Conformational analysis of polypropylene chains bound to model catalytic sites

The models of catalytic sites for isospecific Ziegler-Natta polymerization proposed previously (edges and reliefs on lateral surfaces of violet TiCl₃) are compared in order to verify their validity in the presence of long alkyl groups and of analyzing the conformational constraints imposed by the TiCl₃ surface on the growing chain. Our results indicate that sites on edges of lateral surfaces parallel or nearly parallel to the c axis may be not suitable for the coordination of long alkyl chains; the coordination of long alkyl chains at less hindered sites, such as edges of inclined lateral surfaces or reliefs, do not involve any increase of repulsive interactions for an isobutyl group. Further, these latter sites allow the optimum spiralization of the chain at a very early stage of growth, and their isospecific behaviour is not affected by the presence of configuration defects in the growing chain.     

Conformational analysis of 2-substituted 1-nitro-and 1-bromo-1-nitroethenes

Conformational analysis of 2-trichloromethyl(ethoxycarbonyl)-1-nitro-and 2-trichloromethyl-(ethoxycarbonyl)-1-bromo-1-nitroethenes was performed using the dipole moment method, IR spectroscopy, and DFT quantum-chemical calculations (B3LYP/6-31G*). The nitro and ester (or trichloromethyl) groups in the molecules of these compounds were found to occupy trans positions with respect to the double C=C bond, i.e., the nitroalkenes have E, and their bromine-containing analogs, Z configuration; the compounds having an ethoxycarbonyl group are characterized by s-cis orientation of the C=C and C=O bonds.     

Ion-exchange chromatographic assay of peptidases acting on the C-terminal hexapeptide sequence of substance P

A rapid and sensitive assay for peptidases acting on the C-terminal hexapeptide sequence of the neuropeptide substance P is described. The radiolabelled substrate, N alpha-[125I]desaminotyrosyl-substance P (6-11) is easily prepared by coupling commercially available radioiodinated Bolton-Hunter reagent with substance P (6-11). Peptidase activity is determined by quantitative separation of the degradation products from the intact substrate on small QAE-Sephadex columns. The assay has been used to measure degradation of the substrate by rat parotid and diencephalon slices. The peptidase activity in the latter system was inhibited by substance P and substance P fragments and was sensitive to metal chelators and thiol reagents.     

A convergent approach to the synthesis of aprepitant: a potent human NK-1 receptor antagonist

A simple and convergent approach to enantiomerically pure 5-[[2-[1-[3,5-bis(trifluoromethyl)phenyl]ethoxy-3-(4-fluorophenyl)morpholin-4-yl]methyl]-1,2-dihydro-1,2,4-triazol-3-one 1, a potent orally active antagonist of the human neurokinin-1 (NK-1) receptor, is described. The synthetic procedure starts from p-fluorobenzaldehyde to access the racemic morpholinone 2 via a modified Strecker synthesis and utilizes a diastereomeric salt resolution technique to accomplish the synthesis of 1 in enantiomerically pure form and good yield.     

Conformational selection of the AGA*IA(M) heparin pentasaccharide when bound to the fibroblast growth factor receptor

The interaction of the synthetic pentasaccharide AGA*IA(M) (GlcNS,6S-GlcA-GlcNS,3S,6S-IdoA2S-GlcNS,6S-Me) with the extracellular Ig2 domain of the fibroblast growth factor receptor (FGFR2) has been studied by NMR and computational methods. Analysis of the heparin pentasaccharide in the free state and in the complex indicates the existence of a conformational selection process. Although an equilibrium exists between the (1)C(4) and (2)S(0) conformers (ratio 60:40) of the 2-O-sulfo-α-L-iduronate ring (IdoA2S) in the free state, FGFR2 selects only the unique twisted-boat (2)S(0) conformation of this IdoA2S residue. In addition, the protein residues involved in the binding with AGA*IA(M) have also been characterized. The NMR results obtained, from both the ligand and protein perspective, were employed to model the bound conformation of the pentasaccharide by a combined docking and molecular dynamic simulation approach.     

