Using tandem mass spectrometry to predict chemical transformations of 2-pyrimidinyloxy-N-arylbenzyl amine derivatives in solution

Design, step-economical diversity-oriented synthesis of an N-heterocyclic library containing a pyrimidine moiety: discovery of novel potential herbicidal agents

The synthesis of highly diverse libraries has become of paramount importance for obtaining novel leads for drug and agrochemical discovery. Herein, the step-economical diversity-oriented synthesis of a library of various pyrimidine-N-heterocycle hybrids was developed, in which a 4,6-dimethoxypyrimidine core was incorporated into nine kinds of N-heterocycles. A total of 34 structurally diverse compounds were synthesized via a two-step process from very simple and commercially available starting materials. Further, in vivo biological screening of this library identified 11 active compounds that exhibited good post-emergence herbicidal activity against D. sanguinalis at 750 g ai per ha. More importantly, pyrimidine-tetrahydrocarbazole hybrid 5q showed good to excellent herbicidal activity against five test weeds at the same dosage. Pyrimidine-tetrahydrocarbazole hybrids represent a novel class of herbicidal agents that may become promising lead compounds in the herbicidal discovery process.

Mass Spectrometry-Based Discovery of New Chemical Scaffold Rearrangement Ions: Aza-biphenylene as a Novel Potent Biradical Agent in Cancer Chemotherapy

Discovery of a new drug is time-consuming, laborious, and expensive. Herein, a novel integrative strategy for discovering potential new lead compounds has been developed, which was based on the characteristics of mass spectrometry (MS). MS was used to predict the potential forced degradation products (DPs) and metabolites of drugs by electrospray ionization and collision-induced dissociation (CID). Special rearrangement ions representing unique predicted DPs and metabolites were identified. The consistency between the predicted and the measured results was proven by in vitro metabolism and forced degradation of a commercial drug, respectively. From this, new chemical scaffold rearrangement ions named (aza)-biphenylenes, as potent anticancer agents, were discovered. As a representative aza-biphenylene analogue, 2-azabiphenylene was proven in vitro to induce apoptosis and inhibit the growth of various human cancer cells in a dose-dependent manner. Surprisingly, 2-azabiphenylene exhibited the best comparable bioactivity with the positive control sorafenib, but showed significantly lower in vitro cytotoxicity than sorafenib (at least a 5-fold decrease in cytotoxicity) because it could be targeted to the tumor microenvironment at low pH. A biradical mechanism accompanied by a mitochondrion-dependent oxidative stress mechanism was proposed to explore its anticancer mechanism. The highly reactive intermediate aza-biphenylenediyl worked as an active pharmaceutical ingredient and induced apoptosis of cancer cells. This provided the basis for the potential applications of CID-induced special rearrangement ions in developing new lead compounds.

Protonation of Curcumin Triggers Sequential Double Cyclization in the Gas-Phase: An Electrospray Mass Spectrometry and DFT Study

ESI-protonated natural curcumin (1) undergoes gas-phase cyclization and dissociates via competitive expulsions of 2-methoxy phenol and C₄H₄O₂ (diketene or an isomer). Evidence from mechanistic mass spectrometry and from Density Functional Theory (DFT) reveals that a two-step sequential cyclization occurs for the protonated molecule prior to the unusual loss of the elements of 2-methoxy phenol. Furthermore, the presence of the methoxy group at postion-3 is essential for the second cyclization. The transformation of curcumin upon protonation in the gas phase may be predictive of its solution chemistry and explain how curcumin plays a protective role in biology.

