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Abstract: An efficient one-pot multicomponent synthesis of 3,4- dihydropyrimidin-2(1H)-ones has been developed from aldehyde bisulfite adducts, ethyl acetoacetate and urea using recyclable polymer- supported sulfonic acid catalyst. This new method provides several advantages over the previous synthesis, including high product yields, commercially viable, minimal workup operations and sustainable chemical practices.

The Beckmann rearrangement has been predominantly studied for the synthesis of amide and lactam. By strategically using the in situ generated Appel's salt or Mitsunobu's zwitterionic adduct as the dehydrating agent, a series of Beckmann rearrangement and following cascade reactions have been developed herein. The protocol allows the conversion of various ketoximes into amide, thioamide, tetrazole and imide products in modular procedures. The generality and tolerance of functionalities of this method have been demonstrated.

Here in we report Ag(I)-promoted homo-dimerization of 2-(alk-2-yn-1-onyl)-1-alkynylbenzenes for the synthesis of structurally novel and functionalized naphthalene derivatives. This transformation has exhibited a broad scope for the alkyl as well as aryl groups present on alkynes. Observations made from the control experiments, had suggested the possible mechanism as i) homo-dimerization of in situ generated benzopyrylium ion intermediates through a head–tail [4+2] cycloaddition, followed by ii) the competitive aromative ring-opening vs. decarbonylative aromatization of the adduct to give the formylated and deformylated naphthalenes respectively.

Mycobacterium tuberculosis (Mtb) cells are known to synthesize very long chain (C60-90) structurally complex mycolic acids with various functional groups. In this study, we applied linear ion-trap (LIT) multiple-stage mass spectrometry (MSn), combined with high-resolution mass spectrometry to study the mechanisms underlying the fragmentation processes of mycolic acid standards desorbed as lithiated adduct ions by ESI. This is followed by structural characterization of a Mtb mycolic acid family (Bovine strain). Using the insight fragmentation processes gained from the study, we are able to achieve a near complete characterization of the whole mycolic acid family, revealing the identity of the α-alkyl chain, the location of the functional groups including methyl, methoxy, and keto groups along the meroaldehyde chain in each lipid species. This study showcased the power of LIT MSn toward structural determination of complex lipids in a mixture, which would be otherwise very difficult to define using other analytical techniques.

Lewis acids increase the catalytic activity of classical heterogeneous catalysts and molecular d0 tungsten oxo alkylidenes in a variety of olefin metathesis processes. The formation of labile adducts between the metal complex and the Lewis acid has been observed experimentally and suggested to be involved in the catalyst activity increase. In this contribution, DFT (M06) calculations have been performed to determine the role of Lewis acids on catalyst activity, Z-/E- selectivity and stability by comparing three W(E)(CHR)(2,5-dimethylpyrrolide)(O-2,6-dimesithylphenoxide) (E = oxo, imido or oxo-Lewis acid adduct) alkylidenes. Results show that the formation of the alkylidene—Lewis acid adducts influences the reactivity of tungsten oxo alkylidenes due to both steric and electronic effects. The addition of the Lewis acid on the E group increases its bulkiness and this decreases catalyst Z-selectivity. Moreover, the interaction between the oxo ligand and the Lewis acid decreases the donating ability of the former toward the metal. This is important when the oxo group has either a ligand in trans or in the same plane that is competing for the same metal d orbitals. Therefore, the weakening of oxo donating ability facilitates the cycloaddition and cycloreversion steps and it stabilizes the productive trigonal bipyramid metallacyclobutane isomer. The two factors increase the catalytic activity of the complex. The electron donating tuneability by the coordination of the Lewis acid also applies to catalyst deactivation and particularly the key β-hydride elimination step. In this process, the transition states show a ligand in pseudo trans to the oxo. Therefore, the presence of the Lewis acid decreases the Gibbs energy barrier significantly. Overall, the optimization of the E group donating ability in each step of the reaction makes tungsten oxo alkylidenes more reactive and this applies both for the catalytic activity and catalyst deactivation.

Quinones are potent genotoxic agents through generating reactive oxygen species or undergo covalent bonding to modify the nucleobases of DNA. The formation of DNA adducts is an early indication of cancer, as it may lead to gene mutation, thereby initiating tumor development. The present review aims to summarize different types of quinone-induced DNA damages and the corresponding DNA adducts. In addition to the considerably stable naphthoquinone and halobenzoquinones in the environment, quinones are also metabolically activated from estrogen, bisphenol A, ochratoxin A, polychlorinated biphenyls, benzo[a]pyrene and polybrominated diphenyl ethers, in which the inducement from these pollutants to produce DNA adducts were systematically discussed. Liquid chromatography-mass spectrometry (LC-MS)-based method with high accuracy and sensitivity for the detection of DNA adducts in mononucleotides, DNA duplexes, and biological samples was methodically summarized. It is believed that the presence of dione moiety in quinones is an imperative element that induce the formation of DNA adducts. The investigation on DNA adducts is helpful for understanding the generation, transformation, and repair of DNA damages, and for elucidating the underlying mechanism of carcinogenesis. This review provides a new perspective to assess the toxicological potential of quinones, and intends to put forward strategies of analyzing DNA adducts, which act as biomarkers, for indicating the potential health risks of multiDNA damages.

The first title compound, [Au(C7H11BrN2)2]I, crystallizes in the space group P\overline{1} without imposed symmetry. The cations and anions are linked to form chains by Br...I...Br halogen-bond linkages. The second title compound, [Au(C7H11BrN2)2][AuI2(C7H11BrN2)2]I2, is an adduct of the first and its formally I2-oxidized AuIII analogue. It also crystallizes in space group P\overline{1}, whereby both gold atoms occupy inversion centres. The extended structure is a reticular layer involving Br...I...Br and I...I...Au linkages.

