Single- and double-proton-transfer in the aggregate between cytosine and guaninediazonium ion

Experimental and theoretical study of enol–keto prototropic tautomerism and photophysics of azomethine–BODIPY dyads

Enol ↔ keto prototropic tautomerism can be exploited to modulate the photophysics of BODIPY chromophores based on proton-coupled photoinduced electron transfer processes.

Ammonia elimination from protonated nucleobases and related synthetic substrates

The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH(3) elimination does present a major path for the fragmentations of the ions [1h + H](+), [2h + H](+), and [3h + H](+). The ion [2h + H - NH(3)](+) also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH(2) replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15-55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate's best protonation site, and possible mechanisms for NH(3) elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.

N-salicylideneanilines: tautomers for formation of hydrogen-bonded capsules, clefts, and chains

[structure: see text] The synthesis, characterization, and solid-state structures of new salicylaldimines are reported. Bis(N-salicylideneaniline)s (BSANs) and tris(N-salicylideneaniline)s (TSANs) are sterically encumbered compounds featuring a central six-membered ring in the keto-enamine tautomer. When extended with additional functional groups, these molecules may form hydrogen-bonded capsules, clefts, and extended structures. A TSAN with N-(t)()BOC-o-phenylenediamine groups has been structurally investigated. The complementary hydrogen-bonding motif in this molecule leads it to form dimers in solution and in the solid state. A BSAN with N-(t)()BOC-o-phenylenediamine substituents forms a hydrogen-bonded cleft in solution but forms an extended hydrogen-bonded ladder assembly of cofacial dimers in the solid state. When N-(t)()BOC-1,8-naphthalenediamine was utilized to extend the cleft, an unusual perimidine structure was obtained with the central core in the enol tautomer. In addition, ab initio calculations have been used to support the assignment of the keto-enamine or enol-imine tautomers of the BSANs and TSANs and to predict tautomerization in related BSANs and TSANs.

Cytosine catalysis of nitrosative guanine deamination and interstrand cross-link formation

Effects are discussed of the anisotropic DNA environment on nitrosative guanine deamination based on results of an ab initio study of the aggregate 3 formed by guaninediazonium ion 1 and cytosine 2. Within 3, the protonation of 2 by 1 is fast and exothermic and forms 6, an aggregate between betaine 4 (2-diazonium-9H-purin-6-olate) and cytosinium ion 5. Electronic structure analysis of 4 shows that this betaine is not mesoionic; only the negative charge is delocalized in the pi-system while the positive charge resides in the sigma-system. Potential energy surface exploration shows that both dediazoniation and ring-opening of betaine 4 in aggregate 6 are fast and exothermic and lead irreversibly to E-11, the aggregate between (E)-5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole E-10 and 5. The computed pair binding energies for 3, 6, and E-11 greatly exceed the GC pair binding energy. While 1 can be a highly reactive intermediate in reactions of the "free nucleobase" (or its nucleoside and nucleotide), the cyanoimine 10 emerges as the key intermediate in nitrosative guanine deamination in ds-DNA and ds-oligonucleotides. In essence, the complementary nucleobase cytosine provides base catalysis and switches the sequence of deprotonation and dediazoniation. It is argued that this environment-induced switch causes entirely different reaction paths to products as compared to the respective "free nucleobase" chemistry, and the complete consistency is demonstrated of this mechanistic model with all known experimental results. Products might form directly from 10 by addition and ring closure, or their formation might involve water catalysis via 5-cyanoamino-4-imidazolecarboxylic acid 12 and/or 5-carbodiimidyl-4-imidazolecarboxylic acid 13. The pyrimidine ring-opened intermediates 10, 12, and 13 can account for the formations of xanthosine, the pH dependency and the environment dependency of oxanosine formation, the formation of the classical cross-link dG(N(2)())-to-dG(C2), including the known sequence specificity of its formation, and the formation of the structure-isomeric cross-link dG(N1)-to-dG(C2).

Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-glycine complex have been investigated employing the B3LYP/6-311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and -1.83 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H-bonded glycinamide-glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H-bond.

