Toward artificial developmental regulators

A polyamide-peptide conjugate is designed which recruits sequence specifically the developmental regulator Exd to a cognate DNA site. In particular, an eight-ring hairpin polyamide (Im-Im-Py(C3H6NHR)-Py-gamma-Im-Py-Py-Py-beta-Dp) with a heptapeptide (R = Ac-Phe-Tyr-Pro-Trp-Met-Lys-Gly-) attached on a central ring was shown to induce cooperative binding of the Drosophila Hox protein cofactor Exd with a Kd of 4.4 nM in vitro, an order of magnitude more efficient than the natural Hox protein partner Ubx. The conjugate joins two sequence specific domains, one for DNA and one for the protein. This small molecule thus serves as a cooperative protein-DNA dimerizer, which mimics the natural Hox family of developmental regulators.     

Structures and energies of seleno derivatives of biuret.Ab Initio comparative studies of diselenobiuret, selenobiuret, and selenothiobiuret

Ab initio studies (LCAO-MO method) on conformers of three seleno derivatives of the biuret molecules diselenobiuret [I], selenobiuret [II], and selenothiobiuret [III] were carried out at the Hartree-Fock (HF) and MP2 levels. The molecular geometries of these species were fully optimized at the HF level and characterized by analysis of the harmonic vibrational frequencies using a split-valence triple-zeta basis set augmented by a set ofd polarization functions on heavy atoms andp polarization functions on hydrogen atoms [TZP(d, p)]. The total energies of the HF-optimized structures were calculated at the MP2 (frozen core) level using a larger TZP (2df, 2pd) basis set. The potential energy searches revealed a total of 11 minimum-energy conformers (assigned astrans-trans, trans-cis, cis-trans, andcis-cis) and seven transition-state species for the title molecules. The two predicted conformers for diselenobiuret (Ia=trans-trans andIc=cis-cis) are characterized byC ₂ and the third byC _s symmetry. For selenothiobiuret two forms (IIIa=trans-trans andIIId=cis-cis) possessC ₁ and two (IIIb=trans-cis andIIIc=cis-trans) possessC _s symmetries, respectively. For selenobiuret, four formsIIa=trans-trans (C₁),IIb=trans-cis (C _s),IIc=cis-trans (C ₁), andIId=cis-cis (C₁), were obtained as a result of gradient optimization. Comparison of the relative energies for the considered species indicated that thecis-trans forms are the most stable conformations for all three systems at both the HF and MP2 levels of theory.     

Application of the energy gap law to the decay of charge transfer excited states,solvent effects

Values of non-radiative decay rate constants (k_nr) and emission energies (E_cm) have been obtained for Os(Phen₃)²⁺ in a series of solvents and the results are consistent with the energy gap law. For hydroxylic solvents like water or methanol related studies suggest the existence of strong, specific contributions to the vibrational trapping energy of the solvent.     

Dramatic 5'-residue effect on conformer distribution of short oligonucleotide retro models of the cisplatin-DNA cross-link: implications for the Lippard and cross-link distorted base pair steps present in cisplatin-DNA duplex adducts

The cisplatin anticancer drug preferentially attacks the GG sequence of DNA duplexes. Virtually all DNAs containing the key G*G* lesion (G* = N7 platinated G) have large distortions in the cross-link (G*G*) base pair (bp) step and also in the adjacent Lippard (XG*) bp step, making the adducts very different from B-form DNA in the XG*G* region. The XG*G* strand in duplexes also differs in several ways from single-strand (ss) models with G*G* and XG*G* sequences. In the duplex, the X residue has an N sugar, the 5'-G* and 3'-G* bases have slight "R" canting (3'-G* H8 atom toward the 5'-G* base), and there is no or weak H-bonding by the NH3 ligands. In most XG*G* ss models, X has an S sugar, the 5'-G* base normally cants strongly toward the 3'-G* base (L canting), and the NH3 forms an H-bond. Well-defined ss models exist in the solid state, but dynamic motion obscures the properties of the ss models in solution. In this work, we employ retro models (better defined, less dynamic ss models) to understand the differences between duplex and ss models. The retro models in this study lack carrier ligand NH's, thus eliminating H-bonding. To correlate previous ss solid-state models with our solution work, we constructed hybrid molecules by overlaying parts of known structures. The combined model and experimental information indicates that the X N-pucker is not favorable in L-canted ss models, that X residue steric effects (not H-bonding) favor L canting in ss models, that X N-pucker is needed for favorable WC hydrogen bonding and stacking interactions in duplexes, and that X N-pucker minimizes X base clashes with bases in the complementary strand in duplexes. The R canting minimizing clashes between the X and G* residues of the Lippard bp step (independent of X pucker) and the repositioning of the X residue base caused by the change from S-pucker to N-pucker together lead to the unusual features of the Lippard bp step in the duplex.     