Functionalization-induced phase transitions in polymer systems in which a postpolymerization reaction drives polymers to organize into colloidal aggregates are a versatile method to create nanoscal...

We report that exposing the dipyrrin complex ((EMind)L)Cu(N(2)) to air affords rapid, quantitative uptake of O(2) in either solution or the solid-state to yield ((EMind)L)Cu(O(2)). The air and thermal stability of ((EMind)L)Cu(O(2)) is unparalleled in molecular copper-dioxygen coordination chemistry, attributable to the ligand flanking groups which preclude the [Cu(O(2))](1+) core from degradation. Despite the apparent stability of ((EMind)L)Cu(O(2)), dioxygen binding is reversible over multiple cycles with competitive solvent exchange, thermal cycling, and redox manipulations. Additionally, rapid, catalytic oxidation of 1,2-diphenylhydrazine to azoarene with generation of hydrogen peroxide is observed, through the intermittency of an observable ((EMind)L)Cu(H(2)O(2)) adduct. The design principles gleaned from this study can provide insight for the formation of new materials competent capable of reversible scavenging of O(2) from air under ambient conditions with low-coordinate Cu(I) sorbents.

Understanding binding site preferences in biological systems as well as affinities to binding partners is a crucial aspect in metallodrug development. We here present a mass spectrometry-based method to compare relative stabilities of metal-peptide adducts in the gas phase. Angiotensin 1 and substance P were used as model peptides. Incubation with isostructural N-heterocyclic carbene (NHC) complexes of RuII , OsII , RhIII , and IrIII led to the formation of various adducts, which were subsequently studied by energy-resolved fragmentation experiments. The gas-phase stability of the metal-peptide bonds depended on the metal and the binding partner. Of the four complexes used, the OsII derivative bound strongest to Met, while RuII formed the most stable coordination bond with His. RhIII was identified as the weakest peptide binder and IrIII formed peptide adducts with intermediate stability. Probing these intrinsic gas-phase properties can help in the interpretation of biological activities and the design of site-specific protein binding metal complexes.

The properties of metal/dioxygen species, which are key intermediates in oxidation catalysis, can be modulated by interaction with redox-inactive Lewis acids, but structural information about these adducts is scarce. Here we demonstrate that even mildly Lewis acidic alkali metal ions, which are typically viewed as innocent "spectators", bind strongly to a reactive cis-peroxo dicopper(II) intermediate. Unprecedented structural insight has now been obtained from X-ray crystallographic characterization of the "bare" CuII2(μ-η1:η1-O2) motif and its Li+, Na+, and K+ complexes. UV-vis, Raman, and electrochemical studies show that the binding persists in MeCN solution, growing stronger in proportion to the cation's Lewis acidity. The affinity for Li+ is surprisingly high (∼70 × 104 M-1), leading to Li+ extraction from its crown ether complex. Computational analysis indicates that the alkali ions influence the entire Cu-OO-Cu core, modulating the degree of charge transfer from copper to dioxygen. This induces significant changes in the electronic, magnetic, and electrochemical signatures of the Cu2O2 species. These findings have far-reaching implications for analyses of transient metal/dioxygen intermediates, which are often studied in situ, and they may be relevant to many (bio)chemical oxidation processes when considering the widespread presence of alkali cations in synthetic and natural environments.

Acrolein (ACR), the simplest α,β-unsaturated aldehyde, possesses high reactivity and toxicity both in vitro and in vivo and results in various chronic diseases. This has attracted increasing interest from researchers to screen various bioactive compounds to control it. In this article, we attempted to discover a new attribute of cyanidin-3-O-glucoside (C3G), including its ACR-scavenging capacity, reaction pathway, and possible application. Our findings revealed that C3G could capture ACR to form mono- and diadducts at room temperature by using liquid chromatography-mass spectrometry, and we further synthesized and elucidated the structures of C3G-ACR and C3G-2ACR using HRMS and 2D NMR. The structural data validated that there were two active sites of C3G for trapping ACR: at C-6 in the A-ring and C-5' in the B-ring. In addition, we found that C3G-ACR exhibited a more remarkable clearing ability than C3G within a short time. More than 65.9% of ACR was eliminated by C3G-ACR within 5 min via further formation of C3G-2ACR, but there was no obvious effect of C3G on ACR. When the incubation time was extended to 120 min, C3G could remove up to 83.2% of ACR. Subsequently, we also observed that mynica red (>5% C3G), as a pigmented food additive, could efficiently eliminate ACR generated in the Chinese liquor model and real red bayberry wine products to form C3G-ACR and C3G-2ACR. Both adducts increased significantly, by 10 times to a 100 times, after adding mynica red to red bayberry wine products for 24 h; they also increased rapidly with prolonged incubation time in the liquor-mynica red model system. Therefore, our findings suggest that C3G or mynica red may be developed as a promising novel ACR inhibitor in fruit wine and assembled alcoholic drinks or as a health food.

Aldehyde deformylation reactions by metal dioxygen adducts have been proposed to involve peroxyhemiacetal species as key intermediates. However, direct evidence of such intermediates has not been obtained to date. We report the spectroscopic characterization of a mononuclear cobalt(III)-peroxyhemiacetal complex, [Co(Me3-TPADP)(O2CH(O)CH(CH3)C6H5)]+ (2), in the reaction of a cobalt(III)-peroxo complex (1) with 2-phenylpropionaldehyde (2-PPA). The formation of 2 is also investigated by isotope labeling experiments and kinetic studies. The conclusion that the peroxyhemiacetalcobalt(III) intermediate is responsible for the aldehyde deformylation is supported by the product analyses. Furthermore, isotopic labeling suggests that the reactivity of the cobalt(III)-peroxo complex depends on the second reactant. The aldehyde inserts between the oxygen atoms of 1, whereas the reaction with acyl chlorides proceeds by a nucleophilic attack. The observation of the peroxyhemiacetal intermediate provides significant insight into the initial step of aldehyde deformylation by metalloenzymes.