Pomeranz-Fritsch Synthesis of Isoquinoline: Gas-Phase Collisional Activation Opens Additional Reaction Pathways

We have investigated the gas-phase production of isoquinoline by performing collisional activation on benzalaminoacetal, the first intermediate in the classic solution-phase Pomeranz-Fritsch synthesis of isoquinoline. We have elucidated the reaction pathways in the gas phase using tandem mass spectrometry. Unlike the corresponding condensed-phase reaction, where catalytic proton exchange between intermediate(s) and solvent (Brønsted-Lowry base) is known to drive the reaction, the gas-phase reaction follows the "mobile proton model" to form the products via a number of intermediates, some the same as in their condensed-phase counterparts. Energy-resolved mass spectrometry, deuterium labeling experiments, and theoretical calculations (B3LYP/6-31G**) identified 27 different reaction routes in the gas phase, forming a complex interlinked reaction network. The experimental measurements and theoretical calculations confirm the proton hopping onto different basic sites of the precursors and intermediates to transform them ultimately into isoquinoline.

An unexpected acid-catalyzed decomposition reaction of cilnidipine and pranidipine to the decarboxylative bridged tricyclic products via cascade rearrangements

A gas-phase Carroll rearrangement occurring during electrospray ionization tandem mass spectrometry led to the discovery of bridged tricyclic degradation products from cilnidipine and pranidipine.

Gas-phase fluorine migration reactions in the radical cations of pentafluorosulfanylbenzene (Aryl-SF₅) and benzenesulfonyl fluoride (Aryl-SO₂F) derivatives and in the 2,5-xylylfluoroiodonium ion

The gas-phase reactions of Aryl-SF5(·+) and Aryl-SO2F(·+) have been studied with the electron ionization tandem mass spectrometry. Such reactions involve F-atom migration from the S-atom to the aryl group affording the product ion Aryl-F(·+) by subsequent expulsion of SF4 or SO2, respectively. Especially, the 4-pentafluorosulfanylphenyl cation 4-SF5C6H4(+) (m/z 203) from 4-NO2C6H4SF5(·+) by loss of ·NO2 could occur multiple F-atom migration reactions to the product ion C6H4F3(+) (m/z 133) by loss of SF2 in the MS/MS process. The gas-phase reactions of 2,5-xylylfluoroiodonium (pXyl-I(+)F, m/z 251) have also been studied using the electrospray tandem mass spectrometry, which involve a similar F-atom migration process from the I-atom to the aryl group giving the radical cation of 2-fluoro-p-xylene (or its isomer 4-fluoro-m-xylene, m/z 124) by reductive elimination of an iodine atom. All these gas-phase F-atom migration reactions from the heteroatom to the aryl group led to the aryl-F coupling product ions with a new formed C(Aryl)-F bond. Density functional theory calculations were performed to shed light on the mechanisms of these reactions.

Mass spectrometric study of the gas-phase difluorocarbene expulsion of polyfluorophenyl cations via F-atom migration

An increasing number of fluorinated drugs, pesticides, and fine chemicals are now produced and applied, especially those containing polyfluorinated aromatic moieties. However, at present, the extent of literature covering the special mass spectrometric behaviors of these compounds remains limited. Herein, we report an unexpected but also general gas-phase dissociation mode of polyfluorinated aromatics in mass spectrometry: expulsion of difluorocarbene (50-Da neutral loss). Results from accurate mass measurements, tandem mass spectrometric experiments, and density functional theory (DFT) calculations support an intramolecular F-atom “ring-walk” migration mechanism for gas-phase CF2 loss. Based on an assessment of the electron ionization-mass spectrometry (EI-MS) data of more than 40 polyfluorinated aromatic compounds from the National Institute of Standards and Technology data bank, we generalized on the substitution group effects on the difluorocarbene dissociation process of polyfluorinated aromatic compounds in EI-MS. These studies have enriched our knowledge of the special gas-phase reactivity of polyfluorinated aromatics and will provide valuable information in further analytical research of these compounds by mass spectrometry.

