Fingerprinting DNA Oxidation Processes: IR Characterization of the 5‐Methyl‐2′‐Deoxycytidine Radical Cation

Methylated cytidine plays an important role as an epigenetic signal in gene regulation. Its oxidation products are assumed to be involved in active demethylation processes but also in damaging DNA. Here, we report the photochemical production of the 5‐methyl‐2′‐deoxycytidine radical cation via a two‐photon ionization process. The radical cation is detected by time‐resolved IR spectroscopy and identified by band assignment using density functional theory calculations. Two final oxidation products are characterized with liquid chromatography coupled to mass spectrometry.     

13‐cis‐β,β‐Carotene and 15‐cis‐β,β‐carotene

13‐cis‐β,β‐Carotene, C₄₀H₅₆, crystallizes with a complete molecule in the asymmetric unit, whereas 15‐cis‐β,β‐carotene, also C₄₀H₅₆, has twofold symmetry about an axis through the central bond of the polyene chain. The polyene methyl groups are arranged on one side of the polyene chains for each molecule and the 6‐s‐cisβ end groups, with the cyclohexene rings in half‐chair conformations, are twisted out of the planes of the polyene chains by angles ranging from 41.37 (17) to 52.2 (4)°. The molecules in each structure pack so that the arms of one occupy the cleft of the next, and there is significant π–π stacking of the almost‐parallel polyene chains of the 15‐cis isomer, which approach at distances of 3.319 (1)–3.591 (1) Å.     

Enantioselective Divergent Synthesis of (−)‐cis‐α‐ and (−)‐cis‐γ‐Irone by Using Wilkinson’s Catalyst

A simple, efficient synthesis is reported for (?)‐cis‐α‐ and (?)‐cis‐γ‐irone, two precious constituents of iris oils, in ≥99 % diastereomeric and enantioselective ratios. The two routes diverge from a common intermediate prepared from (?)‐epoxygeraniol. Of general interest in this approach is the installation of the enone moiety of irones through a NHC?Au^I‐catalyzed Meyer–Schuster‐like rearrangement of a propargylic benzoate and the use of Wilkinson’s catalyst for the stereoselective hydrogenation of a prostereogenic exocyclic double bond to secure the critical cis stereochemistry of the alkyl groups at C2 and C6 of the irones. The stereochemical aspects of this reaction are rationally supported by DFT calculation of the conformers of the substrates undergoing the hydrogenation and by a modeling study of the geometry of the rhodium η² complexes involved in the diastereodifferentiation of the double bond faces. Thus, computational investigation of the η² intermediates formed in the catalytic cycle of prostereogenic alkene hydrogenation by using Wilkinson’s catalyst could be highly predictive of the stereochemistry of the products.     

Facile Construction of Quinoline‐2‐carboxylate Esters through Aerobic Oxidation of Alkyl 4‐Anilinocrotonates Induced by a Radical Cation Salt

A facile construction of quinoline‐2‐carboxylate esters through an aerobic oxidation of alkyl 4‐anilinocrotonates is described. In the presence of dioxygen, sp³ C−H bonds in 4‐anilinocrotonates can easily be oxidized by using a catalytic amount of a radical cation salt, providing a radical intermediate. After further oxidation and domino cyclization, the desired quinoline derivatives were afforded in high yields. This reaction provides a new way to construct the pharmaceutically relevant quinoline skeleton, avoiding harsh reaction conditions and tedious starting material synthesis.     

Deamination of the Radical Cation of the Base Moiety of 2′‐Deoxycytidine: A Theoretical Study

Five pathways leading to the deamination of cytosine (to uracil) after formation of its deprotonated radical cation are investigated in the gas phase, at the UB3LYP/6‐311G(d,p) level of theory, and in bulk aqueous solvent. The most favorable pathway involves hydrogen‐atom transfer from a water molecule to the N3 nitrogen of the deprotonated radical cation, followed by addition of the resulting hydroxyl radical to the C4 carbon of the cytosine derivative. Following protonation of the amino group (N4), the C4? N4 bond is broken with elimination of the NH₃^?+ radical and formation of a protonated uracil. The rate‐determining step of this mechanism is hydrogen‐atom transfer from a water molecule to the cytosine derivative. The associated free energy barrier is 70.2 kJ mol^?1.     

