Cyclization and rearrangement reactions of a(n) fragment ions of protonated peptides

a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory. Overall, theory and infrared spectroscopy provide compelling evidence that a(n) ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n). The a(2) ion (GG sequence) undergoes cyclization to form a 5-membered ring isomer. The a(3) ion (GGG sequence) undergoes cyclization initiated by nucleophilic attack of the carbonyl oxygen of the N-terminal glycine residue on the carbon center of the C-terminal immonium group forming a 7-membered ring isomer. The barrier to this reaction is comparatively low at 10.5 kcal mol(-1), and the resulting cyclic isomer (-5.4 kcal mol(-1)) is more energetically favorable than the linear form. The a(4) ion with the GGGG sequence undergoes head-to-tail cyclization via nucleophilic attack of the N-terminal amino group on the carbon center of the C-terminal immonium ion, forming an 11-membered macroring which contains a secondary amine and three trans amide bonds. Then an intermolecular proton transfer isomerizes the initially formed secondary amine moiety (-CH(2)-NH(2)(+)-CH(2)-NH-CO-) to form a new -CH(2)-NH-CH(2)-NH(2)(+)-CO- form. This structure is readily cleaved at the -CH(2)-NH(2)(+)- bond, leading to opening of the macrocycle and formation of a rearranged linear isomer with the H(2)C═NH(+)-CH(2)- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. This rearranged linear structure is much more energetically favorable (-14.0 kcal mol(-1)) than the initially formed imine-protonated linear a(4) ion structure. Furthermore, the barriers to these cyclization and ring-opening reactions are low (8-11 kcal mol(-1)), allowing facile formation of the rearranged linear species in the mass spectrometer. This finding is not limited to 'simple' glycine-containing systems, as evidenced by the IRMPD spectrum of the a(4) ion generated from protonated AAAAA, which shows a stronger tendency toward formation of the energetically favorable (-12.3 kcal mol(-1)) rearranged linear structure with the MeHC═NH(+)-CHMe- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. Our results indicate that one needs to consider a complex variety of cyclization and rearrangement reactions in order to decipher the structure and fragmentation pathways of peptide a(n) ions. The implications this potentially has for peptide sequencing are also discussed.     

Deprotonated N-(2,4-Dinitrophenyl)amino Acids Undergo Cyclization in Solution and the Gas Phase

The collisionally activated mass spectral fragmentations of N-(2,4-dinitrophenyl)alanine and phenylalanine [M - H](-) may be gas-phase analogs of the base-catalyzed cyclization of N-(2,4-dinitrophenyl)amino acids in aqueous dioxane. This latter reaction is one source of the 2-substituted 5-nitro-1H-benzimidazole-3-oxides, which are antibacterial agents. The fragmentation of both compounds, established by tandem mass spectrometric experiments and supported by molecular modeling using DFT methods, indicate that the [M - H](-) ions dissociate via sequential eliminations of CO(2) and H(2)O to produce deprotonated benzimidazole-N-oxide derivatives. The gas-phase cyclization reactions are analogous to the base-catalyzed cyclization in solution, except that in the latter case, the reactant must be a dianion for the reaction to occur on a reasonable time scale. The cyclization of N-(2-nitrophenyl)phenylalanine, which has one less nitro group, requires a stronger base for the cyclization than the compound with a second nitro group at the 4-position. Following losses of CO(2) and H(2)O are expulsions of both neutral molecules and free radicals, the latter being examples of violations of the even-electron ion rule.     

Backbone-assisted reactions of polymers. VII. Kinetics of isomerization of poly[(chloromethyl)thiirane] in the absence of solvent

The kinetics of the repeating unit isomerization of poly[(chloromethyl)thiirane] have been determined at four temperatures in the absence of solvent. The reaction can be treated as a reversible first-order process with rate constants and activation energies similar to those observed in analogous reactions of β-chlorosulfides of low molecular weight. These observations are consistent with a mechanistic scheme that involves rate determining cyclization to a thiiranium ion intermediate, followed by rapid ring opening by chloride ion attack.     

