Radical Cleavage Research Articles

Mn(III)-Mediated Radical Cyclization of o-Alkenyl Aromatic Isocyanides with Boronic Acids: Access to N-Unprotected 2-Aryl-3-cyanoindoles.

The synthesis of N-unprotected 2-aryl-3-cyanoindoles was realized via the Mn(III)-mediated radical cascade cyclization of o-alkenyl aromatic isocyanides with boronic acids. A possible mechanism involving a sequential intermolecular radical addition, intramolecular cyclization, and cleavage of the C-C bond under mild reaction conditions is proposed. Mechanism studies show that H2O or O2 might provide the oxygen source for the elimination of benzaldehyde.

A novel approach in revealing mechanisms and particular step predictors of pH dependent tartrazine catalytic degradation in presence of Oxone®

The degradation of tartrazine in the presence of cobalt activated Oxone® (potassium peroxymonosulfate) was investigated at different initial pH values. Aluminum pillared clay had the role of a support for catalytically active cobalt oxide species. The degradation of tartrazine and the formation of a mixture of degradation products were monitored using the Ultraviolet–Visible (UV–Vis) spectroscopy and gas chromatography–mass spectrometry (GC-MS). The exact qualitative composition of this mixture and the determination of the most probable mechanism of degradation (the primary goal) were obtained using GC-MS. Besides, the main reaction pathway (reaction with SO4˙ˉ radical anion) and secondary pathways were proposed depending on the pH value. At pH = 6 the reaction with HO˙ radical was proposed. At pH = 11 decarboxilation was suggested as the first step of the secondary proposed reaction pathway. The combination of results acquired from the deconvolution of UV–Vis spectra and the theoretical UV–Vis spectra of degradation products, whose occurrence was predicted by quantum-chemical calculations, was proven to be beneficial for the identification of tartrazine degradation products and for defining UV–Vis predictors of particular degradation steps. An additional contribution of this paper, from the reactivity aspect, was the establishment of the critical structural demand for the radical degradation of any diazo compound. The existence of a hydrogen atom bound to a diazo group was found to be the essential prerequisite for the radical cleavage of diazo compounds.

Radiolytic degradation of ornidazole in aqueous solutions by electron beam irradiation: Implications to parameters, kinetics, toxicity and cost evaluation

The study is aimed to assess the effectiveness of electron beam (EB) technology to degrade the antibiotic ornidazole (ORN) in aqueous solution. The influence of several factors viz. initial ORN concentrations, dose, pH of solution, and addition of NO2−, NO3−, isopropanol, H2O2, thiourea, and different water mediums were evaluated on the ORN degradation. The degradation of ORN was followed by pseudo first-order reaction kinetics with rate constant value of 2.01, 1.17, 0.87 and 0.70 kGy−1 for the initial concentrations of 25, 50, 75, and 100 mg L−1 with their corresponding (G-(ORN)) values of 0.93, 1.60, 1.97, and 2.12 μmol J−1, respectively. The presence of NO2−, thiourea and isopropanol revealed reduction in the k-value, whereas, addition of NO3− anion had not substantially effected the degradation of ORN. Presence of H2O2 exhibits significant effect on the mineralization efficiency of ORN rather than degradation extent. The efficacy of EB irradiation to degrade ORN decreased in wastewater in comparison to surface, ground and ultrapure water. Based on the LC-QTOF-MS study, it could be ascribed that degradation of ORN was primarily due to the oxidative species HO radical and direct cleavage of ORN compound. Tentative pathways for EB-induced radiolytic degradation of ORN were proposed. Cytotoxicity assessment and overall cost of electrical energy consumed for the degradation of ORN was also evaluated.

Synthesis of cis‐1,2‐diol‐type chiral ligands and their dioxaborinane derivatives: Application for the asymmetric transfer hydrogenation of various ketones and biological evaluation

Two cis‐1,2‐diol‐type chiral ligands (T1 and T2) and their tri‐coordinated chiral dioxaborinane (T(1–2)B(1–2)) and four‐coordinated chiral dioxaborinane adducts with 4‐tert‐butyl pyridine sustained by N → B dative bonds (T(1–2)B(1–2)‐N) were synthesized and characterized by various spectroscopic techniques such as NMR (1H, 13C, and 11B), FT‐IR and UV–Vis spectroscopy, LC–MS/MS, and elemental analysis. It was suggested that both ferrocene and trifluoromethyl groups played key roles in the catalytic and biological studies because they could tune the solubility of the chiral dioxaborinane complexes and adjust the strength of intermolecular interactions. To assess the biological activities of newly synthesized chiral dioxaborinane compounds, DPPH (2,2‐diphenyl‐1‐picrylhydrazyl) radical scavenging, reducing power, antibacterial, DNA binding, and DNA cleavage activities were tested. Then, all chiral dioxaborinane complexes were investigated as catalysts for the asymmetric transfer hydrogenation of various ketones under suitable conditions. The results indicated that the chiral dioxaborinane catalysts performed well with high yields.

