Bicyclo[3.2.1]amide-DNA: a chiral, non-chiroselective base-pairing system

The design, synthesis and base-pairing properties of bicyclo[3.2.1]amide-(bca)DNA, a novel phosphodiester based DNA analogue, is reported. This analogue consists of a conformationally constrained backbone entity which emulates a B-DNA geometry, to which the nucleobases were attached via an extended, acyclic amide linker. Homobasic adenine-containing bca-decamers form duplexes with complementary oligonucleotides containing the bca-, the DNA the RNA and, surprisingly, also the L-RNA backbone. UV- and CD-spectroscopic investigations revealed the duplexes with D- or L-complement to be of similar stability and enantiomorphic in structure. Bca-oligonucleotides containing all four bases form strictly antiparallel, left-handed complementary duplexes with itself and complementary DNA but not with RNA. Base-mismatch discrimination is comparable to that of DNA while the overall thermal stabilities of bca-oligonucleotide duplexes are inferior relative to that of DNA or RNA. A detailed molecular modeling study of left- and right-handed bca-DNA containing duplexes showed only minor changes in the backbone structure and revealed a structural switch around the base-linker unit to be responsible for the generation of enantiomorphic duplex structures. The obtained data are discussed with respect to the structural and energetic role of the ribofuranose entities in DNA and RNA association

Excited state interactions between the chiral Au 38 L 24 cluster and covalently attached porphyrin

A protected S-acetylthio porphyrin was synthesized and attached to the Au38(2-phenylethanethiolate)24 cluster in a ligand exchange reaction. Chiral high performance liquid chromatography of the functionalized cluster yielded enantiomeric pairs of clusters probably differing in the binding site of the porphyrin. As proven by circular dichroism, the chirality was maintained. Exciton coupling between the cluster and the chromophore is observed. Zinc can be incorporated into the porphyrin attached to the cluster, as evidenced by absorption and fluorescence spectroscopy, however, the reaction is slow. Quenching of the chromophore fluorescence is observed, which can be explained by energy transfer from the porphyrin to the cluster. Transient absorption spectra of Au38(2-phenylethanethiolate)24 and the functionalized cluster probe the bleach of the gold cluster due to ground state absorption and the characteristic excited state absorption signals. Zinc incorporation does not have a pronounced effect on the photophysical behaviour. Decay times are typical for the molecular behaviour of small monolayer protected gold clusters.

Microscopic study of vorticities in relativistic chiral fermions

It is usually believed that unlike the external magnetic field which one can set directly, vorticity is a property of the flow of particles, which is indirectly controlled by external fields and initial conditions. Using the curved-space technics it is shown that the influence of the vorticity on the relativistic chiral fermions can indeed be controlled directly.

Finite volume effects in chiral perturbation theory with twisted boundary conditions

We study the effects of a finite cubic volume with twisted boundary conditions on pseudoscalar mesons. We apply Chiral Perturbation Theory in the p-regime and introduce the twist by means of a constant vector field. The corrections of masses, decay constants, pseudoscalar coupling constants and form factors are calculated at next-to-leading order. We detail the derivations and compare with results available in the literature. In some case there is disagreement due to a different treatment of new extra terms generated from the breaking of the cubic invariance. We advocate to treat such terms as renormalization terms of the twisting angles and reabsorb them in the on-shell conditions. We confirm that the corrections of masses, decay constants, pseudoscalar coupling constants are related by means of chiral Ward identities. Furthermore, we show that the matrix elements of the scalar (resp. vector) form factor satisfies the Feynman–Hellman Theorem (resp. the Ward–Takahashi identity). To show the Ward–Takahashi identity we construct an effective field theory for charged pions which is invariant under electromagnetic gauge transformations and which reproduces the results obtained with Chiral Perturbation Theory at a vanishing momentum transfer. This generalizes considerations previously published for periodic boundary conditions to twisted boundary conditions. Another method to estimate the corrections in finite volume are asymptotic formulae. Asymptotic formulae were introduced by Lüscher and relate the corrections of a given physical quantity to an integral of a specific amplitude, evaluated in infinite volume. Here, we revise the original derivation of Lüscher and generalize it to finite volume with twisted boundary conditions. In some cases, the derivation involves complications due to extra terms generated from the breaking of the cubic invariance. We isolate such terms and treat them as renormalization terms just as done before. In that way, we derive asymptotic formulae for masses, decay constants, pseudoscalar coupling constants and scalar form factors. At the same time, we derive also asymptotic formulae for renormalization terms. We apply all these formulae in combination with Chiral Perturbation Theory and estimate the corrections beyond next-to-leading order. We show that asymptotic formulae for masses, decay constants, pseudoscalar coupling constants are related by means of chiral Ward identities. A similar relation connects in an independent way asymptotic formulae for renormalization terms. We check these relations for charged pions through a direct calculation. To conclude, a numerical analysis quantifies the importance of finite volume corrections at next-to-leading order and beyond. We perform a generic Analysis and illustrate two possible applications to real simulations.

