Conformational studies by dynamic NMR. 97. Structure, conformation, stereodynamics and enantioseparation of aryl substituted norbornanes

The structure of a 1,7,7-triaryl norbornane (compound 3) has been determined by X-ray diffraction and was found essentially equal to that predicted by molecular mechanics calculations. Restricted rotation of the aryl groups also has been observed by dynamic NMR spectroscopy in this compound and in a number of analogously substituted norbornanes. The aryl-norbornane bond rotation barriers were measured by line shape analysis of the (13)C NMR spectra obtained at temperatures lower than -100 degrees C and were found to cover the range 6.0 to 7.9 kcal mol(-1). An exception was the rotation involving the o-anisyl group in compound 5, which occurs near ambient temperature since the corresponding barrier is much higher (14.4 kcal mol(-1)). In one case (compound 4) configurational enantiomers could be separated by chiral HPLC and the corresponding CD spectra recorded.     

Toward efficient Zn(II)-based artificial nucleases

A series of cis-cis-triaminocyclohexane Zn(II) complex-anthraquinone intercalator conjugates, designed in such a way to allow their easy synthesis and modification, have been investigated as hydrolytic cleaving agents for plasmid DNA. The ligand structure comprises a triaminocyclohexane platform linked by means of alkyl spacers of different length (from C(4) to C(8)) to the anthraquinone group which may intercalate the DNA. At a concentration of 5 microM, the complex of the derivative with a C(8) alkyl spacer induces the hydrolytic stand scission of supercoiled DNA with a rate of 4.6 x 10(-6) s(-1) at pH 7 and 37 degrees C. The conjugation of the metal complex with the anthraquinone group leads to a 15-fold increase of the cleavage efficiency when compared with the anthraquinone lacking Zn-triaminocyclohexane complex. The straightforward synthetic procedure employed, allowing a systematic change of the spacer length, made possible to gain more insight on the role of the intercalating group in determining the reactivity of the systems. Comparison of the reactivity of the different complexes shows a remarkable increase of the DNA cleaving efficiency with the length of the spacer. In the case of too-short spacers, the advantages due to the increased DNA affinity are canceled due to the incorrect positioning of the reactive group, thus leading to cleavage inhibition.     

Understanding the mechanism of short-range electron transfer using an immobilized cupredoxin

The hydrophobic patch of azurin (AZ) from Pseudomonas aeruginosa is an important recognition surface for electron transfer (ET) reactions. The influence of changing the size of this region, by mutating the C-terminal copper-binding loop, on the ET reactivity of AZ adsorbed on gold electrodes modified with alkanethiol self-assembled monolayers (SAMs) has been studied. The distance-dependence of ET kinetics measured by cyclic voltammetry using SAMs of variable chain length, demonstrates that the activation barrier for short-range ET is dominated by the dynamics of molecular rearrangements accompanying ET at the AZ-SAM interface. These include internal electric field-dependent low-amplitude protein motions and the reorganization of interfacial water molecules, but not protein reorientation. Interfacial molecular dynamics also control the kinetics of short-range ET for electrostatically and covalently immobilized cytochrome c. This mechanism therefore may be utilized for short-distance ET irrespective of the type of metal center, the surface electrostatic potential, and the nature of the protein-SAM interaction.     

Low-lying electronic excitations and optical absorption spectra of the black dye sensitizer: a first-principles study

We report on ab-initio calculations of the electronic structure and optical absorption response of the black dye sensitizer in gas phase. We show that, despite the large size of this molecule, the second-order multiconfiguration quasi-degenerate perturbation theory (MC-QDPT) can be used to calculate vertical excitation energies, oscillator strengths and optical absorption spectra. The zeroth-order reference states entering perturbation calculations are complete active space (CAS) configuration interaction (CI) wave functions computed for 12 active electrons distributed in 12 active orbitals. We found that the CI approach is not enough for taking into account the strong dynamical correlation effects in this system. In fact, the excitation energies of the CAS-CI target states are strongly renormalized by the MC-QDPT calculations. In the calculated absorption spectra, the analysis of the perturbed wavefunctions revealed that the stronger absorption bands correspond to metal-to-ligand and ligand-to-ligand charge transfer processes. Comparison with independent time-dependent extension (TDDFT) calculations performed with different functionals shows that corrections to the long-range behavior of the functional is pivotal to achieve agreement with the MC-QDPT results.     

