Structural Basis for Recognition of Guanosine by a Synthetic Tricyclic Cytosine Analogue: Guanidinium G‐Clamp

An oligonucleotide analogue containing a novel heterocyclic analogue, the guanidinium G‐clamp, was designed to allow formation of five H‐bonds to guanosine. The guanidinium group was introduced postsynthetically by treatment of the deprotected oligonucleotide containing a free amino group with a solution of 1H‐pyrazole‐1‐carboxamidine and purified by a combination of size‐exclusion chromatography and reversed‐phase HPLC. A single incorporation of this modification into an oligodeoxynucleotide sequence was found to increase duplex stability by 13° and 16° per modification to RNA and DNA, respectively. Crystals of a self‐complementary decamer sequence containing this modification were grown and diffracted to 1‐Å resolution. The structure was solved by molecular replacement and revealed that the modification forms additional H‐bonds to O(6) and N(7) of guanosine through the amino and imino N‐atoms, respectively. The origins of enhanced duplex stability are also attributed to increased stacking interactions mediated by the phenoxazine moiety of the G‐clamp and formation of H‐bond networks between the positively charged guanidinium group, H₂O molecules, and negatively charged O‐atoms from phosphates on the adjacent strand.     

Effect of ammonia,ammonia-water,and sulfuric acid on the HO2 + HO2 → H2O2 + 3O2 reaction in troposphere: Competition between stepwise and one-step mechanisms

A detailed theoretical study on the reaction mechanisms for the formations of H₂O₂ + ³O₂ from the self-reaction of HO₂ radicals under the effect of NH₃, H₃N···H₂O, and H₂SO₄ catalysts was performed using the CCSD(T)/CBS//M06-2X/aug-cc-pVTZ method. The rate constant was computed using canonical variational transition state theory (CVT) with small curvature tunneling (SCT). Our results indicate that NH₃-, H₃N···H₂O-, and H₂SO₄-catalyzed reactions could proceed through both one-step and stepwise routes. Calculated rate constants show that the catalyzed routes in the presence of the three catalysts all prefer stepwise pathways. Compared to the catalytic efficiency of H₂O, the efficiencies of NH₃, H₃N···H₂O, and H₂SO₄ are much lower due to their smaller relative concentrations. The present results have provided a definitive example of how basic and acidic catalysts influence the atmospheric reaction of HO₂ + HO₂ → H₂O₂ + ³O₂. These results further encourage one to consider the effects of basic and acidic catalysts on the related atmospheric reactions. Thus, the present investigation should have broad implications in the gas-phase reactions of the atmosphere.     

Synthesis and excited-state photodynamics of a chlorin-bacteriochlorin dyad--through-space versus through-bond energy transfer in tetrapyrrole arrays.

Understanding energy transfer among hydroporphyrins is of fundamental interest and essential for a wide variety of photochemical applications. Toward this goal, a synthetic free base ethynylphenylchlorin has been coupled with a synthetic free base bromobacteriochlorin to give a phenylethyne-linked chlorin-bacteriochlorin dyad (FbC-pe-FbB). The chlorin and bacteriochlorin are each stable toward adventitious oxidation because of the presence of a geminal dimethyl group in each reduced pyrrole ring. A combination of static and transient optical spectroscopic studies indicate that excitation into the Qy band of the chlorin constituent (675 nm) of FbC-pe-FbB in toluene results in rapid energy transfer to the bacteriochlorin constituent with a rate of approximately (5 ps)(-1) and efficiency of >99%. The excited bacteriochlorin resulting from the energy-transfer process in FbC-pe-FbB has essentially the same fluorescence characteristics as an isolated monomeric reference compound, namely a narrow (12 nm fwhm) fluorescence emission band at 760 nm and a long-lived (5.4 ns) Qy excited state that exhibits a significant fluorescence quantum yield (Phif=0.19). F?rster calculations are consistent with energy transfer in FbC-pe-FbB occurring predominantly by a through-space mechanism. The energy-transfer characteristics of FbC-pe-FbB are compared with those previously obtained for analogous phenylethyne-linked dyads consisting of two porphyrins or two oxochlorins. The comparisons among the sets of dyads are facilitated by density functional theory calculations that elucidate the molecular-orbital characteristics of the energy donor and acceptor constituents. The electron-density distributions in the frontier molecular orbitals provide insights into the through-bond electronic interactions that can also contribute to the energy-transfer process in the different types of dyads.     

