Repair of a Dimeric Azetidine Related to the Thymine–Cytosine (6‐4) Photoproduct by Electron Transfer Photoreduction

Photolyases are intriguing enzymes that take advantage of sunlight to restore lesions like cyclobutane pyrimidine dimers or (6‐4) photoproducts. This work focused on the photoreductive process responsible for splitting of the azetidine ring proposed to occur during (6‐4) photoproduct repair at a thymine–cytosine sequence. A model compound formed by photocycloaddition between thymine and 6‐azauracil has been designed to mimic the elusive azetidine intermediate. The photoinduced electron transfer process has been investigated by means of steady‐state and time‐resolved fluorescence using photosensitizers with oxidation potentials in the singlet excited state ranging from ?3.3 to ?2.1 V vs. SCE. Azetidine ring splitting and recovery of “repaired” bases were proven by HPLC analysis.     

Crystal Structure of the T(6‐4)C Lesion in Complex with a (6‐4) DNA Photolyase and Repair of UV‐Induced (6‐4) and Dewar Photolesions

UV‐light irradiation induces the formation of highly mutagenic lesions in DNA, such as cis‐syn cyclobutane pyrimidine dimers (CPD photoproducts), pyrimidine(6‐4)pyrimidone photoproducts ((6‐4) photoproducts) and their Dewar valence isomers ((Dew) photoproducts). Here we describe the synthesis of defined DNA strands containing these lesions by direct irradiation. We show that all lesions are efficiently repaired except for the T(Dew)T lesion, which cannot be cleaved by the repair enzyme under our conditions. A crystal structure of a T(6‐4)C lesion containing DNA duplex in complex with the (6‐4) photolyase from Drosophila melanogaster provides insight into the molecular recognition event of a cytosine derived photolesion for the first time. In light of the previously postulated repair mechanism, which involves rearrangement of the (6‐4) lesions into strained four‐membered ring repair intermediates, it is surprising that the not rearranged T(6‐4)C lesion is observed in the active site. The structure, therefore, provides additional support for the newly postulated repair mechanism that avoids this rearrangement step and argues for a direct electron injection into the lesion as the first step of the repair reaction performed by (6‐4) DNA photolyases.     

Relative Contributions of UVB and UVA to the Photoconversion of (6‐4) Photoproducts into their Dewar Valence Isomers

Dewar valence isomers are photoisomerization products of pyrimidine (6‐4) pyrimidone photoproducts, a major class of UV‐induced DNA lesions, which exhibits a maximal absorption around 320 nm. However, Dewar isomers are not produced in significant amounts in cells exposed to biologically relevant doses of UVB. In contrast, they are readily produced when cells are exposed to a combination of UVA and UVB. The present computational work demonstrates that, on the basis of known absorption properties and formation quantum yields, the difference in Dewar formation between the two types of radiation can be explained by the role of normal bases. In the UVB range, at the low level of (6‐4) photoproducts present in cells exposed to realistic doses, normal bases are present in overwhelming amounts and absorb the vast majority of the incident photons. In contrast, the absorption of DNA bases is much weaker in the UVA range while that of (6‐4) photoproducts is still significant, making photoisomerization possible. This two‐photon process makes it difficult to define an action spectrum for the formation of Dewar isomers.     

Two polymorphs of N1,N4‐bis(5‐hydroxypenta‐1,3‐diynyl)‐N1,N4‐diphenylbenzene‐1,4‐diamine

The title compound, C₂₈H₂₀N₂O₂, forms two conformational polymorphs, (I) and (II), where the molecular structures are similar except for the orientation of the two hydroxy groups. In (I), which was obtained by slow evaporation from chloroform, the two hydroxy groups have an anti conformation. The molecules form a sheet structure within the ac plane, where the hydroxy groups form zigzag hydrogen bonds. In (II), which was obtained by slow evaporation from acetonitrile, the two hydroxy groups have a syn conformation. The molecules form a double‐sheet structure within the ab plane, where the hydroxy groups form 4‐helix hydrogen bonds.     