Enantioselective isotactic alternating copolymerization of styrene and 4-methylstyrene with carbon monoxide catalyzed by a cationic bioxazoline pd(II) complex

The cationic bioxazoline Pd(II) complex 2 catalyzes the alternating copolymerization of carbon monoxide with styrene and 4-methylstyrene, respectively, to yield a highly isotactic optically active polymer at room temperature and low carbon monoxide pressure (1–4 atm).     

Use of capillary gas chromatography/sensory analysis as an additional tool for sampling technique comparison in peach aroma analysis

Capillary GC/sensory analysis was used to judge if dynamic headspace on sliced pulp and on intact fruit, and solvent extraction could collect the “character impact” and the “contributory” aroma compounds in peaches. Capillary GC/sensory data showed that the headspace techniques selectively recovered the “contributory” volatile compounds, which are strictly related to the characteristic odor of the various peach cultivars, whereas solvent extraction better quantified the “character impact” compounds (lactones).     

A short synthesis of C-glycosyl pyrazoles and pyrroles

The sodium salt of TOSMIC reacted with (E)-3,4,5,6,7-penta-O-acetyl-1,2-dideoxy-1-C-nitro-D-galacto- (1) and -D-manno-hept-1-enitol (2) to give 3-(D-galacto- (3) and 3-(D-manno-penta-O-acetylpentitol-1-yl)-4-nitropyrrole (4) , respectively. Compound 1 reacted with diaryl nitrile imines, affording 1,3-diaryl-4-(1,2,3,4,5-penta-O-acetyl-D-galacto-pentitol-1-yl)pyrazoles 5 and 6 .     

Enantioselective synthesis of the bisabolane sesquiterpene (+)-1-hydroxy-1,3,5-bisabolatrien-10-one and revision of its absolute configuration

The enantioselective synthesis of (S)-1-hydroxy-1,3,5-bisabolatrien-10-one 1 is here described. This sesquiterpene was prepared using (S)-3-(2-methoxy-4-methyl-phenyl)butan-1-ol as a chiral building block. Two different pathways were employed and both turned out to be high yielding, affording 1 in good chemical purity and without any racemization of the existing stereocenter. The spectroscopic data of the synthetic (S)-1 were in very good agreement with those reported for the natural compound, which was extracted from Juniperus formosana heartwood and from the leaves of J. chinensis. The positive sign of the measured optical rotation value of synthetic (S)-1 allows the unambiguous assignment of the absolute configuration of (+)-1 as the (S)-enantiomer. This finding corrects the previous configuration determination which indicated the opposite result. At last, since even (R)-3-(2-methoxy-4-methyl-phenyl)butan-1-ol is preparable in high enantiomer purity by mean of a different biocatalytic process, the formal synthesis of natural (R)-1 was also accomplished.     

Computer-aided molecular design of asymmetric pyrazole derivatives with exceptional enantioselective recognition toward the Chiralcel OJ-H stationary phase

A computer-aided design of novel asymmetric pyrazoles with improved enantioselective properties was performed by docking experiments starting from a model of Chiralcel OJ chiral in the stationary phase. Synthesis and HPLC experiments confirmed the theoretical prediction and led to a detailed investigation of the enantioselective recognition process. For the first time, looking at the time spent by each enantiomer in contact with the CSP during long molecular dynamic simulations, the experimental analytical trend has been reproduced.     

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.