Demonstration of an alternative mechanism for G-to-G cross-link formation

The cross-link dG-to-dG is an important product of DNA nitrosation. Its formation has commonly been attributed to nucleophilic substitution of N2 in a guaninediazonium ion by guanine, while recent studies suggest guanine addition to a cyanoamine derivative formed after dediazoniation, deprotonation, and pyrimidine ring-opening. The chemical viability of the latter mechanism is supported here by the experimental demonstration of rG-to-aG formation via rG addition to a synthetic cyanoamine derivative. Thus, all known products of nitrosative guanine deamination are consistent with the postulate of pyrimidine ring-opening. This postulated mechanism not only explains what is already known but also suggests that other products and other cross-links also might be formed in DNA deamination. The study suggests one possible new product: the structure isomer aG(N1)-to-rG(C2) of the classical G(N2)-to-G(C2) cross-link. While the formation of aG(N2)-to-rG(C2) has been established by chemical synthesis, the structure isomer aG(N1)-to-rG(C2) has been assigned tentatively based on its MS/MS spectrum and because this assignment is reasonable from a mechanistic perspective. Density functional calculations show preferences for the amide-iminol tautomer of the classical cross-link G(N2)-to-G(C2) and the amide-amide tautomer of G(N1)-to-G(C2). Moreover, the results suggest that both cross-links are of comparable thermodynamic stability, and that there are no a priori energetic or structural reasons that would prevent the formation of the structure isomer in the model reaction or in DNA.

Amino Effect on the Protonation of β-Aminoacrylonitrile

The protonation of acrylonitrile (1) and of Z- and E-3-aminoacrylonitrile (5 and 9) was studied with the Gaussian-2 method. Ammoniumacrylonitrile ion formation is not important. Nitrilium ion formation is preferred in all cases, and the proton affinities are about 80 kJ/mol higher for aminoacrylonitrile. Remarkably, it is found that C2-protonation of 3-aminoacrylonitriles to form iminium ions can compete with nitrilium ion formation. Beta-aminoacrylonitriles thus show propinquity to both acrylonitriles and enamines, and mechanistic and toxicological implications are discussed.

Double proton transfer behavior and one-electron oxidation effect in double H-bonded glycinamide-formic acid complex

The behavior of double proton transfer occurring in a representative glycinamide-formic acid complex has been investigated at the B3LYP/6-311 + + G( * *) level of theory. Thermodynamic and, especially, kinetic parameters, such as tautomeric energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the double proton transfer process, such as geometrical changes, interaction energies, and intrinsic reaction coordinate calculations have also been studied. Computational results show that the participation of a formic acid molecule favors the proceeding of the proton transfer for glycinamide compared with that without mediate-assisted case. The double proton transfer process proceeds with a concerted mechanism rather than a stepwise one since no ion-pair complexes have been located during the proton transfer process. The calculated barrier heights are 11.48 and 0.85 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 2.95 and 2.61 kcal/mol to 8.53 and -1.76 kcal/mol if further inclusion of zero-point vibrational energy corrections, where the negative barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to that occurring between glycinamide and formamide. Furthermore, solvent effects on the thermodynamic and kinetic processes have also been predicted qualitatively employing the isodensity surface polarized continuum model within the framework of the self-consistent reaction field theory. Additionally, the oxidation process for the double H-bonded glycinamide-formic acid complex has also been investigated. Contrary to that neutral form possessing a pair of two parallel intermolecular H bonds, only a single H bond with a comparable strength has been found in its ionized form. The vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 9.40 and 8.69 eV, respectively, where ionization is mainly localized on the glycinamide fragment. Like that ionized glycinamide-formamide complex, the proton transfer in the ionized complex is characterized by a single-well potential, implying that the proton initially attached to amide N4 in the glycinamide fragment cannot be transferred to carbonyl O13 in the formic acid fragment at the geometry of the optimized complex.

Nitrosative Guanine Deamination: Ab Initio Study of Deglycation of N-Protonated 5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazoles

5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazoles (1) (R at N1) have been discussed as possible intermediates in nitrosative guanine deamination, which are formed by dediazoniation and deprotonation of guaninediazonium ion. The parent system 1 (R = H) and its N1 derivatives 2 (R = Me) and 3 (R = MOM) are considered here. Protonation of 1-3, respectively, may occur either at the cyano-N to form cations 4 (R = H), 6 (R = Me), and 8 (R = MOM) or at the imino-N to form cations 5 (R = H), 7 (R = Me), and 9 (R = MOM), respectively. This protonation is the first step in the acid-catalyzed water addition to form 5-cyanoimino-imidazole-4-carboxylic acid, which then leads to oxanosine. There also exists the option of a substitution reaction by water at the R group of 6-9, and this dealkylation forms N-[4-(oxomethylene)-imidazol-5-yl]carbodiimide (10) and N-[4-(oxomethylene)-imidazol-5-yl]cyanamide (11). In the case of DNA, the R group is a deoxyribose sugar, and attack by water leads to deglycation. To explore this reaction option, the S(N)1 and S(N)2 reactions of 6-9 with water were studied at the MP2/6-31G*//RHF/6-31G* and CCSD/6-31G*//RHF/6-31G* levels, with the inclusion of implicit solvation at the IPCM(MP2/6-31G*)//RHF/6-31G* level, and the electron density distributions of tautomers 1, 10, and 11 were analyzed. The low barriers determined for the MOM transfer show that the deglycation could occur at room temperature but that the process cannot compete with water addition.