A systematic study on Lewis-acid/base adducts of N-heterocyclic carbenes (NHCs) and the cyclic (alkyl)(amino)carbene cAAC\(^{Me}\) (1-(2,6-di-iso-propylphenyl)-3,3,5,5-tetramethyl-pyrrolidin-2-ylidene) with antimony(III) chlorides of the general formula SbCl\(_{2}\)R (R=Cl, Ph, Mes) is presented. The reaction of the NHCs Me\(_{2}\)Im\(^{Me}\) (1,3,4,5-tetra-methyl-imidazolin-2-ylidene), iPr\(_{2}\)Im\(^{Me}\) (1,3-di-isopropyl-4,5-dimethyl-imidazolin-2-ylidene), Mes\(_{2}\)Im, Dipp\(_{2}\)Im (R\(_{2}\)Im=1,3-di-organyl-imidazolin-2-ylidene; Mes=2,4,6-trimethylphenyl, Dipp=2,6-di-isopropylphenyl) and cAAC\(^{Me}\) with antimony(III) compounds SbCl\(_{2}\)R (R=Cl (1), Ph (2) and Mes (3)) yields the adducts NHC ⋅ SbCl\(_{2}\)R (R=Cl (4), Ph (5) and Mes (6); NHC=Me\(_{2}\)Im\(^{Me}\) (a), iPr\(_{2}\)Im\(^{Me}\) (b), Dipp\(_{2}\)Im (c) and Mes\(_{2}\)Im (d)) and cAAC\(^{Me}\) ⋅ SbCl\(_{2}\)R (R=Cl (4 e) and Ph (5 e)). Thermal treatment of (Dipp\(_{2}\)Im) ⋅ SbCl\(_{2}\)Ar (Ar=Ph (5 c) and Mes (6 c)) in benzene leads to isomerization to the backbone coordinated \(^{a}\)NHC-adduct \(^{a}\)Dipp\(_{2}\)Im ⋅ SbCl\(_{2}\)Ar (Ar=Mes (7) and Ph (8)) (\(^{"a"}\) denotes “abnormal” coordination mode of the NHC) in high yields. One of the chloride substituents at antimony of 7 can be abstracted by GaCl3 or Ag[BF\(_{4}\)] to obtain the imidazolium salts [\(^{a}\)Dipp\(_{2}\)Im ⋅ SbClMes][BF\(_{4}\)] (9) and [\(^{a}\)Dipp\(_{2}\)Im ⋅ SbClMes][GaCl\(_{4}\)] (10).

While some hetero-Diels-Alder (HDA) reactions are accelerated by either carbonyl or phosphate groups attached directly to the heterodiene moiety, the alkyl or aryl groups, on the other hand, have minimal influence. However, in this article, we demonstrate that aryl groups have a significant effect on the spontaneous dimerization reaction of α,β-unsaturated D-xylo-hexofurano-5-ulose derivatives to their respective pyrano adducts via intermolecular HDA reaction. Experimental and computational studies provide strong evidence that dimerization follows the Woodward-Katz two-stage mechanism reaction (asynchronous process), from which the aryl/aryl π-stacking interaction is mainly responsible for the rate-determining step (RDS) and electrostatic interaction for the second bond formation. Since the latter interaction is highly affected by dipolar moment, 5-ulose derivative having a strong electron-withdrawing group (R = CN; μ = 14.3 D) is spontaneously dimerized more than 15 times faster than 5-ulose that possesses an electron-donating group (R = OMe; μ = 2.1 D).

Methylglyoxal (MGO) is a reactive byproduct formed by several metabolic precursors, the most notable being triosephosphates in glycolysis. While many MGO-mediated adducts have been described, the reactivity and specific biomolecular targets of MGO remain incompletely mapped. Based on our recent discovery that MGO can form stable mercaptomethylimidazole crosslinks between cysteine and arginine (MICA) in proteins, we hypothesized that MGO may participate in myriad reactions with biologically relevant guanidines and thiols in proteins, metabolites, and perhaps other biomolecules. Herein, we performed steady-state and kinetic analyses of MGO reactivity with several model thiols, guanidines, and biguanide drugs to establish the plausible and prevalent adducts formed by MGO in proteins, peptides, and abundant cellular metabolites. We identified several novel, stable MICA metabolites that form in vitro and in cells, as well as a novel intermolecular post-translational MICA modification of surface cysteines in proteins. These data confirm that kinetic trapping of free MGO by thiols occurs rapidly and can decrease formation of more stable imidazolone (MG-H1) arginine adducts. However, reversible hemithioacetal adducts can go on to form stable MICA modifications in an inter- and intramolecular fashion with abundant or proximal guanidines, respectively. Finally, we discovered that intracellular MICA-glutathione metabolites are recognized and exported by the efflux pump MRP1, providing a parallel and perhaps complementary pathway for MGO detoxification working alongside the glyoxalase pathway. These data provide new insights into the plausible reactions involving MGO in cells and tissues, as well as several new molecular species in proteins and metabolites for further study.