Fragmentation of deprotonated diacylhydrazine derivatives in electrospray ionization tandem mass spectrometry: generation of acid anions via intramolecular rearrangement

The gas-phase fragmentation pathways of deprotonated diacylhydrazine derivatives (R1(C = O)-N(t-Bu)NH(C = O)R2, Compounds 1-6) were investigated by the combination of electrospray ionization tandem mass spectrometry (ESI-MS/MS) and theoretical calculations. Upon collisional activation, the deprotonated molecular ions [M - H](-) dissociate in two reaction channels, both of which involve intramolecular rearrangement. The main product ion is confirmed to be an anionic acid species, [R1-CO2](-), generated through intramolecular rearrangement of [M - H](-) initiated by the nucleophilic attack of the amide O6 on the carbonyl C2 (Path-1). The minor fragment channel (Path-2) involves methylpropene elimination of the precursor ion, followed by a similar nucleophilic displacement reaction to produce another acid anion [R2-CO2](-). Density functional theory calculations at the B3LYP/6-31+G(d,p) level indicate that Path-1 is more favorable than Path-2 for dissociation of the deprotonated halofenozide.

Study of the gas-phase intramolecular aryltrifluoromethylation of phenyl(trifluoromethyl)iodonium by ESI-MS/MS

The gas-phase reactions of the reactive λ(3)-phenyl(trifluoromethyl)iodonium (PhI(+)(III)CF3, 1 at m/z 273) to the radical cation of iodobenzene (PhI(•+), 2 at m/z 204) via the loss of ·CF3 and the radical cation of trifluoromethylbenzene (PhCF3(•+), 3 at m/z 146) via the loss of ·I, were studied by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Interestingly, the gas-phase intramolecular coupling reaction of CF3 with phenyl via the CF3 migration process of 1 at m/z 273 from iodine to the phenyl to give 3 at m/z 146 could only occur according to an intramolecular aromatic substitution mechanism. Density functional theory (DFT) calculations showed that the gas-phase intramolecular aryltrifluoromethylation of 1 at m/z 273 to 3 at m/z 146 occurred via a Meisenheimer complex intermediate (MC), where the triplevalent I center of 1 was reduced to monovalent I. Most importantly, the structure of 3 at m/z 146 derived from 1 at m/z 273 in ESI-MS/MS process was confirmed by comparison of its MS/MS with that of an authentic PhCF3(•+) at m/z 146 acquired from the electron ionization (EI)-MS/MS analysis of PhCF3. Thus, our studies revealed the intrinsic reactivity tendencies of λ(3)-phenyl(trifluoromethyl)iodonium under solvent-free conditions.

Gas phase decarbonylation and cyclization reactions of protonated N-methyl-N-phenylmethacrylamide and its derivatives via an amide Claisen rearrangement

Gas phase decarbonylation and cyclization reactions of protonated N-methyl-N-phenylmethacrylamide and its derivatives (M·H(+)) were studied by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). MS/MS experiments of M·H(+) showed product ions were formed by loss of CO, which could only occur with an amide Claisen rearrangement. Mechanisms for the gas phase decarbonylation and cyclization reactions were proposed based on the accurate m/z measurements and MS/MS experiments with deuterated compounds. Theoretical computations showed the gas phase Claisen rearrangement was a major driving force for initiating gas phase decarbonylation and cyclization reactions of M·H(+). Finally, the influence of different phenyl substituents on the gas phase Claisen rearrangement was evaluated. Electron-donating groups at the para-position of the phenyl moiety promoted the gas phase Claisen rearrangement to give a high abundance of fragment ions [M - CO + H](+). By contrast, electron-withdrawing groups on the phenyl moiety retarded the Claisen rearrangement, but gave a fragment ion at m/z 175 by loss of neutral radicals of substituents on the phenyl, and a fragment ion at m/z 160 by further loss of a methyl radical.