Mass spectral fragmentation analyses of isotopically labelled hydroxy steroids using gas chromatography/electron ionization low-resolution mass spectrometry: A practical approach.

Gas chromatography coupled to electron ionization mass spectrometry (GC/EI-MS) is used for routine screening of anabolic steroids in many laboratories after the conversion of polar groups into trimethylsilyl (TMS) derivatives. The aim of this work is to elucidate the origin and formation of common and subclass-specific fragments in the mass spectra of TMS-derivatized steroids. Especially in the context of metabolite identification or analysis of designer drugs, isotopic labelling is helpful to better understand fragment ion generation, identify unknown compounds and update established screening methods. Stable isotope labelling procedures for the introduction of [2 H9 ]-TMS or 18 O were established to generate perdeuterotrimethylsilylated, mixed deuterated and 18 O-labelled derivatives for 13 different hydroxy steroids. Fragmentation proposals were substantiated by comparison of the abundances of isotopically labelled and unlabelled fragment ions in unit mass resolution GC/MS. Specific fragmentations were also investigated by high-resolution MS (GC/quadrupole time-of-flight MS, GC/QTOFMS). Methyl radical cleavage occurs primarily from the TMS groups in saturated androstanes and from the steroid nucleus in the case of enol-TMS of oxo or α,β-unsaturated steroid ketones. Loss of trimethylsilanol (TMSOH) is dependent on steric factors, degree of saturation of the steroid backbone and the availability of a hydrogen atom and TMSO group in the 1,3-diaxial position. For the formation of the [M - 105]+ fragment ion, methyl radical cleavage predominates from the angular methyl groups in position C-18 or C-19 and is independent of the site of TMSOH loss. The common [M - 15 - 76]+ fragment ion was found in low abundance and identified as [M - CH3 - (CH3 )2 SiH - OH]+ . For the different steroid subclasses further diagnostic fragment ions were discussed and structure proposals postulated. Stable isotope labelling of oxo groups as well as derivatization with deuterated TMS groups enables the detection of structure-related fragment ion generation in unit mass resolution GC/EI-MS. This may in turn allow us to propose isomeric assignments that are otherwise almost impossible using MS only.

Locating TATA Binding Protein in the RNA Polymerase I Pre‐Initiation Complex

Transcription of eukaryotic DNA into RNA is carried by three main RNA polymerases (Pols I–III). Pol I synthesizes ribosomal DNA (rDNA) into ribosomal RNA (rRNA), which has been directly linked to the rate of protein synthesis, cell growth and proliferation. The efficiency of Pols’ function is controlled by general transcription factors, which enable the enzyme to interact with promoter DNA at the initiation stage. In Saccharomyces cerevisiae, Pol I transcription initiation relies on four main factors, one of which is TATA Binding Protein (TBP). TBP is an essential universal transcription factor used by all three eukaryotic Pols. As its name eludes, TBP typically binds to TATA motifs found in promoter DNA. Interestingly, unlike Pol II and III, Pol I promoters are TATA‐less. Thus, unlike the location of TBPs in other PICs, the location and function of TBP within the Pol I PIC remains unclear.Current Cryo‐EM structures of CF‐DNA‐Pol I initiation complex leaves little room for TBP to bind to its “typical” Pols II/III position. Therefore, we hypothesize that TBP must occupy a unique location, putatively more upstream, within the Pol I PIC. Combining available structural data with previous crosslinking data of CF and TBP, we modeled the interaction between the two proteins with varying distance constraints. In addition, we analyzed TBPs location on the rDNA promoter by site‐directed hydroxyl radical cleavage experiment, known as FeBABE, where DNA phosphothioate modification probes were constructed based on our predicted models. Our results from these combinational methods elucidated that TBP locates more upstream within Pol I PIC.Support or Funding InformationThis work was a part of SUNY Upstate Medical School’s Summer Undergraduate Research Fellowship 2019 and was supported by National Cancer Institute (NCI), National Institute for Dental and Craniofacial Research (NIDCR), and Carol Baldwin Research Foundation.FeBABE site‐directed hydroxyl radical cleavage.A and B. Sites of FeBABE incorporation into rDNA promoter in clusters of 5 include the “typical” location of TBP (1), upstream of the CE (2), 5′ of CE (3), and within the CE (4). C. Western blot showed FeBABE specific cleavage products. Cleavages were observed when FeBABE was incorporated at all four positions. Most intense cleavages were observed when FeBABE is incorporated upstream of the CE. D. Quantitation of TBP cleavages.Figure 1

