Open Adducts Research Articles

Functional analyses of single nucleotide polymorphic variants of the DNA glycosylase NEIL1 in sub-Saharan African populations

Nei-like glycosylase 1 (NEIL1) is a DNA repair enzyme that initiates the base excision repair (BER) pathway to cleanse the human genome of damage. The substrate specificity of NEIL1 includes several common base modifications formed under oxidative stress conditions, as well as the imidazole ring open adducts that are induced by alkylating agents following initial modification at N7 guanine. An example of the latter is the persistent and mutagenic 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua) adduct, resulting from the alkylating agent aflatoxin B1 (AFB1) exo-8–9-epoxide. Naturally occurring single nucleotide polymorphic (SNP) variants of NEIL1 are hypothesized to be associated with an increased risk for development of early-onset hepatocellular carcinoma (HCC), especially in environments with high exposures to aflatoxins and chronic inflammation from viral infections and alcohol consumption. Given that AFB1 exposures and hepatitis B viral (HBV) infections represent a major problem in the developing countries of sub-Saharan Africa, it is pertinent to study SNP NEIL1 variants that are present in this geographic region. In this investigation, we characterized the three most common NEIL1 variants found in this region: P321A, R323G, and I182M. Biochemical analyses were conducted to determine the proficiencies of these variants in initiating the repair of DNA lesions. Our data show that damage recognition and excision activities of P321A and R323G were near that of wild-type (WT) NEIL1 for both thymine glycol (ThyGly) and AFB1-FapyGua. The substrate specificities of these variants with respect to various oxidatively-induced base lesions were also similar to that of WT. In contrast, the I182M variant was unstable, such that it precipitated under a variety of conditions and underwent rapid inactivation at a biologically relevant temperature, with partial stabilization being observed in the presence of undamaged DNA. This study provides insight regarding the potential increased risk for early-onset HCC in human populations carrying the NEIL1 I182M variant.

(Invited) Chemical Reactions of Ionic Metallofullerenes: An Alternative Route for Exohedral Functionalization

The chemistry of cationic forms of clusterfullerenes remain less explored than that of the corresponding neutral or anionic species. In the present work, M3N@Ih -C80 (M = Sc or Lu) cations were generated by both electrochemical and chemical oxidation methods. The as-obtained cations successfully underwent the typical Bingel-Hirsch reaction that fails with neutral Sc3N@Ih -C80. Two isomeric Sc3N@Ih -C80 cation derivatives, [5,6]-open and [6,6]-open adducts, were synthesized, and the former has never been prepared via a Bingel-Hirsch reaction with neutral clusterfullerenes. Density functional theory (DFT) calculations indicated that the oxidized M3N@Ih -C80 was much more reactive than the neutral compound upon addition of the diethyl bromomalonate anion. The Bingel-Hirsch reaction of M3N@Ih -C80 cations occurred via an unusual outer-sphere single-electron transfer (SET) process from the diethyl bromomalonate anion to the stable intermediate [M3N@C80(C2H5COO)2CBr]•. Remarkably, the diethyl bromomalonate anion was found to act as both a nucleophile and an electron donor. Cationic forms of clusterfullerenes exhibited chemical properties that are different from those of the corresponding neutral and anionic forms. These findings promote a better understanding of EMFs cations and offer a complementary strategy to activate and functionalize EMFs.

(Invited) Chemical Reactions of Ionic Metallofullerenes: An Alternative Route for Exohedral Functionalization

The chemistry of cationic forms of clusterfullerenes remain less explored than that of the corresponding neutral or anionic species. In the present work, M3N@Ih -C80 (M = Sc or Lu) cations were generated by both electrochemical and chemical oxidation methods. The as-obtained cations successfully underwent the reactions that fail with neutral Sc3N@Ih -C80. For example, two isomeric Sc3N@Ih -C80 cation derivatives, [5,6]-open and [6,6]-open adducts, were synthesized, and the former has never been prepared via a Bingel-Hirsch reaction with neutral clusterfullerenes. Density functional theory (DFT) calculations indicated that the oxidized M3N@Ih -C80 was much more reactive than the neutral compound upon addition of the nucleophiles. The Bingel-Hirsch reaction of M3N@Ih -C80 cations occurred via an unusual outer-sphere single-electron transfer (SET) process from the diethyl bromomalonate anion to the stable intermediate [M3N@C80(C2H5COO)2CBr]•. Cationic forms of clusterfullerenes exhibited chemical properties that are different from those of the corresponding neutral and anionic forms. These findings promote a better understanding of EMFs cations and offer a complementary strategy to activate and functionalize EMFs.

