An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory

The potential energy surface for formation of 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-OG), guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from 8-oxoguanine (8-oxoG) has been mapped out using B3LYP density functional theory, the aug-cc-pVTZ and 6-31+G(d,p) basis sets and the IEF-polarizable continuum model (PCM) solvation model. Three pathways for formation of 5-OH-OG from 8-oxoG were evaluated: (A) stepwise loss of two electrons and two protons to form the quinonoid intermediate 2-amino-7,9-dihydro-purine-6,8-dione (8-oxoG(ox)) followed by hydration; (B) stepwise loss of two electrons and one proton and net addition of hydroxide, in which the key step is nucleophilic addition to the 8-oxoG radical cation; and (C) stepwise loss of one electron and one proton and addition of hydroxyl radical to the 8-oxoG radical cation. The data suggest that all three pathways are energetically feasible mechanisms for the formation of 5-OH-OG, however, Pathway A may be kinetically favored over Pathway B. Although lower in energy, Pathway C may be of limited biological significance since it depends on the local concentration of hydroxyl radical. Pathways for hydrolysis and decarboxylation of 5-OH-OG to form Gh via either a carboxylic acid or substituted carbamic acid intermediate have been evaluated with the result that cleavage of the N1-C6 bond is clearly favored over that of the C5-C6 bond. Formation of Sp from 5-OH-OG via stepwise proton transfer and acyl migration or ring opening followed by proton transfer and ring closure have also been explored and suggest that deprotonation of the hydroxyl group facilitates a 1,2 acyl shift. Results of the calculations are consistent with experimental studies showing dependence of the Gh/Sp product ratio on pH. Under neutral and basic conditions, the data predict that formation of Sp is kinetically favored over the pathways for formation of Gh. Under acidic conditions, Gh is predicted to be the kinetically favored product.     

Effects of Intra-Base Pair Proton Transfer on Dissociation and Singlet Oxygenation of 9-Methyl-8-Oxoguanine−1-Methyl-Cytosine Base-Pair Radical Cations

8-Oxoguanosine is the most common oxidatively generated base damage and pairs with complementary cytidine within duplex DNA. The 8-oxoguanosine−cytidine lesion, if not recognized and removed, not only leads to G-to-T transversion mutations but renders the base pair being more vulnerable to the ionizing radiation and singlet oxygen (¹O₂) damage. Herein, reaction dynamics of a prototype Watson−Crick base pair [9MOG ⋅ 1MC]⋅⁺, consisting of 9-methyl-8-oxoguanine radical cation (9MOG⋅⁺) and 1-methylcystosine (1MC), was examined using mass spectrometry coupled with electrospray ionization. We first detected base-pair dissociation in collisions with the Xe gas, which provided insight into intra-base pair proton transfer of 9MOG⋅⁺ ⋅ 1MC [9MOG − H_N1]⋅ ⋅ [1MC+H_N3′]⁺ and subsequent non-statistical base-pair separation. We then measured the reaction of [9MOG ⋅ 1MC]⋅⁺ with ¹O₂, revealing the two most probable pathways, C5-O₂ addition and H_N7-abstraction at 9MOG. Reactions were entangled with the two forms of 9MOG radicals and base-pair structures as well as multi-configurations between open-shell radicals and ¹O₂ (that has a mixed singlet/triplet character). These were disentangled by utilizing approximately spin-projected density functional theory, coupled-cluster theory and multi-referential electronic structure modeling. The work delineated base-pair structural context effects and determined relative reactivity toward ¹O₂ as [9MOG − H]⋅>9MOG⋅⁺>[9MOG − H_N1]⋅ ⋅ [1MC+H_N3′]⁺≥9MOG⋅⁺ ⋅ 1MC.     