Two-stage calcination composite of Bi2O3-TiO2 supported on powdered activated carbon for enhanced degradation of sulfamethazine under solar irradiation

In a previous study, we used a sol-hydrothermal method with a one-stage calcination in an air atmosphere at 400 °C to prepare composites of Bi2O3-TiO2 supported on powdered activated carbon (Bi-Ti/PAC-1). However, the photocatalytic efficiency of those composites was relatively low due to their high band gap and the single crystal phase of their TiO2. To improve the photocatalytic efficiency, we developed a two-stage calcination method with a first calcination in air at 300 °C followed by a second calcination in a N2 atmosphere (at 500, 600, or 700 °C) to form the Bi2O3-TiO2 composites (Bi-Ti/PAC-2). Compared with Bi-Ti/PAC-1, the photocatalytic degradation efficiency of sulfamethazine (SMT) by Bi-Ti/PAC-2-700 increased by 32 % under solar light irradiation. Bi-Ti/PAC-2-700 contained two TiO2 crystal phases, rutile and anatase, and its band gap was 2.58 eV, far less than that of Bi-Ti/PAC-1. Electron paramagnetic resonance measurements and trapping experiments showed that the superoxide radical, hole, and hydroxyl radical each played an important role in the degradation of SMT, among which the superoxide radical predominated. The degradation pathway of SMT included four processes: oxidation of hydroxyl radical, SO2 extrusion, NC and SN bond cleavage. We also determined that solution pH, humic acid, and inorganic ions had varying effects on the photocatalytic degradation capability of Bi-Ti/PAC-2-700. We measured the efficiency of Bi-Ti/PAC-2-700 for SMT degradation in natural river and lake water and found it to be >85 %, sufficient for practical applications. This study provides a green and efficient photocatalyst that can be applied to water treatment processes.

DFT исследование триплетных и синглетных элементарных актов окисления ациклических и циклических алканов, инициированных первичным взаимодействием с 3O2

The primary oxidation stages of 3O2 model acyclic and cyclic alkanes and their subsequent triplet and singlet elementary events were studied for the first time by the DFT method with the density functional B3LYP and basis set 6-311++g(df,p). According to quantum chemical DFT calculations the C–H radical cleavage of the bonds of acyclic and cyclic alkanes upon interaction with 3O2 is almost completely thermodynamically shifted toward the initial state of the reaction system. This energy of primary oxidizing events explains the extremely low reactivity of saturated alkanes in comparison with asphaltene structural fragments under the conditions of SCF technology for the extraction of heavy oils and asphaltenes by a propane-butane mixture. It has been demonstrated that for all elementary acts of primary alkane oxidation the product of the direct reaction direction is not a free pair of radicals but a triplet hydrogen complex with a pronounced hydrogen bond between the hydroperoxyl radical and the radical form of the corresponding hydrocarbon. A new, previously not taken into account very exothermic (H = -29.25 – -30.77 kcal/mol) reaction direction is described which corresponds to triplet recombination of alkyl radicals and a hydroperoxyl radical in its oxygen-concentrated part. The products of this recombination are triplet forms of alkane hydroperoxides in which there is a fairly loosened triplet O---O bond with a length of 2.20-2.23 Å, which is ~0.72-0.77 Å more than bond length in the singlet state.

Why a Constant Number of Vertebrae? Digital Control of Segmental Identity during Vertebrate Development: The Somite Cycle Controls a Digital, Chromatin-Based Counter That Defines Segmental Identity and Body Plans in Vertebrate Animals.