Chemical Reactions of Cationic Metallofullerenes: An Alternative Route for Exohedral Functionalization.

The chemistry of cationic forms of clusterfullerenes remain less explored than that of the corresponding neutral or anionic species. In the present work, M3 N@Ih -C80 (M=Sc or Lu) cations were generated by both electrochemical and chemical oxidation methods. The as-obtained cations successfully underwent the typical Bingel-Hirsch reaction that fails with neutral Sc3 N@Ih -C80 . Two isomeric Sc3 N@Ih -C80 cation derivatives, [5,6]-open and [6,6]-open adducts, were synthesized, and the former has never been prepared by means of a Bingel-Hirsch reaction with neutral clusterfullerenes. In the case of the Lu3 N@Ih -C80 cation, however, only a [6,6]-open adduct was obtained. Density functional theory (DFT) calculations indicated that the oxidized M3 N@Ih -C80 was much more reactive than the neutral compound upon addition of the diethyl bromomalonate anion. The Bingel-Hirsch reaction of M3 N@Ih -C80 cations occurred by means of an unusual outer-sphere single-electron transfer (SET) process from the diethyl bromomalonate anion to the stable intermediate [M3 N@C80 (C2 H5 COO)2 CBr]. . Remarkably, the diethyl bromomalonate anion was found to act as both a nucleophile and an electron donor.

Reaction of 2‐Phenyl‐4‐arylidene‐1,3‐oxazolones with Different Nucleophiles for Synthesis of Some New Heterocycles

Refluxing of 1,3‐oxazolone (1a) with malononitrile in dry benzene and in the presence of ammonium acetate afforded imidazolone derivative (2). However, carrying out the same reaction in absolute ethanol and in the presence of piperidine as a base gave the benzamide derivative (4). Fusion of (1a) with p‐anisidine gave the open adduct benzamide (6), which cyclized in acidic medium to give imidazolone derivative (7). Heating of imidazolone (7) with malononitrile above its melting point afforded 1,3‐diazepine derivative (8). Reaction of the carbohydrazide (9) with isatin in ethanol gives the corresponding Schiff base (11), which then reacted with acetyl acetone, ethyl acetoacetate, ethyl cyanoacetate, and malononitrile in n‐butanol and piperidine to afford benzamide derivative (13, 14, 15) and (16), respectively. The structures of the newly synthesized compounds were established on the basis of IR, 1H‐NMR, mass spectra, and elemental analyses.

Inside Back Cover: Adamantylidene Addition to M3N@Ih‐C80 (M=Sc, Lu) and Sc3N@D5h‐C80: Synthesis and Crystallographic Characterization of the [5,6]‐Open and [6,6]‐Open Adducts (Chem. Eur. J. 27/2017)

Inside Back Cover: Adamantylidene Addition to M₃N@<i>I_h</i>‐C₈₀ (M=Sc, Lu) and Sc₃N@<i>D</i>_5<i>h</i>‐C₈₀: Synthesis and Crystallographic Characterization of the [5,6]‐Open and [6,6]‐Open Adducts (Chem. Eur. J. 27/2017)

Formation mechanism of glyoxal-DNA adduct, a DNA cross-link precursor

DNA nucleobases undergo non-enzymatic glycation to nucleobase adducts which can play important roles in vivo. In this work, we conducted a comprehensive experimental and theoretical kinetic study of the mechanisms of formation of glyoxal–guanine adducts over a wide pH range in order to elucidate the molecular basis for the glycation process. Also, we performed molecular dynamics simulations to investigate how open or cyclic glyoxal–guanine adducts can cause structural changes in an oligonucleotide model. A thermodynamic study of other glycating agents including methylglyoxal, acrolein, crotonaldehyde, 4-hydroxynonenal and 3-deoxyglucosone revealed that, at neutral pH, cyclic adducts were more stable than open adducts; at basic pH, however, the open adducts of 3-deoxyglucosone, methylglyoxal and glyoxal were more stable than their cyclic counterparts. This result can be ascribed to the ability of the adducts to cross-link DNA. The new insights may contribute to improve our understanding of the connection between glycation and DNA cross-linking.

Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers.

Sequence-specific multivalent molecular recognition has been recognized to play a major role in biological processes. Furthermore, sequence-specific recognition motifs have been used in various artificial systems in the last years, e.g., to emulate biological processes or to build up new materials with highly specific recognition domains. In this article, we present the preparation of cyclodextrin (CD)-based strands and complementary and non-complementary strands modified with guest molecules and the investigation of their complexation behavior towards each other by isothermal titration calorimetry (ITC). As complementary binding motifs n-butyl and α-CD and adamantane and β-CD were selected. It was found that it is possible to realize sequence-specific molecular recognition by the use of host–guest chemistry, but the recognition motifs as well as the linkages have to be chosen very carefully. In the case of trivalent systems one adamantane moiety must be included to induce preferred formation of 1:1 adducts. Due to the too weak interaction between n-butyl and α-CD these systems have a negative chelate cooperativity and open adducts are preferentially formed. As soon as two adamantane moieties are present, the complementary systems have a positive chelate cooperativity and double-stranded structures are favored over open adducts. In this system the n-butyl moiety provides insufficient discrimination towards α- and β-CD and no sequence specificity is observed. By the combination of three adamantane moieties sequence specificity can be generated. Exclusively with the complementary CD sequence double-stranded structures are formed, with non-complementary strands aggregates of higher stoichiometry are generated.

An unprecedented [5,6]-open adduct via a direct benzyne-C60 cycloaddition

Cycloaddition is one of the best-studied types of reactions in the organic chemistry of fullerenes, engendering [6,6]-closed adducts in the vast majority of cases. Notwithstanding that a formation of open fulleroid structures is undoubtedly of theoretical interest, no one has demonstrated the conformation of [5,6]-open fulleroid via the direct cycloadditions. Here, we establish that cycloaddition between C60 and benzyne in situ generated from 2-amino-4,5-dibutoxybenzoic acid affords a new type of elusive [5,6]-open structure that is characterized on the basis of NMR, UV–vis spectroscopy, and cyclic voltammetry. Additionally, from density functional theory (DFT) calculations for possible [5,6]-open and [6,6]-closed adducts induced of benzyne-C60 reaction, as expected, features such as the charge distributions, binding characteristics, and frontier molecular orbital levels, are affected by the different binding modes in C60 cage.

Aromaticity as the driving force for the stability of non-IPR endohedral metallofullerene Bingel–Hirsch adducts

We have studied the relative stabilities of Bingel-Hirsch non-IPR endohedral metallofullerene monoadducts having one, two, or three adjacent pentagon pairs. The most stable addition always leads to an open adduct and never occurs on [5,5] bonds. Our results show that the thermodynamics of the addition is governed by the additive local aromaticity of the rings of the final adducts.

Stable and Unstable 6,6‐ and 5,6‐ Closed and Open Adducts of Fullerene C60

DFT/PBE/TZ2P research of total energy of various adducts at variation of 5,6‐ and 6,6‐ bond was carried out. On the basis of the analysis of local minima, the conclusion on structures stability and instability was drawn. Acyclic and cyclic derivatives containing 4‐6‐membered rings are established to form the closed adducts only. Thus the [6,6]‐closed structures are 15–18 kcal/mole more stable than [5,6]‐closed. The [6,6]‐closed adducts with strained 3‐membered cycles and their [5,6]‐open isomers are found to be stable. The analysis of strain energy is accomplished.

Revisit to the reaction of [60]fullerene with nitrile ylides generated from imidoyl chlorides and triethylamine

The reaction of [60]fullerene (C 60) with nitrile ylides generated from N-benzyl-4-nitrobenzimidoyl chloride/ N-(4-chlorobenzyl)-4-nitrobenzimidoyl chloride and triethylamine gave only isomeric monoadducts of C 60 with [6,6]-closed structure. No [5,6]-open adduct of C 60 could be identified from these reactions. The previously reported [5,6]-open product of C 60 should be reassigned as a [6,6]-closed product.