N6‐Furfuryladenine (kinetin) hydrochloride

In the title compound, N⁶‐furfuryl­adenin‐3‐ium chloride, C₁₀H₁₀N₅O⁺·Cl⁻, the adenine moiety exists as the N3‐protonated N7–H tautomer. The orientation of the N6 substituent (furfuryl moiety) is distal to the imidazole ring of the adenine base. The dihedral angle between the adenine plane and the furfuryl ring plane is 76.1 (2)°. Three N—H⋯Cl hydrogen bonds are responsible for the formation of a supramolecular chain‐like pattern. These supramolecular chains are interconnected by C—H⋯Cl hydrogen bonds to form a hydrogen‐bonded sheet and a three‐dimensional hydrogen‐bonded network.     

Alkylations of N4‐(4‐Pyridyl)‐3,5‐di(2‐pyridyl)‐1,2,4‐triazole: First Observation of Room‐Temperature Rearrangement of an N4‐Substituted Triazole to the N1 Analogue

Attempts to use alkylation to introduce a positive charge at the nitrogen atom of the 4‐pyridyl ring in the bis(bidentate) triazole ligand N⁴‐(4‐pyridyl)‐3,5‐di(2‐pyridyl)‐1,2,4‐triazole ( pydpt ) were made to ascertain what effect a strongly electron‐withdrawing group would have on the magnetic properties of any subsequent iron(II) complexes. Alkylation of pydpt under relatively mild conditions led in some cases to unexpected rearrangement products. Specifically, when benzyl bromide is used as the alkylating agent, and the reaction is carried out in refluxing acetonitrile, the N⁴ substituent moves to the N¹ position. However, when the same reaction is performed in dichloromethane at room temperature, the rearrangement does not occur and the desired product containing an alkylated N⁴ substituent is obtained. Heating a pure sample of N⁴‐Bzpydpt?Br to reflux in MeCN resulted in clean conversion to N1Bzpydpt.Br . This is consistent with N4‐Bzpydpt.Br being the kinetic product whereas N1Bzpydpt.Br is the thermodynamic product. When methyl iodide is used as the alkylating agent, the N⁴ to N¹ rearrangement occurs even at room temperature, and at reflux pydpt is doubly alkylated. The observation of the lowest reported temperatures for an N⁴ to N¹ rearrangement is due to this particular rearrangement involving nucleophilic aromatic substitution: a possible mechanism for this transformation is suggested.     

(4‐Aminopyridine‐κN1)(phthalocyaninato‐κ4N)zinc(II) tetrahydrofuran disolvate

The title compound, [Zn(C₃₂H₁₆N₈)(C₅H₆N₂)]·2C₄H₈O, consists of one (phthalocyaninato)zinc (ZnPc) unit, a coordinated 4‐aminopyridine (4‐ap) molecule and two tetrahydrofuran (THF) solvent molecules. The central Zn atom is (4+1)‐coordinated by four isoindole N atoms of the Pc core and by the pyridine N atom of 4‐aminopyridine. The Zn atom is displaced by 0.4464 (8) Å from the isoindole N₄ plane towards the pyridine N atom. The crystal structure is stabilized by intermolecular amine–phthalocyaninate N—H...N hydrogen bonds and π–π interactions between the aggregated Pc rings, which form molecular layers, and by weak van der Waals interactions between the layers. As well as hindering the aggregation of ZnPc molecules by occupying an axial position, the amino group will add new interactions which will favor applications of ZnPc, for example, as a sensitizer of photodynamic therapy.     

(E)‐(4‐Hydroxyphenyl)(4‐nitrophenyl)diazene, (E)‐(4‐methoxyphenyl)(4‐nitrophenyl)diazene and (E)‐[4‐(6‐bromohexyloxy)phenyl](4‐cyanophenyl)diazene

Syntheses and X‐ray structural investigations have been carried out for (E)‐(4‐hydroxy­phenyl)(4‐nitro­phenyl)­diazene, C₁₂H₉N₃O₃, (Ia), (E)‐(4‐methoxy­phenyl)(4‐nitro­phenyl)­diazene, C₁₃H₁₁N₃O₃, (IIIa), and (E)‐[4‐(6‐bromo­hexyl­oxy)­phenyl](4‐cyano­phenyl)­diazene, C₁₉H₂₀BrN₃O, (IIIc). In all of these compounds, the mol­ecules are almost planar and the azo­benzene core has a trans geometry. Compound (Ia) contains four and compound (IIIc) contains two independent mol­ecules in the asymmetric unit, both in space group P (No. 2). In compound (Ia), the independent mol­ecules are almost identical, whereas in crystal (IIIc), the two independent mol­ecules differ significantly due to different conformations of the alkyl tails. In the crystals of (Ia) and (IIIa), the mol­ecules are arranged in almost planar sheets. In the crystal of (IIIc), the mol­ecules are packed with a marked separation of the azo­benzene cores and alkyl tails, which is common for the solid crystalline precursors of mesogens.     