It is not understood how the numbers and identities of vertebrae are controlled during mammalian development. The remarkable robustness and conservation of segmental numbers may suggest the digital nature of the underlying process. The study proposes a mechanism that allows cells to obtain and store the segmental information in digital form, and to produce a pattern of chromatin accessibility that in turn regulates Hox gene expression specific to the metameric segment. The model requires that a regulatory element be present such that the number of occurrences of the motif between two consecutive Hox genes equals the number of segments under the control of the anterior gene. This is true for the recently discovered hydroxyl radical cleavage 3bp-periodic (HRC3) motif, associated with histone modifications and developmental genes. The finding not only allows the correct prediction of the numbers of segments using only sequence information, but also resolves the 40-year-old enigma of the function of temporal and spatial collinearity of Hox genes. The logic of the mechanism is illustrated in the attached animated video. How different aspects of the proposed mechanism can be tested experimentally is also discussed.

Decomposition Mechanisms of Di-tert-butylaminoarsane (DTBAA)

III–V semiconductors containing small amounts of nitrogen (“dilute nitrides”) are very promising material systems for optoelectronic applications. Devices based on dilute nitrides currently suffer from problematic C incorporation. To overcome this problem, a novel nitrogen (N) and arsenic (As) precursor for metal–organic vapor phase epitaxy (MOVPE) of the dilute nitride di-tert-butylaminoarsane (DTBAA) has been introduced. DTBAA in comparison to the commonly used 1,1-dimethylhydrazine (UDMHy) showed a significantly improved N incorporation efficiency. The molecule exhibits no strong carbon (C)–N bond, and the C is only present in large alkyl groups which form fewer C radicals since β-H elimination is the dominating decomposition process. This should significantly lower the problematic C incorporation in dilute nitrides and lead to highly efficient devices. To understand the high N incorporation efficiency as well as the As incorporation, the gas-phase decomposition of this novel precursor has been studied with a real time Fourier transform (FT) quadrupole ion trap mass spectrometer (iTrap) from Carl Zeiss SMT GmbH in a horizontal Aixtron Aix 200 GFR MOVPE reactor. Formation of isobutane and isobutene proves a radical cleavage and β-H-elimination as decomposition processes of the tert-butyl groups attached to the molecule. Furthermore, the appearance of ammonia (NH3) has been detected. This indicates a direct cleavage of the As–N bond of the molecule, resulting in the formation of an aminyl radical (NH2•). The formation of NH2• explains the high N incorporation efficiency of DTBAA as well as its limitations due to desorption of NH3 at higher temperatures.

Free Radical Pathway Cleavage of C—O Bonds for the Synthesis of Alkylboron Compounds

Summary of main observation and conclusionWe report a silver‐catalyzed borylation of alkyl tosylates, which provides a new method for the synthesis of alkylboron compounds with good functional group compatibility and excellent chemoselectivity. The present work added highly polarized alkyl tosylate C—O bonds to the fairly limited number of C—O bonds able to participate in free radical cleavage pathways. The mechanistic studies suggested that in situ‐generated silver(0) catalytic species were the active catalytic species and played a key role in the radical pathway cleavage of C—O bonds.

Copper Catalyzed Alcohol Oxidation and Cleavage of β‐O‐4 Lignin Model Systems: From Development to Mechanistic Examination

AbstractLignin, an abundant natural polymer with high aromaticity, is a potential source of renewable chemicals and fuels among other biomaterials. Herein, a study on copper catalyzed alcohol oxidation and cleavage of lignin β‐O‐4 model substrates is reported. The potential of CuX/BiPy/TEMPO(/additive) systems (X=halide or triflate, BiPy=2,2’‐bipyridine; TEMPO=2,2,6,6‐tetramethylpiperidine‐N‐oxyl) was explored and the optimized protocol was studied with several type of model compounds. Mechanistic studies elucidated two types of cascade reactions: Both involve a cleavage of Cα–Cβ bond, which is most likely activated by 1) primary alcohol oxidation in β‐O‐4 glycerolaryl ethers resulting in retro‐aldol cleavage and 2) Cβ–H oxidation after secondary alcohol oxidation in β‐O‐4 ethanolaryl ethers leading to oxidative radical cleavage. The first process affords aromatic aldehydes while the latter delivers aryl acids.

Epimerization of Tertiary Carbon Centers via Reversible Radical Cleavage of Unactivated C(sp3)-H Bonds.