Reversed Cation Selectivity of G8‐Octamer and G16‐Hexadecamer towards Monovalent and Divalent Cations

A reverse‐binding‐selectivity between monovalent and divalent cations was observed for two different self‐assembly G₁₆‐hexadecamer and G₈‐octamer systems. The dissociation constant between G₄‐quadruplex and monomer was calculated via VT‐¹H NMR experiments. Quantitative energy profiles revealed entropy as the key factor for the weaker binding toward Ba²⁺ compared with K⁺ in the G₈‐octamer system despite stronger ion‐dipole interactions. This study is the first direct comparison of the G₄‐quartet binding affinity between mono and divalent cations and will benefit future applications of G‐quadruplex‐related research. Further competition experiments between the G₈‐octamer and 18‐crown‐6 with K⁺ demonstrated the potential of this G₈ system as a new potassium receptor.     

Site‐Directed Spin‐Labeling of DNA by the Azide–Alkyne ‘Click’ Reaction: Nanometer Distance Measurements on 7‐Deaza‐2′‐deoxyadenosine and 2′‐Deoxyuridine Nitroxide Conjugates Spatially Separated or Linked to a ‘dA‐dT’ Base Pair

Nucleobase‐directed spin‐labeling by the azide‐alkyne ‘click’ (CuAAC) reaction has been performed for the first time with oligonucleotides. 7‐Deaza‐7‐ethynyl‐2′‐deoxyadenosine ( 1 ) and 5‐ethynyl‐2′‐deoxyuridine ( 2 ) were chosen to incorporate terminal triple bonds into DNA. Oligonucleotides containing 1 or 2 were synthesized on a solid phase and spin labeling with 4‐azido‐2,2,6,6‐tetramethylpiperidine 1‐oxyl (4‐azido‐TEMPO, 3 ) was performed by post‐modification in solution. Two spin labels ( 3 ) were incorporated with high efficiency into the DNA duplex at spatially separated positions or into a ‘dA‐dT’ base pair. Modification at the 5‐position of the pyrimidine base or at the 7‐position of the 7‐deazapurine residue gave steric freedom to the spin label in the major groove of duplex DNA. By applying cw and pulse EPR spectroscopy, very accurate distances between spin labels, within the range of 1–2 nm, were measured. The spin–spin distance was 1.8±0.2 nm for DNA duplex 17 ( dA*^7,10 ) ?11 containing two spin labels that are separated by two nucleotides within one individual strand. A distance of 1.4±0.2 nm was found for the spin‐labeled ‘dA‐dT’ base pair 15 ( dA*⁷ ) ?16 ( dT*⁶ ). The ‘click’ approach has the potential to be applied to all four constituents of DNA, which indicates the universal applicability of the method. New insights into the structural changes of canonical or modified DNA are expected to provide additional information on novel DNA structures, protein interaction, DNA architecture, and synthetic biology.     

Synthesis of 2‐Styrylbenzoxazole Derivatives by the Reaction of Styrylphenolic Schiff Bases with Thianthrene Cation Radical

A simple and fast preparative method of 2‐styrylbenzoxazoles by oxidative intramolecular cyclization of styrylphenolic Schiff bases with thianthrene cation (Th^+.ClO₄^?) is described. The oxidative cyclization of Schiff bases in the presence of 2,6‐di‐tert‐butyl‐4‐methylpyridine (DTBMP) gives 2‐styrylbenzoxazole derivatives in better yields than those in the absence of DTBMP.     