5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazole and 5-Cyanoamino-4-imidazolecarboxylic Acid Intermediates in Nitrosative Guanosine Deamination: Evidence from 18O-Labeling Experiments

The nitrosative deaminations (37 degrees C, NaNO2, NaAc buffer, pH 3.7) of guanosine 1r in (18O)water (97.6%) and of [6-18O]-1r in normal water were studied. [6-(18)O]-1r was prepared from 2-amino-6-chloropurine riboside using adenosine deaminase. The reaction products xanthosine 3r and oxanosine 4r were separated by HPLC and characterized by LC/MS analysis and 13C NMR spectroscopy. The 18O-isotopic shifts on the 13C NMR signals were measured and allowed the identification of all isotopomers formed. The results show that oxanosine is formed via 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole, 5, and its 1,4-addition product 5-cyanoamino-4-imidazolecarboxylic acid, 6. This hydration of 5 to 6 leads to aromatization and greatly dominates over water addition to the cyanoimino group of 5 to form 5-guanidinyliden-4-oxomethylene-4,5-dihydroimidazole, 7. 5-Guanidinyl-4-imidazolecarboxylic acid, 8, the product of water addition to 6, is not involved.

5-Cyanoamino-4-imidazolecarboxamide and nitrosative guanine deamination: experimental evidence for pyrimidine ring-opening during deamination

5-Cyanoamino-4-imidazolecarboxamide 4a (R = CH2-O-CH2-CH2-OH) has been synthesized, purified, and fully characterized by MS, MS/MS, HRMS, IR spectroscopy, and by 1H and 13C NMR spectroscopy. It is shown that cyclization of 4a yields the guanine 6a and the isoguanine 12a. Our findings provide experimental evidence in support of our hypothesis that the formation of oxanine and xanthine in nitrosative guanine deamination may proceed via pyrimidine ring-opened intermediates. The observed formation of 6a from the amide 4a (XH2 = NH2) shows that, in analogy, oxanine can be formed from 3 (XH = OH). The formation of 12a from 4a reveals for the first time the possibility that oxanine might be formed by a second pathway that involves electrocyclic reaction of 3. Finally, the new chemistry suggests the possibility for a new dG-to-dG cross-link.

Substituent Effects on Pyrid-2-yl Ureas toward Intramolecular Hydrogen Bonding and Cytosine Complexation

Equilibria between two conformational isomers of pyrid-2-yl ureas, the (E,Z) and (Z,Z) forms, have been studied in DMF-d(7) at -70 degrees C. Most of them show a small preference for the (E,Z) form with an equilibrium constant K(i) around 1-2. However, the K(i) value for 1-methyl-2-(3-(pyrid-2-yl)ureido)pyridinium iodide (12) was found to be 14.2 +/- 1.2. That is 1 order of magnitude larger than those of the others, which indicates that the positively charged 1-methylpyridinium-2-yl substituent would facilitate the (E,Z) form formation. Pyrid-2-yl ureas bind cytosine in DMF-d(7) with binding constants K(B) ranging from 30 to 1700 M(-1). Electron withdrawing substituents, such as the 4-O(2)NC(6)H(4)- or 1-methylpyridinium-4-yl substituent, preferentially facilitate the intermolecular cytosine complexation with large binding constants.

5-Cyanoimino-4-oxomethylene-4,5-dihydroimidazole and Nitrosative Guanine Deamination. A Theoretical Study of Geometries, Electronic Structures, and N-Protonation

The 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole 1 (R = H), its N1-derivatives 2 (R = Me) and 3 (R = MOM) and their cyano-N (4, 6, 8) and imino-N protonated (5, 7, 9) derivatives were studied with RHF, B3LYP, and MP2 theory. Solvation effects were estimated with the isodensity polarized continuum model (IPCM) at the MP2 level using the dielectric constant of water. Carbodiimide 10, cyanamide 12, N-cyanomethyleneimine 13, and its protonated derivatives 14 and 15 were considered for comparison as well. Adequate theoretical treatment requires the inclusion of dispersion because of the presence of intramolecular van der Waals, charge-dipole, and dipole-dipole (including H-bonding) interactions. All conformers were considered for the MOM-substituted systems, and direct consequences on the preferred site of protonation were found. The vicinal push (oxomethylene)-pull (cyanoimino) pattern of the 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazoles results in the electronic structure of aromatic imidazoles with 4-acylium and 5-cyanoamido groups. The gas-phase proton affinities of 1-3 are over 30 kcal/mol higher than that for N-cyanomethyleneimine 13, and this result provides compelling evidence in support of the zwitterionic character of 1-3. Protonation enhances the push-pull interaction; the OC charge is increased from about one-half in 1-3 to about two-thirds in the protonated systems. In the gas phase, cyano-N protonation is generally preferred but imino-N protonation can compete if the R-group contains a suitable heteroatom (hydrogen-bond acceptor, Lewis base). In polar solution, however, imino-N protonation is generally preferred. Solvation has a marked consequence on the propensity for protonation. Whereas protonation is fast and exergonic in the gas phase, it is endergonic in the polar condensed phase. It is an immediate consequence of this result that the direct observation of the cations 8 and 9 should be possible in the gas phase only.