Photoreactivating Enzyme for (6–4) Photoproducts in Cultured Goldfish Cells

We previously reported that when cultured goldfish cells are illuminated with fluorescent light, photorepair ability for both cyclobutane pyrimidine dimers and (6–4) photoproducts increased. In the present study, it was found that the duration of the induced photorepair ability for cyclobutane pyrimidine dimers was longer than that for (6–4) photoproducts, suggesting the presence of different photolyases for repair of these two major forms of DNA damage. A gel shift assay was then performed to show the presence of protein(s) binding to (6–4) photoproducts and its dissociation from (6–4) photoproducts under fluorescent light illumination. In addition, at 8 h after fluorescent light illumination of the cell, the binding of pro-tein(s) to (6–4) photoproducts increased. The restriction enzymes that have recognition sites containing TT or TC sequences failed to digest the UV-irradiated DNA pho-toreactivated by using Escherichia coli photolyase for cyclobutane pyrimidine dimers, indicating that restriction enzymes could not function because (6–4) photoproducts remained in recognition sites. But, when UV-irradiated DNA depleted of cyclobutane pyrimidine dimers was incubated with extract of cultured goldfish cells under fluorescent light illumination, it was digested with those restriction enzymes. These results suggested the presence of (6–4) photolyase in cultured goldfish cells as in Dro-sophila, Xenopus and Crotalus.     

Supramolecular hydrogen‐bonding patterns in two cocrystals of the N(7)–H tautomeric form of N6‐benzoyladenine: N6‐benzoyladenine–3‐hydroxypyridinium‐2‐carboxylate (1/1) and N6‐benzoyladenine–DL‐tartaric acid (1/1)

Two novel cocrystals of the N(7)—H tautomeric form of N⁶‐benzoyladenine (BA), namely N⁶‐benzoyladenine–3‐hydroxypyridinium‐2‐carboxylate (3HPA) (1/1), C₁₂H₉N₅O·C₆H₅NO₃, (I), and N⁶‐benzoyladenine–DL‐tartaric acid (TA) (1/1), C₁₂H₉N₅O·C₄H₆O₆, (II), are reported. In both cocrystals, the N⁶‐benzoyladenine molecule exists as the N(7)—H tautomer, and this tautomeric form is stabilized by intramolecular N—H...O hydrogen bonding between the benzoyl C=O group and the N(7)—H hydrogen on the Hoogsteen site of the purine ring, forming an S(7) motif. The dihedral angle between the adenine and phenyl planes is 0.94 (8)° in (I) and 9.77 (8)° in (II). In (I), the Watson–Crick face of BA (N6—H and N1; purine numbering) interacts with the carboxylate and phenol groups of 3HPA through N—H...O and O—H...N hydrogen bonds, generating a ring‐motif heterosynthon [graph set R₂²(6)]. However, in (II), the Hoogsteen face of BA (benzoyl O atom and N7; purine numbering) interacts with TA (hydroxy and carbonyl O atoms) through N—H...O and O—H...O hydrogen bonds, generating a different heterosynthon [graph set R₂²(4)]. Both crystal structures are further stabilized by π–π stacking interactions.     

4‐Amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one (metamitron) and 4‐amino‐6‐methyl‐3‐phenyl‐1,2,4‐triazin‐5(4H)‐one (isometamitron)

The title structures, both C₁₀H₁₀N₄O, are substitutional isomers. The N—N bond lengths are longer and the C=N bond lengths are shorter by ca 0.025 Å than the respective average values in the C=N—N=C group of asymmetric triazines; the assessed respective bond orders are 1.3 and 1.7. There are N—H⋯O and N—H⋯N hydrogen bonds in both structures, with 4‐­amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one containing a rare bifurcated N—H⋯N,N hydrogen bond. The structures differ in their mol­ecular stacking and the hydrogen‐bonding patterns.     