Purines, pyrimidines, and related fused systems. 21. Oxidative amination of 3-chloro-6,8-dimethylpyrimido[4,5-c]pyridazine-5,7(6H,8H)-dione

Oxidative amination of 3-chloro-6,8-dimethylpyrimido[4,5-c]pyridazine-5,7(6H,8H)-dione with primary alkylamines and potassium amide in liquid ammonia gives rise to the corresponding 4-amino derivatives as the major products. The reactions with acyclic secondary amines are accompanied by annelation of the pyrrole moiety to the starting heterosystem to form 1-R-3-R"-6,8-dimethylpyrrolo[2",3";3,4]pyrimido[4,5-c]pyridazine-7,9(6H,8H)-diones. The reaction with piperidine as the aminating agent occurs exclusively as aminodehalogenation. The Sonogashira cross-coupling of 4-amino-3-chloro-6,8-dimethylpyrimido[4,5-c]pyridazine-5,7(6H,8H)-diones with terminal alkynes affords 1-R-2-R"-6,8-dimethylpyrrolo[3",2";3,4]pyrimido[4,5-c]pyridazine-7,9(6H,8H)-diones.     

The synthesis of proximal-benzolumazine,proxirnal-benzoxanthine,proximal-benzotheophylline and proximal-benzocaffeine

The synthesis of pyrazino[2,3-f]quinazolin-8,10-(7H,9H)dione(proximal-benzolumazine, 1 ), imidazo[4,5-f]-quinazolin-7,9-(6H,8H)-dione (proximal-benzoxanthine, 2 ), 6,8-dimethylimidazo[4,5-f]-quinazolin-7,9-(6H,8H) dione (proximal-benzotheophylline, 3 ), and 1,6,8-trimethylimidazo[4,5-f]quinazolin-7,9-(6H,8H)dione (proximal-benzocaffeine, 4 ) is reported by commencing with 2-amino-6-chlorobenzamide and proceeding via a variety of 5,6-disubstituted-2,4-(1H,3H)quinazolinediones. Methylation of 3 is shown to yield 3,6,8-trimethylimidazo[4,5-f]quinazolin-7,9-(6H,8H)dione ( 15 ) and 4 in a ratio of 4:1.     

Reactions of 3,5-dibromo-1-(thiiran-2-ylmethyl)-1,2,4-triazole with NH-azoles

Reactions of 3,5-dibromo-1-(thiiran-2-ylmethyl)-1,2,4-triazole with 3,5-dimethylpyrazole, 1,3-dimethyl-3,7-dihydropurine-2,6-dione, 3,5-dibromo-1,2,4-triazole, 2,4,5-tribromoimidazole, and 2-chlorobenzimidazole lead to the formation of 5-azolylmethyl-2-bromo-5,6-dihydrothiazolo[3,2-b]-1,2,4-triazoles. In the case of 8-bromo-1,3-dimethyl-3,7-dihydropurine-2,6-dione the intermediate thiolate anion undergoes cyclization into 7-[(3,5-dibromo-1,2,4-triazol-1-yl)methyl]-1,3-dimethyl-6,7-dihydrothiazolo[2,3-f]purine-2,4(1H,3H)-dione. The structure of reaction products depends on the relative rate of substitution of leaving groups in the reagents.     

Evaluation of Novel Third‐Strand Bases for the Recognition of a C⋅G Base Pair in the Parallel DNA Triple‐Helical Binding Motif

We describe the synthesis and the incorporation into oligonucleotides of the novel nucleoside building blocks 9, 10 , and 16 , carrying purine‐like double H‐bond‐acceptor bases. These base‐modified nucleosides were conceived to recognize selectively a cytosine⋅guanine (C⋅G) inversion site within a homopurine⋅homopyrimidine DNA duplex, when constituent of a DNA third strand designed to bind in the parallel binding motif. While building block 16 turned out to be incompatible with standard oligonucleotide‐synthesis conditions, UV/triplex melting experiments with third‐strand 15‐mers containing β‐D ‐nucleoside 6 (from 9 ) showed that recognition of the four natural Watson‐Crick base pairs follows the order G⋅C≈C⋅G>A⋅T>T⋅A. The recognition is sequence‐context sensitive, and G⋅C or C⋅G recognition does not involve protonated species of β‐D ‐nucleoside 6 . The data obtained fit (but do not prove) a structural model for C⋅G recognition via one conventional and one C−H⋅⋅⋅O H‐bond. The unexpected G⋅C recognition is best explained by third‐strand base intercalation. A comparison of the triplex binding properties of these new bases with those of 4‐deoxothymine (5‐methylpyrimidine‐2(1H)‐one, ^{4 H}T), previously shown to be C⋅G selective but energetically weak, is also described.     