Reversible cleavage of C(sp3)-H bonds can enable racemization or epimerization, offering a valuable tool to edit the stereochemistry of organic compounds. While epimerization reactions operating via cleavage of acidic C(sp3)-H bonds, such as the Cα-H of carbonyl compounds, have been widely used in organic synthesis and enzyme-catalyzed biosynthesis, epimerization of tertiary carbons bearing a nonacidic C(sp3)-H bond is much more challenging with few practical methods available. Herein, we report the first synthetically useful protocol for the epimerization of tertiary carbons via reversible radical cleavage of unactivated C(sp3)-H bonds with hypervalent iodine reagent benziodoxole azide and H2O under mild conditions. These reactions exhibit excellent reactivity and selectivity for unactivated 3° C-H bonds of various cycloalkanes and offer a powerful strategy for editing the stereochemical configurations of carbon scaffolds intractable to conventional methods. Mechanistic study suggests that the unique ability of N3• to serve as a catalytic H atom shuttle is critical to reversibly break and reform 3° C-H bonds with high efficiency and selectivity.

Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays.

RNA footprinting by hydroxyl radical cleavage provides 'snapshots' of RNA tertiary structure or protein interactions that bury the RNA backbone. Generation of hydroxyl radicals with a high-flux synchrotron X-ray beam provides analysis on a short timescale (5-100 msec), which enables the structures of folding intermediates or other transient conformational states to be determined in biochemical solutions or cells. This article provides protocols for using synchrotron beamlines for hydroxyl radical footprinting. © 2018 by John Wiley & Sons, Inc.

СРАВНИТЕЛЬНЫЙ АНАЛИЗ СОСТАВА НИЗКОМОЛЕКУЛЯРНЫХ ПРОДУКТОВ СВЕРХКРИТИЧЕСКОЙ ЭКСТРАКЦИИ СОЛОМЫ ПШЕНИЦЫ ЭТАНОЛОМ И ДИМЕТИЛКАРБОНАТОМ

Supercritical extraction is a promising method for the preparation of lignocellulosic raw material for subse-quent biochemical processing. This paper presents a comparative analysis of low-molecular-weight prod-ucts extracted from wheat straw in a batch-type autoclave at a temperature of 285С for 10 min. Ethanol and dimethyl carbonate were used as solvents, since these compounds are known to be similar in terms of their dissolution ability but different in terms of their alkylating properties. It is found that wheat straw ex-traction using dimethyl carbonate demonstrates a high level of efficiency. Compared to ethanolysis, a greater extract yield characterized by a high content of hexanol-soluble compounds was obtained. These compounds predominantly included methyl esters of carboxylic acids. On the other hand, lignin fragmentation products were dominated by veratrous-type compounds. A mechanism is proposed for obtaining low-molecular lignin fragmentation products under the conditions of supercritical extraction, which is based on the processes of a radical cleavage of alkyl aryl ester bonds and C-C bonds in the side radical, as well as on the reactions of dehydration, esterification and re-esterification. When this mechanism is applied under the conditions of supercritical ethanolysis, it additionally involves the reactions of hydrogenation and keto-enol rearrangement with the formation of ketones.

Latent Radical Cleavage of α-Allenylic C–O Bonds: Potassium Persulfate Mediated Thiolation of Allenylphosphine Oxides

A novel potassium persulfate (K2S2O8) mediated thiolation of allenylphosphine oxides with diaryl sulfides is disclosed. Mechanistic studies indicate that K2S2O8 homolyzes the diaryl sulfide to produce a thiyl radical (PhS•), which is followed by C–O bond cleavage of the allenylphosphine oxide under metal-free conditions, affording novel S,P-bifunctionalized butadienes in moderate to excellent yields.

Gas chromatographic-mass spectrometric investigation of n-alkanes and carboxylic acids in bottom sediments of the northern Caspian Sea

Abstract Prior to the start of experimental oil production in the Kashagan field (northern part of the Caspian Sea), n-alkanes and carboxylic acids contained in samples obtained from bottom sediments in the area of artificial island “D” were investigated by gas chromatography–mass spectrometry. Concentrations of 10 n-alkanes (composed of C10-C13, C15-C20) and 11 carboxylic acids (composed of C6-C12, C14-C16) were identified and measured. Concentrations of individual alkanes and carboxylic acids in bottom sediments of the various samples varied between 0.001 ÷ 0.88 μg/g and 0.001 ÷ 1.94 μg/g, respectively. Mass spectra, in particular the M+ molecular ion peak and the most intense peaks of fragment ions, are given. The present study illustrates the stability of molecular ions to electronic ionisation and the main fragment ions to the total ion current and shows that the initial fragmentation of alkanes implies radical cleavage of C2H5 rather than CH3. All aliphatic monocarboxylic acids studied were characterised by McLafferty rearrangement leading to the formation of F4 cation-radical with m/z 60 and F3 cation-radical with m/z 88 in the case of ethylhexanoic acid. The formation of oxonium ions presents another important aspect of acid fragmentation. Using mass numbers of oxonium ions and rearrangement ions allows determination of the substitution character in α- and β- C atoms. The essence of our approach is to estimate the infiltration of hydrocarbon fluids from the enclosing formation into sea water, comprising an analysis of derivatives of organic compounds in bottom sediments. Thus, concentrations of derived organic molecules can serve as a basis for estimates of the depth at which hydrocarbon fluids leak, i.e., to serve as an auxiliary technique in the search for hydrocarbon deposits and to repair well leaks.