It is widely accepted that the use of alkyl zinc and alkyl zinc alkoxide precursors are usually preferred instead of the popularly used zinc acetate precursor to obtaining better control on the synthesis of different zinc-oxo clusters and nanostructures. However, there are very few reports about zinc dialkoxides precursors and not many ones studying these precursors in a typical hydrolysis-condensation route. In the present report, we focus on the study of zinc dimethoxide structural features and their Raman spectroscopy signatures in the absence and presence of tetrahydrofuran (THF) adduct. Our theoretical calculations using Density Functional Theory (DFT) reveal that monomeric, dimeric and trimeric zinc dimethoxide exhibit distinctive Raman signatures, particularly at the low frequency region. In addition, some particular vibrational modes of zinc dimethoxide also evidenced some characteristic shifting and splitting in the presence of explicit THF coordination molecules. Our experimental approach using surface-enhanced Raman spectroscopy (SERS) reveals a quite complex combination of Raman signatures associated to zinc dimethoxide clusters corroborating tetrahydrofuran coordination and further early hydrolysis-condensation scenario. We aim to shed some light on the chemical structure of this particular zinc dimethoxide precursor and some of its early hydrolysis-condensation products employing a powerful, popular and versatile technique such as Raman spectroscopy as it can be a promising candidate to access and simultaneously monitor the formation of novel zinc-oxo clusters and nanostructures.

Diels–Alder chemistry is a well-explored avenue for the synthesis of bioactive materials; however, its potential applications have recently expanded following the development of reactions that can be performed in buffered aqueous environments at low temperatures, including fulvene–maleimide [4 + 2] cycloadditions. In this study, we synthesized two novel amine-reactive fulvene linkers to demonstrate the application of this chemistry for generating mass spectrometry-cleavable labels (“mass tags”), which can be used for the labeling and detection of proteins. Successful conjugation of these linkers to maleimide-labeled peptides was observed at low temperatures in phosphate-buffered saline, allowing the non-destructive modification of proteins with such mass tags. The labile nature of fulvene–maleimide adducts in the gas phase also makes them suitable for both matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometric analysis. Unlike previous examples of MALDI mass tags, we show that fulvene–maleimide cycloaddition adducts fragment predictably upon gas-phase activation without the need for bulky photocleavable groups. Further exploration of this chemistry could therefore lead to new approaches for mass spectrometry-based bioassays. Refereed/Peer-reviewed

The Diels–Alder reaction of N-benzylcytisine with N-methyl- and N-benzylmaleimides is 100% endo-selective and gives the corresponding syn- and anti-diastereomers in 11–42% isolated yields. The studies of the reaction progress with LCMS and NMR along with detailed quantum chemical calculations revealed that some Diels–Alder adducts are kinetically and their isomers are thermodynamically controlled products. The Pd/C-catalyzed hydrogenation of benzyl-protected cytisine amine derivatives resulted in the removal of the benzyl group and the addition of hydrogen to the C=C double bond to give the corresponding secondary amines in 45–84% yield. The complete reduction of carbonyl groups in a cytisine derivative with LiAlH4 in THF under reflux afforded the respective tricyclic triamine. Quantum mechanical calculations for the mechanism of the Diels–Alder reaction between the simplest model compounds are presented.

This communication reports experimental and theoretical evidences of σ‐hole interactions in adducts between nitrogen or oxygen nucleophiles and tetroxides of osmium or other group 8 elements. Cocrystals between pyridine or pyridine N‐oxide derivatives and osmium tetroxide are characterized through various techniques and rationalized as σ‐hole interactions using DFT calculations and several other computational tools. We propose the term “osme bond” (OmB, Om=Fe, Ru, Os, (Hs)) for naming the noncovalent interactions wherein group 8 elements have the role of the electrophile. The word osme is the transcription of ὀσμή, the ancient Greek word for smell that was used to name the heaviest group 8 element in relation to the smoky odor of its tetroxide., σ‐Hole interactions in adducts between nitrogen or oxygen nucleophiles and tetroxides of osmium or other group 8 elements are reported. Cocrystals between pyridine or pyridine N‐oxide derivatives and osmium tetroxide are characterized through various techniques including computational tools. We propose the term “osme bond” (OmB, Om=Fe, Ru, Os, (Hs)) for naming the noncovalent interactions wherein group 8 elements have the role of the electrophile.

Sterically hindered Lewis acid and base centers are unable to form Lewis adducts, instead forming frustrated Lewis pairs (FLPs), where latent reactivity can be utilized for the activation of small molecules. Applying FLP chemistry into polymeric frameworks transforms this chemistry into responsive and functional materials. Here, we report a versatile synthesis strategy for the preparation of macromolecular FLPs and explore its potential with the ring-opening reactions of cyclic ethers. Addition of the cyclic substrates triggered polymer network formation, where the extent of cross-linking, strength of network, and reactivity are tuned by the steric and electronic properties of the ethers. The resultant networks behave like covalently cross-linked polymers, demonstrating the versatility of FLPs to simultaneously tune both small-molecule capture and mechanical properties of materials.

Lewis-base coordinated iminoborane adducts, in contrast to their isoelectronic analogue imines, remain largely unexplored given the lack of efficient synthetic strategies for generating robust compounds. Herein, we report the preparation of a cyclic amino iminoborane carbene complex 2 obtained in quantitative yield by adding NHC to the 1,8-(trimethylsilyl)aminonaphthalene complex of boron 1 to induce the elimination of trimethylsilyl chloride (TMSCl). The iminoborane-NHC adduct 2 shows unprecedented thermal stability both in the solid and solution phases, due to the rigid, pre-established geometry of the 1,8-diaminonaphthalene scaffold. Theoretical calculations reveal an exceptionally strong iminoborane-NHC bond as a consequence of the enhanced boron-center acidity in combination with the lower steric and electronic shielding. We show that the chemical bond can be understood as donor-acceptor interaction, leading to a different kind of electronic situation of the B═N π-bond. The high conjugation between the pz-lone pair of the tricoordinated sp2 hybridized N atom and the B═N π-system results in a particularly long B═N double bond distance. Taking advantage of the pendant lone pair of the dicoordinated sp2 hybridized N atom, the iminoborane-NHC adduct gives access to NHC-stabilized borenium cation 3 through the reaction with trimethylsilyl triflate (Me3SiOTf) or to the gallium adduct 4 by reacting with GaCl3. Incorporating an iminoborane functional group into a π-conjugated system brings a new bonding situation for broadening the scope of BN-containing polyaromatic systems.