Indeno[2,1-a]fluorene-11,12-dione Radical Anions: Synthesis,Characterization, and Properties

The one-electron reduction of indeno[2,1-a]fluorene-11,12-dione ( IF ) with various alkali metals prepare the radical anion salts. The data about different structures, properties, and characterization was obtained by single-crystal X-ray diffraction, electron paramagnetic resonance (EPR) spectroscopy, superconducting quantum interference device (SQUID) measurements, and physical property measurement system (PPMS). Compound IF ^.−K⁺(18-c-6) is regarded as a one-dimensional magnetic chain through C−H⋅⋅⋅C interaction. Theoretical calculations and magnetic results showed that [ IF ^.−K⁺(15-c-5)]₂ is a dimer with an open-shell ground state. Compounds IF ^.−Na⁺(15-c-5) and IF ^.−K⁺(cryptand) are monoradical anion salts: IF ₂^.−Li⁺ possesses unique π-stack structure with an interplanar separation less than 3.46 Å, making it a semiconductor (δ_RT=1.9×10⁻⁴ S ⋅ cm⁻¹). This work gives insights into multifunctional radical anions, and describes the design and development of different functional radicals.     

Syntheses and Properties of (Nitronyl nitroxide)-substituted Tri-phenylamine ortho-Bridged by Two Oxygen and Sulfur Atoms

A nitronyl nitroxide unit ( NN ) was linked with a triphenylamine-based condensed polycyclic skeleton DOTT to form a radical substituted donor NN - DOTT . X-ray crystal structure analysis demonstrated a flat bowl shape of the DOTT unit. EPR spectra showed the localization of electron spin on the NN unit. Chemical oxidation of the DOTT unit produced radical-substituted radical cation salts NN - DOTT ⁺ ⋅ SbF₆⁻ and NN - DOTT ⁺ ⋅ FeBr₄⁻ that are stable under ambient conditions. The magnetic behavior of NN - DOTT ⁺ ⋅ SbF₆⁻ is characterized by the strong intramolecular ferromagnetic interaction between NN and DOTT ⁺. The X-ray structural analysis of NN - DOTT ⁺ ⋅ FeBr₄⁻ shows planar structure of DOTT and 1D mixed-stack column of NN-DOTT ⁺ and FeBr₄⁻. Magnetic measurements established that NN - DOTT ⁺ ⋅ FeBr₄⁻ undergoes magnetic phase transition into a weak ferromagnet at 7 K.     

Purines,pyrimidines, and related fused systems. 19. Use of S N H methodology for the synthesis of a new heterocyclic system,pyrrolo[3",2":3,4]pyrimido[4,5-c]pyridazine

Sonogashira cross-coupling of 3-chloro-6,8-dimethylpyrimido[4,5-c]pyridazine-5,7(6H,8H)-dione with terminal alkynes afforded the corresponding 3-(alkyn-1-yl) derivatives. Oxidative amination of the latter compounds with primary alkylamines was accompanied by heterocyclization to give 6,8-dimethylpyrrolo[3",2":3,4]pyrimido[4,5-c]pyridazine-7,9(6H,8H)-diones.     

Purine and pyrimidine derivatives from the South China Sea gorgonian Subergorgia suberosa

Three new purine derivatives, namely, 4-caryboxy-5,6-dihydro-4H,8H-pyrimido[1,2,3-cd]purine-8,10(9H)-dione (1), 7,9-dihydro-1-(3-oxobutyl)-1H-purine-6,8-dione (2), and 7-hydro-9-(3-oxobutyl)-1H-purine-6,8-dione (3) together with six known purine and pyrimidine derivatives were isolated from the EtOH/CH(2)Cl(2) extracts of the South China Sea gorgonian Subergorgia suberosa. The structures of 1-3 were determined on the bases of extensive spectroscopic analysis, including 1D and 2D NMR data.     