Nitrosative Adenine Deamination: Facile Pyrimidine Ring-Opening in the Dediazoniation of Adeninediazonium Ion

[reaction: see text]. Dediazoniation of adeninediazonium ion, 1, forms the heteroaromatic cation, 2. Ab initio studies at the CCSD(fc)/6-31G**//MP2(full)/6-31G** level now reveal that the cyclic cation 2 is kinetically and thermodynamically unstable with respect to the pyrimidine ring-opened cation, 3. The results suggest that 4-cyano-5-isocyano-imidazole, 4, and 4,5-dicyanoimidazole, 5, might be formed to some extent in nitrosative deaminations of adenine.

Highly Stable Keto-Enamine Salicylideneanilines

[reaction: see text] Highly stable NH salicylideneanilines have been prepared by reaction of 1,3,5-triformylphloroglucinol with aniline derivatives. The NH form was confirmed by X-ray crystallographic data, as well as by NMR studies. A convenient one-step synthesis of triformylphloroglucinol is also reported.

Nucleic acid related compounds. 116. Nonaqueous diazotization of aminopurine nucleosides. Mechanistic considerations and efficient procedures with tert-butyl nitrite or sodium nitrite

Nonaqueous diazotization-dediazoniation of two types of aminopurine nucleoside derivatives has been investigated. Treatment of 9-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)-2-amino-6-chloropurine (1) with SbCl(3)/CH(2)Cl(2) was examined with benzyltriethylammonium (BTEA) chloride as a soluble halide source and tert-butyl nitrite (TBN) or sodium nitrite as the diazotization reagent. Optimized yields (>80%) of the 2,6-dichloropurine derivative were obtained with SbCl(3). Combinations with SbBr(3)/CH(2)Br(2) gave the 2-bromo-6-chloropurine product (>60%), and SbI(3)/CH(2)I(2)/THF gave the 2-iodo-6-chloropurine derivative (>45%). Antimony trihalide catalysis was highly beneficial. Mixed combinations (SbX(3)/CH(2)X'(2); X/X' = Br/Cl) gave mixtures of 2-(bromo, chloro, and hydro)-6-chloropurine derivatives that were dependent on reaction conditions. Addition of iodoacetic acid (IAA) resulted in diversion of purine radical species into a 2-iodo-6-chloropurine derivative with commensurate loss of other radical-derived products. This allowed evaluation of the efficiency of SbX(3)-promoted cation-derived dediazoniations relative to radical-derived reactions. Efficient conversions of adenosine, 2'-deoxyadenosine, and related adenine nucleosides into 6-halopurine derivatives of current interest were developed with analogous combinations.

Formation of 2'-deoxyoxanosine from 2'-deoxyguanosine and nitrous acid: mechanism and intermediates

The reaction mechanism for the formation of 2'-deoxy-oxanosine from 2'-deoxyguanosine by nitrous acid was explored using methyl derivatives of guanosine and an isolated intermediate of the reaction. When 1-methylguanosine was incubated with NaNO(2)under acidic conditions, N (5) -methyloxanosine and 1-methylxanthosine were generated, whereas the same treatment of N (2), N (2)-dimethylguanosine generated no product. In a similar experiment without NO(2)(-), participation of a Dimroth rearrangement was ruled out. In the guanosine-HNO(2)reaction system, an intermediate with a half-life of 5.6 min (pH 7.0, 20 degrees C) was isolated and tentatively identified as a diazoate derivative of guanosine. The diazoate intermediate was converted into oxanosine and xanthosine at a molar ratio (oxanosine:xanthosine) of 0.26 at pH 7.0 and 20 degrees C. The ratio was not affected by the incubation pH between 2 and 10, but increased linearly with temperature from 0.22 (0 degrees C) to 0.32 (50 degrees C). The addition of acetone also increased the ratio up to 0.85 (98% acetone). Based on these results, a con-ceivable pathway for the formation of 2'-deoxyoxanosine from 2'-deoxyguanosine by HNO(2)is proposed.