Hydrogen‐bonded supramolecule of N,N′‐bis(4‐pyridylmethyl)oxalamide and a zigzag chain structure of catena‐poly[[[dichloridocobalt(II)]‐μ‐N,N′‐bis(4‐pyridylmethyl)oxalamide‐κ2N4:N4′] hemihydrate]

N,N′‐Bis(4‐pyridylmethyl)oxalamide, C₁₄H₁₄N₄O₂, exists as a dimer which is extended into a two‐dimensional network with other dimers through pyridine–amide hydrogen bonds. The crystal structure of the title coordination polymer, {[CoCl₂(C₁₄H₁₄N₄O₂)]·0.5H₂O}_n, features a one‐dimensional zigzag chain, in which the cobalt ion sits at a twofold symmetry position and adopts a tetrahedral geometry, and the bridging ligand lies on an inversion center and connects to Co^II ions in a bis‐monodentate mode. Furthermore, two interwoven chains create a cavity of ca 8.6 × 8.6 Å, which produces a three‐dimensional channel. Water molecules are held in the channel by hydrogen bonds.     

N,N, N′, N′‐Tetrakis(diphenylphosphanyl)‐1, 3‐diaminobenzene as a Bis‐chelate Ligand in [1, 3‐{cis‐Mo(CO)4(PPh2)2N}2C6H4]

1, 3‐Diaminobenzene reacts readily with PPh₂Cl to give N, N, N′, N′‐tetrakis(diphenylphosphanyl)‐1, 3‐diaminobenzene ( 1 ) in excellent yield. The dinuclear complex [1, 3‐{cis‐Mo(CO)₄(PPh₂)₂N}₂C₆H₄] ( 2 ) is obtained in high yield from 1 and cis‐[Mo(CO)₄(NCEt)₂]. Compounds 1 and 2 were characterized by NMR spectroscopy (¹H, ¹³C, ³¹P) and by crystal structure determination. The latter shows the formation of a bis‐chelate complex with Mo‐P‐N‐P four‐membered rings.     

Conformational flipping of the N(6) substituent in diprotonated N6‐(N‐glycylcarbonyl)adenines: The role of N(6)H in purine‐ring‐protonated ureido adenines

Conformational transitions of the N(6) substituent, in hypermodified nucleic acid base N⁶‐(N‐glycylcarbonyl)adenine, gc⁶Ade, on diprotonation of the adenine ring at any two of N(1), N(3), and N(7) sites, are studied using the quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. The N(6) substituent retains the usual “distal” orientation (α=0°) in (N(1),N(3)) diprotonated gc⁶Ade, but the “proximal” orientation (α=180°) is preferred instead, for (N(3),N(7)) and (N(7),N(1)) diprotonated gc⁶Ade. The proximal orientation may alter the reading frame during translation. Intramolecular N(6)HO(13b) hydrogen bonding is the key common feature, present in the preferred structure, for each of these variously diprotonated gc⁶Ade. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 398–405, 2000     

Highly branched and high‐molecular‐weight polyethylenes produced by 1‐[2,6‐bis(bis(4‐fluorophenyl)methyl)‐4‐MeOC6H2N]‐2‐aryliminoacenaphthylnickel(II) halides

A series of unsymmetrical 1‐[2,6‐bis(bis(4‐fluorophenyl)methyl)‐4‐MeOC₆H₂N]‐2‐aryliminoacenaphthene‐nickel(II) halides has been synthesized and fully characterized by Fourier transform infrared spectroscopy, proton nuclear magnetic resonance (¹H NMR), ¹³C NMR, and ¹⁹F NMR spectroscopy as well as elemental analysis. The structures of Ni1 and Ni6 have been confirmed by the single‐crystal X‐ray diffraction. On activation with cocatalysts either ethylaluminum sesquichloride or methylaluminoxane, all the title nickel complexes display high activities toward ethylene polymerization up to 16.14 × 10⁶ g polyethylene (PE) mol^?1(Ni) h^?1 at 30 °C, affording PEs with both high branches (up to 103 branches/1000 carbons) and molecular weight (1.12 × 10⁶ g mol^?1) as well as narrow molecular weight distribution. High branching content of PE can be confirmed by high temperature ¹³C NMR spectroscopy and differential scanning calorimetry. In addition, the PE exhibited remarkable property of thermoplastic elastomers (TPEs) with high tensile strength (σ_b = 21.7 MPa) and elongation at break (ε_b = 937%) as well as elastic recovery (up to 85%), indicating a better alternative to commercial TPEs. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 130–145     