Pyrimidines. 21. Novel reactions of 5-cyano-1,3-dimethyluracil with carbon nucleophiles. A facile preparation of certain pyrido[2,3-d]pyrimidines

Treatment of 5-cyano-1,3-dimethyluracil ( 8 ) with an activated acetonitrile, such as malononitrile, ethyl cyanoacetate or cyanoacetamide, in base afforded 7-amino-6-cyano-, 7-amino-6-ethoxycarbonyl-, and 7-amino-6-aminocarbonyl-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione ( 18b, 18c and 18d , respectively) in high yields. On the other hand, reaction of 8 with acetonitrile in base gave the Michael adduct, 5-cyano-6-cyanomethyl-5,6-dihydrouracil ( 15 , R = H), and the hydrated product, 1,3-dimethyluracil-5-carboxamide ( 9 ) as the major products, and 7-amino-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione ( 18a ) in only very low yield. Similar reaction with butanone gave 7-ethyl-1,3-dimethyl- and 1,3,6,7-tetramethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione ( 10b and 10c ) in low yields. When 8 was treated with diethylmalonate in base, only a small amount of 6-ethoxycarbonyl-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4,7(1H,3H,8H)-trione ( 19 ) was obtained together with 1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione ( 20 ) and 18c (also in low yields). Treatment of 8 in ethanolic sodium ethoxide without added carbon nucleophile gave significant amounts (14%) of 20 and a small amount of 18c .     

Possible cause of G-C-->C-G transversion mutation by guanine oxidation product, imidazolone

BACKGROUND: The genome is constantly assaulted by oxidation reactions which are likely to be associated with oxygen metabolism, and oxidative lesions are generated by many types of oxidants. Such genotoxin-induced alterations in the genomic message have been implicated in aging and in several pathophysiological processes, particularly those associated with cancer. The guanine base (G) in genomic DNA is highly susceptible to oxidative stress due to having the lowest oxidation potential. Therefore, G-C-->T-A and G-C-->C-G transversion mutations frequently occur under oxidative conditions. One typical lesion of G is 8-oxo-7,8-dihydro-guanine (8-oxoG), which can pair with A. This pairing may cause G-C-->T-A transversion mutations. Although the number of G-C-->C-G transversions is rather high under specific oxidation conditions such as riboflavin photosensitization, the molecular basis of G-C-->C-G transversions is not known. RESULTS: To determine which oxidative products are responsible for G-C-->C-G transversion mutations, we photooxidized 5'-d(AAAAAAGGAAAAAA)/5'-d(TTTTTTCCTTTTTT) using either riboflavin or anthraquinone (AQ) carboxylate under UV irradiation. Prolonged low-temperature (4 degrees C) enzymatic digestion of photoirradiated sample indicated that under both conditions the amount of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) initially increased with decreasing amounts of 2'-deoxyguanosine (dG), then decreased with the formation of 2-amino-5-[(2-deoxy-beta-D-erythro-pentofuranosyl)amino]-4H-imidazol-4-one (dIz), suggesting that nascent 8-oxoG was further oxidized to 2,5-diamino-4H-imidazol-4-one (Iz) in duplex DNA. Photoirradiation of an AQ-linked oligomer with a complementary strand containing 8-oxoG indicated that 8-oxoG residues were oxidized to Iz. These results indicate that Iz is formed from 8-oxoG through long-range hole migration. Primer extension experiments using a template containing Iz demonstrated that only dGTP is specifically incorporated opposite Iz suggesting that specific Iz-G base pairs are formed. The 'reverse' approach consisting of DNA polymerization using dIzTP showed that dIzTP is incorporated opposite G, further confirming the formation of a Iz-G base pair. CONCLUSIONS: HPLC product analysis demonstrated that Iz is a key oxidation product of G through 8-oxoG in DNA photosensitized with riboflavin or anthraquinone. Photoreaction of AQ-linked oligomer confirmed that Iz is formed from 8-oxoG through long-range hole migration. Two sets of primer extension experiments demonstrated that Iz can specifically pair with G in vitro. Specific Iz-G base pair formation can explain the G-C-->C-G transversion mutations that appear under oxidative conditions.     

