Interaction of 2'-deoxyadenosine with cis-2-butene-1,4-dial: computational approach to analysis of multistep chemical reactions

The computational analysis of multistep chemical interactions between 2'-deoxyadenosine and cis-2-butene-1,4-dial has been performed. The applied protocol includes generation of a multistep Gibbs free-energy reaction profile (PCM/M05-2X/6-311+G(d) level) for the transformations of the reagents to products, followed by evaluation of the rate constants, construction of the corresponding kinetic equations, and solving them. Such a procedure allows one to significantly extend the number of experimentally determined steps by addition of the ones computationally predicted. The primary products of the reaction are found to be four diastereomeric adducts characterized by virtually the same stability. The acid-catalyzed dehydration of these adducts leads to a more stable secondary product. Computational verification of UV and NMR spectra has also been performed. It has been revealed that simulated UV and NMR spectra of primary and secondary 2'-deoxyadenosine adducts of cis-2-butene-1,4-dial are in agreement with the experimental observations.     

Photochemical syn-anti isomerization reactions in N2-hydroxyisocytosines--an experimental matrix isolation and theoretical study

N2-hydroxyisocytosine and 1-methyl-N2-hydroxyisocytosine were studied using a matrix isolation technique combined with infrared absorption spectroscopy. For N2-hydroxyisocytosine isolated in an Ar matrix (at 10 K), two imino-oxo isomers, one with the hydroxyimino =N-OH group directed toward the N1-H group (the form called further anti) and the second with the =N-OH group directed toward N3-H (syn), were observed in the ratio 1.4:1. The syn isomer is converted totally to the anti form after UV (lambda > 295 nm) irradiation of the matrix. A small amount of the N(3)H-hydroxy-amino tautomer of N2-hydroxyisocytosine was also detected in the matrix. This form did not react photochemically. For 1-methyl-N2-hydroxyisocytosine, only the syn form of the imino-oxo tautomer was observed after deposition of the matrix. UV (lambda > 295 nm) irradiation induced a photoreaction converting this isomer into the anti form. After 15% of the starting material had been converted into the product, a photostationary state was achieved, and no further progress of the reaction was observed. Subsequent UV irradiation (lambda > 335 nm) caused a back reaction, leading to a disappearance of the anti form and to the recovery of the initial syn isomer. All isomers were identified by comparing their experimental IR spectra with the spectra theoretically calculated at the DFT(B3LYP)/6-31G(d,p) level, where DFT is the density functional theory. Good agreement between the observed and predicted patterns of the spectral lines allowed for reliable identification. The experimental IR spectra were interpreted and discussed. The relative energies of the 12 isomers of N2-hydroxyisocytosine were calculated at the MP2/6-31G(d,p) and MP4//MP2/6-31G(d,p) levels. For six isomers of 1-methyl-N2-hydroxyisocytosine, the calculations were carried out at the MP2/6-31G(d,p) level. The anti form of the imino-oxo tautomer of N-hydroxyisocytosine and the syn form of the imino-oxo tautomer of 1-methyl-N2-hydroxyisocytosine were predicted to be the most stable.     

Oxidation chemistry of 2'-deoxyadenosine at pyrolytic graphite electrode

The electrochemical oxidation of 2'-deoxyadenosine has been investigated in phosphate containing supporting electrolytes in pH range 2-10 at a pyrolytic graphite electrode by cyclic sweep voltammetry, spectral studies, controlled potential electrolysis and related techniques. The oxidation of 2'-deoxyadenosine occurred in a single well-defined oxidation peak (I(a)), over the entire pH range. The electrooxidation occurred by the loss of 6.0+/-0.5 e(-) per mole over the entire pH range. The kinetics of the decay of the UV-absorbing intermediates has been studied and found to follow pseudo first order kinetics having rate constant (k) in the range (5.7-7.7)x10(-4) s(-1). The major products of electrooxidation were separated by HPLC and characterized by GC-MS/MS, (1)H NMR and a tentative mechanism for electrooxidation of 2'-deoxyadenosine has been suggested.     