Chiral recognition with a benzofuran receptor that mimics an oxyanion hole

A new chiral benzofuran receptor has been synthesized and its properties in the association of amino acid derivatives have been studied. X-ray structures were obtained and these corroborate the presence of an oxyanion-hole motif in these structures.

NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains

Polymers of N-substituted glycines (“peptoids”) containing chiral centers at the α position of their side chains can form stable structures in solution. We studied a prototypical peptoid, consisting of five para-substituted (S)-N-(1-phenylethyl)glycine residues, by NMR spectroscopy. Multiple configurational isomers were observed, but because of extensive signal overlap, only the major isomer containing all cis-amide bonds was examined in detail. The NMR data for this molecule, in conjunction with previous CD spectroscopic results, indicate that the major species in methanol is a right-handed helix with cis-amide bonds. The periodicity of the helix is three residues per turn, with a pitch of ≈6 Å. This conformation is similar to that anticipated by computational studies of a chiral peptoid octamer. The helical repeat orients the amide bond chromophores in a manner consistent with the intensity of the CD signal exhibited by this molecule. Many other chiral polypeptoids have similar CD spectra, suggesting that a whole family of peptoids containing chiral side chains is capable of adopting this secondary structure motif. Taken together, our experimental and theoretical studies of the structural properties of chiral peptoids lay the groundwork for the rational design of more complex polypeptoid molecules, with a variety of applications, ranging from nanostructures to nonviral gene delivery systems.

Chiral molecular self-assembly of phospholipid tubules: A circular dichroism study

We report on spectroscopic studies of the chiral structure in phospholipid tubules formed in mixtures of alcohol and water. Synthetic phospholipids containing diacetylenic moieties in the acyl chains self-assemble into hollow, cylindrical tubules in appropriate conditions. Circular dichroism provides a direct measure of chirality of the molecular structure. We find that the CD spectra of tubules formed in mixtures of alcohol and water depends strongly on the alcohol used and the lipid concentration. The relative spectral intensity of different circular dichroism bands correlates with the number of bilayers observed using microscopy. The results provide experimental evidence that tubule formation is based on chiral packing of the lipid molecules and that interbilayer interactions are important to the tubule structure.

Chemical communication in scarab beetles: reciprocal behavioral agonist-antagonist activities of chiral pheromones.

A novel mechanism of reciprocal behavioral agonist-antagonist activities of enantiomeric pheromones plays a pivotal role in overcoming the signal-to-noise problem derived from the use of a single-constituent pheromone system in scarab beetles. Female Anomala osakana produce (S, Z)-5-(+)-(1-decenyl)oxacyclopentan-2-one, which is highly attractive to males; the response is completely inhibited even by 5% of its antipode. These two enantiomers have reverse roles in the Popillia japonica sex pheromone system. Chiral GC-electroantennographic detector experiments suggest that A. osakana and P. japonica have both R and S receptors that are responsible for behavioral agonist and antagonist responses.

Pseudoscalar susceptibilities and quark condensates: chiral restoration and lattice screening masses

We derive the formal Ward identities relating pseudoscalar susceptibilities and quark condensates in three-flavor QCD, including consistently the 77-n' sector and the U-A(1) anomaly. These identities are verified in the low-energy realization provided by ChPT, both in the standard SU(3) framework for the octet case and combining the use of the SU(3) framework and the large-Nc expansion of QCD to account properly for the nonet sector and anomalous contributions. The analysis is performed including finite temperature corrections as well as the calculation of U(3) quark condensates and all pseudoscalar susceptibilities, which together with the full set of Ward identities, are new results of this work. Finally, the Ward identities are used to derive scaling relations for pseudoscalar masses which explain the behavior with temperature of lattice screening masses near chiral symmetry restoration.

