Gas-phase acidity studies of multiple sites of adenine and adenine derivatives

The acidities of multiple sites in the purine nucleobase adenine (1) and adenine alkyl derivatives 9-ethyladenine (2), 3-methyladenine (3), 1-methyladenine (4), and N,N-dimethyladenine (5) have been investigated for the first time, using computational and experimental methods to provide an understanding of adenine reactivity. We have previously measured two acidic sites on adenine, with the N9 site being 19 kcal mol(-)(1) more acidic than the N10 site (333 +/- 2 versus 352 +/- 4 kcal mol(-)(1), respectively). In this work, we have established that 9-ethyladenine has two sites more acidic than water: the N10 (352 +/- 4 kcal mol(-)(1)) and the C8 (374 +/- 2 kcal mol(-)(1)). We have likewise measured two acidities for 3-methyladenine, the N10 (347 +/- 4 kcal mol(-)(1)) and the C2 (370 +/- 3 kcal mol(-)(1)). For 1-methyladenine and N,N-dimethyladenine, we measure the N9H acidity to be 331 +/- 2 and 333 +/- 2 kcal mol(-)(1), respectively. We believe that the bracketing of only one site for the latter species is a kinetic effect, which we discuss further in the paper. Computationally, we have found the interesting result that some of the vinylic C-H sites in these purine bases are predicted to be much more acidic than water (DeltaH(acid) = 390.7 kcal mol(-)(1)) in the gas phase, on the order of 373 kcal mol(-)(1). The acidic vinylic C-H sites are always adjacent to an N-R group, and this pattern is maintained regardless of whether the site is on the five- or six-membered ring of the purine. Vinylic C-H sites elsewhere on the purine have calculated acidities of about 400 kcal mol(-)(1). The differing acidities are interpreted through electrostatic potential calculations. We also relate our results to the intriguing biochemical decarboxylation of orotate ribose monophosphate, which involves a vinylic anion adjacent to an N-R group; this decarboxylation is the last step in the de novo biosynthesis of pyrimidine nucleotides, and the enzyme that catalyzes the reaction, orotate ribose monophosphate decarboxylase, has been the subject of intense study recently, as its mechanism remains elusive.     

Structure and hydrogen bonding in polyhydrated complexes of guanine

Abstract Molecular structure of complexes of guanine with 12, 13, 16, and 17 water molecules were calculated using B3LYP/6-311G(d,p) level of theory. Interaction with water results in some deformation of geometrical parameters of guanine, which can be described as contribution of zwitter-ionic resonant form into the structure of DNA base. Saturation of water binding sites within guanine creates possibilities for the formation of the N···H–O hydrogen bond where the nitrogen atom of amino group acts as proton acceptor. The NBO analysis of guanine–water interactions reveals that hydrogen bonds involving the N(3) and N(7) atoms of guanine represent a case of mixed N···H–O/π···H–O hydrogen bonds where contribution of π-system into total energy of interaction varies from 3% to 41%. This contribution significantly depends on orientation of the hydrogen atom of water molecule with respect to plane of purine bicycle and influence of neighboring water molecules. Graphical Abstract      

On the bonding of first-row transition metal cations to guanine and adenine nucleobases

The binding of first-row transition metal monocations (Sc+-Cu+) to N7 of guanine and N7 or N3 of adenine nucleobases has been analyzed using the hybrid B3LYP density functional theory (DFT) method. The nature of the bonding is mainly electrostatic, the electronic ground state being mainly determined by metal-ligand repulsion. M+-guanine binding energies are 18-27 kcal/mol larger than those of M+-adenine, the difference decreasing along the row. Decomposition analysis shows that differences between guanine and adenine mainly arise from Pauli repulsion and the deformation terms, which are larger for adenine. Metal cation affinity values at this level of calculation are in very good agreement with experimental data obtained by Rodgers et al. (J. Am. Chem. Soc. 2002, 124, 2678) for adenine nucleobases.     