Model studies of DNA C5' radicals. Selective generation and reactivity of 2'-deoxyadenosin-5'-yl radical

The reaction of hydrated electrons (e(aq)(-)) with 8-bromo-2'-deoxyadenosine has been investigated by radiolytic methods coupled with product studies and addressed computationally by means of DFT-B3LYP calculations. Pulse radiolysis revealed that this reaction was complete in approximately 0.3 mus, and, at this time, no significant absorption was detected. The spectrum of a transient developed in 20 mus has an absorbance in the range 300-500 nm (epsilon(max) congruent with 9600 M(-1) cm(-1) at 360 nm), and it was assigned to aromatic aminyl radical 3. Computed vertical transitions (TD-UB3LYP/6-311+G) are in good agreement with the experimental observations. Radical 3 is obtained by the following reaction sequence: one-electron reductive cleavage of the C-Br bond that gives the C8 radical, a fast radical translocation from the C8 to C5' position, and an intramolecular attack of the C5' radical at the C8,N7 double bond of the adenine moiety. The rate constant for the cyclization is 1.6 x 10(5) s(-1). On the basis of the theoretical findings, the cyclization step is highly stereospecific. The rate constants for the reactions of C5' and aminyl 3 radicals with different oxidants were determined by pulse radiolysis methods. The respective rate constants for the reaction of 2'-deoxyadenosin-5'-yl radical with dioxygen, Fe(CN)(6)(3)(-), and MV(2+) in water at ambient temperature are 1.9 x 10(9), 4.2 x 10(9), and 2.2 x 10(8) M(-1) s(-1). The value for the reaction of aminyl radical 3 with Fe(CN)(6)(3-) is 8.3 x 10(8) M(-1) s(-1), whereas the reaction with dioxygen is reversible. Tailored experiments allowed the reaction mechanism to be defined in some detail. A synthetically useful radical cascade process has also been developed that allows in a one-pot procedure the conversion of 8-bromo-2'-deoxyadenosine to 5',8-cyclo-2'-deoxyadenosine in a diastereoisomeric ratio (5'R):(5'S) = 6:1 and in high yield, by reaction with hydrated electrons in the presence of K(4)Fe(CN)(6).     

Adduct formation identification between phenyl glycidyl ether and 2'-deoxyadenosine and thymidine by chromatography, mass spectrometry and nuclear magnetic resonance spectroscopy

Thymidine and 2'-deoxyadenosine were reacted with phenyl glycidyl ether in order to study the formation of the corresponding 2'-deoxynucleoside adducts. Separation methods were elaborated using either reversed-phase high-performance liquid chromatography with photodiode-array detection, or centrifugal circular thin-layer chromatography. The adducts were isolated on a preparative scale and were fully characterized by UV spectroscopy, desorption chemical ionization and fast atom bombardment mass spectrometry and 270- and 360-MHz 1H NMR spectrometry. For thymidine the main adduct was characterized as N-3-(2-hydroxy-3-phenoxypropyl)thymidine. With 2'-deoxyadenosine, predominantly N-1-(2-hydroxy-3-phenoxypropyl)-2'-deoxyadenosine was formed. With longer reaction times, the formation of a minor amount of dialkylated 2'-deoxyadenosine was observed. These nucleoside adducts will be used as marker compounds for studies of DNA adduct formation.     

Molecular Structure of 1-Ethyl-4-hydroxy-N-(6-hydroxybenzothiazolyl-2)-2-oxo-1,2-dyhydroquinoline-3-carboxamide

X-ray diffraction analysis of 1-ethyl-4-hydroxy-N-(6-hydroxybenzothiazolyl-2)-2-oxo-1,2-dihydroquinoline-3-carboxamide has been performed. In crystal, the compound exists as a 2-oxo-4-hydroxy tautomer.     