Gas phase chemistry of Li+ with amides: the observation of LiOH loss in mass spectrometry

Collision-induced dissociation (CID) of Li(+) adducts of three sets of compounds that contains an amide bond, including 2-(4, 6-dimethoxypyrimidin-2-ylsulfanyl)-N-phenylbenzamide, its derivatives and simpler structures was investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Observed fragment ions include those that reflect loss of LiOH. Other product ions result from the Smiles rearrangement and direct C-S bond cleavage. MS/MS of H/D exchange products demonstrated occurrence of a 1,3-H shift from the amide nitrogen atom to the phenyl ring of these compounds. The LiOH loss from Li(+) adducts of amides was further examined by CID of [M + Li](+) ions of N-phenylbenzamide and N-phenylcinnamide. Loss of LiOH was essentially the sole fragmentation reaction observed for the former. For the latter, both losses of LiOH and H(2)O were discovered. The presence of electron-donating substituents of the phenyl ring of these compounds was found to facilitate elimination of LiOH, while that loss was retarded by electron-withdrawing substituents. Proposed fragment ion structures were supported by elemental compositions deduced from ultrahigh resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR-MS/MS) m/z value determinations. Density functional theory-based (DFT) calculations were performed to evaluate potential mechanisms for these reactions.

Studies on CH3CN-assisted decomposition of 1st Grubbs catalyst by electrospray ionization tandem mass spectrometry

The CH(3)CN-assisted decomposition reaction of the 1(st) Grubbs catalyst (1) was studied using electrospray ionization tandem mass spectrometry (ESI-MS/MS). We detected a series of Ru-intermediates and decomposition products by off-line and on-line ESI-MS(/MS) monitoring of the decomposition process. In particular, an on-line microreactor method was applied with ESI-MS/MS to profile the change and relationship of various Ru-intermediates by controlling the reaction within the first 30 s of its time scale. The main fast decomposition mechanism of Ru-catalyst 1 in the presence of CH(3)CN was similar to that proposed by Grubbs, and this was confirmed by detecting the (PhCH(2)PCy(3))(+) ion at m/z 371 as the major decomposition products with ESI-MS. We also studied the time evolution of the transient reactive Ru-intermediate ions step by step with ESI-MS/MS and detected the C-H bond activation products of toluene--dehydrogenated PCy(3), such as P(Cy)(2)(C(6)H(9)), P(Cy)(2)Ph--by analyzing the decomposition reaction solution by gas chromatography (GC)/MS. The mechanism of another minor decomposition pathway involving the phosphine activation of catalyst 1 was proposed on the basis of the ESI-MS(/MS) interception and characterization of the transient reactive Ru-species in the decomposition reaction solution. Finally the coordination effect of the CH(3)CN in assisting the decomposition and stabilizing the transient Ru-complexes is discussed.

Integration of high accuracy N-terminus identification in peptide sequencing and comparative protein analysis via isothiocyanate-based isotope labeling reagent with ESI ion-trap TOF MS

A multifunctional isothiocyanate-based isotope labeling reagent, [d (0)]-/[d (6)]-4,6-dimethoxy pyrimidine-2-isothiocyanate (DMPITC), has been developed for accurate N-terminus identification in peptide sequencing and comparative protein analysis by ESI Ion-trap TOF mass spectrometry. In contrast with the conventional labeling reagent phenyl isothiocyanate (PITC), DMPITC showed more desirable properties such as rapid labeling, sensitivity enhancement, and facilitating peptide sequencing. More significantly, DMPITC-based labeling strategy possessed the capacity of higher reliable N-terminus identification owning to the high-yield b(1) ion combined with the isotope validation of 6 Da. Meanwhile, it also showed potential in differentiating isomeric residues of leucine and isoleucine at N-terminus on the basis of the relative abundance ratios between the fragment ions of their respective b(1) ions. The strategy not only allows accurate interpretation for peptide but also ensures rapid and sensitive comparative analysis for protein by direct MS analysis. Using trypsin-digested bovine serum albumin (BSA), both peptide N-terminus identification and quantitative analysis were accomplished with high accuracy, efficiency, and reproducibility. The application of DMPITC-based labeling strategy is expected to serve as a promising tool for proteome research.

