Gas phase interaction of zinc ion with purine and pyrimidine DNA and RNA bases

The interaction of uracil, thymine, cytosine, adenine, and guanine with zinc ion was studied at the density functional B3LYP/6‐311+G(2df,2p) level. Different binding sites allowing both mono‐metal and bi‐metal coordination were considered for the different low‐lying tautomers of nucleic acid bases. Zinc ion forms stable compounds with all nucleobases. Except for cytosine, mono‐coordination appears to be less favored than bi‐coordination in the other pyrimidines. Instead, the preferred sites in the case of adenine and guanine were found to be the N7 and O6 and N7 and N6 pairs of atoms, respectively. Zinc ion affinity was evaluated for all the complexes and compared with values previously obtained for other transition metal ions. In the present case, the following order of metal ion affinity (MIA) was found: G>A>C>T>U. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Unified model for the ultrafast decay of pyrimidine nucleobases

Ultrafast decay processes detected after absorption of UV radiation in gas-phase pyrimidine nucleobases uracil, thymine, and cytosine are ascribed to the barrierless character of the pathway along the low-lying 1(pipi*) hypersurface connecting the Franck-Condon region with an out-of-plane distorted ethene-like conical intersection with the ground state. Longer lifetime decays and low quantum yield emission are on the other hand related to the presence of a 1(pipi*) state planar minimum on the S1 surface and the barriers to access other conical intersections. A unified model for the three systems is established on the basis of accurate multiconfigurational CASPT2 calculations, whereas the effect of the different levels of theory on the results is carefully analyzed.     

Eutectic mixtures with plastic columnar discotics: molecular structure,phase morphology and kinetics of phase separation

We report the properties of eutectic mixtures of triphenylenes displaying a highly ordered columnar phase with a low molar mass non‐discotic compound. Such highly ordered triphenylenes display large charge carrier mobilities which are strongly controlled by the state of order in the discotic phase. The motivation was to establish how the state of order—molecular order, phase morphology, temperature ranges of phase stabilities and macroscopic orientational order—can be influenced by mixing. The studies reveal that the molecular order, in particular the mutual arrangement of the columns and the intracolumnar order, are unaffected by dilution of the discotic compound, whereas the phase morphology and the kinetics of phase separation change significantly with dilution. Rod‐shaped discotic domains with a hexagonal cross‐sectional area are formed via a nucleation process and the rods grow linearly as a function of time. Both the pure discotic phase as well as the discotic domains forming during phase separation can be macroscopically ordered by orientation layers.     

Eutectic mixtures with plastic columnar discotics: molecular structure, phase morphology and kinetics of phase separation

We report the properties of eutectic mixtures of triphenylenes displaying a highly ordered columnar phase with a low molar mass non-discotic compound. Such highly ordered triphenylenes display large charge carrier mobilities which are strongly controlled by the state of order in the discotic phase. The motivation was to establish how the state of order—molecular order, phase morphology, temperature ranges of phase stabilities and macroscopic orientational order—can be influenced by mixing. The studies reveal that the molecular order, in particular the mutual arrangement of the columns and the intracolumnar order, are unaffected by dilution of the discotic compound, whereas the phase morphology and the kinetics of phase separation change significantly with dilution. Rod-shaped discotic domains with a hexagonal cross-sectional area are formed via a nucleation process and the rods grow linearly as a function of time. Both the pure discotic phase as well as the discotic domains forming during phase separation can be macroscopically ordered by orientation layers.     

Association patterns of platinated purine nucleobases in metal-modified pairs and triples

Blocking of Watson-Crick or Hoogsteen edges in purine nucleobases by a metal entity precludes involvement of these sites in interbase hydrogen bonding, thereby leaving the respective other edge or the sugar edge as potential H bonding sites. In mixed guanine, adenine complexes of trans-a2PtII (a = NH3 or CH3NH2) of composition trans-[(NH3)2Pt(9-EtA-N1)(9-MeGH-N7)](NO3)2 (1a), trans-[(NH3)2Pt(9-EtA-N1)(9-MeGH-N7)](ClO4)2 (1b), and trans,trans-[(CH3NH2)2(9-MeGH-N7)Pt(N1-9-MeA-N7)Pt(9-MeGH-N7)(CH3NH2)2](ClO4)4*2H2O (2) (with 9-EtA = 9-ethyladenine, 9-MeA= 9-methyladenine, 9-MeGH = 9-methylguanine), this aspect is studied. Thus, in 1b pairing of two adenine ligands via Hoogsteen edges and in 2 pairing of two guanine bases via sugar edges is realized. These situations are compared with those found in a series of related complexes.     

