Synthesis of enantiomeric-pure cyclohexenyl nucleoside building blocks for oligonucleotide synthesis

Lipases were used for the resolution of (±) (4aR, 7R, 8aS)-2-phenyl-4a,7,8,8a-tetrahydro-4H-1,3-benzodioxine. This separation was carried out on preparative scale and used for the synthesis of eight phosphoramidites of cyclohexenyl nucleosides (d- and l-series).     

Synthesis and conformational studies of amide-linked cyclic homooligomers of a thymidine-based nucleoside amino acid

Cyclic homooligomers of a thymidine-based nucleoside amino acid were synthesized from the linear dimer using BOP reagent in the presence of DIPEA under dilute conditions. Conformational analysis by NMR and constrained MD studies revealed that all the cyclic products had symmetrical structures. The NH and CO groups in these molecules point in opposite directions with near perpendicular orientation with respect to the plane of the macrocyclic ring having CO on the same side as the base.     

Synthesis and conformational analysis of efrapeptins

The efrapeptin family of peptide antibiotics produced by the fungus Tolypocladium niveum, and the neo‐efrapeptins from the fungus Geotrichum candidumare inhibitors of F₁‐ATPase with promising antitumor, antimalaria, and insecticidal activity. They are rich in C^α‐dialkyl amino acids (Aib, Iva, Acc) and contain one β‐alanine and several pipecolic acid residues. The C‐terminus bears an unusual heterocyclic cationic cap. The efrapeptins C–G and three analogues of efrapeptin C were synthesized using α‐azido carboxylic acids as masked amino acid derivatives. All compounds display inhibitory activity toward F₁‐ATPase. The conformation in solution of the peptides was investigated with electronic CD spectroscopy, FT‐IR spectroscopy, and VCD spectroscopy. All efrapeptins and most efrapeptin analogues were shown to adopt helical conformations in solution. In the case of efrapeptin C, VCD spectra proved that a 3₁₀‐helix prevails. In addition, efrapeptin C was conformationally studied in detail with NMR and molecular modeling. Besides NOE distance restraints, residual dipolar couplings (RDC) observed upon partial alignment with stretched PDMS gels were used for the conformational analysis and confirmed the 3₁₀‐helical conformation.     

Synthesis and conformational analysis of redox-active ferrocenyl-calixarenes

A novel synthetic approach toward redox-active calixarene-based receptors is described wherein ferrocene fragments have been introduced at the lower rim through anion-binding urea or amide connections. A thorough ¹H NMR investigation on a series of calixarene-ferrocene receptors was performed in order to estimate their hydrogen bonding-driven self-association properties and improve our understanding of the correlation between molecular structures and redox properties.     

Synthesis and conformational analysis of 1,3-azasilinanes

1-Isopropyl-3-methyl-3-phenyl-1,3-azasilinane 1 and 1-isopropyl-3,3-dimethyl-1,3-azasilinane 2 were synthesized and a detailed analysis of their NMR spectra, conformational equilibria and ring inversion processes is presented. Low temperature ¹H/¹³C NMR spectroscopy, iteration of the ¹H NMR spectra and quantum chemical calculations showed slight predominance of the Ph_eqMe_ax over the Ph_axMe_eq conformer of 1 at low temperature. The barrier for the chair to chair interconversion of both compounds was measured to be 8.25 kcal/mol.     

Synthesis and conformational analysis of phosphine selenides

Methods of preparation of complex phosphine selenide via the original Trofimov–Gusarova reaction are described. The results of the products conformational analysis by means of a set of physical methods (IR spectroscopy, dipole moments, and quantum chemical calculation) are presented.     

Synthesis of cannabidiols via alkenylation of cyclohexenyl monoacetate

[reaction: see text] Because of the lack of potency binding to the receptors responsible for psychoactivity, cannabidiol has received much attention as a lead compound to develop a nonpsychotropic drug. Herein, we establish a method to access not only cannabidiol but also its analogues. The key reaction is nickel-catalyzed allylation of 2-cyclohexene-1,4-diol monoacetate with a new reagent, (alkenyl)ZnCl/TMEDA, which gives a S(N)2-type product with 94% regioselectivity in good yield.     