(Nitronyl Nitroxide)‐Substituted Trioxytriphenylamine Radical Cation Tetrachlorogallate Salt: A 2p‐Electron‐Based Weak Ferromagnet Composed of a Triplet Diradical Cation

The synthesis and the solid state magnetic properties of (nitronyl nitroxide)‐substituted trioxytriphenylamine radical cation tetrachlorogallate, NNTOT+·GaCl4? , are reported. In the temperature region between 300 and 3 K, the magnetic behavior is characterized by the strong intramolecular ferromagnetic interaction (J/k_B=+400 K) between the radical ( NN ) and the radical cation ( TOT ⁺) and the weak intermolecular antiferromagnetic interaction (J/k_B=?1.9 K) between NNTOT⁺ ions. Below 3 K, a 3D‐type long‐range magnetic ordering into a weak ferromagnet was observed (T_N=2.65 K). The magnetic entropy (S_mag=8.97 J K^?1 mol^?1) obtained by the heat capacity measurement is in good agreement with the theoretical value of R ln3=9.13 J K^?1 mol^?1 based on the S=1 state.     

Radical Formation in the Oxidation of 2,2'-Azo-2-methyl-6-heptene by Thianthrene Cation Radical

Reaction of 2,2'-azo-2-methyl-6-heptene (1) with thianthrene cation radical perchlorate (Th(*)(+)ClO(4)(-)) in CH(2)Cl(2) solution containing 2,6-di-tert-butyl-4-methylpyridine (DTBMP) gave a mixture of nine C(8) hydrocarbons, namely, 1,1,2-trimethylcyclopentane (4, 2.2%), 6-methyl-1-heptene (5, 2.2%), 2-methyl-1,6-heptadiene (6, 9.8%), 2,2-dimethyl-1-methylenecyclopentane (7, 2.9%), 6-methyl-1,5-heptadiene (8, 39%), 3,3-dimethyl- (9, 7.6%), 4,4-dimethyl- (10, 11%), 1,2-dimethyl- (11, 5.4%), and 1,6-dimethylcyclohexene (12, 1.5%). The amounts of acyclic dienes (6, 8) fell and of cyclohexenes (9, 10) rose when DTBMP was omitted from or diminished in the solution. The results provide firm evidence (products 4, 5, and 7) for the formation of the 2-methyl-6-hepten-2-yl radical (2), although the major fate of 2 is its oxidation to the corresponding cation 13, the origin of the bulk of the other products.     

Reversal of the Stereochemical Course of 1‐Methyl‐1H‐indole Addition to Cinnamaldehyde with cis‐5‐Benzyl‐(2‐fluoromethyl)‐2,3‐dimethylimidazolidin‐4‐ones as Catalysts – a Puzzling ‘Fluorine Effect’

Replacement of the cis‐Me group by CH₂F in the imidazolidinone organocatalyst specified in the title (so‐called McMillan generation‐I catalyst) leads to reversal of the product configuration in the title reaction. The topicity reversal in the nucleophilic addition step must arise either from cis‐addition with respect to the benzylic substituent of an (E)‐iminium ion intermediate or from trans‐addition to the corresponding (Z)‐iminium ion. Mechanistic investigations have not provided evidence for either one of these two possibilities, so far.     

Experimental and Theoretical Conformational Analysis of 5‐Benzylimidazolidin‐4‐one Derivatives – a ‘Playground’ for Studying Dispersion Interactions and a ‘Windshield‐Wiper’ Effect in Organocatalysis

