)₂ is found to be very efficient. Comparing with the proton transfer mechanism of 5-HIO shows that the methyl substitution prevents the intramolecular proton transfer.     

Synthesis of latonduine derivatives via intramolecular Heck reaction

The synthesis of indole ring-fused benzazepinone series as latonduine derivatives has been developed via an intramolecular Heck reaction. The scope has been enlarged not only to indole moiety but also to pyrrolo and benzo[b]thiophene nuclei. Several derivatives prepared have been evaluated in vitro for their antiproliferative activities on breast cancer cell lines. Some of them showed promising cytotoxic activities.     

Synthesis of 1-oxa-2-silacyclopentane derivatives via intramolecular nucleophilic attack at silicon

Metalation of (HSiMe₂)₃CH with lithium diisopropylamide (LDA) in THF gives (HSiMe₂)₃CLi, which reacts with ethylene oxide, propylene oxide, 1,2-epoxy butane, 1,2-epoxy pentane, 1,2-epoxy hexane, and epichlorohydrin to give the corresponding 1-oxa-2-silacyclopentane derivatives. Then, glycidylmethacrylate (GM) random copolymers with styrene (St) (in a 1:1 and 1:3 mol ratio) were synthesized by solution free radical polymerization at 70(±1) °C using α,α′-azobis(isobutyronitrile) (AIBN) as an initiator. Both types of copolymers were treated with (HSiMe₂)₃CLi to give new modified copolymers. The reaction of (HSiMe₂)₃CLi with epoxides on the side chains of the copolymers does not lead to intramolecular nucleophilic attack contrary to simple epoxides. All the products have been characterized by spectroscopic techniques.     

Neat total synthesis of six monoterpenic alkaloids of the actinidine series

A concise enantiopure synthesis of six monoterpenic alkaloids of the actinidine series possessing a cyclopenta[c]pyridine skeleton, (+)-deoxyrhexifoline (4), (+)-boschniakinic acid (5), (+)-boschniakine (6), (−)-plantagonine (7), (−)-indicaine (8) and (−)-tecostidine (9) is reported starting with the chiral precursor 3-bromo-5-((4R)-phenyloxazolin-2-yl)pyridine (10). It involves a C-4 regioselective connection of a butene appendice and an intramolecular 5-exo-trig Heck annulation sequence followed by hydrogenation of the exocyclic alkene. Mixture of (3R)- and (3S)-7-((4R)-phenyloxazolin-2-yl)cyclopenta[c]pyridines was separated by HPLC before being transformed into enantiopure natural products (4-9) by modification of the oxazoline group.     

Total synthesis of the alkaloid (−)-codonopsinine from l-xylose

The enantiopure total synthesis of (−)-codonopsinine is described from commercially available l-xylose in 20% overall yield. The key steps included Julia trans olefination and cascade epoxidation-cyclisation strategies.     

Synthesis of fused bicyclic pyridines with microwave-assisted intramolecular hetero-Diels-Alder cycloaddition of acetylenic pyrimidines

A series of acetylenic pyrimidines was synthesized and subjected to microwave irradiation. In contrast to conventional heating, the microwave irradiations generally gave clean conversion to fused bicyclic pyridines for all substrates reported with shorter reaction time. This method has been successfully applied to the synthesis of both fused lactones and lactams.     

How π-electron delocalisation reflects replacement of H+ with Li+ in variously substituted malonaldehydes

Correlations were studied between the properties of Bader's ring and bond critical points calculated for variously substituted malonaldehyde (containing intramolecular H-bond) and its π-electron delocalisation expressed by aromaticity indices HOMA and NICSs. It was observed that π-electron delocalisation of the system strongly depends on the substituent and its position. Replacement of the H⁺ with Li⁺ in malonaldehyde allowed us to study the role of unoccupied 2p orbital in π-electron delocalisation. In the case of lithium system the aromaticity is increased as compared with the malonaldehyde itself and moreover with the malonaldehyde anion. This proves that the unoccupied 2p orbital of Li⁺ may play a significant role in delocalisation of π-electrons due to its low orbital energy. In the case of lithium system the substituent effect is negligible, which resembles the situation in benzene derivatives. Dedicated to Prof. Karl Jug on the occasion of his 65th birthday anniversary.     

The Role of Intramolecular Hydrogen Bonds vs. Other Weak Interactions on the Conformation of Hyponitrous Acid and Its Mono- and Dithio-Derivatives

High level ab initio and density functional theory calculations have been carried out to investigate the relative stability of the different conformers of hyponitrous acid and its mono- and dithio-derivatives. Geometries and vibrational frequencies were obtained at the B3LYP/6-311+G(d,p) level and final energies through B3LYP/6-311++G(3df,2pd) single point calculations. The reliability of this theoretical scheme has been assessed by comparing these DFT results with those obtained at the G3 level of theory, for some suitable cases. The cis conformers of hyponitrous acid and its mono- and dithio-derivatives are systematically more stable than the trans ones because in the cis conformation a dative interaction between the nitrogen-lone pairs and the σ_NX^* antibonding orbital is significantly favored. Quite interestingly, in general, the conformers presenting an intramolecular hydrogen bond (IHB) are not the global minima of the corresponding potential energy surfaces and only for hyponitrous acid the conformer with a OH ⋅s O IHB is slightly more stable than the cis conformer without IHB. The low stability of the tautomers with IHB is closely related with another weak intramolecular interaction which involves the lone-pairs of the chalcogen atoms and the π_NN^* antibondig orbital, and which is significantly perturbed when the IHB is formed.