Oxidative amination of cuprated pyrimidine and purine derivatives

Using regioselective cuprations (via magnesiations), various primary, secondary and tertiary aminated pyrimidine and purine derivatives were prepared by the oxidative coupling of lithium amidocuprates using chloranil. DNA and RNA units such as aminated uracil or thymine, and adenine, as well as a CDK inhibitor, purvalanol A, were all obtained under mild conditions and satisfactory yields.     

Reactions of trimethylsilyl fluorosulfonyldifluoroacetate with purine and pyrimidine nucleosides

Difluorocarbene, generated from trimethylsilyl fluorosulfonyldifluoroacetate (TFDA), reacts with the uridine and adenosine substrates preferentially at the enolizable amide moiety of the uracil ring and the 6-amino group of the purine ring. 2′,3′-Di-O-benzoyl-3′-deoxy-3′-methyleneuridine reacts with TFDA to produce 4-O-difluoromethyl product derived from an insertion of difluorocarbene into the 4-hydroxyl group of the enolizable uracil ring. Reaction of the difluorocarbene with the adenosine substrates having the unprotected 6-amino group in the purine ring produced the 6-N-difluoromethyl derivative, while reaction with 6-N-benzoyl protected adenosine analogues gave the difluoromethyl ether product derived from the insertion of difluorocarbene into the enol form of the 6-benzamido group. Treatment of the 6-N-phthaloyl protected adenosine analogues with TFDA resulted in the unexpected one-pot conversion of the imidazole ring of the purine into the corresponding N-difluoromethylthiourea derivatives. Treatment of the suitably protected pyrimidine and purine nucleosides bearing an exomethylene group at carbons 2′, 3′ or 4′ of the sugar rings with TFDA afforded the corresponding spirodifluorocyclopropyl analogues but in low yields.     

The low frequency vibrations of pyrimidine and purine bases

We report the far i.r. spectra of crystalline powders of uracil, cytosine, thymine, xanthine and hypoxanthine, from 25 to 1000 cm⁻¹. The carbonyl bending modes of uracil and cytosine have been identified through the substitution of sulfur for oxygen at the C2 position. Wagging and torsional modes of the amino group of cytosine as well as the N1H out-of-plane bending mode have been identified by deuteration studies. Several ring vibrations below 800 cm⁻¹ have also been identified. A Fermi resonance was observed in the case of 2-thiocytosine which involves the sulfur out-of-plane bending mode, the lowest lying ring bending mode and the wagging and torsional modes of the amino group. There also appears to be a Fermi resonance in cytosine involving the carbonyl modes and two external modes. Two modes at 285 and 320 cm⁻¹ which involve the methyl group of thymine are tentatively identified. The temperature dependence of the spectra of hypoxanthine for frequencies <350 cm⁻¹ indicates a large mixing between the internal and external vibrations in the 200–250 cm⁻¹ region.     

Synthesis of novel chiral compounds of purine and pyrimidine bases

The physiologically active groups such as purine and pyrimidine bases are introduced to the asymmetric ynthesis. The optically pure compounds bearing purine and pyrimidine bases (5a—5e) were prepared via the asymetric Michael addition reaction of purines and pyrimidines as Michael donators with the chiral source 5-(R)-[(1R, 2S, 5R)-menthyloxy]-2(5H)-furanone (3a), which was prepared from the natural chiral auxiliary (-)-menthol. The synthetic method was studied in detail and the new compounds were identified on the basis of their analytical data and spectroscopic data, such as [α]_D~(20), IR, UV, ~1H NMR, ~(13)C NMR and MS. The absolute configuration of 5a was established by X-ray crystallography. The results provided an efficient synthetic route to chiral purines and pyrimidine analogues, and offered chiral sources for further research on the physiologically active compounds of chiral nucleotides.     