Selective methane chlorination to methyl chloride by zeolite Y-based catalysts

The CH4 chlorination over Y zeolites was investigated to produce CH3Cl in a high yield. Three different catalytic systems based on Y zeolite were tested for enhancement of CH4 conversion and CH3Cl selectivity: (i) HY zeolites in H+-form having various Si/Al ratios, (ii) Pt/HY zeolites supporting Pt metal nanoparticles, (iii) Pt/NaY zeolites in Na+-form supporting Pt metal nanoparticles. The reaction was carried out using the gas mixture of CH4 and Cl2 with the respective flow rates of 15 and 10 mL min−1 at 300–350 °C using a fixed-bed reactor under a continuous gas flow condition (gas hourly space velocity = 3000 mL g−1 h−1). Above the reaction temperature of 300 °C, the CH4 chlorination is spontaneous even in the absence of catalyst, achieving 23.6% of CH4 conversion with 73.4% of CH3Cl selectivity. Under sufficient supplement of thermal energy, Cl2 molecules can be dissociated to two chlorine radicals, which triggered the C-H bond activation of CH4 molecule and thereby various chlorinated methane products (i.e., CH3Cl, CH2Cl2, CHCl3, CCl4) could be produced. When the catalysts were used under the same reaction condition, enhancement in the CH4 conversion was observed. The Pt-free HY zeolite series with varied Si/Al ratios gave around 27% of CH4 conversion, but there was a slight decrease in CH3Cl selectivity with about 64%. Despite the difference in acidity of HY zeolites having different Si/Al ratios, no prominent effect of the Si/Al ratios on the catalytic performance was observed. This suggests that the catalytic contribution of HY zeolites under the present reaction condition is not strong enough to overcome the spontaneous CH4 chlorination. When the Pt/HY zeolite catalysts were used, the CH4 conversion reached further up to 30% but the CH3Cl selectivity decreased to 60%. Such an enhancement of CH4 conversion could be attributed to the strong catalytic activity of HY and Pt/HY zeolite catalysts. However, both catalysts induced the radical cleavage of Cl2 more favorably, which ultimately decreased the CH3Cl selectivity. Such trade-off relationship between CH4 conversion and CH3Cl selectivity can be slightly broken by using Pt/NaY zeolite catalyst that is known to possess Frustrated Lewis Pairs (FLP) that are very useful for ionic cleavage of H2 to H+ and H−. Similarly, in the present work, Pt/NaY(FLP) catalysts enhanced the CH4 conversion while keeping the CH3Cl selectivity as compared to the Pt/HY zeolite catalysts.

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.

Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein–DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein–DNA complexes are numerous, the structure of naked cognate DNA is seldom available experimentally. We present here an experimental and computational analysis pipeline that uses hydroxyl radical cleavage to map, at single-nucleotide resolution, DNA minor groove width, a recognition feature widely exploited by proteins. For 11 protein–DNA complexes, we compared experimental maps of naked DNA minor groove width with minor groove width measured from X-ray co-crystal structures. Seven sites had similar minor groove widths as naked DNA and when bound to protein. For four sites, part of the DNA in the complex had the same structure as naked DNA, and part changed structure upon protein binding. We compared the experimental map with minor groove patterns of DNA predicted by two computational approaches, DNAshape and ORChID2, and found good but not perfect concordance with both. This experimental approach will be useful in mapping structures of DNA sequences for which high-resolution structural data are unavailable. This approach allows probing of protein family-dependent readout mechanisms.

Transition-metal-free radical cleavage of a hydrazonyl N–S bond: tosyl radical-initiated cascade C(sp3)–OAr cleavage, sulfonyl rearrangement and atropisomeric cyclopropanation

Combination of 1,10-phenanthroline and potassium carbonate enables a radical cleavage of a hydrazonyl N–S bond, allowing a coupling reaction of N-tosylhydrazone and phosphinyl allene via cascade C–O cleavage, sulfonyl rearrangement and atropisomeric cyclopropanation.