Complexation and Versatile Reactivity of a Highly Lewis Acidic Cationic Mg Complex with Alkynes and Phosphines

[(BDI)Mg⁺][B(C₆F₅)₄⁻] ( 1 ; BDI=CH[C(CH₃)NDipp]₂; Dipp=2,6-diisopropylphenyl) was prepared by reaction of (BDI)MgnPr with [Ph₃C⁺][B(C₆F₅)₄⁻]. Addition of 3-hexyne gave [(BDI)Mg⁺ ⋅ (EtC≡CEt)][B(C₆F₅)₄⁻]. Single-crystal X-ray analysis, NMR investigations, Raman spectra, and DFT calculations indicate a significant Mg-alkyne interaction. Addition of the terminal alkynes PhC≡CH or Me₃SiC≡CH led to alkyne deprotonation by the BDI ligand to give [(BDI-H)Mg⁺(C≡CPh)]₂ ⋅ 2 [B(C₆F₅)₄⁻] ( 2 , 70 %) and [(BDI-H)Mg⁺(C≡CSiMe₃)]₂ ⋅ 2 [B(C₆F₅)₄⁻] ( 3 , 63 %). Addition of internal alkynes PhC≡CPh or PhC≡CMe led to [4+2] cycloadditions with the BDI ligand to give {Mg⁺C(Ph)=C(Ph)C[C(Me)=NDipp]₂}₂ ⋅ 2 [B(C₆F₅)₄⁻] ( 4 , 53 %) and {Mg⁺C(Ph)=C(Me)C[C(Me)=NDipp]₂}₂ ⋅ 2 [B(C₆F₅)₄⁻] ( 5 , 73 %), in which the Mg center is N,N,C-chelated. The (BDI)Mg⁺ cation can be viewed as an intramolecular frustrated Lewis pair (FLP) with a Lewis acidic site (Mg) and a Lewis (or Brønsted) basic site (BDI). Reaction of [(BDI)Mg⁺][B(C₆F₅)₄⁻] ( 1 ) with a range of phosphines varying in bulk and donor strength generated [(BDI)Mg⁺ ⋅ PPh₃][B(C₆F₅)₄⁻] ( 6 ), [(BDI)Mg⁺ ⋅ PCy₃][B(C₆F₅)₄⁻] ( 7 ), and [(BDI)Mg⁺ ⋅ PtBu₃][B(C₆F₅)₄⁻] ( 8 ). The bulkier phosphine PMes₃ (Mes=mesityl) did not show any interaction. Combinations of [(BDI)Mg⁺][B(C₆F₅)₄⁻] and phosphines did not result in addition to the triple bond in 3-hexyne, but during the screening process it was discovered that the cationic magnesium complex catalyzes the hydrophosphination of PhC≡CH with HPPh₂, for which an FLP-type mechanism is tentatively proposed.     

Reaction of thianthrene cation radical with grignard reagents : Evidence for electron transfer and trapping of alkyl radicals by the thianthrene cation radical

Reactions are reported between RMgCl and thianthrene cation radical perchlorate (Th^.+ClO^-₄) suspended in ether and tetrahydrofuran (THF). In ether solution reactions R = Bu, s-Bu, t-Bu, 5-hexenyl, and cyclopentylmethyl. Major products were the alkane, the alkene R(-H) in some cases, and, in the cases of R = Bu, 5-hexenyl, and cyclopentylmethyl, the 5-alkylthianthrenium perchlorate (ThR⁺ClO^-₄). When 5-hexenylMgCl was used a mixture of 5-(5-hexenyl)- and 5-(cyclopentylmethyl)thianthrenium per-chlorates in the ratio of approximately 2 was obtained. Since the ratio of 5-hexenyl/cyclopentylmethyl in the Grignard reagent was 10.4, it is concluded that the C₆ sulfonium ions were formed by radical trapping by Th^.+ after single electron transfer from Grignard to cation radical had occurred, thus allowing for cyclization of 5-hexenyl radical. Formation of ThBu⁺ClO^-₄ is attributed to the trapping of butyl radical by Th^·+, while formation of RH and R(-H) is in all cases also attributed to alkyl radical reactions. Reactions in THF(R = Me, i-Pr, Bu, s-Bu, t-Bu, Ph) led almost exclusively to RH and Th. Polymerization of THF was also initiated and took place slowly giving rise to low molecular weight poly(THF). By using THF-d₈, as solvent for reaction between BuMgCl and Th^.+, it was possible to find Bu groups (¹H-NMR) in the poly(THF-d₈). Polymerization of THF is attributed, in some cases (R = Me, Bu), to alkyl-cation transfer from ThR⁺ to THF. In other cases initiation of polymerization by R⁺ and THF(-H)⁺ is considered.     

