Theoretical examination of Mg(2+)-mediated hydrolysis of a phosphodiester linkage as proposed for the hammerhead ribozyme

The hammerhead ribozyme is an RNA molecule capable of self-cleavage at a unique site within its sequence. Hydrolysis of this phosphodiester linkage has been proposed to occur via an in-line attack geometry for nucleophilic displacement by the 2'-hydroxyl on the adjoining phosphorus to generate a 2',3'-cyclic phosphate ester with elimination of the 5'-hydroxyl group, requiring a divalent metal ion under physiological conditions. The proposed S(N)2(P) reaction mechanism was investigated using density functional theory calculations incorporating the hybrid functional B3LYP to study this metal ion-dependent reaction with a tetraaquo magnesium (II)-bound hydroxide ion. For the Mg(2+)-catalyzed reaction, the gas-phase geometry optimized calculations predict two transition states with a kinetically insignificant, yet clearly defined, pentacoordinate intermediate. The first transition state located for the reaction is characterized by internal nucleophilic attack coupled to proton transfer. The second transition state, the rate-determining step, involves breaking of the exocyclic P-O bond where a metal-ligated water molecule assists in the departure of the leaving group. These calculations demonstrate that the reaction mechanism incorporating a single metal ion, serving as a Lewis acid, functions as a general base and can afford the necessary stabilization to the leaving group by orienting a water molecule for catalysis.     

Asymmetric synthesis of rubiginones A(2) and C(2) and their 11-methoxy regioisomers

Convergent enantioselective syntheses of angucyclinone-type natural products rubiginones A(2) (2) and C(2) (1) and their 11-methoxy regioisomers 3 a and 3 b have been achieved by using two domino processes from a common enantiomerically pure 1-vinylcyclohexene 4. Key steps in the synthesis of this diene were the stereoselective conjugate addition of AlMe(3) on (SS)-[(p-tolylsulfinyl)methyl]-p-quinol (9) and the elimination of the beta-hydroxy sulfoxide fragment, after oxidation to sulfone, to recover a carbonyl group. The first domino sequence comprised Diels-Alder reaction with a sulfinyl naphthoquinone followed by sulfoxide elimination. An efficient opposite regioselection in the cycloaddition step was achieved in the convergent construction of the tetracyclic skeleton using a sulfoxide at C-2 or C-3 of the dienophiles 5 or 6, derived from 5-methoxy-1,4-naphthoquinone. The second domino process, triggered by oxygen and sunlight, allowed the transformation of the initial tetracyclic adducts into the final products after B ring aromatization, silyl deprotection and C-1 oxidation.     

Identification of esters by collisional charge inversion of their enolate ions

The collisional charge inversion and neutralization-reionization (^?NR) mass spectra of the enolate ions of m/z 115 derived from the four butyl acetates, the two propyl propionates, ethyl butyrate, ethyl isobutyrate, methyl valerate, methyl 2-methylbutyrate and methyl 3-methylbutyrate were recorded. The major primary fragmentation reactions of the unstable carbenium ion formed by charge inversion involve elimination of an alkoxy radical to form a ketene or alkylketene molecular ion and formation of an alkyl ion consisting of the R¹ group of RCOOR¹. A minor fragmentation reaction involves elimination of an alkyl radical by cleavage of a C? C bond α to the ether oxygen. The alkylketene ions fragment by β-cleavage eliminating an alkyl radical to form an olefinic acylium ion. In most cases the charge inversion mass spectra of the enolate ions allow identification of the ester.     

Synthesis of 3alpha,7alpha,14alpha-trihydroxy-5beta-cholan-24-oic acid: a potential primary bile acid in vertebrates

A method for the synthesis of 3alpha,7alpha,14alpha-trihydroxy-5beta-cholan-24-oic acid which is a possible candidate of bile acid metabolite in vertebrates was developed. The principal reactions involved were 1). stereoselective remote-hydroxylation of methyl ursodeoxycholate diacetate with dimethyldioxirane, 2). site-selective protection at C-3 by tert-butyldimethylsilylation of the resulting 3alpha,7alpha,14alpha-trihydroxy ester, 3). oxidation of the diol with pyridinium dichromate adsorbed on activated alumina, 4). stereoselective reduction of the 7-ketone with zinc borohydride, and 5). cleavage of the protecting group at C-3 with p-toluenesulfonic acid. A facile elimination of the 14alpha-hydroxy group under an acidic or neutral condition is also described. The synthetic reference compound is now available for comparison with unidentified biliary bile acids detected in vertebrate bile.     

