Synthesis of an mRNA fragment of alanyl-tRNA synthetase gene in Escherichia coli using the 6-methyl-3-pyridyl group for protection of the imide functions of uridine and guanosine

The synthesis of 5'-GpGpUpGpU-3' is reported to demonstrate the synthetic use of the 6-methyl-3-pyridyl group for the protection of the O-4 and O-6 imide functions of uridine and guanosine, respectively. The 2'- and 5'-hydroxyl functions of the key intermediates were protected with two acid-labile groups: 3-methoxy-1,5-dicarbomethoxypentane-3-yl (MDMP) and 9-(4-octadecyloxyphenyl)xanthen-9-yl (C18Px), respectively. The internucleotide phosphotriesters were protected with 2-chlorophenyl and the 9-fluorenylmethyl group was employed for 3'-terminal phosphate protection.     

Analytical irreducible representation bases of the single and double icosahedral groups and their applications

An equivalent basis of icosahedral molecules is introduced in which the basis functions can be transformed under the operations in the icosahedral group (I_h). In this equivalent basis, the irreducible representation basis (IRB) of I_h, including the double‐valued IRB of I, is deduced analytically based on the method introduced in the literature [J. Comput. Chem. 17 , 851 (1996)]. Therefore the concepts of symmetry‐matrix and symmetry‐supermatrix can be used in the single‐ and multiconfiguration self‐consistent field methods (including relativistic effects) to reduce the storage of two‐electron integrals and calculations of Fock matrix during iterations by a factor of ca. 10,000. In addition, the equivalent basis of I_h can also be used to reduce the calculations of atoms and representations of rank ≥ 2 tensors. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 615–624, 2000     

Electron attachment to the DNA bases adenine and guanine and dehydrogenation of their anionic derivatives: Density functional study

Density functional theory (DFT) calculations have been used to explore electron attachment to the purines adenine and guanine and their hydrogen atom loss. Calculations show that the dehydrogenation at the N9 site in the adenine and guanine transient anions is the lowest‐cost channel of hydrogen loss, and the N9? H bond scission has Gibbs free energies of dissociation ΔG° of 8.8 kcal mol^?1 for the anionic adenine and 13.9 kcal mol^?1 for the anionic guanine. The relatively high feasibility of low‐energy electron (LEE)‐induced N9? H bond cleavage in the purine nucleobases arises from high electron affinities of their H‐deleted counterparts. Unlike adenine, other N? H bond dissociations are competitive with the N9? H bond fission in the anionic guanine. The replacement of hydrogen in the ring of purine has a significant effect on the N9? H bond fragmentation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Study of photopolymers. XVI. Novel syntheses of the polymers with azidonitrobenzoyl groups and their photochemical and thermochemical reactions

Poly-2-(2-azido-5-nitrobenzoyloxy)ethylmethacrylate (P-II-A) and poly-2-(4-azido-3-nitrobenzoyloxy)ethylmethacrylate (P-II-B) were synthesized from the reactions of 2-hydroxyethylmethacrylate with 2-chloro-5-nitrobenzoic acid and 4-chloro-3-nitrobenzoic acid, respectively, by substitution reactions of sodium azide with the corresponding chloronitrobenzoyl group. In addition, the degradation reaction of the 2-azido-5-nitrobenzoyl group in P-II-A and the transformation of the 4-azido-3-nitrobenzoyl group to 5-carboxylbenzofurazane-1-oxide ring in P-II-B by irradiation with ultraviolet (UV) light or by heating were investigated in detail. In the photochemical reaction the reaction of the azide group in P-II-A was affected by the presence of a spacer in the polymer chain. Moreover, in the thermochemical reaction the rates of the reactions of azide groups in P-II-A and P-II-B were controlled by the facility of molecular motion and the conformation of polymer chains.     

Mechanism for the deamination of ammeline,guanine, and their analogues

Structural Chemistry - Mechanisms for the deamination of ammeline (AMN), guanine (Gua), and their analogues with nH2O (n = 1–3) have been investigated using B3LYP and...     

Organosilicon and organophosphorus compounds with pseudohalogen groups. 1. Synthesis of alkoxydimethylsilyl cyanides and their reactions with metal fluorides

Alkoxydimethylsilyl cyanides were synthesized by the exchange reaction of the corresponding alkoxydimethylchlorosilanes with trimethylsilyl cyanide, and also by the reaction of the former compounds with HCN in the presence of triethylamine (the latter method is preferential). Reactions of silyl cyanides with SbF₃ and ZnF₂ were studied. It was found that the reaction of silyl cyanides with SBF₃ leads to the formation of Me₂SiF₂ and the corresponding alkoxydimethylfluorosilanes, which were also obtained by counter-synthesis from alkoxydimethylsilylchlorosilanes and metal fluorides (SbF₃, ZnF₂, CsF). Dimethylfluorosilyl cyanide was obtained by the reaction of silyl cyanides with ZnF₂.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 7, pp. 1593–1587, July, 1991.     

An effective method for the preparation of O6 -substituted guanosine and n3-substituted uridine derivatives via the corresponding stannylated intermediates

O₆-substituted guanosine and N³-substituted uridine derivatives were obtained in high yields by stannylation of the corresponding unsubstituted nucleosides with bis(tributyltin)-oxide followed by treatment with various electrophiles.     

Novel trichloroacetyl based silylations: simple methods for t-butyldimethylsilylations and for the protection of amino groups.

A new reagent for t-butyldimethylsilylation has been developed and the known trimethylsilyl trichloroacetate (1) has been shown to be of use for N-silylating amines.     