Synthesis and conformational analysis of isomeric 3-propananilidotropanes

The isomeric 3-anilino and 3-propananilidotropanes have been synthesized and obtained in isomerically pure form. The configurations and solute conformations of these isomers were studied via glc and nrar analysis. The 3β-isomers have been shown to exist in the normal piper-idine chair conformation whereas the 3α-anilino tropane exists in a flattened piperidine chair conformation and the 3α-propananilidotropane isomer preferentially exists in a conformation in which the piperidine ring system is a boat.     

Synthesis and conformational analysis of furfuryl vinyl ethers

Five furfuryl vinyl ethers were synthesized from the corresponding furfuryl alcohols and acetylene at high and atmospheric pressures in superbasic medium KOH-DMSO. On the example of 2-vinyloxymethylfuran and 2-vinyloxymethyltetrahydrofuran, their conformational structures have been studied by quantum chemistry methods, NMR and IR spectroscopy. In particular, from the results of the quantum-chemical calculations, as well as on the basis of experimental measurement and nonempirical calculations of the high level spin-spin coupling constants ¹³C-¹³C and ¹³C-¹H, a conclusion has been drawn on the s-cis-orientation of the vinyl groups with respect to the C_α-O bond in the predominant conformers of 2-vinyloxymethylfuran and 2-vinyloxymethyltetrahydrofuran.     

Synthesis and conformational analysis of new cyclobutane-fused nucleosides

[structure: see text]. A stereselective synthesis of 3-oxabicyclo[3.2.0]heptane nucleoside analogues, which were designed as conformational mimics of the anti-HIV agents 2',3'-didehydro-2',3'-dideoxythimidine (stavudine, d4T) and 2',3'-didehydro-2',3'-dideoxyadenosine (d4A), is described. The target compounds were prepared by condensation of a common intermediate bicyclic acetate, derived from a homochiral 2(5H)-furanone, with pyrimidine and purine bases under modified Vorbrüggen conditions. The conformational behavior of the synthesized nucleoside analogues was studied by NMR spectroscopy and X-ray crystallography.     

Synthesis of a bicyclic double-headed nucleoside

An attempt of preparing a carbocyclic LNA-analogue using different RCM-methods failed. However, a compound with a hemiacetal linker between the C2′ and the C4′-positions was isolated and found to be a suitable substrate for making a conformationally restricted double-headed nucleoside. This contains two uracil nucleobases organized on a bicyclic skeleton and is locked in an N-type conformation.     

Synthesis and conformational analysis of glycomimetic analogs of thiochitobiose

The synthesis of six analogs of N,N′-diacetylchitobiose is reported, including a novel transglycosylation reaction for the preparation of S-aryl thioglycosides. The conformations of the compounds were studied by a combination of NMR spectroscopy and molecular modeling, using force field calculations. In the case of the S-aryl thioglycosides with exclusively S-glycosidic linkages, dihedral angles of the disaccharidic S-glycosidic bonds, Φ′ and Ψ′ and of the S-arylglycoside bonds, Φ and Ψ, were found to be similar, whereas they were different in mixed glycosides and in a thiazoline derivative. An adequate correlation between the calculated H,H-distances of the local minima and the measured NOE contacts was achieved by applying population-weighted averages over participating conformers based on weighted relative energies.     

Synthesis and conformational analysis of 18-membered Aib-containing cyclohexapeptides