Conformational analysis of methyl 2-methyl-2-(1-naphthyl)propionate

(S)-2-Methoxy-2-(1-naphthyl)propionic acid (MαNP acid 1) is used for enantioseparation of many secondary alcohols and for determining the stereogenic centers. In the liquid state, based on the ¹H NMR anisotropy effect and reported results, it was shown that the MαNP ester preferred a coplanar relation between the methyl and naphthyl groups and a synperiplanar relation between the Cα-OMe and CO groups. In the case of 1,2,3,4-tetrahydro-4-phenanthrenol, which is a secondary alcohol, the stereogenic center was determined by X-ray analysis. It was shown that MαNP ester adopted similar arrangements in the solid state. However, it was presumed that the strong repulsion between oxygen atoms may be disadvantageous in the solid state. Therefore, we carried out conformational analysis using the simplest MαNP methyl ester to clarify this unique relationship. From detailed results based on the energy surface determined using the RHF/STO-3G basis set, the synperiplanar positional relation was the most stable, and the calculated results agreed with many reported experimental results. At the same time, all conformational isomers of the MαNP methyl ester were used to clarify the internal conversion pathways.     

Conformational analysis of 2-substituted nitroethenes

Experimental and theoretical conformational analysis of polyfunctional 2-substituted nitroethenes was carried out by the method of dipole moments and density functional theory calculations. It was established that the nitro and ester (or trichloromethyl) groups are trans-arranged in the molecules of 2-trichloromethyl-(ethoxycarbonyl)-1-nitro- and 1-bromo-1-nitroethenes, i.e., nitroalkenes have E-configuration, their bromo-containing analogues have Z-configuration, and s-cis-orientation of the C=C and C=O double bonds is preferred for nitroacrylates. 2,3-Dibromo-3-nitroacrylates have untrivial Z-configuration in solution.     

Conformational analysis of N-vinyl-2-phenylpyrrole

A conformational analysis of N-vinyl-2-phenylpyrrole was undertaken according to the results from experimental measurements and nonempirical quantum-chemical calculation of the high-level ¹³C–¹H and ¹³C–¹³C spin-spin coupling constants. Angular relationships were established in the direct and vicinal J _C,C and J _C,H constants in the N-vinylpyrrole fragment, making it possible to use them in stereochemical investigations of the vinyl derivatives of pyrrole. Dedicated to Boris Aleksandrovich Trofimov on his 70th jubilee. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 35–42, January, 2009.     

Conformational transition of DNA bound to Hfq probed by infrared spectroscopy

Hfq is a bacterial protein involved in RNA metabolism. Besides this, Hfq's role in DNA restructuring has also been suggested. Since this mechanism remains unclear, we examined the DNA conformation upon Hfq binding by combining vibrational spectroscopy and neutron scattering. Our analysis reveals that Hfq, which preferentially interacts with deoxyadenosine rich sequences, induces partial opening of dA-dT sequences accompanied by sugar repuckering of the dA strand and hence results in a heteronomous A/B duplex. Sugar repuckering is probably correlated with a global dehydration of the complex. By taking into account Hfq's preferential binding to A-tracts, which are commonly found in promoters, potential biological implications of Hfq binding to DNA are discussed.     

Stereocontrolled preparation of a nonpeptidal (-)-spirobicyclic NK-1 receptor antagonist

The synthesis of a spirobicyclic NK-1 receptor (Substance-P) antagonist 1 antipode is described. Retrosynthetic analysis reveals an allylic halide A bearing the cyclopropoxy-substituted aryl group and a 2-phenyl-3-piperidone B. The stereochemistry in the spirobicyclic system bearing three chiral centers is initially set via a highly diastereoselective zinc-mediated coupling of the allylic bromide 23 to the optically active ketopiperidine 3. The remaining benzylic asymmetric center is set by a diastereoselective hydroboration followed by cyclization to the spirobicyclic system.     