Stereochemical memory effects in alkene radical cation/anion contact ion pairs: effect of substituents, and models for diastereoselectivity

A series of 12 stereochemically defined 2,m-dimethyl- and 2,m,n-trimethyl-6-benzylamino-2-nitro-3-(diphenylphosphatoxy)hexanes have been synthesized and their cyclization reactions leading to di- and trisubstituted N-benzyl pyrrolidines examined in the presence of tributyltin hydride and azoisobutyronitrile in benzene at reflux. The cyclizations are interpreted in terms of generation of an alkyl radical by abstraction of the nitro group with a stannyl radical. The phosphate leaving group is then expelled in a heterolytic cleavage to give a contact alkene radical cation/phosphate anion pair. For the majority of the examples studied, the cyclizations are best understood in terms of nucleophilic attack by the amine on the opposite face of the alkene radical cation to the one shielded by the leaving group, within the confines of the initial contact ion pair, resulting in overall cyclization with inversion of configuration. Dependent on the relative stereochemistry of the substituents, the cyclization is envisaged as taking place through either chair-like or twist-boat-like transition states with the maximum number of substituents pseudo-equatorial. The model breaks down when cyclization on the initial contact ion pair would engender significant destabilizing steric interactions, especially (1,3)A strain in the alkene radical cation. In these cases a fully equilibrated Beckwith-Houk-type transition state provides a satisfactory model. Interesting examples of matching and mismatching in the Corey-type oxazaborolidine-mediated reduction of alkyl (methyl-1-nitroethyl) ketones by a beta-methyl group in the alkyl chain are reported, and the mismatching is attributed to a developing syn-pentane interaction in the transition state.     

Bifunctionalized allenes. Part XXI. Electrophilic cyclization and addition reactions of 3-(α- or β-hydroxyalkyl)-allenylphosphonates and allenyl phosphine oxides

Abstract

The present paper discusses the electrophilic cyclization and addition reactions of 3-(α- or β-hydroxyalkyl)-allenylphosphonates and phosphine oxides. Treatment of 3-(α- or β-hydroxy-alkyl)-allenylphosphonates with electrophiles takes place with 5-endo-trig cyclization and gives 2-methoxy-2,5-dihydro-1,2-oxaphosphole 2-oxides as a result of the neighboring phosphonate group participation in the electrophilic cyclization. On the other hand, 3-(α- or β-hydroxyalkyl)-alk-(1E)-en-1-yl phosphine oxides were prepared by chemo-, regio-, and stereoselective electrophilic addition to the C²-C³-double bond in the 3-(α- or β-hydroxyalkyl)-alka-1,2-dienyl phosphine oxides and subsequent attack of the external nucleophile (halide anion). The paper proposes a possible mechanism that involves electrophilic cyclization and addition reactions of the phosphorylated (α- or β-hydroxyalkyl)allenes.     

Ambident reactivity of the thiocyanate anion revisited: can the product ratio be explained by the hard soft acid base principle?

Laser flash photolysis and stopped-flow methods have been employed to determine the kinetics of the reactions of benzhydrylium ions with both termini of the thiocyanate ion. In contrast to previous investigations which reported sulfur/nitrogen ratios of k(S)/k(N) = 2-10 for the reactions of carbocations with SCN(-), values of k(S)/k(N) = 10(3)-10(4) are now derived from absolute rate constants. This discrepancy is explained by the fact that the data determined in this investigation are the first which refer to activation-controlled attack of carbocations at both termini of the thiocyanate ion, while previous reactivity ratios included diffusion-controlled reactions. It is concluded that the selectivities of the reactions of carbocations with the thiocyanate ion cannot be explained by the hard soft acid base principle.     

Formal [4+2]‐Annulation of Vinyl Azides with N‐Unsaturated Aldimines

Highly functionalized quinolines and pyridines could be synthesized by BF₃?OEt₂‐mediated reactions of vinyl azides with N‐aryl and N‐alkenyl aldimines, respectively. The reaction mechanism could be characterized as formal [4+2]‐annulation, including unprecedented enamine‐type nucleophilic attack of vinyl azides to aldimines and subsequent nucleophilic cyclization onto the resulting iminodiazonium ion moieties.     