Stability of the chlorinated derivatives of the DNA/RNA nucleobases,purine and pyrimidine toward radical formation via homolytic CCl bond dissociation

The chlorinated derivatives of nucleobases (and nucleosides), as well as those of purine, have well‐established anticancer activity, and in some cases, are also shown to be involved in the link between chronic inflammatory conditions and the development of cancer. In this investigation, the stability of all of the isomeric forms of the chlorinated nucleobases, purine and pyrimidine are investigated from the perspective of their homolytic C?Cl bond dissociation energies (BDEs). The products of these reactions, namely chlorine atom and the corresponding carbon‐centered radicals, may be of importance in terms of potentiating biological damage. Initially, the performance of a wide range of contemporary theoretical procedures were evaluated for their ability to afford accurate C?Cl BDEs, using a recently reported set of 28 highly accurate C?Cl BDEs obtained by means of W1w theory. Subsequent to this analysis, the G3X(MP2)‐RAD procedure (which achieves a mean absolute deviation of merely 1.3 kJ mol^?1, with a maximum deviation of 5.0 kJ mol^?1) was employed to obtain accurate gas‐phase homolytic C?Cl bond dissociation energies for a wide range of chlorinated isomers of the DNA/RNA nucleobases, purine and pyrimidine.     

Synthesis of new purine,pteridine, and other pyrimidine derivatives

The reaction of malononitrile dimer with phenyl isothiocyanate gave (6-amino-1-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidin-4-ylidene)malononitrile which was then used as starting material in the synthesis of pharmacologically important fused pyrimidine derivatives, such as 4-dicyanomethylidene-1,5-diphenyl-2-thioxo-1,2,3,4-tetrahydropyrrolo[2,3-d]pyrimidine, 6-cyano-4-dicyanomethylidene-7-methylsulfanyl-5-oxo-1-phenyl-2-thioxo-1,2,3,4,5,8-hexahydropyrido[2,3-d]pyrimidine, 6-dicyanomethylidene-3-phenyl-2-thioxo-1,2,3,6-tetrahydro-9H-purine, and 6-substituted 4-dicyanomethylidene-7-oxo-1-phenyl-2-thioxo-1,2,3,4,7,8-hexahydropteridines. Published in Russian in Zhurnal Organicheskoi Khimii, 2007, Vol. 43, No. 3, pp. 443–449. The text was submitted by the authors in English.     

Exploring the metal coordination properties of the pyrimidine part of purine nucleobases: isomerization reactions in heteronuclear Pt(II)/Pd(II) of 9-methyladenine

The synthesis and characterization of three heteronuclear Pt(2)Pd(2) (4, 5) and PtPd(2) (6) complexes of the model nucleobase 9-methyladenine (9-MeA) is reported. The compounds were prepared by reacting [Pt(NH(3))(3)(9-MeA-N7)](ClO(4))(2) (1) with [Pd(en)(H(2)O)(2)](ClO(4))(2) at different ratios r between Pt and Pd, with the goal to probe Pd(II) binding to any of the three available nitrogen atoms, N1, N3, N6 or combinations thereof. Pd(II) coordination occurs at N1 and at the deprotonated N6 positions, yet not at N3. 4 and 5 are isomers of [{(en)Pd}(2){N1,N6-9-MeA(-)-N7)Pt(NH(3))(3)}(2)](ClO(4))(6)·nH(2)O, with a head-head orientation of the two bridging 9-MeA(-) ligands in 4 and a head-tail orientation in 5. 6 is [{(en)Pd}(2)(OH)(N1,N6-9MeA(-)-N7)Pt(NH(3))(3)](ClO(4))(4)·4H(2)O, hence a condensation product between [Pt(NH(3))(3)(9-MeA-N7)](2+) and a μ-OH bridged dinuclear (en)Pd-OH-Pd(en) unit, which connects the N1 and N6 positions of 9-MeA(-) in an intramolecular fashion. 4 and 5, which slowly interconvert in aqueous solution, display distinct structural differences such as significantly different intramolecular Pd···Pd contacts (3.124 0(16) ? in 4; 2.986 6(14) ? in 5), among others. Binding of (en)Pd(II) to the exocyclic N6 atom in 4 and 5 is accompanied by a large movement of Pd(II) out of the 9-MeA(-) plane and a trend to a further shortening of the C6-N6 bond as compared to free 9-MeA. The packing patterns of 4 and 5 reveal substantial anion-π interactions.