The complementarity principle in chemical reactions. modifications of the indolinedione-indole rearrangement and enamine synthesis

The experimental discovery of a significant modification of a chemical reaction has always been considered a noteworthy achievement. As shown below, four modifications of the indolinedione-indole rearrangement and three modifications of the synthesis of β-diketones provide evidence for the usefulness of the complementarity principle [1] for the discovery of such specific reactions.     

DNA-protein cross-links between guanine and lysine depend on the mechanism of oxidation for formation of C5 vs C8 guanosine adducts

The reaction between N(alpha)-acetyllysine methyl ester (Lys) and 2'-deoxyguanosine (dGuo) was used to study structural aspects of DNA-protein cross-link (DPC) formation. The precise structure of DPCs depended on the nature of the oxidant and cross-linking reactions in which a series of different oxidation conditions generated a distribution of adducts, principally spirodiiminodihydantoins with lysine appended at the purine position of C5 (5-Lys-Sp), C8 (8-Lys-Sp), or both C5 and C8 (5,8-diLys-Sp). Singlet oxygen oxidation of dGuo produced 5-Lys-Sp exclusively when Rose Bengal or methylene blue was used to photochemically generate (1)O2 in the presence of Lys, whereas riboflavin or benzophenone-mediated photochemistry generated lysine radicals and led to C8 adduct formation, yielding 8-Lys-Sp and 5,8-diLys-Sp. Notably, the yield of dGuo modifications from riboflavin photooxidation increased dramatically in the presence of lysine. Oxidation of deoxyguanosine/lysine mixtures with Na2IrCl6 or sulfate radicals produced both 5-Lys-Sp and 8-Lys-Sp. The same adducts were formed in single and double-stranded oligodeoxynucleotides, and these could be analyzed after nuclease digestion. Adduct formation in duplex DNA was somewhat dependent on the accessibility of lysine to C5 vs C8 of the purine. No adduct formation was detected between lysine and the other nucleobases T, C, or A. Overall, the precise location of adduct formation at C5 vs C8 of guanine appears to be diagnostic of the oxidation pathway.     

Systematic study of the tautomerism of uracil induced by proton transfer. Exploration of water stabilization and mutagenicity

To systematically investigate all the possible tautomerisms from uracil (U) and its enol form (U) induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase, in a continuum solvent, and in a microhydrated environment with 1 or 2 explicit water molecules, using density functional theory (DFT) calculations by means of the B3LYP exchange and correlation functions. A total of 62 geometries including 25 transition states were optimized, and the geometrical parameters have been discussed. Some rules of the configuration variation in tautomerization were summarized. The relative stabilities of all the tautomers were established. When a proton transfers from the di-keto form to the keto-enol form, water molecules in different regions show absolutely opposite effects: some assist, whereas others hinder the tautomerization. However, when a proton transfers from the keto-enol form to the di-enol form, water molecules in different regions show similar effects: the Gibbs free energy always increases and the activation energy always decreases. Additionally, some important factors that obviously affect the activation energy and Gibbs free energy were found and discussed in detail. The reasons that water molecules can assist or prevent the proton transfer were given. Furthermore, on the basis of our calculated results, we explain why it is hard to detect the di-enol form of uracil in general experiments.     

Novel method for the preparation of poly(urethane–imide)s and their properties

A polymer blend consisting of polyimide (PI) and polyurethane (PU) was prepared by means of a novel approach. PU prepolymer was prepared by the reaction of polyester polyol and 2,4-tolylenediisocyanate (2,4-TDI) and then end-capped with phenol. Poly(amide acid) was prepared from pyromellitic dianhydride (PMDA) and oxydianiline (ODA). A series of oligo(amide acid)s were also prepared by controlling the molar ratio of PMDA and ODA. The PU prepolymer and poly(amide acid) or oligo(amide acid) solution were blended at room temperature in various weight ratios. The cast films were obtained from the blend solution and treated at various temperatures. With the increase of polyurethane component, the films changed from plastic to brittle and then to elastic. The poly(urethane–imide) elastomers showed excellent mechanical properties and moderate thermal stability. The elongation of films with elasticity was more than 300%. The elongation set after the breaking of films was small. From the dynamic mechanical analysis, all the samples showed a glass transition temperature (T_g) at ca. −15°C, corresponding to T_g of the urethane component, suggesting that phase separation occurred between the two polymer components, irrespective of polyimide content. TGA and DSC studies indicated that the thermal degradation of poly(urethane–imide) was in the temperature range 250–270°C. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 3745–3753, 1997     

Chlorination reactions of ephedrines revisited. Stereochemistry and functional groups effect on the reaction mechanisms

The stereochemistry of the chlorination reactions with SOCl₂ of free ephedrine and pseudoephedrine and their hydrochlorides, oxamides and sulfonamides was analyzed. Chlorination of free and hydrochloride erythro isomers occurs with 100% inversion of configuration at C-1 (S_N2 mechanism). Chlorination of oxamides and sulfonamides of erythro isomers occurs with retention of the configuration at C-1, (S_Ni mechanism). Chlorination reactions in all threo isomers and derivatives hydrochlorides, oxamides or sulfonamides gave the same ratio of erythro (40%) and threo isomers (60%) (S_N1 mechanism). Treatment of the isomeric mixture of the chlorodeoxyephedrine and chlorodeoxypseudoephedrine hydrochloride in DMSO with HCl changes the isomeric ratio, increasing the erythro isomer content (65%). Using the erythro ethanolamines it is possible to arrive stereoselectively at the erythro chloroamines if the compound is previously tosylated or converted to the amide, or to the threo chloroamines if the compound is directly chlorinated with SOCl₂.