Chiral gold(I) vs chiral silver complexes as catalysts for the enantioselective synthesis of the second generation GSK-hepatitis C virus inhibitor

The synthesis of a GSK 2nd generation inhibitor of the hepatitis C virus, by enantioselective 1,3-dipolar cycloaddition between a leucine derived iminoester and tert-butyl acrylate, was studied. The comparison between silver(I) and gold(I) catalysts in this reaction was established by working with chiral phosphoramidites or with chiral BINAP. The best reaction conditions were used for the total synthesis of the hepatitis C virus inhibitor by a four step procedure affording this product in 99% ee and in 63% overall yield. The origin of the enantioselectivity of the chiral gold(I) catalyst was justified according to DFT calculations, the stabilizing coulombic interaction between the nitrogen atom of the thiazole moiety and one of the gold atoms being crucial.

Binap-silver salts as chiral-catalysts for the enantioselective 1,3-dipolar cycloaddition of azomethine ylides and alkenes

Binap-AgSbF6 catalyzed 1,3-dipolar cycloadditions between azomethine ylides and electrophilic alkenes are described and compared with analogous transformations mediated by other Binap-silver(I) salt complexes. Maleimides and 1,2-bis(phenylsulfonyl)ethylene are suitable dipolarophiles for obtaining very good enantioselectivities, even better values are generated by a multicomponent version. There are some very interesting applications of the disulfonylated cycloadducts in the total synthesis of cis-2,5-disubstituted pyrrolidines, precursors of natural products, or valuable intermediates in the synthesis of antiviral compounds.

Phosphoramidite-Cu(OTf)2 complexes as chiral catalysts for 1,3-dipolar cycloaddition of iminoesters and nitroalkenes

Chiral complexes formed by phosphoramidites such as (Sa,R,R)-9 and Cu(OTf)2 are excellent catalysts for the general 1,3-dipolar cycloaddition between azomethine ylides and nitroalkenes affording the corresponding tetrasubstituted proline esters mainly as exo-cycloadducts in high er at room temperature. The exo-cycloadducts can be obtained in enantiomerically pure form just after simple recrystallization. DFT calculations support the stereochemical results.

Synthetic scope and DFT analysis of the chiral binap-gold (I) complex-catalyzed 1,3-dipolar cycloaddition of azlactones with alkenes

The 1,3-dipolar cycloaddition between glycine-derived azlactones with maleimides is efficiently catalyzed by the dimeric chiral complex [(Sa)-Binap·AuTFA]2. The alanine-derived oxazolone only reacts with tert-butyl acrylate giving anomalous regiochemistry, which is explained and supported by Natural Resonance Theory and Nucleus Independent Chemical Shifts calculations. The origin of the high enantiodiscrimination observed with maleimides and tert-butyl acrylate is analyzed using DFT computed at M06/Lanl2dz//ONIOM(b3lyp/Lanl2dz:UFF) level. Several applications of these cycloadducts in the synthesis of new proline derivatives with a 2,5-trans-arrangement and in the preparation of complex fused polycyclic molecules are described.

Chiral β-amino alcohols as ligands for the ruthenium-catalyzed asymmetric transfer hydrogenation of N-phosphinyl ketimines

Some chiral β-amino alcohols have been evaluated as potential ligands for the ruthenium-catalyzed asymmetric transfer hydrogenation (ATH) of N-phosphinyl ketimines in isopropyl alcohol. The ruthenium complex prepared from [RuCl2(p-cymene)]2 and (1S,2R)-1-amino-2-indanol has shown to be an efficient catalyst for the ATH of several N-(diphenylphosphinyl)imines, affording the reduction products in very good isolated yields and enantiomeric excesses up to 82%. The inherent rigidity of the indane ring system present in the ligand seems to be very important to achieve good enantioselectivities.