The PF₆ salts of 5‐benzyl‐1‐isopropylidene‐ and 5‐benzyl‐1‐cinnamylidene‐3‐methylimidazolidin‐4‐ones 1 (Scheme) with various substituents in the 2‐position have been prepared, and single crystals suitable for X‐ray structure determination have been obtained of 14 such compounds, i.e., 2 – 10 and 12 – 16 (Figs. 2–5). In nine of the structures, the Ph ring of the benzyl group resides above the heterocycle, in contact with the cis‐substituent at C(2) (staggered conformation A ; Figs. 1–3); in three structures, the Ph ring lies above the iminium π‐plane (staggered conformation B ; Figs. 1 and 4); in two structures, the benzylic C? C bond has an eclipsing conformation ( C ; Figs. 1 and 5) which places the Ph ring simultaneously at a maximum distance with its neighbors, the CO group, the N?C‐π‐system, and the cis‐substituent at C(2) of the heterocycle. It is suggested by a qualitative conformational analysis (Fig. 6) that the three staggered conformations of the benzylic C? C bond are all subject to unfavorable steric interactions, so that the eclipsing conformation may be a kind of ‘escape’. State‐of‐the‐art quantum‐chemical methods, with large AO basic sets (near the limit) for the single‐point calculations, were used to compute the structures of seven of the 14 iminium ions, i.e., 3, 4 / 12, 5 – 7, 13 , and 16 (Table) in the two staggered conformations, A and B , with the benzylic Ph group above the ring and above the iminium π‐system, respectively. In all cases, the more stable computed conformer (‘isolated‐molecule’ structure) corresponds to the one present in the crystal (overlay in Fig. 7). The energy differences are small (≤2 kcal/mol) which, together with the result of a potential‐curve calculation for the rotation around the benzylic C? C bond of one of the structures, 16 (Fig. 8), suggests that the benzyl group is more or less freely rotating at ambident temperatures. The importance of intramolecular London dispersion (benzene ring in ‘contact’ with the cis‐substituent in conformation A ) for DFT and other quantum‐chemical computations is demonstrated; the benzyl‐imidazolidinones 1 appear to be ideal systems for detecting dispersion contributions between a benzene ring and alkyl or aryl CH groups. Enylidene ions of the type studied herein are the reactive intermediates of enantioselective organocatalytic conjugate additions, Diels–Alder reactions, and many other transformations involving α,β‐unsaturated carbonyl compounds. Our experimental and theoretical results are discussed in view of the performance of 5‐benzyl‐imidazolidinones as enantioselective catalysts.     

Consequences of Substitution in the Photoelectron Spectra of [2, 2]Paracyclophanes: Separation of ‘through-space’ and ‘through-bond’ interactions as a consequence of fluorosubstitution

The PE. spectra of [2, 2]paracyclophane ( 1 ), 4-amino[2, 2]paracyclophane ( 2 ) and 1, 1, 2, 2, 9, 9, 10, 10-octafluoro[2, 2]paracyclophane ( 3 ) are presented. The bands corresponding to ejection of the photoelectron from the five highest occupied π-orbitals have been assigned. The ‘observed’ orbital energies (i.e. the negative ionization potentials) are discussed in terms of ‘through space’ and ‘through-bond’ interactions between the semi-localized π-orbitals ( e_1g ) of the benzene moieties and the C, C-σ-orbitals of the ethylene bridges. The PE. spectrum of 3 shows that the fluorine-induced lowering of the C, C-σ-orbital energy effectively ‘turns-off’ the ‘through-bond’ interaction. The resulting pattern of the first four bands confirms the assignment given for 1 . Finally the band shifts induced by an amino group in position 4 are again in agreement with this assignment. Attention is drawn to the phenomenon of ‘orbital switching’ as a consequence of substitution in loosely coupled systems such as 1 .     

Tetrathiafulvalene‐Based Macrocycles Formed by Radical Cation Dimerization: The Role of Intramolecular Hydrogen Bonding and Solvent

Compounds 1 a and 1 b were prepared by appending two tetrathiafulvalene (TTF) units to an aromatic amide segment that is driven by six or two intramolecular N? H???O hydrogen bonds to adopt a folded conformation. UV/Vis absorption experiments revealed that if the TTF units were oxidized to TTF^.+ radical cations, the two compounds could form a stable single molecular noncovalent macrocycle in less polar dichloromethane or dichloroethane or a bimolecular noncovalent macrocycle in a binary mixture of dichloromethane with a more polar solvent owing to remarkably enhanced dimerization of the TTF^.+ units. The stability of the (TTF^.+)₂ dimer was evaluated through UV/Vis absorption, electron paramagnetic resonance, and cyclic voltammetry experiments and also by comparing the results with those of control compound 2 . The results showed that introduction of the intramolecular hydrogen bonds played a crucial role in promoting the stability of the (TTF^.+)₂ dimer and thus the noncovalent macrocyclization of the two backbones in both uni‐ and bimolecular manners.     