3-(Hetero)aryl-4-indolylamino-α-tetralones by diastereoselective internal redox cyclization: an "azaenamine" conjugate addition

(E)-3-(hetero)aryl-1-(2-((E)-(indolin-1-ylimino)methyl)phenyl)prop-2-en-1-ones 1 undergo 6-exo-trig cyclization reactions upon treatment with BF(3)·Me(2)S in dichloromethane at low temperature to give the tetralones 10 in good yield. This cyclization process can be considered to be an intramolecular Michael-type addition which is accompanied by an internal redox reaction as the indoline fragment is oxidized to indole with simultaneous hydrogen shift to nitrogen atom N1 and the α-carbon atom of the Michael system. The reactions at the iminic centers take place via umpolung of the classical carbonyl reactivity. The reaction is diastereoselective and affords exclusively 3,4-disubstituted α-tetralones 10 as trans-diastereomers. According to quantum chemical calculations the reactions take place under kinetic control with the trans-diastereomer being the kinetically favored product as it has the lower activation barrier compared to the cis-diastereomer.     

Tandem polar/radical crossover sequences for the formation of fused and bridged bicyclic nitrogen heterocycles involving radical ionic chain reactions,and alkene radical cation intermediates,performed under reducing conditions: scope and limitations

It is demonstrated that phosphorylated forms of beta-nitro alcohols provide an excellent means of entry into beta-(phosphatoxy)alkyl radicals on exposure to tributyltin hydride and AIBN in benzene at reflux. These radicals then undergo heterolytic cleavage of the phosphate group to yield alkene radical cation/phosphate anion contact ion pairs which are trapped intramolecularly in a tandem polar/radical crossover sequence involving radical ionic chain reactions by allylic and propargylic amines. The substitution pattern of the alkene radical cation dictates the cyclization mode, and this may be engineered to form fused ring systems by an initial exo-mode nucleophilic cyclization or bridged bicyclic systems when the nucleophilic attack takes place in the endo-mode.     

Intramolecular cyclization with nitrenium ions generated by treatment of N-acylaminophthalimides with hypervalent iodine compounds: formation of lactams and spiro-fused lactams

N-Phthalimido-N-acylnitrenium ions are generated from N-acylaminophthalimides, a new class of precursors, by treatment with hypervalent iodine compounds (PIFA and HTIB). In HFIP, the nitrenium ions undergo intramolecular electrophilic substitution reactions to afford N-aminonitrogen heterocycles in high yields. In TFEA, spirodienones bearing the 1-azaspiro[4.5]decane skeleton are obtained by treatment of N-phthalimido-3-(4-halogenophenyl)propanamides with HTIB as a result of ipso attack of the intermediate nitrenium ion. Similarly, using PIFA in TFEA, ipso cyclization of unactivated benzenoid compounds occurs to afford spirodiene derivatives. This involves loss of aromaticity despite the absence of other activating substituents on the phenyl group.     

On the mechanism of the selenolactonization reaction with selenenyl halides

The mechanism of selenocyclization reactions of beta,gamma-unsaturated acids and their derivatives has been studied. The reactions of (E)-4-phenyl-3-butenoic acid 10 and its silyl and alkyl esters with benzeneselenenyl chloride (PhSeCl) and bromide (PhSeBr) have been examined by VT-NMR and in situ IR spectroscopic methods. Whereas the reactions of the acid 10 in the presence of a base were irreproducible and complicated, reactions of the silyl esters were clean and spontaneously and quantitatively afforded a chloroselenylation adduct at -70 degrees C as a single (Markovnikov) isomer. This adduct underwent three processes as the temperature was raised: (1) reversal to the starting materials, (2) isomerization to the anti-Markovnikov product, and (3) cyclization to the selenolactone 12. All of these processes are believed to proceed via a seleniranium ion the intermediacy of which was established by independent synthesis and spectroscopic identification. The reversible formation of chloro selenide adducts was unambiguously established by crossover experiments. The reaction of 10 with PhSeBr was found to be rapid but thermodynamically unfavorable at room temperature.     