Effect of glutathione on the covalent binding of the 13C-labeled skin sensitizer 5-chloro-2-methylisothiazol-3-one to human serum albumin: identification of adducts by nuclear magnetic resonance, matrix-assisted laser desorption/ionization mass spectrometry, and nanoelectrospray tandem mass spectrometry.

The covalent binding of 4-[(13)C]- and 5-[(13)C]-5-chloro-2-methylisothiazol-3-one (MCI) toward human serum albumin (HSA) was followed by (13)C and (1)H[(13)C] NMR spectroscopy. MCI was found to react with histidine through an addition-elimination at position 5, leading to stable substitution adducts, and with lysine to form open adducts of the thioamide or amide type. No other modification could be detected on either cysteine or tyrosine. In the presence of glutathione (GSH), we observed an increased covalent binding to lysine residues. This could be explained by the rapid reaction of GSH with MCI to form a chlorothioacyl intermediate very reactive toward primary amino groups of lysine residues. To further confirm these observations and map covalent binding sites, HSA samples modified by MCI with or without GSH were analyzed by matrix-assisted laser desorption/ionization mass spectrometry of tryptic digests and electrospray tandem mass spectrometry of modified peptides purified by reverse phase HPLC. About 80% of the HSA sequence was mapped, and several modified peptides were identified. When HSA was incubated with MCI without GSH, three peptides modified at histidine residues were characterized while when HSA was incubated in the presence of GSH, five peptides modified at histidine and lysine residues were identified. These experiments confirmed that modifications on lysine residues were of the amide and thioamide types. Observed modifications were in accordance with mass increases corresponding to structures identified by NMR, and an extra adduct corresponding to a double modification of His 338 was observed. Comparison of HSA-MCI and HSA-MCI-GSH samples confirmed that the presence of GSH increased the modification of lysine residues.

Covalent binding of the 13C-labeled skin sensitizers 5-chloro-2-methylisothiazol-3-one (MCI) and 2-methylisothiazol-3-one (MI) to a model peptide and glutathione

The reactivity of 4-[ 13C]- and 5-[ 13C]-5-chloro-2-methylisothiazol-3-one (MCI) and 2-methylisothiazol-3-one (MI) towards a model peptide and glutathione was followed by 13C and 1H{ 13C} NMR spectroscopy. Both molecules were found to react with GSH but in addition MCI was found to react with histidine and lysine to form adducts of a different nature. Reaction with histidine led to stable substitution adducts through an addition–elimination reaction at position 5 while reaction with lysine led to the formation of open adducts of the thioamide or amide type.

Studies of chemical selectivity of hapten, reactivity, and skin sensitization potency. 3. Synthesis and studies on the reactivity toward model nucleophiles of the 13C-labeled skin sensitizers, 5-chloro-2-methylisothiazol-3-one (MCI) and 2-methylisothiazol-3-one (MI).

The skin sensitizers, 5-chloro-2-methylisothiazol-3-one (MCI) and 2-methylisothiazol-3-one (MI), have been synthesized isotopically labeled with (13)C at all carbon positions. The reactivity of 3-[(13)C]-, 4-[(13)C]-, and 5-[(13)C]MCI and MI toward a series of model nucleophiles for protein amino acid residues, i.e., butylamine, imidazole, sodium propanethiolate, and sodium phenoxide, was followed by (13)C and (1)H[(13)C] NMR spectroscopy. While MCI was found to react quantitatively with sodium propanethiolate and butylamine and significantly with imidazole and sodium phenoxide, MI reacted only with sodium propanethiolate. Reaction of MCI with nonthiol nucleophiles proceeded through an initial addition-elimination at position 5, leading to stable substitution adducts in the case of imidazole and sodium phenoxide. In the case of butylamine, the initial adduct was subjected to extra reactions at the sulfur atom through a cleavage of the S-N bond, leading to open adducts of the thioamide or amide type. Experiments carried out with N-acetyl-Cys, in excess or in deficiency, indicated that thiol nucleophiles reacted first at the sulfur atom through a cleavage of the S-N bond followed by extra nucleophilic reactions leading to open adducts of the mercaptothioester or mercaptoester type. Reaction of MCI with thiol nucleophiles gave products consistent with the formation of a reactive thioacyl chloride intermediate able to react with other nucleophiles present in the reaction medium. As a consequence, N-acetyl-Cys was found to be able to activate MCI toward N(alpha)-acetyl-Lys under physiological conditions to form adducts of the thioamide or amide type. Thus MCI, a strong sensitizer, and MI, a weak sensitizer, were found to react with different nucleophiles through different mechanisms. Although both MCI and MI can react with thiol nucleophiles, only MCI is capable of significantly reacting with amino nucleophiles of the Lys or His type. Moreover, MCI could be activated by a prior reaction with thiols.