Synthesis of novel retinoid X receptor-selective retinoids

Retinoids 1-5 have been identified as potent RXR agonists for evaluation in the treatment of non-insulin-dependent (type II) diabetes mellitus (NIDDM). Highly convergent syntheses of 1-5 have been developed. The core tetrahydronaphthalene 7, employed in the synthesis of 1 and 2, was prepared in 98% yield using an AlCl(3)-catalyzed (0.03 equiv) Friedel-Crafts alkylation of toluene with 2,5-dichloro-2,5-dimethylhexane 6. A nitromethane-mediated Fridel-Crafts acylation of 7 with chloromethylnicotinate 9 was developed to prepare ketone 10 in 68% yield. Chelate-controlled addition of MeMgCl to 10 followed by dehydration afforded olefin 11 in 65% yield. Cyclopropanation of 11 with trimethylsulfoxonium ylide, followed by saponification, completed a five-step synthesis of 1 in 33% yield. FeCl(3)-catalyzed (0.05 equiv) Friedel-Crafts acylation of 7 with chloromethylterephthalate 14 afforded ketone 15 in 81% yield. Saponification of 15 and reaction with 50% aqueous NH(2)OH in AcOH afforded a 9:1 mixture of cis and trans oximes, from which the desired cis-oxime 2 was isolated in 43% yield. The core bromo-dihydronaphthalene 29 required for the synthesis of 3-5 was prepared by a Shapiro reaction. Transmetalation of 29 and reaction with Weinreb amides 30b or 36 afforded ketones 32 and 37, which were converted into 3-5 using chemistry comparable to the tetrahydronaphthylene series. Suzuki coupling of boronic acids 41 and 42 with vinyl triflate 43 provided an alternative approach to the synthesis of this class of compounds.     

Longitudinal dispersion in flows that are homogeneous in the streamwise direction

The longitudinal dispersion of a pulse of passive scalar contaminant within a flow that is unchanging in the downstream direction is established to be a function of the mean-velocity-history of molecules from a uniform distribution on the flow cross-section. The specific case of laminar flow between parallel plates is investigated in detail, wherein it is found that $$\frac{1}{2}\frac{{\overline {d\eta (t)^2 } }}{{dt}} = \frac{9}{{2\pi ^6 }}\frac{{\bar U^2 d^2 }}{k}\sum\limits_{n = 1}^\infty {\frac{1}{{n^6 }}} \left( {1 - \exp \left( {\frac{{ - (2n\pi )^2 tK}}{{d^2 }}} \right)} \right),$$ where η(t) is the displacement relative to an axis located byūt whenū is the discharge velocity,K is the molecular diffusivity andd is the plate separation. This flow is used to show that the molecule mean velocity-histories can be approximated by a function that does not directly depend on the release position of the molecule on the flow cross-section. The results of a numerical simulation of the dispersion in this flow are presented for comparison.     

The approach to normality of the distance-neighbour function when used to describe relative turbulent dispersion

Batchelor [1] suggested that the Distance-Neighbour Function when used to describe the relative turbulent dispersion of a cloud of marked fluid, whose diameter is well within the length scale range of the universal inertial sub-range of turbulence, would become of Gaussian form. This paper determines that a necessary condition for the Gaussian form to apply is that the non-dimensional time of (/v)^1/2 t 300, following the release of the marked fluid with an initial diameter <(v ³/t)^1/4, be attained.

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Zusammenfassung Batchelor [1] hat die Behauptung aufgestellt, dass die Abstands-Nachbar-Funktion (räumliche Korrelation) die Gauss'sche Form annimmt, wen man sie zur Beschreibung der relativen turbulenten Dispersion einer Wolke von markierter Flüssigkeit benützt, falls der Durchmesser der Wolke nicht über die Längenskala des universellen Inertial-Unterbereichs der Turbulenz hinausgeht. In dieser Arbeit wird gezeigt, dass eine notwendige Bedingung der Anwendbarkeit der Gauss'schen Form darin besteht, dass die dimensionsloze Zeit (/v)^1/2 t 300 nach dem Ablösen einer markierten Flüssigkeits-wolke mit dem Anfangsdurchmesser <(v ³/t)^1/4 erreicht wird.