Synthetic chlorins bearing auxochromes at the 3- and 13-positions

Synthetic chlorins bearing diverse auxochromes at the 3- and 13-positions of the macrocycle are valuable targets given their resemblance to chlorophylls a and b, which bear 3-vinyl and 13-keto groups. A de novo route has been exploited to construct nine zinc chlorins bearing substituents at the 3- and 13-positions and two benchmark zinc chlorins lacking such substituents. The chlorins are sterically uncongested and bear (1) a geminal dimethyl group in the reduced pyrroline ring, (2) a H, an acetyl, a triisopropylsilylethynyl (TIPS-ethynyl), or a vinyl at the 3-position, (3) a H, an acetyl, or TIPS-ethynyl at the 13-position, and (4) a H or a mesityl at the 10-position. The synthesis of the 13-substituted chlorins relied on p-TsOH x H2O-catalyzed condensation of an 8,9-dibromo-1-formyldipyrromethane (eastern half) and 2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin (western half), followed by metal-mediated oxidative cyclization, affording the 13-bromochlorin. Similar use of a bromo- or TIPS-ethynyl-substituted western half provided access to 3-substituted chlorins. A 3-bromo, 13-bromo, or 3,13-dibromochlorin was further transformed by Pd-coupling to introduce the vinyl group (via tributylvinyltin), TIPS-ethynyl group (via TIPS-acetylene), or acetyl group (via tributyl(1-ethoxyvinyl)tin, followed by acidic hydrolysis). In the 10-mesityl-substituted zinc chlorins, the series of substituents, 3-vinyl, 13-TIPS-ethynyl, 3-TIPS-ethynyl, 13-acetyl, 3,13-bis(TIPS-ethynyl), 3-TIPS-ethynyl-13-acetyl, or 3,13-diacetyl, progressively causes (1) a redshift in the absorption maximum of the B band (405-436 nm) and the Q(y) band (606-662 nm), (2) a relative increase in the intensity of the Q(y) band (I(B)/I(Q) = 4.2-1.5), and (3) an increase in the fluorescence quantum yield phi(f) (0.059-0.29). The zinc chlorins bearing a 3-TIPS-ethynyl-13-acetyl or a 3,13-diacetyl group exhibit a number of spectral properties resembling those of chlorophyll a or its zinc analogue. Taken together, this study provides access to finely tuned chlorins for spectroscopic studies and diverse applications.     

Synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] modified nucleosides and oligonucleotides.

A versatile synthetic route has been developed for the synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2'-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2'-O-DMAOE purine nucleosides, the key intermediate B (Scheme 1) was obtained from the 2'-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon-carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2'-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2'-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2'-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2'-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3'-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2'-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t(1/2) > 24 h.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.     

Synthesis,Spectral, and Structural Characterization of Bisthiocarbohydrazone Derivatives

Abstract

Bisthiocarbohydrazone derivatives of three heterocyclic ketone ligands, having a flexible coordination ability; 1, 5-bis (2-acetylthiophene) thiocarbohydrazone; 1, 5-bis (2-acetylfuran) thiocarbohydrazone; and 1, 5-bis (2-acetylpyrrole) thiocarbohydrazone were synthesized and characterized by elemental analysis, UV-visible, FT-IR, cyclic voltammetry, and ¹H and ¹³C-NMR spectral studies. All bisthiocarbohydrazone exhibited the thioketone—thioenol tautomeric forms, as evidenced by IR spectral data and single crystal X-ray diffraction studies of 1, 5-bis (2-acetylfuran) thiocarbohydrazone and 1, 5–bis (2-acetylpyrrole) thiocarbohydrazone.

Supplementary materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfer, and Silicon and the Related Elements for the following free supplemental files: Additional figures and tables.