Excited State Proton Transfers in Hybrid Compound Based on Indoline Spiropyran of the Coumarin Type and Azomethinocoumarin in the Presence of Metal Ions

Spectral-luminescence properties of a hybrid compound containing a coumarin-type spiropyran and an azomethinocoumarin fragment in toluene-acetonitrile solution in the presence of Li⁺, Ca²⁺, Zn²⁺ and Mg²⁺ ions are reported. Two excited state proton transfers can occur in the hybrid compound—the transfer of a proton from the OH group of the 7-hydroxy coumarin tautomer to the N atom of the C=N bond of the azomethine fragment leading to green ESIPT fluorescence with a maximum at 540 nm and from the OH group of the 7-hydroxy coumarin tautomer to the carbonyl group of the pyrone chromophore, which leads to the formation of the 2-hydroxyl-tautomer T of coumarin with blue fluorescence with a maximum at 475 nm. Dependence of these excited state proton transfers on the metal nature and irradiation with an external UV source is discussed.     

Synthesis,structure, and luminescent properties of 2-[2-(9-anthryl)vinyl]quinolines

Previously unknown 2-[2-(9-anthryl)vinyl]quinolin-8-ol and 2-[2-(9-anthryl)vinyl]-8-methoxyquinoline were synthesized by condensation of 8-hydroxy(methoxy)-2-methylquinoline with 9-anthraldehyde in acetic anhydride, as well as by the Wittig reaction. The product structure was determined on the basis of their 1H NMR, IR, UV, and mass spectra and quantum-chemical calculations. 2-[2-(9-Anthryl)vinyl]-8-methoxyquinoline showed luminescence with a quantum yield φ of 0.25, which was considerably higher than that of its 8-hydroxy analog (φ = 0.067).     

A novel strategy of chemical modification for rate enhancement of 10-23 DNAzyme: a combination of A9 position and 8-aza-7-deaza-2'-deoxyadenosine analogs

With the help of a divalent-metal ion, 10-23 DNAzyme cleaves RNA. Chemical modification of its catalytic loop to make a more efficient enzyme has been a challenge. Our strategy started from its five 2'-deoxyadenosine residues (A5, A9, A11, A12, and A15) in the loop based on the capability of the N7 atom to form hydrogen bonds in tertiary structures. 8-Aza-7-deaza-2'-deoxyadenosine and its analogs with 7-substituents (3-aminopropyl, 3-hydroxylpropyl, or phenethyl) were each used to replace five dA residues, respectively, and their effect on cleavage rate were evaluated under single-turnover conditions. The results indicated that the N7 atom of five dA residues were necessary for catalytic activity, and the N8 atom and 7-substituents were detrimental to the catalytic behavior of 10-23 DNAzyme, except that all these modifications at A9 were favourable for the activity. Especially, DZ-3-9 with 7-(3-aminopropyl)-8-aza-7-deaza-2'-deoxyadenosine (3) at A9 position gave a 12- fold increase of k(obs), compared to the corresponding parent 10-23 DNAzyme. DZ-3-9 was supposed to catalyze the cleavage reaction with the same mechanism as 10-23 DNAzyme based on their very similar pH-dependent and divalent metal ions-dependent cleavage patterns. Introduction of functional groups at A9 position was demonstrated to be a successful and feasible approach for more efficient 10-23 DNAzyme analogs.     

A highly facile and efficient one-step synthesis of N6-adenosine and N6-2'-deoxyadenosine derivatives

[reaction: see text] A highly facile and efficient one-step synthesis of N6-adenosine and N6-2'-deoxyadenosine derivatives has been developed. Treatment of inosine or 2'-deoxyinosine, without protection of sugar hydroxyl groups, with alkyl or arylamines, in the presence of BOP and DIPEA in DMF, led to the formation of N6-adenosine and N6-2'-deoxyadenosine derivatives in good to excellent yields. Carcinogenic polyaromatic hydrocarbon (PAH) N6-2'-deoxyadenosine adduct 10 and a rare DNA constituent 11 were thus synthesized directly from 2'-deoxyinosine both in 98% yield.     