Remote fragmentations of protonated aromatic carbonyl compounds via internal reactions in intermediary ion-neutral complexes

Protonated aromatic aldehydes and methyl ketones 1a–10a, carrying initially the proton at the carbonyl group, are prepared by electron impact-induced loss of a methyl radical from 1?arylethanols and 2?aryl?2?propanols, respectively. The aryl moiety of the ions corresponds to a benzene group, a naphthalene group, a phenanthrene group, a biphenyl group, and a terphenyl group. respectively, each substituted by a CH₃OCH₂ side-chain as remote from the acyl substituent as possible. The characteristic reactions of the metastable ions, studied by mass-analyzed ion kinetic energy spectrometry, are the elimination of methanol, the formation of CH₃OCH ₂ ⁺ ions, and the elimination of an ester RCOOCH₃ (R = H and CH₃) . The mechanisms of these fragmentations were studied by using D-labeled derivatives. Confirming earlier results, it is shown that the ester elimination, at least from the protonated aryl methyl ketones, has to proceed by an intermediate [acyl cation/arylmethyl methyl ether]-complex. The relative abundances of the elimination of methanol and of the ester decrease and increase, respectively, with the size of the aromatic system. Clearly, the fragmentation via intermediate ion-neutral complexes is favored for the larger ions. Furthermore, the acyl cation of these complexes can move unrestricted over quite large molecular distances to react with the remote CH₃OCH₂-side-chain, contrasting the restricted migration of a proton by 1,2-shifts (“ring walk”) in these systems.     

Gas phase glycosidic cleavage of oxynions from alkyl glycosides

The oxyanion [M? H]^? from several methylglycosides were generated by fast atom bombardment and their decomposition was studied by mass-analysed ion kinetic energy spectrometry. The main decomposition pathway is the loss of methanol. The hydroxylic hydrogen arises by proton transfer from the hydroxyl groups of the sugar. In the gluco-series, no anomeric effect is found. The absence of either the hydroxyl groups at C-2 or C-6 does not inhibit the glycosidic cleavage. However, the blocking of both the hydroxyl groups at C-4 and C-6, by a benzylidene group or two methyl groups, inhibit completely the glycosidic cleavage. From these results, it is proposed that the glycosidic cleavage occurs after opening the sugar ring by a vicinal attack of an oxyanion at C-6 or C-4 to the C-5 carbon atom. Then, the ionized hemi-acetals fragment into a methanolate anion and a 5,6- or 4,5-anhydrosugar which exchange another proton before their separation into charged and neutral species.     

Ring cleavage reactions of methyl α-D-allopyranoside derivatives with phenylboron dichloride and triethylsilane

In the course of our studies on the regioselective carbon-oxygen bond cleavage of the benzylidene acetal group of hexopyranosides with a reducing agent, we found that a combination of a Lewis acid and a reducing agent triggered a ring-opening reaction of the pyranose ring of methyl α-D-allopyranosides. The formation of an acyclic boronate ester by the attachment of a hydride ion at C-1 indicated that the unexpected endocyclic cleavage of the bond between the anomeric carbon atom and the pyranose ring oxygen atom proceeded via an oxacarbenium ion intermediate produced by the chelation between O5/O6 of the pyranoside and the Lewis acid, followed by nucleophile substitution with a hydride ion at C1.     

Hydrolytic reactions of diribonucleoside 3',5'-(3'-N-phosphoramidates): kinetics and mechanisms for the P-O and P-N bond cleavage of 3'-amino-3'-deoxyuridylyl-3',5'-uridine

Hydrolytic reactions of 3'-amino-3'-deoxyuridylyl-3',5'-uridine (2a), an analogue of uridylyl-3',5'-uridine having the 3'-bridging oxygen replaced with nitrogen, have been followed by RP HPLC over a wide pH range. The only reaction taking place under alkaline conditions (pH > 9) is hydroxide ion-catalyzed hydrolysis (first-order in [OH(-)]) to a mixture of 3'-amino-3'-deoxyuridine 3'-phosphoramidate (7) and uridine (4). The reaction proceeds without detectable accumulation of any intermediates. At pH 6-8, a pH-independent formation of 3'-amino-3'-deoxyuridine 2'-phosphate (3) competes with the base-catalyzed cleavage. Both 3 and in particular 7 are, however, rather rapidly dephosphorylated under these conditions to 3'-amino-3'-deoxyuridine (5). In all likelihood, both 3 and 7 are formed by an intramolecular nucleophilic attack of the 2'-hydroxy function on the phosphorus atom, giving a phosphorane-like intermediate or transition state. Under moderately acidic conditions (pH 2-6), the predominant reaction is acid-catalyzed cleavage of the P-N3' bond (first-order in [H(+)]) that yields an equimolar mixture of 5 and uridine 5'-phosphate (6). The reaction is proposed to proceed without intramolecular participation of the neighboring 2'-hydroxyl group. Under more acidic conditions (pH < 2), hydrolysis to 3 and 4 starts to compete with the cleavage of the P-N bond, and this reaction is even the fastest one at pH < 1. Formation of 2'-O,3'-N-cyclic phosphoramidate as an intermediate appears probable, although its appearance cannot be experimentally verified. The rate constants for various partial reactions have been determined. The reaction mechanisms and the effect that replacing the 3'-oxygen with nitrogen has on the behavior of the phosphorane intermediate are discussed.     