Structural analysis of the neuropeptide substance P by using vibrational spectroscopy

Substance P (SP) is one of the most studied peptide hormones and knowing the relationship between its structure and function may have important therapeutic applications in the treatment of a variety of stress-related illnesses. In order to obtain a deeper insight into its folding, the effects of different factors, such as pH changes, the presence of Ca²⁺ ions, and the substitution of the Met-NH₂ moiety in the SP structure, was studied by Raman and infrared spectroscopies. SP has a pH-dependent structure. Under acidic–neutral conditions, SP possesses a prevalent β-sheet structure although also other secondary structure elements are present. By increasing pH, a higher orderliness in the SP secondary structure is induced, as well as the formation of strongly bound intermolecular β-strands with a parallel alignment, which favour the self-assembly of SP in β-aggregates. The substitution of the Met-NH₂ moiety with the acidic functional group in the SP sequence, giving rise to a not biologically active SP analogue, results in a more disordered folding, where the predominant contribution comes from a random coil. Conversely, the presence of Ca²⁺ ions affects slightly but sensitively the folding of the polypeptide chain, by favouring the α-helical content and a different alignment of β-strands; these are structural elements, which may favour the SP biological activity. In addition, the capability of SERS spectroscopy to detect SP in its biologically active form was also tested by using different metal nanoparticles. Thanks to the use of silver NPs prepared by reduction of silver nitrate with hydroxylamine hydrochloride, SP can be detected at very low peptide concentration (~ 90 nM). However, the SERS spectra cannot be obtained under alkaline conditions since both the formation of SP aggregates and the lack of ion pairs do not allow a strong enough interaction of SP with silver NPs.

Graphical abstract

     

Conformational study of 2-arylazo-1-vinylpyrroles

Conformational study of 2-phenylazo-1-vinylpyrrole and 2-(4-bromophenyl)azo-5-methyl-1-vinylpyrrole was performed on the basis of the experimental measurements and high-level ab initio calculations of their 13C--13C and 13C--1H spin-spin coupling constants, showing marked stereochemical behaviour upon the internal rotation of the vinyl group and the pyrrolyl moiety. In liquid phase, both compounds were found to adopt predominant s-trans-s-trans conformation with the noticeable population (ca. 30%) of the higher-energy s-cis-s-trans conformation in the latter compound. As follows from the X-ray data, 2-phenylazo-1-vinylpyrrole crystallizes in s-trans-s-trans conformation while the crystalline molecular structure of 2-(4-bromophenyl)azo-5-methyl-1-vinylpyrrole is s-cis-s-trans.     

One-pot carbanionic synthesis of P1,P2-diglycosyl, P1,P1,P2-triglycosyl, and P1,P1,P2,P2-tetraribosyl methylenediphosphonates

Novel lithiated carbanions derived from ethyl glycosyl- and diglycosyl methylphosphonates were used in a direct and convenient synthesis of P1,P2-diglycosyl, P1,P1,P2-triglycosyl, and P1,P1,P2,P2-tetraribosyl methylenediphosphonates involving a one-pot methylidenediphosphonylation of sugars.     

Conformational analysis of polymethine dyes derived from the 2-azaazulene

A systematic investigation of the conformational structure was performed for the series of symmetrical and unsymmetrical mono-, tri-, pentamethine cyanines, and styryl dyes bearing 2-azaazulenium terminal group. The rotation energy barriers of terminal groups were determined via the dynamic variable temperature NMR experiments. The conformational transformation energy was calculated by quantum chemical methods (B3LYP and M05-2X) both for the cases of considering the solvent influence and not tacking it into account. Based on the comparison of theoretical and experimental data, relative electron-donating abilities and geometrical features of the heterocyclic terminal groups in 2-azaazulenium dyes were estimated. The arrangement of certain heterocyclic nuclei in order of basicity by considering the results of the dynamic NMR investigations was proposed. Influence of the conjugated chain length and the solvent nature on the conformational lability of the investigated dye molecules was discussed.