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Many RNA structures are comprised of simple secondary structure elements linked by a few, critical, tertiary interactions. SHAPE chemistry has made interrogation of RNA dynamics at single-nucleotide resolution straightforward. However, de novo identification of nucleotides involved in tertiary interactions remains a challenge. Here we show that nucleotides that form non-canonical or tertiary contacts are detected by comparing information obtained using two SHAPE reagents, N-methylisatoic anhydride (NMIA) and 1-methyl-6-nitroisatoic anhydride (1M6). Nucleotides that react preferentially with NMIA exhibit slow local nucleotide dynamics and preferentially adopt the less common C2′-endo ribose conformation. Experiments and first-principle calculations show 1M6 reacts preferentially with nucleotides in which one face of the nucleobase allows an unhindered stacking interaction with the reagent. Differential SHAPE reactivities were used to detect non-canonical and tertiary interactions in four RNAs with diverse structures and to identify pre-formed non-canonical interactions in partially folded RNAs. Differential SHAPE reactivity analysis will enable experimentally concise, large-scale identification of tertiary structure elements and ligand binding sites in complex RNAs and in diverse biological environments.

Under the conditions of transfer hydrogenation employing a cyclometallated iridium catalyst (R)-I derived from [Ir(cod)Cl]2, allyl acetate, 4-cyano-3-nitrobenzoic acid and the chiral phosphine ligand (R)-SEGPHOS, α-methyl allyl acetate engages 1,3-propanediol 1a and 2-methyl-1,3-propanediol 1b in double carbonyl crotylation from the alcohol oxidation level to deliver the C2-symmetric and pseudo-C2-symmetric stereopolyads 2a and 3a, respectively, with exceptional control of anti-diastereo- and enantioselectivity. Notably, the polypropionate stereopentad 3a is formed predominantly as 1 of 16 possible stereoisomers. Desymmetrization of polypropionate stereopentad 3a is readily achieved upon iodoetherification to form pyran 4. Direct generation of polypropionate stereopentad 3a enables a dramatically simplified approach to previously prepared polypropionate substructures, as demonstrated by the synthesis of C19–C27 of rifamycin S (8 steps, originally prepared in 26 steps) and C19–C25 of scytophycin C (8 steps, originally prepared in 15 steps). The present transfer hydrogenative protocol represents an alternative to chiral auxiliaries, chiral reagents and premetallated nucleophiles in polyketide construction.

Using the ortho-cyclometalated pi-allyl iridium precatalyst (R)-I derived from [Ir(cod)Cl](2), 4-cyano-3-nitrobenzoic acid, (R)-SEGPHOS, and allyl acetate, enantioselective transfer hydrogenation of alpha-(trimethylsilyl)allyl acetate in the presence of aldehydes 2a-i mediated by 2-propanol delivers products of (trimethylsilyl)allylation 4a-i in good isolated yields and with exceptional levels of anti-diastereoselectivity and enantioselectivity (90-99% ee). In the absence of 2-propanol, but under otherwise identical reaction conditions, carbonyl (trimethylsilyl)allylation is achieved directly from the alcohol oxidation level to furnish an equivalent set of adducts 4a-i with roughly equivalent isolated yields and stereoselectivities. To evaluate the synthetic utility of the reaction products 4a-i, adduct 4g was converted to the 1,4-ene-diol 5g via dioxirane-mediated oxidative desilylation with allylic transposition, the allylic alcohol 6g via protodesilylation with allylic transposition, and the gamma-lactam 7g via chlorosulfonyl isocyanate-mediated cycloaddition.

Rate constant ratios for addition of the three nucleophilic sites of phenol to the 1-(4-methoxyphenyl)ethyl carbocation (1 + ) in 50/50 (v/v) trifluoroethanol/water were determined from the relative yields of the three phenol adducts, and absolute rate constants were determined from product rate constant ratios for addition of phenol and azide ion to 1 + using k az = 5 × 10 9 M -1 s -1 for the diffusion-limited reaction of azide ion. A selectivity of 230:20:1 was determined for alkylation of phenol at oxygen, C-4 and C-2 to form 1-OPh and biphenyls 1-(4-C 6 H 4 OH) and 1-(2-C 6 H 4 OH), respectively, and of 2:2:1 for alkylation of the corresponding nucleophilic sites of phenoxide ion in diffusion-limited reactions. The Mayr nucleophilicity parameter for C-4 of phenol is N= 2.0. Encounter-limited addition of phenoxide ion to 1 + to form 1-OPh is faster than encounter-limited addition of oxygen anions that are either more or less basic than phenoxide ion. Only the products of solvolysis are observed from acid-catalyzed cleavage of 1-OPh in 50/50 (v/v) trifluoroethanol/water, but a 50% yield of biphenyls 1-(4-C 6 H 4 OH) and 1-(2-C 6 H 4 OH) are observed from spontaneous cleavage of 1-OPh, where the leaving group is phenoxide ion, because of the very low kinetic barriers to collapse of the ion pair intermediate 1 + PhO - . The 230-fold larger rate constant for O-compared to C-2-alkylation of phenol is due primarily to the larger thermodynamic driving force for oxygen addition. There are similar Marcus intrinsic barriers for these two reactions.