Carboxyketenes from 4-hydroxy-1,3-oxazin-6-ones and Meldrum's acid derivatives

New 4-hydroxy-1,3-oxazin-6-ones 8 and 16 were prepared from chlorocarbonyl(phenyl)ketene and amides. The flash vacuum thermolysis (FVT) reactions of these compounds and the 4-methoxy derivative 17 were investigated by Ar matrix isolation IR spectroscopy and online mass spectrometry including MS/MS analysis. Carboxy(phenyl)ketene 10 is formed as the major product by thermal fragmentation of 4-hydroxy-1,3-oxazin-6-one 8. This takes place via the unstable 6-hydroxy tautomer 9. Another tautomer, the 5H-isomer 12, leads to the formation of benzoyl isocyanate 13 as a minor product together with phenylketene 14. Carboxy(phenyl)ketene 10 remains detectable at high FVT temperatures but undergoes thermal decarboxylation to phenylketene 14. The same carboxy(phenyl)ketene 10 is also produced in significant amounts by FVT of 5-phenyl-Meldrum's acid 18 via the unstable enol tautomer 19. A small amount of the unsubstituted carboxyketene 20 is observable on FVT of Meldrum's acid 1 itself.     

Comprehensive studies on an overall proton transfer cycle of the ortho-green fluorescent protein chromophore

Initiated by excited-state intramolecular proton transfer (ESIPT) reaction, an overall reaction cycle of 4-(2-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one (o-HBDI), an analogue of the core chromophore of the green fluorescent protein (GFP), has been investigated. In contrast to the native GFP core, 4-(4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one (p-HBDI), which requires hydrogen-bonding relay to accomplish proton transfer in vivo, o-HBDI possesses a seven-membered-ring intramolecular hydrogen bond and thus provides an ideal system for mimicking an intrinsic proton-transfer reaction. Upon excitation, ESIPT takes place in o-HBDI, resulting in a ～600 nm proton-transfer tautomer emission. The o-HBDI tautomer emission, resolved by fluorescence upconversion, is comprised of an instantaneous rise to a few hundred femtosecond oscillation in the early relaxation stage. Frequency analysis derived from ultrashort pulse gives two low-frequency vibrations at 115 and 236 cm(-1), corresponding to skeletal deformation motions associated with the hydrogen bond. The results further conclude that ESIPT in o-HBDI is essentially triggered by low-frequency motions and may be barrierless along the reaction coordinate. Femtosecond UV/vis transient absorption spectra also provide supplementary evidence for the structural evolution during the reaction. In CH(3)CN, an instant rise of a 530 nm transient is resolved, which then undergoes 7.8 ps decay, accompanied by the growth of a rather long-lived 580 nm transient species. It is thus concluded that following ESIPT the cis-proton transfer isomer undergoes cis-trans-isomerization. The results of viscosity-dependent dynamics are in favor of the one-bond-flip mechanism, which is in contrast to the volume-conserving isomerization behavior for cis-stilbene and p-HBDI. Further confirmation is given by the picosecond-femtosecond transient IR absorption spectra, where several new and long-lived IR bands in the range of 1400-1500 cm(-1) are assigned to the phenyl in-plane breathing motions of the trans-proton transfer tautomer. Monitored by the nanosecond transient absorption, the 580 nm transient undergoes a ～7.7 μs decay constant, accompanied by the growth of a new ～500 nm band. The latter is assigned to a deprotonated tautomer species, which then undergoes the ground-state reverse proton recombination to the original o-HBDI in ～50 μs, achieving an overall, reversible proton transfer cycle. This assignment is unambiguously supported by pump-probe laser induced fluorescence studies. On these standpoints, a comparison of photophysical properties among o-HBDI, p-HBDI, and wild-type GFP is discussed in detail.     