Evidence of A Possible Cycloaddition Channel in the Ethene + NO3 Reaction

In this work, the NO3 addition to alkenes has been studied using ab initio quantum chemistry methods. In addition to the commonly accepted NO3 radical addition to one of the CC carbon atoms in alkenes, a symmetric transition state corresponding to the cycloaddition of the nitrate radical to the double bond has been identified, leading to the formation of a particularly stable NO3-alkene cyclic radical. Consideration of the cyclic adduct is necessary to explain the formation of carbonyl products derived from the cleavage of the CC bond in the absence of oxygen. Yet, the possibility of its formation from the nitroalkyl open adduct radical R1R2C(ONO2)CR3R4· is hampered by the presence of a high energy barrier leading from the open to the cyclic adduct. The proposed cycloaddition channel is analogous to the Criegee mechanism for the cycloaddition of ozone to double bonds.

Theoretical studies of the chemistry of singlet and triplet species. II. Cycloaddition reaction

Ab initio SCF potential energy surfaces for the cycloaddition reactions C2H4(1Alg) + O(1D,3P) are reported. The lowest energy singlet path corresponds to the symmetric, concerted addition reaction yielding ethylene oxide. The lowest energy triplet path corresponds to an asymmetric approach of the reactants to form an open ring adduct [Formula: see text] The spatial distribution of the spin density in this adduct conforms to that expected for a diradical. The barrier to internal rotation of the terminal methylene is calculated to be ∼5 kcal mol−1. The lowest intersystem crossing from the triplet to the singlet surface, as required for ring closure to yield ground state product, is found to occur ∼36 kcal mol−1 above the energy of the triplet reactants.The differences in singlet and triplet charge distributions and energies for similar approach geometries may be rationalized in terms of the additional restraints imposed on the course of the triplet reaction by the Pauli principle, restraints which are made evident by the spatial distribution of the spin density. Two principal mechanisms of spin polarization, spin unpairing and spin decoupling, are found to provide a rationale for the observed differences of singlet and triplet reactants in abstraction, insertion and addition reactions. The favoured course of a triplet reaction is found to be governed by the axiom that localized distributions of spin density are to be maximally separated in space.

Nucleophilic attacks on carbon–carbon double bonds. Part XX. Reaction of active methylene compounds with electrophilic olefins. Formation of substituted 2-amino-4-cyano-4H-pyrans

Reactions of active methylene compounds with several electrophilic olefins are initiated by a nucleophilic attack on the double bond and the following reaction types have been observed. (a) Base-catalysed reaction of malononitrile with 1,1-dinitro-2,2-diphenylethylene gives ‘diphenylmethylene transfer’ forming 1,1-dicyano-2,2-diphenylethylene. (b) Addition of acetylacetone to tetracyanoethylene (IX) and to diethyl 2,3-dicyanofurmarate (X) or of dimedone to (X) gives the non-cyclic Michael adducts 3-(1,1,2,2-tetracyanoethyl)pentane-2,4-dione (XIII), diethyl 2,3-dicyano-2-diacetylmethylsuccinate (XX), and diethyl 2,3-dicyano-2-(4,4-dimethyl-2,6-dioxocyclohexyl)succinate (XXII), respectively. (c) Non-catalysed addition of several active methylene compounds to (IX) or to (X) gives substituted 2-amino-4-cyano-4H-pyrans. These are probably formed by cyclisation of the open adducts, since a non-catalysed cyclisation of (XIII) and of (XXII) gives the 4H-pyran derivatives. (d) Reaction of anthrone with (IX) and (X) gives the 10-substituted anthrone Michael adducts. Addition of bases to the adduct from (IX) gives bianthrone and products derived from (IX), apparently via decomposition of the adduct to anthrone and (IX).