Ladder pyrrolone structures with anthraquinone recurring units

1,2,4,5-Tetraaminoanthraquinone and 1,4,5,8-naphthalene-tetracarboxylic acid dianhydride react in dimethylacetamide to give a tetrameric prepolymer with balanced endgroups of anhydride and diamine. When this prepolymer is carefully treated with polyphosphoric acid at elevated temperature it is converted to a soluble polypyrrolone type structure with an inherent viscosity of 2.3–2.7. Polymers of this molecular weight can be wet-spun into pliable fibers from methanesulfonic acid. The TGA curve in air shows little weight loss below 550°C. The polymer can also be solubilized by reduction with sodium dithionite in alkaline aqueous dimethyl sulfoxide.     

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.     

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.     

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.     

Conformational Properties of the Phosphate Rings of Neutral Phosphoramidate Derivatives of Ribo- and 2′-Deoxyribonucleoside Cyclic 3′,5′-Monophosphates

Abstract

An investigation of the effects of changing the nature of X, nitrogen base (B), and amino substituent (R₂N) on the equilibrium 1?2 was carried out.

The influence of the above structural changes on the time-averaged coupling constants J_AP and J_BP, determined at 300 MHz, were used to follow changes in K_eq. With constant R₂N, small effects from variation of X and B were found. A large range in K_eq arose from changes in the steric size of R₂N. These results will be related to the question of the ease of chair to twist interconversion of the phosphate ring essential to the biological activities of the naturally occurring diesters, cAMP and cGMP.     

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.     

2'-O-[2-(guanidinium)ethyl]-modified oligonucleotides: stabilizing effect on duplex and triplex structures

[structure: see text] Oligonucleotides with a novel 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modification have been synthesized using a novel protecting group strategy for the guanidinium group. This modification enhances the binding affinity of oligonucleotides to RNA as well as duplex DNA (DeltaT(m) 3.2 degrees C per modification). The 2'-O-GE modified oligonucleotides exhibited exceptional resistance to nuclease degradation. The crystal structure of a palindromic duplex formed by a DNA oligonucleotide with a single 2'-O-GE modification was solved at 1.16 A resolution.