REINVESTIGATION OF THE PHOTOPHYSICS OF 2-(2'-HYDROXY-4'-DIETHYLAMINOPHENYL)BENZOTHIAZOLE

Abstract— The photophysical properties of 2-(2'-hydroxy-4'-diethylaminophenyl) benzothiazole (HABT) have been investigated by steady-state and time-resolved spectroscopies. In n-heptane HABT exhibits both normal and tautomer emissions with ∼equal fluorescence intensity at room temperature, in contrast to a previous report in which negligible tautomer emission was observed. The normal/tautomer (400/500 nm) ratio of emission intensity increases as the temperature decreases. Two possible excited-state intramolecular proton transfer (ESIPT) mechanisms are proposed, which cannot be resolved at the present stage. One proposed mechanism incorporates state mixing between -OH and -N(C₂H₅)₂ charge transfer states, resulting in a significant energy barrier for ESIPT. An alternative mechanism is also proposed in which fast proton tunneling may take place between enol and keto forms, which are in equilibrium in the excited singlet state.     

Excited-state double-proton transfer in the 7-azaindole dimer in the gas phase. 2. Cooperative nature of double-proton transfer revealed by H/D kinetic isotopic effects

The dispersed fluorescence (DF) spectra of the 7-azaindole dimer (7AI2) and deuterated dimers 7AI2-hd and 7AI2-dd, where hd and dd indicate the deuteration of an imino proton and two imino protons, have been measured in a supersonic free jet expansion. The undeuterated 7AI2-hh dimer exhibits only the tautomer fluorescence, but both the normal and tautomer fluorescence have been detected by exciting the origins of 7AI2-h*d, 7AI2-hd* and 7AI2-dd in the S1-S0 region, where h* and d* indicate the localization of the excitation on 7AI-h or 7AI-d moiety. The DF spectra indicate that 7AI2-h*d and 7AI2-hd* undergo excited-state proton/deuteron transfer (ESPDT), while excited-state double-deuteron transfer (ESDDT) occurs in 7AI2-dd. The H/D kinetic isotopic effects on ESDPT have been investigated by measuring the intensity ratios of the normal fluorescence to the tautomer fluorescence. The ESPDT rate is about 1/60th of the ESDPT rate, and the ESDDT rate is about 1/12th of the ESPDT rate, where ESPDT rate is an average of the rates for 7AI2-h*d and 7AI2-hd*. The observed H/D kinetic isotope effects imply that the ESDPT reaction of 7AI2 has a "cooperative" nature; i.e., the motion of the two moving protons strongly couples each other through the electron motions. The difference in the estimated ESPDT reaction rates, 9.8 x 10(9) and 6.9 x 109 s(-1) for 7AI2-h*d and 7AI2-hd*, respectively, is consistent with the concerted mechanism rather than the stepwise mechanism.     

The parent of 2-(4,5-dihydro-1H-tetrazol-5-ylidene)-2-cyanoacetate: Synthesis and reactivity X-ray structure of (E)2-[1-(2,2-dimethylpropyl)-4,5-dihydro-1H-tetrazol-5-ylidene]-2-cyanoacetate

Reaction of 3,3-diazido-2-cyanoacrylate 5 with four moles of ammonia gives tetrazolyl-bisammonium salt 7 . The key-intermediate is the amino-vinyl azide 6 which spontaneously undergoes a 1,5′ ring-closure reaction followed by double deprotonation. Treatment of 7 with hydrochloric acid yields the parent of 2-(4,5-dihydro-1H-tetrazol-5-ylidene)-2-cyanoacetate 9 (R = Me, Et) as the only tautomer. Regiospecific monoalkylation of bisammonium salt 7a with dimethyl sulfate and reaction of ammonium salt 12 with hydrochloric acid gives (E)2-(1-methyl-4,5-dihydro-1H-tetrazol-5-ylidene)-2-cyanoacetate ( 13 ) (X-ray structure of derivative 14 ). Compound 13 can also be obtained from vinyl azide 10 and methylamine. This experiment as well as AM1 calculations of 9a, 23 and 24 strongly favour tautomer 9a .     