o-Carbonyl arylboronic acids such as 2-formylphenylboronic acid (2-FPBA) are employed in biocompatible conjugation reactions with the resulting iminoboronate adduct stabilized by an intramolecular N-B interaction. However, few studies have utilized these reagents as active site-directed enzyme inhibitors. We show that 2-FPBA is a potent reversible, slow-onset inhibitor of mandelate racemase (MR), an enzyme that has served as a valuable paradigm for understanding enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKa. Kinetic analysis of the progress curves for the slow onset of inhibition of wild-type MR using a two-step kinetic mechanism gave Ki and Ki* values of 5.1 ± 1.8 and 0.26 ± 0.08 μM, respectively. Hence, wild-type MR binds 2-FPBA with an affinity that exceeds that for the substrate by ∼3000-fold. K164R MR was inhibited by 2-FPBA, while K166R MR was not inhibited, indicating that Lys 166 was essential for inhibition. Unexpectedly, mass spectrometric analysis of the NaCNBH3-treated enzyme-inhibitor complex did not yield evidence of an iminoboronate adduct. 11B nuclear magnetic resonance spectroscopy of the MR·2-FPBA complex indicated that the boron atom was sp3-hybridized (δ 6.0), consistent with dative bond formation. Surprisingly, X-ray crystallography revealed the formation of an Nζ-B dative bond between Lys 166 and 2-FPBA with intramolecular cyclization to form a benzoxaborole, rather than the expected iminoboronate. Thus, when o-carbonyl arylboronic acid reagents are employed to modify proteins, the structure of the resulting product depends on the protein architecture at the site of modification.

2- and 4-(Arylmethylideneamino)phenols react with Reformatsky reagent, obtained from methyl 1-bromocyclohexanecarboxylate and zinc, to form 3-aryl-2-[2-(or 4-)hydroxyphenyl]-2-azaspiro[3.5]nonan-1-ones. The reaction involves the initial addition of the organozinc reagent across the C=N double bond of the Schiff base and the subsequent intramolecular cyclization of the adduct via the nucleophilic attack of the nitrogen atom on the ester carbonyl carbon atom. The structures of the products were confirmed by X-ray diffraction analysis.

Structural determination of N-glycans by mass spectrometry is ideally performed by negative ion collision-induced dissociation because the spectra are dominated by cross-ring fragments leading to ions that reveal structural details not available by many other methods. Most glycans form [M – H]- or [M + adduct]- ions but larger ones (above approx. m/z 2000) typically form doubly charged ions. Differences have been reported between the fragmentation of singly and doubly charged ions but a detailed comparison does not appear to have been reported. In addition to [M + adduct]- ions (this paper uses phosphate as the adduct) other doubly, triply, and quadruply charged ions of composition [Mn + (H2PO4)n]n- have been observed in mixtures of N-glycans released from viral and other glycoproteins. This paper explores the formation and fragmentation of these different types of multiply charged ions with particular reference to the presence of diagnostic fragments in the CID spectra and comments on how these ions can be used to characterize these glycans. Graphical abstract

There is a significant need to develop more rapid and efficient routes to styrene derivatives, since they are extensively used in polymer sciences. This manuscript reports a one-pot synthesis of an array of α-alkyl styrene derivatives from readily available natural products (i.e., estragole and safrole). This method is regioselective, producing a rearranged adduct, under transition metal-free conditions. This methodology has broad nucleophile scope, even tolerating sterically hindered nucleophiles; it is general for carbon, nitrogen, oxygen, and sulfur nucleophiles.

Anionic Diels-Alder chemistry of electron-deficient cross-conjugated vinylogous alkenones, providing highly stable sodium dienolate ion pairs as electron-rich dienes in the presence of a weak sodium base in THF, has been newly developed, leading to a single Diels-Alder adduct, in racemic form, in moderate to high yields (up to 97%, 37 examples).

The mechanism of the aluminum-mediated hydroboration of terminal alkynes was investigated using a series of novel aluminum amidinate hydride and alkyl complexes bearing symmetric and asymmetric ligands. The new aluminum complexes were fully characterized and found to facilitate the formation of the (E)-vinylboronate hydroboration product, with rates and orders of reaction linked to complex size and stability. Kinetic analysis and stoichiometric reactions were used to elucidate the mechanism, which we propose to proceed via the initial formation of an Al-borane adduct. Additionally, the most unstable complex was found to promote decomposition of the pinacolborane substrate to borane (BH3), which can then proceed to catalyze the reaction. This mechanism is in contrast to previously reported aluminum hydride-catalyzed hydroboration reactions, which are proposed to proceed via the initial formation of an aluminum acetylide, or by hydroalumination to form a vinylboronate ester as the first step in the catalytic cycle., This work focuses on the synthesis and characterization of a series of aluminum amidinate hydride and alkyl complexes. The compounds have been studied as hydroboration catalysts for the reaction of HBpin and phenylacetylene, and detailed kinetic and mechanistic investigations were carried out to elucidate possible reaction mechanisms. We propose the reaction to proceed via a HBpin adduct, in contrast to related literature on aluminum-catalyzed hydroboration reactions.