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     

Concerning the acidity and hydrogen bonding of hydroxyphenanthroperylene quinones like fringelite D,hypericin, and stentorin

Summary The strongly enhanced acidity of the bay hydroxyl group as compared to the respectiveperi hydroxyl groups of fringelite D, hypericin, and stentorin could be rationalized on the basis of a vinylogous carboxylic acid and was nicely corroborated by semiempirical calculations of the AM1 type. Experimental data obtained from several independent experimental methods, like polarized absorption spectroscopy, hole burning, and isotope effects, as well as from semiempirical AM1 and 6–31G levelab initio calculations conclusively pointed to dissymmetrical hydrogen bonding systems in both theperi andbay regions of the correspondingbay phenolate ions.

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Zu Acidität und Wasserstoffbrückenbindung von Hydroxyphenanthroperylenchinonen wie Fringelit D, Hypericin und Stentorin

Zusammenfassung Die stark erhöhte Acidität der bay-Hydroxylgruppen gegenüber jener derperi-Hydroxylgruppen von Fringelit D, Hypericin und Stentorin läßt sich auf der Basis einer vinylogen Carbonsäure verstehen und wurde auch durch semiempirische Rechnungen vom AM1-Typ erhärtet. Daten aus unabhängigen Experimenten wie Polarisationsspektroskopie, Lochbrennen und Isotopeneffekte sowie semiempirische AM1- undab initio-Rechnungen auf 6–31G Niveau belegen ein unsymmetrisches Wasserstoffbrückenbindungssystem sowohl für denperi-als auch denbay-Bereich der entsprechendenbay-Phenolationen.

     

Studies on the hydrogen bonding of aniline's derivatives by FT-IR

The hydrogen bonding of 23 aniline's derivatives in various solvents and in solid states are studied by Fourier transform infrared spectroscopy. The Infrared absorption of their amino group is greatly influenced by solvents. Compared with those data determined in hexane, the symmetric stretching frequency (nu(s)) and asymmetric stretching frequency (nu(as)) of amino group have an obvious bathochromic shift in benzene, but a relatively smaller shift in CCl4. It is also found that the concentration of these compounds has very little effect on the frequencies, the band shapes and relative absorption intensities of amino group. This indicates that the intermolecular hydrogen bonds are very weak between the aniline's derivatives in the solution. The substituent of methyl (-CH3) has different electronic effects in organic solvents with various polarities. Methyl group behaves as an electron-donating functional group in hexane, however, it shows an electron-withdrawing effect in benzene. When methoxyl (CH3O-) is ortho-substituted, v(as) of amino group increases and nu(s) almost does not change. While methoxyl (CH3O-) is meta-substituted, v(as) of amino group increases, but nu(s) decreases. The groups of chloro- (Cl-) and nitro- (-NO2) cause a hyposochromic shift of the nu(as) and nu(s) of amino group, while substituent of -NH2 makes a bathochromic shift. The solvents influence the relative intensities of nu(as) and nu(s) of amino group more greatly than the substituents do. In solid states, the amino group of aniline's derivatives has more than two absorption bands because of forming the inter- or intra-molecular hydrogen bonds.     

Relative importance of hydrogen bonding and coordinating groups in modulating the zinc-water acidity

The presence of second-sphere -NH(2) groups in the proximity of a zinc(ii)-bound water molecule enhances its acidity by ca. 2 pK(a) units.     

The aminomethylation of adenine,cytosine and guanine

Aminomethylated derivatives of adenine, cytosine and guanine have been isolated and characterized for the first time. These results are important because of the potential for similar adducts being formed transiently between nucleosides and nucleotides, and endogenous aldehydes and amines in vivo, and of the potential use of similar adducts for drug delivery. Mono-alkylated products obtained were from the reaction of adenine with one equivalent of aminomethylating agent derived from amines exhibiting lower basicity (e.g., morpholine and N-methylpiperazine); bis-alkylated products were obtained with agents derived from more basic amines regardless of the stoichiometry. On the other hand, only bis-alkylated products were obtained from the reaction of cytosine or guanine with the aminomethylating agent regardless of the basicity of the secondary amine used or the stoichiometry of the reaction. The mono-alkylated adenine products were alkylated on N-9 while the bis-alkylated cytosine products were alkylated on N-9 and N⁴ and the bis-alkylated adenine products were alkylated on N-9 and N⁶. The adenine and cytosine aminomethyl adducts hydrolyzed rapidly in dilute aqueous solution.     