Under the conditions of transfer hydrogenation employing an ortho-cyclometallated iridium catalyst generated in situ from [Ir(cod)Cl](2), 4-cyano-3-nitrobenzoic acid and the chiral phosphine ligand (S)-SEGPHOS, alpha-methyl allyl acetate couples to alcohols 1a-1j with complete levels of branched regioselectivity to furnish products of carbonyl crotylation 3a-3j, which are formed with good levels of anti-diastereoselectivity and exceptional levels of enantioselectivity. An identical set of optically enriched carbonyl crotylation products 3a-3j is accessible from the corresponding aldehydes 2a-2j under the same conditions, but employing isopropanol as the terminal reductant. Experiments aimed at probing the origins of stereoselection establish a matched mode of ionization for the (R)-acetate and the iridium catalyst modified by (S)-SEGPHOS, as well as reversible ionization of the allylic acetate with rapid pi-facial interconversion of the resulting pi-crotyl intermediate in advance of C-C bond formation. Additionally, rapid alcohol-aldehyde redox equilibration in advance of carbonyl addition is demonstrated. Thus, anti-diastereo- and enantioselective carbonyl crotylation from the alcohol or aldehyde oxidation level is achieved in the absence of any stoichiometric metallic reagents or stoichiometric metallic byproducts.

A high-throughput screening protocol is proposed for chiral selector discovery. It is modeled after the protocol for biological screening of candidate drugs from chemical libraries. The procedure works based on target distribution between an aqueous phase and an organic phase. The target may be a racemate or separate enantiomers. Screening for noncovalent intermolecular association between target and candidate selectors is carried out by partitioning experiments in the presence and absence of the candidate chiral selectors in the organic phase (plasticized poly(vinyl chloride)). The partition ratio measurement uses 96-well plates for high throughput. The feasibility of this approach is validated by working with a known target/chiral selector pair, N-(3,5-dinitrobenzoyl)-alpha-phenylglycine and 2,2,2-trifluoro-1-(9-anthryl)ethanol. The validated protocol is applied to a small library of 12 cyclopropyl dipeptide isosteres. Eight bind the racemic target, econazole. Among them, one has measurable chiral selectivity. The advantage of the method is that it does not require the covalent attachment of either the analyte or the selector, and the required amount of the potential chiral selector is about 100 mug.

A series of molecular umbrella conjugates, derived from cholic acid, deoxycholic acid, spermidine, lysine, and 5-mercapto-2-nitrobenzoic acid, have been synthesized and found capable of transporting an attached 16-mer oligonucleotide (S-dT16) across liposomal membranes made from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyldglycerol (POPG), and cholesterol [POPC/POPG/cholesterol (65/5/30; mol/mol/mol, v/v/v)] at 37 degrees C. Those molecular umbrellas containing four choloyl (or deoxycholoyl) groups resulted in significantly faster rates of transport as compared to those containing only two such moieties. A model that accounts for these membrane transport processes is proposed.

The antibiotic aureothin is a rare natural nitroaromatic compound produced by Streptomyces thioluteus. By labeling experiments, we demonstrate for the first time that p-nitrobenzoate (PNBA) serves as a polyketide synthase starter unit. Cloning, heterologous expression, and inactivation experiments reveal that this unusual primer is synthesized from p-aminobenzoate (PABA) by means of AurF, a novel N-oxygenase.

The amine oxygenase AurF from Streptomyces thioluteus catalyzes the six-electron oxidation of p-aminobenzoate (pABA) to p-nitrobenzoate (pNBA). In this work, we have studied the reaction of its reduced Fe(2)(II/II) cofactor with O(2), which results in generation of a peroxo-Fe(2)(III/III) intermediate. In the absence of substrate, this intermediate is unusually stable (t(1/2) = 7 min at 20 degrees C), allowing for its accumulation to almost stoichiometric amounts. Its decay is accelerated approximately 10(5)-fold by the substrate, pABA, implying that it is the complex that effects the two-electron oxidation of the amine to the hydroxylamine. The nearly quantitative conversion of pABA to pNBA by solutions containing an excess of the intermediate suggests that it may also be competent for the two subsequent two-electron oxidations leading to the product.