Studies of gas-phase reactions of cationic iron complexes of 2-pyrimidinyloxy-N-arylbenzylamines by electrospray ionization tandem mass spectrometry

Electrospray ionization triple quadrupole mass spectrometry (ESI-TSQ-MS) and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) were used to investigate the interesting gas-phase reactions of the cationic iron (Fe) complexes of 2-pyrimidinyloxy-N-arylbenzylamines (1-6), which are generated by ESI when mixing their methanolic solutions. Further studies of these Fe complexes by collision-induced dissociation (CID) show that Fe(III) complexes undergo an interesting gas-phase single electron transfer (SET) reaction to give 1(•+) -6(•+) ,with loss of neutral FeCl(2) , whereas Fe(II) can catalyze gas-phase Smiles rearrangement reactions of compounds 1-6. By using different Fe(II)X(2) salts (X = Cl or Br) with a set of reactants, the role of the counterion (X(-) ) and the structure effect of the reactants on Fe(II)-catalyzed gas-phase Smiles rearrangement reactions are studied. Evidence obtained from by TSQ-MS and FTICR-MS experiments, hydrogen/deuterium (H/D) exchange experiments and theoretical computations supported some unique gas-phase chemistries initiated by introduction of Fe(II) into 1. Importantly, by comparing the distinct gas-phase reaction results of the cationic Fe(III) complexes with those of Fe(II) complexes, the charge state effects of iron on the gas-phase chemistries of Fe complexes are revealed.

Investigation of coordination of Mg(II) cations to 2-pyrimidinyloxy-N-arylbenzylamines by electrospray mass spectrometry: insights for Mg(II) catalyzed Smiles rearrangement reactions

The CH(3)OH solutions of pyrimidinyloxy-N-arylbenzylamines (1-5) in the presence of Mg(II)X(2) salts (X = Cl or ClO(4)) were investigated by electrospray ionization mass spectrometry and tandem mass spectrometry (MS/MS) subsequently, showing that the cationic Mg(II) complexes 1-5·MgX(+) were important active complexes or intermediates for initiating interesting Smiles rearrangement reactions in both the gas and solution phases. By using different MgX(2) salts and selecting a set of reactants with different substitutes, the role of the counter-ion (X(-)) and the structure effect of the reactants on the Mg(II) catalyzed Smiles rearrangement reactions were studied. Moreover, the solvent effect on Mg(II) catalyzed Smiles rearrangement reactions was revealed by studying the CH(3)OH adduct complexes of 1-5·MgCl(+), which showed that the coordination of CH(3)OH to the Mg(II) center in the complexes decreased the reaction tendency. The mechanisms involved in the gas-phase Mg(II) catalyzed Smiles rearrangement reactions were proposed on the basis of MS/MS experiments and theoretical computations, showing some unique chemistries initiated by introducing Mg(II) into the template molecules.

Gas-phase synthesis of hydrodiphenylcyclopropenylium via nonclassical Favorskii rearrangement from alkali-cationized alpha,alpha'-dibromodibenzyl ketone

The gas-phase synthesis of hydrodiphenylcyclopropenylium from alkali-cationized alpha,alpha'-dibromodibenzyl ketone (1) via nonclassical Lewis-acid-induced Favorskii rearrangement has been studied by electrospray ionization/tandem mass spectrometry (ESI-MS/MS) and theoretical methods, showing that cations [1-Br](+) by debromination from 1 and 1.M(+)(M = Li or Na) by alkali-metal cationization of 1 could convert into the protonated diphenylcyclopropenone 2.H(+) by collision-induced dissociation in the gas phase. A concerted mechanism for the Lewis-acid-induced Favorskii rearrangement from alkali-metal-cationized alpha,alpha'-dibromodibenzyl ketone was proposed and studied, based on mass spectrometric results and theoretical methods.