Molecular switching plays a critical role in biological and displaying systems. Donor-acceptor Stenhouse adducts (DASAs) is a newly re-discovered series of switchable photochromes, and light is the most used approach to control its switching behavior. In this report, we speculated that hydrophobic binding pockets of biologically relevant peptides/proteins could be harnessed to alter its switching behavior without the assistance of light. We designed and synthesized a DASA compound SHA-2, and we demonstrated that the Aβ40 species could stabilize SHA-2 in the linear conformation and decrease the rate of molecular switching via fluorescence spectral studies. Moreover, molecular dynamics simulation revealed that SHA-2 could bind to the hydrophobic fragment of the peptide and resulted in substantial changes in the tertiary structure of Aβ40 monomer. This structural change is likely to impede the aggregation of Aβ40, as evidenced by the results from thioflavin T fluorescence and ProteoStat aggregation detection experiments. We believe that our study opens a new window to alter the switching behavior of DASA via DASA-peptide/protein interactions.

Tegumental carbonic anhydrase from the worm Schistosoma mansoni (SmCA) is considered a new anti-parasitic target because suppressing its expression interferes with schistosome metabolism and virulence. Here, we present the inhibition profiles of selenoureido compounds on recombinant SmCA and resolution of the first X-ray crystal structures of SmCA in adduct with a selection of such inhibitors. The key molecular features of such compounds in adduct with SmCA were obtained and compared to the human isoform hCA II, in order to understand the main structural factors responsible for enzymatic affinity and selectivity. Compounds that more specifically inhibited the schistosome versus human enzymes were identified. The results expand current knowledge in the field and pave the way for the development of more potent antiparasitic agents in the near future.

The pharmacological profile of medicinally relevant Ru(III) coordination compounds has been ascribed to their interactions with proteins, as several studies have provided evidence that DNA is not the primary target. In this regard, numerous spectroscopic and crystallographic studies have indicated that the Ru(III) ligands play an important role in determining the metal binding site, acting as the recognition element in the early stages of the protein-complex formation. Herein, we present a series of near-atomic-resolution X-ray crystal structures of the adducts formed between the antimetastatic metallodrug imidazolium trans-[tetrachlorido(S-dimethyl sufoxide)(1H-imidazole)ruthenate(III)] (NAMI-A) and hen egg-white lysozyme (HEWL). These structures elucidate a series of binding events starting from the noncovalent interaction of intact NAMI-A ions with HEWL (1.5 h), followed by the stepwise exchange of all Ru ligands except for 1H-imidazole (26 h) to the final "ruthenated" protein comprising one aquated Ru ion coordinated to histidine-15 of HEWL (98 h). Our structural data clearly support a two-step mechanism of protein ruthenation, illustrating the ligand-mediated recognition step of the process.

Donor-Acceptor Stenhouse Adducts: a novel type of photoswitchable compounds that consist of donors, acceptors, and trienol-enol bridges, have gained great attention for their unique light responsiv...

Iodide-adduct chemical ionization mass spectrometry (I-CIMS) is a widely used technique in the atmospheric chemistry community to detect oxygenated volatile organic compounds (OVOCs) in real time. In this work, we report the occurrence of secondary ion chemistry from interactions between a strong oxygen donor (such as O3 and peracids) and acidic OVOCs (such as carboxylic acids and organic hydroperoxides) in the ion-molecule reaction (IMR) region of I-CIMS. Such interactions can lead to acidic organic molecules (HA or HB) clustering with [IO]- (e.g., [HA + IO]-) and dimer adducts ([A + B + I]-), in addition to the well-known iodide clusters ([HA + I]-). This ion chemistry was probed using common chemical standards as well as the gas-phase oxidation products of α-pinene and isoprene in a flowtube reactor. The results show that secondary ion chemistry can lead to misinterpretations of molecular compositions and distributions of the gas-phase products and an overestimation of the elemental O/C ratio overall. Nevertheless, the varying degrees of signal change in response to the secondary ion chemistry might be a clue to inform OVOCs' functionalities. Specifically, in the α-pinene ozonolysis system, the extents of ion signal reduction in the presence of additional acids in the IMR suggest that C9H14O4 produced in the gas phase is a peracid, rather than the often-assumed pinic acid. Thus, we suggest that the potential application of the secondary ion chemistry to inform organic functionalities is promising, which could help better understand the molecular compositions of gas-phase OVOCs and the reaction mechanisms therein.

Most studies on SO2 capture using ionic liquids (ILs) have been carried out under mild conditions (e.g., about 1 bar of SO2 and 20–40 °C). However, these ILs only exhibit a fraction of their original SO2 uptake under harsher conditions, i.e., much lower SO2 partial pressure and evidently higher temperature (e.g., ≤0.2 mbar of SO2 and ≥110 °C). In this work, we screen 127 reported ILs for multi-molar SO2 absorption under the harsher conditions, covering nearly all the chemical space explored of the SO2 capturing IL. A unique cooperative anion-SO2 interaction mode with two forms (the insertion adduct and the ringed adduct) has been identified for branched anions, where SO2 acts as both acid and base to attack different reactive sites on anions. The simulated Langmuir isotherms further help screen out potential sorbents (amino-based branched singly charged anions with an Al atom as the center and carboxyl-based divalent anions) with both high overall capacity and high per-cycle absorption capacity. The energies of the reacting orbitals of the anions are linearly correlated to their SO2 binding energies. This work provides new insights for the design of task-specific ILs under harsh conditions.

A synthesis of benzyl trisubstituted triptycenes is described. These triptycenes are precursors for producing a first generation (G1) poly(triptycylether) dendrimer, a derivative of known poly(arylether) dendrimers. The molecule necessary for the further elaboration into the eventual dendrimer is a carboxylic acid ester triptycene terminated with two ether substituents on another ring; the zero generation (G0). The synthesis begins with formation of the Diels-Alder adduct of benzoquinone and methyl 2-anthroate. This adduct is aromatized under basic conditions and the resulting anion trapped with a benzyl halide as an electrophile to form the trisubstituted triptycene. Access to the trisubstituted system is obtained through a highly improved, efficient and chromatography free preparation of anthracene derivatives, mainly methyl 2-anthroate.