Delineating noncovalent interactions between the azinomycins and double-stranded DNA: importance of the naphthalene substitution pattern on interstrand cross-linking efficiency

[reaction: see text] Using a series of synthetic azinomycin analogues, it is shown that the efficiency of in vitro DNA interstrand cross-linking is markedly reduced when either the C-5' methyl group or both the C-5' methyl and C-3' methoxy groups are deleted from the naphthalene ring.     

Isolation and structure determination of a benzofuran and a bis-nor-isoprenoid from Aspergillus niger grown on the water soluble fraction of Morinda citrifolia Linn. leaves

The leaves of Morinda citrifolia, Linn. afforded a new benzofuran and a bis-nor-isoprenoid, blumenol C, hitherto unreported from this source. The structures of these have been elucidated as 5-benzofuran carboxylic acid-6-formyl methyl ester (1) and 4-(3'(R)-hydroxybutyl)-3,5,5, trimethyl-cyclohex-2-en-1-one (2) respectively through spectroscopic studies. The NMR data (including 1D, 2D techniques) and stereochemistry at C-3' of Compound 2 is also being reported for the first time.     

Synthesis and structural characterization of pyrimidine bi- and tricyclic nucleosides with sugar puckers conformationally locked into the eastern region of the pseudorotational cycle

Reaction of 5'-O-tosyl TSAO-m(3)T (1) with amines has led to the synthesis of new classes of bi- and tricyclic nucleosides. Full details about the synthesis of these compounds and a plausible mechanism to explain their obtention are reported. In addition, we describe the development of a second, more efficient, and higher yielding synthetic route as a general approach for the synthesis of some of these bicyclic nucleosides. To study the conformational behavior of the bi- and tricyclic nucleosides described in this paper, intensive NMR investigations and molecular modeling studies were performed. Conformational analysis indicates that the furanose ring of the compounds described here prefers the eastern side of the pseudorotation cycle with the base substituents preferentially in the anti range. The torsion angle gamma describing the C-4'[bond]C-5' is found to prefer the +sc range. These compounds represent a novel class of E-type conformationally restricted bicyclic ribo-nucleosides containing a [3.3.0]-fused carbohydrate moiety. The bicyclic nucleosides described herein present an interesting potential for diverse and selective chemical treatments on the 2'-hydroxyl and/or the functionalities incorporated at the bridge between C-3' and C-5'.     

The role of 23S ribosomal RNA residue A2451 in peptide bond synthesis revealed by atomic mutagenesis

Peptide bond formation is a fundamental reaction in biology, catalyzed by the ribosomal peptidyl-transferase ribozyme. Although all active-site 23S ribosomal RNA nucleotides are universally conserved, atomic mutagenesis suggests that these nucleobases do not carry functional groups directly involved in peptide bond formation. Instead, a single ribose 2'-hydroxyl group at A2451 was identified to be of pivotal importance. Here, we altered the chemical characteristics by replacing its 2'-hydroxyl with selected functional groups and demonstrate that hydrogen donor capability is essential for transpeptidation. We propose that the A2451-2'-hydroxyl directly hydrogen bonds to the P-site tRNA-A76 ribose. This promotes an effective A76 ribose C2'-endo conformation to support amide synthesis via a proton shuttle mechanism. Simultaneously, the direct interaction of A2451 with A76 renders the intramolecular transesterification of the peptide from the 3'- to 2'-oxygen unfeasible, thus promoting effective peptide bond synthesis.     