Synthesis and structure of novel 6-(pyrazol-1-yl)-4-methyl-1H-pyrazolo[3,4-b]pyridin-3-ol derivatives

New 6-(pyrazol-1-yl)pyrazolo[3,4-b]pyridin-3-ol compounds were synthesized by cyclization reaction from 2,6-dichloro-4-methylnicotinonitrile. Their derivatives exist as the 3-hydroxy tautomer. The structure of the compound 1a of one of the resulting compounds was studied in detail by X-ray diffraction.     

Dehydration of 3- and 4-aryl- substituted 3-hydroxy acids in acetic anhydride in presence of zinc chloride

The reaction of several di- and triaryl-substituted 3-aryl-3-hydroxy acids and a 4-aryl-3-hydroxy acid in acetic anhydride in the presence of anhydrous zinc chloride has been investigated. It has been shown that the reaction discovered with 3-(2′-thienyl)-substituted 3-hydroxy acids, namely, their conversion under the above stated conditions into α, β-unsaturated methyl ketones,^1,2 occurs also with 3-aryl 3-hydroxy acids but to a smaller degree due to the concurrent cyclization reaction which leads to indene-1-ones. It has been established that the unsaturated methyl-ketones obtained, containing three aromatic substituents at the CC bond, exist in s-cis-(CC, CO)-conformation. It has been found that with the 4-aryl-substituted 3-hydroxy acid almost no unsaturated ketone is obtained, whereas instead the main product is a 2,3-disubstituted 1-naphthol which is acetylated under the conditions of the reaction. Its structure has been proved by its UV, IR and NMR spectra and confirmed by the mass spectrum of the compound.     

3-氨基-2-吡啶酮互变异构的密度泛函理论计算

采用密度泛函理论,在B3LYP/6-3 l1G**基组水平上,计算并考察了3-氨基-2-吡啶酮分子酮式和烯醇式结构进行结构互变的质子迁移过程中的2种可能途径:(a)分子内质子迁移,(b)水助质子迁移.计算结果表明,途经b所需要的活化能较小,氢键在降低反应活化能方面起着重要作用.     

Electronic spectroscopy and photochromic mechanism of bis-Schiff bases, N, N''''-bis(2-hydroxy-1-naphthylidene)-1,4-phenyldiamine

The steady state and transient state absorption spectra and fluorescence spectra of N,N'-bis(2-hy-droxy-1-napbthylidcne)-1,4-phenyldiamme ( BNP ) in cyclohexane and acetonitrile were determined.The pho-tochromic mechanism was discussed In nonpolar solvents,BNP exists mainly in the enol form and has the absorption maximum in the UV region In polar solvents,however,both the enol and proton transfer tautomer are formed,but the farmer is the main one Fluorescence emissions result from the excited state of proton transfer product.     

Simple HPLC-UV determination of nucleosides and its application to the authentication of Cordyceps and its allies

A simple HPLC-UV method combined with a simple extraction procedure of nucleosides (adenosine, cordycepin, 2'-deoxyadenosine, guanosine and uridine) was developed and applied to the authentication of Cordyceps and its allies. The separation was performed on a C(18) column by isocratic elution with acetonitrile-water, and UV detection at 260 nm. The amounts of adenosine, cordycepin, 2'-deoxyadenosine, guanosine and uridine in Cordyceps were 0.28-14.15, 0.006-6.36, 0.01-0.14, 0.68-14.79 and 0.19-20.29 mg/g, respectively. Among the nucleosides studied, cordycepin was characteristically included in Cordyceps militaris (L.) Link. (CM), which is one of key Cordyceps allies, and might be a good marker for authenticating CM. The ratio of nucleosides to adenosine contents in Cordyceps seemed to be a useful marker for authentication and quality control of Cordyceps.