Synthesis of 8-hydroxymethyl derivatives of guanine and thioguanine

The reaction of 2, 4, 5-triamino-6-hydroxypyrimidine with phosphorus pentasulfide in quinoline has yielded 2, 4, 5-triamino-6-mercaptopyrimidine. 8-Hydroxymethyl derivatives of guanine and thioguanine have been synthesized by the acylation of 2, 4, 5-triamino-6-hydroxypyrimidine and the corresponding 6-mercapto compound with glycolic acid or ethyl glycolate, with subsequent treatment of the resulting 5-hydroxyacetylamino derivatives with aqueous alkali.     

8-aminoquinoline functionalized graphene oxide for simultaneous determination of guanine and adenine

The nanocomposite graphene oxide/8-aminoquinoline (GAQ) was prepared as modified electrode material for simultaneous determination of guanine and adenine. The prepared GAQ was characterized by SEM, TEM, FTIR, Raman, and UV-vis, which confirmed that the 8-aminoquinoline had been functionalized by covalent modification. The differential pulse voltammetry (DPV) proved the electrochemical properties of the GAQ, which exhibited good electrocatalytic activity and prominent synergistic effect for sensitive determination of guanine and adenine. The guanine and adenine both were detection by DPV showed good linearity with linear range covering 0.1–160 μM, and the detection limits (LOD) (S/N = 3) both were estimated to be 0.033 μM for guanine and adenine, respectively.     

General method for the synthesis of 8-arylsulfanyl adenine derivatives

We report a general method for the synthesis of 8-arylsulfanyl adenine derivatives using a mild protocol of coupling 8-mercaptoadenine with a variety of aryl iodides.     

Mesomorphic phenanthroline derivatives: novel architectures based on hydrogen bonding

Strong hydrogen bonding has been observed in mesomorphic phenanthroline compounds engineered from diacylaminobenzene platforms: a columnar organization is found in the free ligands (n = 12 or 16) whereas a smectic arrangement is evidenced in a palladium complex (n = 16).     

Metal coordination and imine-amine hydrogen bonding as the source of strongly shifted adenine pKa values

The X-ray crystal structure of a Pt(II) complex of composition trans-[(NH(3))(2)Pt(1,9-DimeA) (1,9-DimeAH)](ClO(4))(3) (2) with 1,9-DimeA = 1,9-dimethyladenine and 1,9-DimeAH(+) = 1,9-dimethyladeninium) is presented. Complex 2 forms upon deprotonation of one of the exocyclic amino groups of the adeninium ligands in trans-[(NH(3))(2)Pt(1,9-DimeAH)(2)](ClO(4))(4) (1), where the two nucleobases are in a head-tail arrangement. The low pK(a1) of 1 (4.1 +/- 0.2) is a consequence of a combination of the effects of metal coordination to N7 of the purine base and efficient stabilization of the deprotonated species. This feature is supported by the results of the structure determination of 2, which displays a head-head orientation of the two bases and intramolecular H-bonding between the imine group of 1,9-DimeA and the amino group of 1,9-DimeAH. In the fully deprotonated species trans-[(NH(3))(2)Pt(1,9-DimeA)(2)](ClO(4))(2) (3), the two nucleobases are again in a head-tail arrangement. The findings are of relevance with regard to the concept of "shifted pK(a) values" of nucleobases. This concept is applied to rationalize acid-base catalysis reactions involving nucleobases of DNA and RNA which occur in the near-physiological pH range.     

Precise recognition of nucleotides and their derivatives through hydrogen bonding in water by poly(vinyldiaminotriazine)

In water, poly(2-vinyl-4,6-diamino-1,3,5-triazine)(PVDAT) selectively binds the derivatives of thymine and uracil through the formation of three hydrogen bonds with the diaminotriazine (DAT) residues. The nucleotides and dinucleotides are bound much more strongly than are nucleic acid bases, due to the additional interactions of their phosphates with the DAT residues. The binding constant of the thymidine 5′-monophosphate-PVDAT adduct (5400 M^-1) is one of the largest values ever reported for the artificial receptors in protic solvents. In contrast, cytosine and its monophosphate are hardly bound to PVDAT. A water-soluble vinyldiaminotriazine–acrylamide copolymer also forms hydrogen bonds with thymine in water, whereas the corresponding monomers do not. A polymer effect is predominantly important for the molecular recognition through hydrogen bonding in water.