The role of the cleavage site 2'-hydroxyl in the Tetrahymena group I ribozyme reaction

BACKGROUND: The 2'-hydroxyl of U preceding the cleavage site, U(-1), in the Tetrahymena ribozyme reaction contributes 10(3)-fold to catalysis relative to a 2'-hydrogen atom. Previously proposed models for the catalytic role of this 2'-OH involve coordination of a catalytic metal ion and hydrogen-bond donation to the 3'-bridging oxygen. An additional model, hydrogen-bond donation by the 2'-OH to a nonbridging reactive phosphoryl oxygen, is also consistent with previous results. We have tested these models using atomic-level substrate modifications and kinetic and thermodynamic analyses. RESULTS: Replacing the 2'-OH with -NH(3)(+) increases the reaction rate approximately 60-fold, despite the absence of lone-pair electrons on the 2'-NH(3)(+) group to coordinate a metal ion. Binding and reaction of a modified oligonucleotide substrate with 2'-NH(2) at U(-1) are unaffected by soft-metal ions. These results suggest that the 2'-OH of U(-1) does not interact with a metal ion. The contribution of the 2'-moiety of U(-1) is unperturbed by thio substitution at either of the nonbridging oxygens of the reactive phosphoryl group, providing no indication of a hydrogen bond between the 2'-OH and the nonbridging phosphoryl oxygens. In contrast, the 10(3)-fold catalytic advantage of 2'-OH relative to 2'-H is eliminated when the 3'-bridging oxygen is replaced by sulfur. As sulfur is a weaker hydrogen-bond acceptor than oxygen, this effect suggests a hydrogen-bonding interaction between the 2'-OH and the 3'-bridging oxygen. CONCLUSIONS: These results provide the first experimental support for the model in which the 2'-OH of U(-1) donates a hydrogen bond to the neighboring 3'-bridging oxygen, thereby stabilizing the developing negative charge on the 3'-oxygen in the transition state.     

1-β-D-呋喃核糖基-1,2,4-三唑-3-酰胺铂(II)配合物的合成

在缓冲液中，利用1-β-D-呋喃核糖基-1，2，4-三唑-3-酰胺(ribavirin)和1- （2'-脱氧-β-D-呋喃核糖基）-1，2，4-三唑-3-酰胺(deoxyribavirin)作为配体 ，分别与cis-[Pt(DMSO)_2Cl_2]或K[Pt(DMSO)Cl_3]进行配位反应，得到了高产率 的[Pt-(N~4,N~7-ribavirin)(DMSO)Cl] (1)和[Pt(N~4,N~7-deoxyribavirin) (DMSO)Cl] (2)两种配合物。1-（2'-脱氧-β-D呋喃核糖基）-1，2，4-三唑-3-酰 胺的合成是由1-β-D-呋喃核糖基-1，2，4-三唑-3-酰胺与1，3-二氯-1，1，3，3- 四异丙基二硅氧烷保护，在1-甲基咪唑存在下与硫代苯氧基碳酰氯反应，再用tri- n-butyltin hydride和AIBN还原，四丁基氟化铵的四氢呋喃溶液脱去保护基四步反 应完成的。     

Unprecedented migration of a methyl group in 2-(2',6'-dimethylphenylazo)-4-methylphenol mediated by ruthenium

An unprecedented chemical transformation of 2-(2',6'-dimethylphenylazo)-4-methylphenol has been observed upon its reaction with [Ru(PPh(3))(2)(CO)(2)Cl(2)] whereby the methyl group at the 2' position migrates to the 4' or 6' position.     

Interannular proton exchange and fragmentation of carbonyl-protonated benzophenones

Benzopbenones a initially protonated at the carbonyl group were prepared by electron-impact induced dissocation of 1,1-diphenylpropanols (compounds 1-5). These protonated ketones decompose in the ion source and the second field-free region of a reversed geometry mass spectrometer by proton migration to one of the phenyl groups and subsequent elimination of benzene. In the case of derivatives substituted by methoxy groups and trifluoromethyl groups respectively, the proton migrates predominantly to the more bask benzene ring, resulting in the elimination of anisole in the former case and of benzene in die latter case. A study of protonated benzopbenones labelled at the phenyl ring and at the carbonyl group shows that only a few interannular H/D exchange steps precede the fragmentation. This is observed not only for metastable ions in the magnetic sector instilment but also for ions of long lifetimes investigated by Fourier-transform-ion cyclotron resonance (FT-ICR) Spectrometry. This is in contrast to the arene elimination from protonated 1,ω-dipbenylalkanes and related polyphenylalkanes which fragment by complete positional exchange of all hydrogen atoms at the aromatic rings. The special behaviour of protonated benzophenones is attributed to a low barrier for the decomposition of a chemically activated arenium ion b, which arises from the initial proton transfer. Once b is formed, it decomposes quickly without much interannular proton exchange.     