The synthesis and conformational analysis of two Aib-containing cyclic hexapeptides, cyclo(Gly-Aib-Leu-Aib-Phe-Aib) 1 and cyclo(Leu-Aib-Phe-Gly-Aib-Aib) 2, is described. The linear precursors of 1 and 2 were prepared using solution phase techniques, and the cyclization efficiency of three different coupling reagents (HATU, PyAOP, DEPC) was examined. The success of the cyclization was found to be reagent dependent. Solid-state conformational analysis of 1 and 2 was performed by X-ray crystallography and has revealed some unusual features as all three Aib residues of 1 assume nonhelical conformations. Furthermore, the residue Aib⁴ adopts an extended conformation (?=−175.9(3)°, ψ=+178.6(2)°), which is, to the best of our knowledge, the first observation of an Aib residue adopting an extended conformation in a cyclopeptide. The structure of 1 is also a rare example in which an Aib residue occupies the (i+1) position of a type II′ β-turn, stabilized by a bifurcated hydrogen bond. The cyclic peptide 2 adopts a more regular conformation in the solid state, consisting of two fused β-turns of type I/I′, stabilized by a pair of intramolecular hydrogen bonds. In addition, the conformational study of the cyclic peptide 1 in DMSO-d₆ by NMR spectroscopy and molecular dynamics simulations revealed a structure, which is very similar to its structure in the crystalline state.     

Synthesis and conformational analysis of benzimidazole-based reverse turn mimics

New benzimidazole-based tetrapeptide mimics were synthesized and their conformational features were studied by NMR and molecular modeling techniques. All the analyses led to the conclusion that a β-turn is stabilized in both 2 and 3. Since values of the torsion angles do not allow an univocal definition of the β-turn type, structures 2 and 3 could be assigned to the generic type IV classification.     

Robust synthesis of enantiopure cyclohexenyl analogues of 2/3-deoxyribose sugars as carbocyclic nucleoside precursors

An expedient synthesis of 2-deoxy (10) and 3-deoxy (11) cyclohexenyl analogues of 2-deoxy and 3-deoxy-d-ribose sugar from commercially available starting materials is reported. Highly efficient enzymatic resolution of the key compound 10 is described using lipase under hydrolytic conditions. The robust methodology applied here will be useful to synthesize cyclohexenyl nucleosides, which possess potent antiviral activity and are capable of gene silencing via RNAi or antisense applications.     

Synthesis and conformational analysis of a chiral fluorinated bilirubin analog lacking carboxyl groups

An optically active analog 1 of etiobilirubin-IVγ with a single fluorine on each of the C(8) and C(12) alkyl groups has been synthesized in order to examine its potential for hydrogen bonding with fluorine. Circular dichroism spectroscopy reveals an unusually strong influence of 2,2,2-trifluoroethanol solvent on diastereo-selection of the M-helical conformation of (8¹S,12¹S)-1.     

Synthesis and conformational analysis of some cyanomethylene derivatives of piperidines

Five 4-dicyanomethylene derivatives 6–10, N-cyanoacetyl-cis-2,6-diphenylpiperidin-4-one 11 and 4-cyano(ethoxycarbonyl)-methylene-cis-2,6-bis(o-chlorophenyl)piperidine 12 were synthesised by condensing the appropriate piperidin-4-ones 13–17 with malononitrile/ethylcyanoacetate and their ¹H and ¹³C NMR spectra were recorded. The ¹H-¹H COSY spectrum for 6 and NOESY spectra for 8, 10, and 11 were also recorded. Based on coupling constants and the results obtained from NOESY spectra boat conformation for 10 and epimerised chair conformations for 8 and 9 have been proposed. Other derivatives adopt normal chair conformations. Theoretical calculations and the ¹H and ¹³C chemical shifts also support the above conformations. Mass spectra were also recorded for 6–12.     

Synthesis and conformational analysis of novel trimeric maleimide cross-linking reagents

Nine homotrifunctional cross-linking reagents are presented. Their synthesis and chemical properties as well as their characterization by classical mechanical conformational searching techniques is reported. Mixed Low Mode and Monte Carlo searching techniques were used to exhaustively sample the OPLS2005/GBSA(water) potential energy surface of trisubstituted cyclohexane and benzene derivatives of C3 symmetry. Geometric structure, molecular length, and hydrogen-bonding patterns were analyzed. Nonaromatic compounds exhibited exclusively chair conformations at low energies, with a preference for axial or equatorial arms depending upon the presence of additional ring substituent Me groups. Increasing chain length often resulted in overall shorter molecular length due to additional chain flexibility. These results were consistent with one- and two-dimensional temperature-dependent NMR studies.