Elucidation of the Mechanism for the S - N-type Smiles Rearrangement on Pyridine Rings

The Smiles rearrangement (SR) is an important strategy for synthesizing heterocyclic compounds. Many pyridine moiety-containing complexes are biologically active. Although the success has been archived in the development of the SR on the pyridine ring to obtain pyridine moiety-containing heterocyclic compounds, not much is known about the detailed SR mechanism. Here, we report a theoretical study on a typical S–N-type SR reaction involved in the synthesis of thiazinone-fused pyridines. We studied both the ipso-SR process and the direct nucleophilic substitution reactions on the ortho-positions to rationalize the experimentally observed ipso-SR product. The calculated results show the ipso-SR consists of two elementary steps, the intramolecular ipso-position substitution and subsequent ring closure, and the barrier for the rate-determining step is 65.98 kJ mol–1 and the overall reaction is exothermic by 116.94 kJ mol–1, confirming the reaction is kinetically feasible and thermodynamically favourable under mild experimental conditions (such as controlled microwave heating). The present results provide a clear picture for understanding the S–N-type SR on the pyridine ring to synthesize pyridine moiety-containing heterocycles.

Structural characterization of isoprenylated flavonoids from Kushen by electrospray ionization multistage tandem mass spectrometry

Eighteen isoprenylated flavonoids (8 flavanones, 3 flavanols, and 7 chalcones) isolated from Kushen or synthesized were studied by positive and negative ion electrospray ionization multistage tandem mass spectrometry (ESI-MS(n)). Plausible fragmentation patterns were obtained by comparing their MS(n) spectra with each other, which were further supported by high-resolution MS data and two model compounds. It was shown that the 2'-OH group would make the C-ring of flavonoids studied more labile through a six-membered mechanism, resulting in base peaks of (1,3)A+ (positive mode) and (1,4)A(-) (negative mode). In addition, the 2'-OH is also responsible for the neutral loss of water in (+)ESI/MS(2) of flavanones. The neutral loss of water (or methanol) in (-)ESI/MS(2) of flavanols was elucidated by a E2 elimination mechanism. Different relative abundances (RA) of (1,3)A(+) and S(+) in (+)ESI/MS(2) spectra were used to discriminate flavanones with their open-ring products, chalcones, since the equilibrium for flavanone<-->chalcone isomerization in ESI ion source could not be obtained in positive mode.

Gas-phase smiles rearrangement reactions of deprotonated 2-(4, 6-dimethoxypyrimidin-2-ylsulfanyl)-N-phenylbenzamide and its derivatives in electrospray ionization mass spectrometry

The negative ions of deprotonated 2-(4, 6-dimethoxypyrimidin-2-ylsulfanyl)-N-phenylbenzamide and its derivatives are studied by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Upon collisional activation, the [M - H](-) ions dissociate in two competitive pathways that can be considered as the gas-phase Smiles rearrangement reactions, giving rise to the characteristic fragment ions [M - H - C(7)H(4)OS](-) and [M - H - C(13)H(8)NSR](-) (R = substituent). Theoretical computations were invoked to shed light on the reaction mechanisms of the representative Compound 1 by the semiempirical PM3 method. These theoretical calculations show that the formation of [M - H - C(13)H(8)NSR](-) (R = H for Compound 1) is more favorable. Furthermore, it is found that the intensities of the two product ions are strongly influenced by the position and the nature of the substituents. For the para-substituted compounds, the ln[(M - H - C(7)H(4)OS(-))/(M - H - C(13)H(8)NSR(-))] values are well correlated with the sigma(p)(-) substituent constants. In addition, the dependence of the intensity ratios of these two ions, ln[(M - H- C(7)H(4)OS(-))/(M - H - C(13)H(8)NSR(-))](R = CH(3)), on the collision energy can be used to distinguish the positional isomers.