The diastereoselectivity of adducts in the addition reaction via the Felkin-Anh model is affected significantly by the steric effect of bulky groups. However, the influence of steric alkyl chain length has not been studied for the diastereoselectivity. In this work, we present a new strategy for the racemic synthesis of β-methyl alcohols to obtain various diastereomer ratios using the Felkin-Anh model. The addition of alkyl Grignard reagents to α-methyl aldehydes afforded diastereomer ratios of threo/erythro ≈ 2:1, while the reduction in structurally related ketones using LiAlH4 afforded ratios of threo/erythro ≈ 1:1. The experimental data showed no effect of alkyl chain length on either side on the stereoselectivity of adducts. All synthesized analogues were evaluated for attractiveness to Rhynchophorus ferrugineus weevils in the field. Five novel derivatives, including two alcohols and three ketones, were found to attract weevils in the field trials. Among them, 3-methyldecan-4-one (5b) and 4-methyldecan-5-ol (11a) were found to be the most attractive to the insects.

A complex role for chlorine radicals Radicals are atoms or molecules that are highly reactive because they have an unpaired electron. A common means of investigating whether they are involved in a particular reaction is to try to trap them with an acceptor compound. Yang et al. reinvestigated a photoinduced alkane oxidation reaction for which a trapping study had previously implicated alkoxy radicals. Their spectroscopic, kinetic, and isotopic labeling studies revealed that chlorine, rather than alkoxy, was the key radical intermediate; the prior trapping results had stemmed from its complexation with alcohols. Science , abd8408, this issue p. 847

Human exposure to aromatic amines (AAs) can result in carcinogenic DNA adducts. To complement previous work geared toward understanding the mutagenicity of AA-derived adducts, which has almost exclusively studied (monoadducted) DNA containing a single lesion, the present work provides the first in-depth comparison of the structure of monoadducted and diadducted DNA duplexes. Specifically, molecular dynamics (MD) simulations were initially performed on DNA containing the nonmutagenic single-ringed N-(deoxyguanosin-8-yl)-aniline (ANdG) or the mutagenic four-ringed N-(deoxyguanosin-8-yl)-1-aminopyrene (APdG) lesion at G1, G2, or G3 in the AA deletion hotspot (5'-G1G2CG3CC) in the anti or syn glycosidic orientation (B/S duplex conformation). Subsequently, diadducted strands were assessed that span each combination of damaged sites (G1G2 (nearest neighbors), G2G3 (next-nearest neighbors), and G1G3 (two intervening nucleotides)) and anti/syn lesion glycosidic orientations. Despite other N-linked C8-dG adducts exhibiting sequence dependence conformational heterogeneity, a single ANdG or APdG lesion induces helical conformational homogeneity that is exclusively controlled by aryl moiety size. However, the preferred damaged DNA conformation can change upon the addition of a second adduct depending on lesion separation, with neighboring lesions stabilizing a nonmutagenic conformation and next-nearest damaged sites stabilizing a promutagenic conformation regardless of adduct size. As a result, diadducted DNA is found to adopt conformations that are unfavored for the corresponding monoadducted system, pointing to differential replication and repair outcomes for diadducted DNA compared to those for monoadducted DNA. Thus, although the toxicity of monoadducted DNA is most significantly dictated by lesion size, the toxicity can increase or decrease upon a second damaging event depending on lesion size and relative position. Overall, our work adds the number of lesions and their spatial separation to the growing list of factors that determine the structure and biological outcomes of adducted DNA.

Covalent functionalization of two‐dimensional molybdenum disulfide (2D MoS2) holds great promise in developing robust organic‐MoS2 hybrid structures. Herein, for the first time, we demonstrate an approach to building up a bisfunctionalized MoS2 hybrid structure through successively reacting activated MoS2 with alkyl iodide and aryl diazonium salts. This approach can be utilized to modify both colloidal and substrate supported MoS2 nanosheets. We have discovered that compared to the adducts formed through the reactions of MoS2 with diazonium salts, those formed through the reactions of MoS2 with alkyl iodides display higher reactivity towards further reactions with electrophiles. We are convinced that our systematic study on the formation and reactivity of covalently functionalized MoS2 hybrids will provide some practical guidance on multi‐angle tailoring of the properties of 2D MoS2 for various potential applications., For the first time, we demonstrate an approach to building up a bisfunctionalized MoS2 hybrid structure through successively treating activated MoS2 with alkyl iodide and aryl diazonium salt. This approach can be used to modify both colloidal and substrate‐supported MoS2 nanosheets.

Graphical abstract The position and configuration of carbon-carbon double bonds in unsaturated fatty acids is crucial for their biological functions and influences health and disease. However, double bond isomers are not routinely distinguished by classical mass spectrometry workflows. Instead, they require sophisticated analytical approaches usually based on chemical derivatization and/or instrument modification. In this work, a novel strategy to investigate fatty acid double bond isomers (18:1) without prior chemical treatment or modification of the ion source was implemented by non-covalent adduct formation in the gas phase. Fatty acid adducts with sodium, pyridinium, trimethylammonium, dimethylammonium, and ammonium cations were characterized by a combination of cryogenic gas-phase infrared spectroscopy, ion mobility-mass spectrometry, and computational modeling. The results reveal subtle differences between double bond isomers and confirm three-dimensional geometries constrained by non-covalent ion-molecule interactions. Overall, this study on fatty acid adducts in the gas phase explores new avenues for the distinction of lipid double bond isomers and paves the way for further investigations of coordinating cations to increase resolution. Supplementary Information The online version contains supplementary material available at 10.1007/s00216-021-03334-3.