Chelation versus Binucleation: Metal Complex Formation with the Hexadentate all‐cis‐N1,N2‐Bis(2,4,6‐trihydroxy‐3,5‐diaminocyclohexyl)ethane‐1,2‐diamine

The hexadentate ligand all‐cis‐N¹,N²‐bis(2,4,6‐trihydroxy‐3,5‐diaminocyclohexyl)ethane‐1,2‐diamine (L^e) was synthesized in five steps with an overall yield of 39 % by using [Ni(taci)₂]SO₄?4 H₂O as starting material (taci=1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol). Crystal structures of [Na_0.5(H₆L^e)](BiCl₆)₂Cl_0.5?4 H₂O ( 1 ), [Ni(L^e)]‐ Cl₂?5 H₂O ( 2 ), [Cu(L^e)](ClO₄)₂?H₂O ( 3 ), [Zn(L^e)]CO₃?7 H₂O ( 4 ), [Co(L^e)](ClO₄)₃ ( 5 c ), and [Ga(H_?2L^e)]‐ NO₃?2 H₂O ( 6 ) are reported. The Na complex 1 exhibited a chain structure with the Na⁺ cations bonded to three hydroxy groups of one taci subunit of the fully protonated H₆(L^e)⁶⁺ ligand. In 2 , 3 , 4 , and 5 c , a mononuclear hexaamine coordination was found. In the Ga complex 6 , a mononuclear hexadentate coordination was also observed, but the metal binding occurred through four amino groups and two alkoxo groups of the doubly deprotonated H_?2(L^e)^2?. The steric strain within the molecular framework of various M(L^e) isomers was analyzed by means of molecular mechanics calculations. The formation of complexes of L^e with Mn^II, Cu^II, Zn^II, and Cd^II was investigated in aqueous solution by using potentiometric and spectrophotometric titration experiments. Extended equilibrium systems comprising a large number of species were observed, such as [M(L^e)]²⁺, protonated complexes [MH_z(L^e)]^2+z and oligonuclear aggregates. The pK_a values of H₆(L^e)⁶⁺ (25 °C, μ=0.10 m ) were found to be 2.99, 5.63, 6.72, 7.38, 8.37, and 9.07, and the determined formation constants (log β) of [M(L^e)]²⁺ were 6.13(3) (Mn^II), 20.11(2) (Cu^II), 13.60(2) (Zn^II), and 10.43(2) (Cd^II). The redox potentials (vs. NHE) of the [M(L^e)]^3+/2+ couples were elucidated for Co (?0.38 V) and Ni (+0.90 V) by cyclic voltammetry.     

Initial Radical Cation Pathway in the Mo2Cl10‐Mediated Dehydrogenative Arene Coupling

Experimental (EPR) and theoretical (DFT) evidence is provided for radical cation formation as initial step in the Mo₂Cl₁₀‐mediated dehydrogenative arene coupling. The initial electron transfer from methoxyarenes to molybdenum proceeds via an inner sphere mechanism.     

Synthesis of (S)‐3‐heteroaryl‐2‐hydroxy‐l‐propyl benzoates by ‘ring switching’ methodology

(S)‐5‐Benzoyloxymethyl‐3‐[(E)‐(dimethylamino)methylidene]tetrahydrofuran‐2‐one (6), prepared in 5 steps from L‐glutamic acid (1), was used as precursor in a one step ‘ring switching’ synthesis of (S)‐2‐hydroxy‐3‐heteroaryl‐l‐propyl benzoates 13‐18, 23, 24. In the reaction of 6 with 2‐aminopyridine (21) and 2‐amino‐4,6‐dimethylpyrimidine (22) the corresponding dimethylamine substitution products (25, 26) were obtained.