New insight into the photochromic mechanism of 1,3‐diphenyl‐4‐(4‐fluoro)benzal‐5‐pyrazolone N(4)‐phenyl semicarbazone

Density functional theory (DFT) calculation has been carried out to investigate the photochromic mechanism of 1, 3‐diphenyl‐4‐(4‐fluoro)benzal‐5‐pyrazolone N(4)‐phenyl semicarbazone. The novel mechanism, proposed by us, has different reaction pathway between the forward and the reverse process. The energy barrier of the forward direction was calculated to be significantly larger than that of the reverse direction (30.35 kcal/mol to 9.88 kcal/mol), which confirms the experimental observation that the forward process needs irradiation of light while the reverse one will take place easily when heated. The solvent effect on the relative stabilities of those isomers that may involve in the reaction has also been investigated by applying the polarizable continuum model (PCM) of the self‐consistent reaction field theory. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Die Kristallstruktur von (Ph4P)2[Be4Cl4(μ‐N3)6]

Suitable single crystals for X‐ray analysis of the recently published azido beryllate (Ph₄P)₂[Be₄Cl₄(μ‐N₃)₆] ( 1 ) [1] were obtained by a modified synthetic route, and the crystal structure of 1 was determined. The compound crystallizes isotypically with the corresponding bromo derivative [1] in the space group C2/c with 12 formula units per unit cell. Lattice dimensions at 193 K: a = 4125.5(1), b = 2001.7(1), c = 2050.4(1) pm, β = 101.05 (1)°, R₁ = 0.0359. The structure contains adamantanlike dianions [Be₄Cl₄(μ‐N₃)₆]^2? with a Be₄N₆ core forming by the bridging function of the α‐nitrogen atoms of the azido groups.     

(R)‐4‐(4‐Aminophenyl)‐2,2,4‐trimethylchroman and (S)‐4‐(4‐aminophenyl)‐2,2,4‐trimethylthiachroman

The title compounds, C₁₈H₂₁NO and C₁₈H₂₁NS, in their enantiomerically pure forms are isostructural with the enantiomerically pure 4‐(4‐hydroxyphenyl)‐2,2,4‐trimethylchroman and 4‐(2,4‐dihydroxyphenyl)‐2,2,4‐trimethylchroman analogues and form extended linear chains via N—H...O or N—H...S hydrogen bonding along the [100] direction. The absolute configuration for both compounds was determined by anomalous dispersion methods with reference to both the Flack parameter and, for the light‐atom compound, Bayesian statistics on Bijvoet differences.     

A novel dinuclear bismuth(III) coordination compound: bis(μ‐pyridine‐2,6‐dicarboxylato)‐κ4O2,N,O6:O6′;κ4O2:O2′,N,O6‐bis[(azido‐κN)(1,10‐phenanthroline‐κ2N,N′)bismuth(III)] tetrahydrate

A novel dinuclear bismuth(III) coordination compound, [Bi₂(C₇H₃NO₄)₂(N₃)₂(C₁₂H₈N₂)₂]·4H₂O, has been synthesized by an ionothermal method and characterized by elemental analysis, energy‐dispersive X‐ray spectroscopy, IR, X‐ray photoelectron spectroscopy and single‐crystal X‐ray diffraction. The molecular structure consists of one centrosymmetric dinuclear neutral fragment and four water molecules. Within the dinuclear fragment, each Bi^III centre is seven‐coordinated by three O atoms and four N atoms. The coordination geometry of each Bi^III atom is distorted pentagonal–bipyramidal (BiO₃N₄), with one azide N atom and one bridging carboxylate O atom located in axial positions. The carboxylate O atoms and water molecules are assembled via O—H...O hydrogen bonds, resulting in the formation of a three‐dimensional supramolecular structure. Two types of π–π stacking interactions are found, with centroid‐to‐centroid distances of 3.461 (4) and 3.641 (4) Å.