Donor-Acceptor Stenhouse Adducts (DASAs) are molecular photoswitches that reversibly isomerize from a linear to a cyclized form upon visible light irradiation. In the cyclized form, these molecules selectively react with a thiol in a thiol-Michael addition. Driven by the complexity of the switching mechanism and chemical properties of DASAs, the effect of concentration (ranging from 1 to 5 mM DASA) on the thiol-Michael addition was investigated. We find that the rate limiting step in the reaction is the photochemically induced DASA isomerization, as higher concentrations of thiol do not alter the rate at which the thiol-Michael adduct (TMA) is formed. Moreover, the kinetics of the product formation were found to be more significantly affected by irradiation at higher concentrations. In two distinct scenarios, where either the concentration or the molar equivalence of the reaction partner was kept constant, the TMA was found to be more efficiently formed under irradiation at higher concentrations. These findings indicate that the DASA reactivity towards thiol-Michael reactions appear to be equilibrium-driven at lower concentrations and light-driven at higher concentrations.

The SARS-CoV-2 pandemic has triggered global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro), critical for viral replication, is a key target for therapeutic development. An organoselenium drug called ebselen has been demonstrated to have potent Mpro inhibition and antiviral activity. We have examined the binding modes of ebselen and its derivative in Mpro via high resolution co-crystallography and investigated their chemical reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were observed for a number of derivatives. A free selenium atom bound with cysteine of catalytic dyad has been revealed in crystallographic structures of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct and formation of a phenolic by-product, confirmed by mass spectrometry. The target engagement with selenation mechanism of inhibition suggests wider therapeutic applications of these compounds against SARS-CoV-2 and other zoonotic beta-corona viruses., Ebselen is an organoselenium drug that inhibits the SARS-CoV-2 main protease (Mpro). Here, the authors co-crystallised Mpro with ebselen and an ebselen derivative and observed an enzyme bound organoselenium covalent adduct in the crystal structures, which was also confirmed by mass spectrometry analysis.

Two new pharmacologically active series of N-alkyne-substituted indole–thiazoles and C-alkyne-substituted benzylidene–thiazoles were synthesized by a two-step procedure involving initial reactions of thiosemicarbazide with, respectively, [1-(prop-2-yne-1-yl)oxy)-1H-indol-3-yl]formaldehyde and 2-(prop-2-yne-1-yloxy)benzaldehyde, followed by the reactions of the resulting hydrazine-1-carbothioamides with a variety of substituted phenacyl bromides. The synthesized adducts composition and structure were established by elemental analysis and IR and 1H and 13C NMR spectroscopy and mass spectrometry. In vitro antidiabetic activity screening by the α-amylase inhibition assay with Acarbose as a reference drug revealed an excellent antidiabetic potency in four-terminal alkyne-substituted benzylidene–and indole–thiazoles derived from dichloro- and bromophenacyl bromides.

Cyanoacetylenic alcohols, R1R2C(OH)C≡C–CN, the closest derivatives of cyanoacetylene, an abundant interstellar molecule, are now becoming important compounds in the area of modern organic synthesis that tends to mimic Nature. The presence of highly reactive C≡C and C≡N bonds in close proximity to a hydroxy group endows cyanoacetylenic alcohols with a chemical trinity of mutually influencing functions, leading to a myriad number of chemical transformations. All reactions of cyanoacetylenic alcohols parallel modern organic synthesis, whilst being biomimetic. To react, they do not need transition metals (and in most cases, no metals at all, except for physiologically indispensable Na+ and K+), proceed at ambient temperature and often in aqueous media. Fundamentally, their reactions are 100% atom-economic because they are almost exclusively addition processes. Typically, the cyano, acetylene and hydroxy functions of cyanoacetylenic alcohols behave as an inseparable entity, leading to reaction products with multiple functional groups. This allows hydroxy, carbonyl, carboxylic, imino, amino, amido, cyanoamido, cyano, various P-containing, ether and ester functions, along with double bonds, different fundamental heterocycles (furans, furanones, pyrazoles, oxazoles, pyridines, pyrimidines, purines, etc.) and diverse polycyclic systems to be integrated in a single molecular architecture. This review focuses on an analysis and generalization of the knowledge that has accumulated on the chemistry of cyanoacetylenic alcohols, mostly over the past 15 years.1 Introduction2 Nucleophilic Addition to Cyanoacetylenic Alcohols and Subsequent Transformations of the Adducts3 Annulation with Nonaromatic Nitrogen Heterocycles4 Annulation with Aromatic Nitrogen Heterocycles5 Modification of Amino Acids6 Modifications of Nucleobases7 Modification of Nucleosides8 Conclusion

Terminal unactivated alkynes are nowadays considered the golden standard for cysteine-reactive warheads in activity-based probes (ABPs) targeting cysteine deubiquitinating enzymes (DUBs). In this work, we study the versatility of the thiol-alkyne addition reaction in more depth. Contrary to previous findings with UCHL3, we now show that covalent adduct formation can progress with substituents on the terminal or internal alkyne position. Strikingly, acceptance of alkyne substituents is strictly DUB-specific as this is not conserved among members of the same subfamily. Covalent adduct formation with the catalytic cysteine residue was validated by gel analysis and mass spectrometry of intact ABP-treated USP16CD(WT) and catalytically inactive mutant USP16CD(C205A). Bottom-up mass spectrometric analysis of the covalent adduct with a deuterated propargyl ABP provides mechanistic understanding of the in situ thiol-alkyne reaction, identifying the alkyne rather than an allenic intermediate as the reactive species. Furthermore, kinetic analysis revealed that introduction of (bulky/electron-donating) methyl substituents on the propargyl moiety decreases the rate of covalent adduct formation, thus providing a rational explanation for the commonly lower level of observed covalent adduct compared to unmodified alkynes. Altogether, our work extends the scope of possible propargyl derivatives in cysteine targeting ABPs from unmodified terminal alkynes to internal and substituted alkynes, which we anticipate will have great value in the development of ABPs with improved selectivity profiles.