The synthesis of lin-benzoreumycin,lin-benzo-1-methylxanthine,and lin-benzo-1,9-dimethylxanthine

Commencing with 7-chloro-3-methylquinazoline-2,4(1H,3H)-dione ( 9a ), a five step synthesis of 7-methylpyrimido[5,4-g]-1,2,4-benzotriazine-6,8(7H,9H)-dione (lin-benzoreumycin, 6 ) has been accomplished. A synthesis of 1,7-dimethylpyrimido[5,4-g]-1,2,4-benzotriazine-6,8(1H,7H)-dione (lin-benzotoxoflavin, 5 ) employing an intermediate from the preparation of 6 (i.e., 7-chloro-3-methyl-6-nitroquinazoline-2,4(1H,3H)-dione, 9b ) was attempted but could not be accomplished beyond the dihydro precursor of 5 (i.e., 12 ). Compound 9b did lead to successful preparations of 7-methylimidazo[4,5-g]quinazoline-6,8(5H,7H)-dione (lin-benzo-1-methylxanthine, 7 ) and 3,7-dimethylimidazo[4,5-g]quinazoline-6,8(5H,7H)-dione (lin-benzo-1,9-dimethylxanthine, 8 ) by first reacting 9b with ammonia (for 7) or methylamine (for 8 ) followed by reductive cyclization in formic acid.     

Oxidative and hydrolytic cleavage of cyclopropane and spirocyclobutane derivatives of 6,8-dioxabicyclo[3.2.1]octane,the products of transformation of levoglucosenone

A new method for the synthesis of (1R,4S,5S)-4-hydroxymethyl-3-oxabicyclo[3.1.0]hexan2-one, the cyclopropane analog of (S)-5-hydroxypent-2-en-4-olide, has been suggested based on oxidation of (1S,2S,4R,6R)-7,9-dioxatricyclo[4.2.1.0^2,4]nonan-5-one. Oxidation of cyclobutanones, spirojoined with the fragments of 6,8-dioxabicyclo[3.2.1]oct-2-ene, 6,8-dioxabicyclo[3.2.1]octane (at position 4), or 7,9-dioxatricyclo[4.2.1.0^2,4]nonane (at position 5), upon the action of m-chloroperoxybenzoic acid or the KMnO₄-H₂SO₄-H₂O system leads to the corresponding spirojoined butanolides in 73–85% yields. The same cyclobutanones easily undergo the four-membered ring opening upon the action of dilute H₂SO₄ at 50–90 °C to form 6,8-dioxabicyclo[3.2.1]octane-4- or 7,9-dioxatricyclo[4.2.1.0^2,4]nonane-5-propionic acid.     

