Regio- and stereocontrolled synthesis and conformational analysis of benzimidazole nucleosides

Regio- and stereocontrolled synthesis and conformational analysis of a series of benzimidazole nucleosides were achieved. A simple method by ¹H NMR 1D NOE experiment was developed for estimation of syn or anti conformation of benzimidazole nucleosides. Substituents at C2 of benzimidazole demonstrated to play a key role both in the unexpected regioselectivity of the glycosidic reaction and in the conformation distributions of the final products.     

Synthesis and conformational analysis of new troponyl aromatic amino acid

Synthetic peptides are in huge demand in expansion of potential peptide mimics, which may have improved or comparable function as natural one. With these concerns, phenyl bearing aromatic amino acids and peptides has extensively explored, because phenyl residue has high probability in forming stable secondary structure, owing to the presence of an extra stabilizing factor as π–π non-covalent interactions. Apart from phenyl bearing benzenoid aromatic amino acids, a few non-benzenoid aromatic derivatives such as tropolone and related compounds are also occurred in nature, but troponyl containing amino acids and peptides are very poorly understood. Tropolonyl derivatives also contain carbonyl functional group, which may play an important role to provide stable conformation in peptide. Herein we report the synthesis, and conformational analysis of rationally designed new unnatural δ-amino acid, troponyl aminoethylglycine (Tr-aeg), which contains troponyl residue as side chain in flexible aminoethylglycine (aeg) amino acid backbone. We also demonstrate the role of troponyl carbonyl of Tr-aeg residue in hydrogen bonding with adjacent amide NH of their hybrid di/tri-peptides with NMR methods and DFT calculations. In future, Tr-aeg amino acid would be a potential building block in development of promisable peptide mimics.     

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,conformational analysis and free radical scavenging activity of some new spiropyranoquinolinones

A series of novel spiroadamantyl- and spirocyclical substituted pyranoquinolin-2-ones were synthesized and the conformation of the pyran ring was investigated. The free radical scavenging activity of the synthesized compounds was determined by their interaction with the stable free radical 1,1-diphenyl-2-picrylhydrazyl (DPPH). All compounds tested scavenged the DPPH radical and among them derivatives possessing extended conjugation showed the highest activity.     

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 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 tetrahydroisoquinoline- and piperidine-fused 1,3,4,2-oxadiazaphosphinanes, new ring systems

Through cyclization of tetrahydroisoquinoline and piperidine 1,2-hydrazino alcohols with phenylphosphonic dichloride and phenyl dichlorophosphate, P-epimeric diastereomers of 1,6,7,11b-tetrahydro-4H-1,3,4,2-oxadiazaphosphino[5,4-a]isoquinoline-3-oxides (13 and 14), 1,6,11,11a-tetrahydro-4H-1,3,4,2-oxadiazaphosphino[4,5-b]isoquinoline-3-oxides (15 and 16) and 1,6,7,8,9,9a-hexahydro-4H-pyrido[1,2-d][1,3,4,2]oxadiazaphosphinane-3-oxides (17 and 18), the first representatives of these ring systems, were prepared. NMR and X-ray diffraction studies revealed that, independently of the P-substituent and the relative configuration of the phosphorus atom, 13, 14, 17 and 18 could be characterized by trans-connected hetero rings and the chair conformation of the 1,3,4,2-oxadiazaphosphinane moiety, while the stereochemistry of the connection of the hetero rings in the 1,3,4,2-oxadiazaphosphinanes linearly fused to tetrahydroisoquinoline (15 and 16) was found to be dependent on the P-configuration relative to that of the carbon at the annelation.     

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 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.     

Design, synthesis, conformational analysis and biological activities of purine-based 1,2-di-substituted carbocyclic nucleosides

New 1,2-di-substituted carbocyclic nucleosides with 6-chloropurine, adenine and hypoxanthine bases were synthesized by construction of purine on the primary amino group of (+/-)-trans-2-aminocyclopentylmethanol. AM1 calculations showed close correspondence between the positions of the heteroatoms in the adenine derivative and dideoxyadenosine. The most active of the new compounds in antiviral assays and antitumoral assays against L1210/0, MOLT4/C8 and CEM/0 cells was the 6-chloropurine derivative.     

Synthesis, characterization, and conformational analysis of new perfunctionalized calix[9]arenes

The synthesis of a series of six new per-substituted p-tert-butylcalix[9]arenes derivatives has been achieved. Functions such as ester, nitrile, or carbonate have been grafted on the phenolic oxygens of calix[9]arene: p-tert-butylcalix[9]arene nona-ethyl acetate, p-tert-butylcalix[9]arene nona-carboxylic acid, p-tert-butylcalix[9]arene nona-cyanopropyloxy, p-tert-butylcalix[9]arene nona-tert-butoxycarbonyle, p-tert-butylcalix[9]arene nona-acetyl, and p-tert-butylcalix[9]arene nona-trifluoroacetyl have been obtained in good yields (from 48% to 78%) and fully characterized. The X-ray structures of p-tert-butylcalix[9]arene nona-tert-butoxycarbonyl and p-tert-butylcalix[9]arene nona-ethyl acetate have been determined. A dynamic NMR study has revealed the high conformational mobility of such structures, even at low temperature.     

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 a ribo-type cyclohexenyl nucleoside

A straightforward approach to a novel class of ribo-type cyclohexenyl nucleosides is described. An electron-demand Diels-Alder reaction forms the key-step of the chosen synthetic pathway. Although the difference is small, conformational analysis using NMR shows that this nucleoside analogue adopts preferentially an 2H3 conformation (S-type), while the "deoxy" cyclohexenyl analogue has a preference for a C3' endo conformation (N-type). Analyses of the conformational equilibrium reveal that, in the given experimental conditions, the difference between adenosine and its cyclohexenyl congener resides in their different DeltaG values; furthermore, in adenosine, the conformational preference is of enthalpic origin, whereas in the cyclohexenyl congener, the conformational preference is of entropic origin.     

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.     

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.