Substituent control of hydrogen bonding in palladium(II)-pyrazole complexes

Inter- and intramolecular hydrogen bonding of an N-H group in pyrazole complexes was studied using ligands with two different groups at pyrazole C-3 and C-5. At C-5, groups such as methyl, i-propyl, phenyl, or tert-butyl were present. At C-3, side chains L-CH(2)- and L-CH(2)CH(2)- (L = thioether or phosphine) ensured formation of chelates to a cis-dichloropalladium(II) fragment through side-chain atom L and the pyrazole nitrogen closest to the side chain. The significance of the ligands is that by placing a ligating side chain on a ring carbon (C-3), rather than on a ring nitrogen, the ring nitrogen not bound to the metal and its attached proton are available for hydrogen bonding. As desired, seven chelate complexes examined by X-ray diffraction all showed intramolecular hydrogen bonding between the pyrazole N-H and a chloride ligand in the cis position. In addition, however, intermolecular hydrogen bonding could be controlled by the substituent at C-5: complexes with either a methyl at C-5 or no substituent there showed significant intermolecular hydrogen bonding interactions, which were completely avoided by placing a tert-butyl group at C-5. The acidity of two complexes in acetonitrile solutions was estimated to be closer to that of pyridinium ion than those of imidazolium or triethylammonium ions.     

Studies on the enzyme immunoassay of bio-active constituents contained in oriental medicinal drugs. V. Preparation of bovine serum albumin conjugate and beta-galactosidase labelled antigen for enzyme immunoassay of 3 beta-(monoglucuron-1' beta-yl)-18 beta-glycyrrhetic acid

In order to prepare an immunogen for enzyme immunoassay of 3 beta-(monoglucuron-1'-beta-yl)-18 beta-glycyrrhetic acid (3MGA), which was isolated from a patient with glycyrrhizin-induced pseudoaldosteronisms, benzyl glycyrrhetate (3) was allowed to react with an acetobromosugar (2) in the presence of silver carbonate to give benzyl 3 beta-(methyl 2',3',4'-triacetyl-glucuron-1' beta-yl)-glycyrrhetate (5) and methyl 3',4'-diacetyl-alpha-1',2'-O-[1-(benzyl glycyrrhet-3 beta-yl)- ethylidene]-D-glucuronate (4). On the other hand, this reaction was carried out in the presence of mercuric cyanide in nitromethane to give compound 5, benzyl 3 beta-acetyl glycyrrhetate (6) and benzyl 11-oxo-A-neooleana-3(5),12-dien-3-oate (7). 4-Aminomethylcyclohexanecarboxylic acid and glycine were introduced as chemical bridges at C-30 of 3 beta-(tert-butylglucuron-1' beta-yl)-glycyrrhetic acid (11) derived from compound 5. The former bridge was used to prepare an immunogenic conjugate with bovine serum albumin, and the latter bridge was used for antigen labelled with beta-galactosidase.     

Identification of amino acid phosphorodiamidates of antiviral nucleosides using electrospray ionization tandem mass spectrometry

Several amino acid phosphorodiamidate derivatives of d4T as anti-HIV prodrugs were synthesized and investigated using electrospray ionization multistage tandem mass spectrometry (ESI-MS(n)). A novel methyl group migration in gas phase was observed in ESI-MS(2) of the sodium adducts of amino acid methyl ester of phosphorodiamidates of 2',3'-didehydro-2',3'-dideoxythymidine (d4T). The proposed structures of the rearrangement ions were confirmed by high resolution tandem mass spectrometry. A possible mechanism involving the pentacoordinate phosphoric-carboxylic phosphate anhydride was proposed, in which a seven-membered ring intermediate was formed by coordination with the metal ion between the phosphoryl group and carbonyl oxygen atom. Thus, the intrinsic properties of phosphoryl group might be the key factors responsible for this migration.     

Cyclization into perhydronaphthalenones using samarium diiodide

Samarium(II) diiodide has been employed to promote the intramolecular cyclization reactions of aldehydes or ketones onto α,β-unsaturated ketones. The cyclization reactions described herein provide a general approach to the syntheses of perhydronaphthalenones with a cis-relationship between the OH at C-5 and the proton or methyl group at C-4a with good diastereoselectivity under mild reaction conditions.