Proton Transfer Accounting for Anomalous Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pair of Cytosine and Guanine

To understand the anomalous collision-induced dissociation (CID) behavior of the proton-bound Hoogsteen base pair of cytosine (C) and guanine (G), C:H⁺???G, we investigated CID of a homologue series of proton-bound heterodimers of C, 1-methylcytosine, and 5-methylcytosine with G as a common base partner. The CID experiments were performed in an energy-resolved way (ER-CID) under both multiple and near-single collision conditions. The relative stabilities of the protonated complexes examined by ER-CID suggested that the proton-bound complexes produced by electrospray ionization in this study are proton-bound Hoogsteen base pairs. On the other hand, in contrast to the other base pairs, CID of C:H⁺???G exhibited more abundant productions of C:H⁺, the fragment protonated on the moiety with a smaller proton affinity, than that of G:H⁺. This appeared to contradict general prediction based on the kinetic method. However, further theoretical exploration of potential energy surfaces found that there can be facile proton transfers in the proton-bound Hoogsteen base pairs during the CID process, which makes the process accessible to an additional product state of O-protonated C for C:H⁺ fragments. The presence of an additional dissociation channel, which in other words corresponds to twofold degeneracy in the transition state leading to C:H⁺ fragments, effectively doubles the apparent reaction rate for production of C:H⁺. In this way, the process gives rise to the anomaly, the observed pronounced formation of C:H⁺ in the CID of the proton-bound Hoogsteen base pair, C:H⁺???G.

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Graphical Abstract ?

     

Study of the rate of methyl loss and the structure of the product ion as a function of the lifetime of the molecular ion of pent-3-en-2-ol

The normalized unimolecular rate constant for loss of a methyl radical from pent-3-en-2-ol molecular ions with lifetimes ranging from 10^?11 to 10^?9 s was studied by field ionization kinetics (FIK). The normalized rate curve shows maxima at molecular ion lifetimes of 10^?10.5 and 10^?10.1 s. Based on results for deuterium and ¹³C-labelled pent-3-en-2-ol, the maximum at 10^?10.5 s is ascribed to loss of the methyl group at the 1-position by a direct cleavage reaction. The maximum at 10^?10.1 s is attributed to a 1,2-H shift-initiated rearrangement of the molecular ion, which leads to loss of the methyl group at the 5- and 1-positions. The time dependence of the processes in the form of the maxima on the normalized rate curve is discussed qualitatively in terms of a lower critical energy and a tighter transition state of the 1,2-H shift than those of the direct cleavage reaction. Collision-induced dissociation of the [C₄H₇O]⁺ product ions in combination with FIK provides evidence that at molecular ion lifetimes corresponding to the first maximum on the rate curve protonated crotonaldehyde is formed, whereas protonated methyl vinyl ketone and the butyryl cation are formed at times corresponding to the second maximum.     

Synthesis of 6,7,8,9-tetrahydro-5H-pyrimido-[4,5-b][1,4]diazepine-6,8-diones

The sodium ethoxide catalyzed condensation of 4,5-diaminopyrimidine ( 3 ) with diethyl malonate afforded 6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepine-6,8-dione ( 4 ). Methylation of 6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepine-6,8-dione ( 4 ) using sodium hydride and two equivalents of iodomethane gave 5,9-dimethyl-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepine-6,8-dione ( 5 ) which on further methylation using sodium hydride and one equivalent iodomethane yielded 6,7,8,9-tetrahydro-5,7,9-trimethyl-5H-pyrimido[4,5-b][1,4]diazepine-6,8-dione ( 6 ). Reaction of 6,7,8,9-tetrahydro-5H-pyrirnido[4,5-b][1,4]diazepine-6,8-dione ( 4 ) with 4.2 equivalents of sodium hydride and 4.1 equivalents of iodomethane afforded 6,7,8,9-tetrahydro-5,7,7, 9-tetramethyl-5H-pyrimido[4,5-b][1,4]diazepine-6,8-dione ( 7 ). 6,7,8,9-Tetrahydro-5,7,7,9-tetramethyl-5H-pyrimido[4,5-b][1,4]diazepine-6,8-dione ( 7 ) exhibited weak anticonvulsant activities in the subcutaneous pentylenetetrazole and maximal electroshock anticonvulsant screens indicating it is a partial bioisostere of the anticonvulsant drug clobazam ( 2 ).     

The Two Faces of the Guanyl Radical: Molecular Context and Behavior

The guanyl radical or neutral guanine radical G(-H)^• results from the loss of a hydrogen atom (H^•) or an electron/proton (e^–/H⁺) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC^•+ pair. The role of the two G(-H)^• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.