Electrophilic-induced cyclization reaction of hexahydroindolinone derivatives and its application toward the synthesis of (+/-)-erysotramidine

A convenient synthesis of variously substituted octahydroindolo[7a,1a]-isoquinolinones has been achieved by an acid-induced cyclization of hexahydroindolinones bearing tethered phenethyl groups. The formation of a single lactam diastereomer is the result of the stereoelectronic preference for axial attack by the aromatic ring onto the initially formed N-acyliminium ion from the least hindered side. Additional experiments showed that a variety of hexahydroindolinones containing tethered pi-bonds undergo a related acid-induced cyclization reaction. Treatment of the 3-methylbut-3-enyl-substituted hexahydroindolinone with acid furnished a 3:1 mixture of isomeric octahydropyrido[2,1-i]indolinones in near-quantitative yield. Interestingly, cyclization of the closely related 1-(3-methoxybut-3-enyl)-substituted hexahydroindolin-one afforded a pyrrolo[3,2,1-ij]quinolinone as the exclusive product. With this system, initial protonation takes place on the more nucleophilic enol ether pi-bond and the resulting carbonium ion undergoes a subsequent cyclization with the enamido pi-bond to give the observed product. The electrophilic promoted cyclizations were extended to include the related hexahydro[1]pyrindinone and 1H-quinolinone systems. An NBS-promoted intramolecular electrophilic aromatic substitution reaction of 1-[2-(3,4-dimethoxyphenyl)ethyl]-1,4,5,6-tetrahydroindolinone was used to assemble the tetracyclic core of the erythrinone skeleton. The resulting cyclized product was transformed into (+/-)-erysotramidine in three additional steps.     

Scope and facial selectivity of the Prins-pinacol synthesis of attached rings

Using a B-alkyl Suzuki cross-coupling as a key step, a concise and stereocontrolled synthesis of five- to eight-membered triisopropylsiloxy ethers having (2Z)-(6,6-dimethoxyhexylidene) or (2Z)-(5,5-dimethoxypentylidene) side chains was developed. Prins-pinacol reactions of these precursors promoted by SnCl4 provide bicyclic products in which 5-, 6-, or 7-membered rings are joined by a C-C single bond. Synthetically challenging attached ring systems in which both rings are chiral can be prepared in this fashion with high stereo- and enantioselectivity. Stabilizing through-space electrostatic interactions between the alpha-alkoxycarbenium ion and an axially positioned oxygen substituent are believed to play a significant role in organizing the transition structure of the Prins cyclization.     

6-Endo-dig versus 5-exo-dig: Exploring Radical Cyclization Preference with First-, Second-, and Third-row Linkers using High-level Quantum Chemical Methods

As an expansion upon Baldwin rules, the cyclization reactions of hex-5-yn-1-yl radical systems with different first-, second-, and third-row linkers are explored at the CCSD(T) level via means of the SMD(benzene)-G4(MP2) thermochemical protocol. Unlike C, O, and N linkers, systems with B, Si, P, S, Ge, As, and Se linkers are shown to favor 6-endo-dig cyclization. This offers fundamental insights into the rational synthetic design of cyclic compounds. A thorough analysis of stereoelectronic effects, cyclization barriers, and intrinsic barriers illustrates that structural changes alter the cyclization preference by mainly impacting 5-exo-dig reaction barriers. Based on the high-level computational modeling, we proceed to develop a new tool for cyclization preference prediction from the correlation between cyclization barriers and radical structural parameters (e. g., linker bond length and bond angle). A strong correlation is found between the radical attack trajectory angle and the reaction barrier heights, i. e., cyclization preference. Finally, the influence of stereoelectronic effects on the two radical cyclization pathways is further investigated in stereoisomers of hypervalent silicon system, which provides novel insight into cyclization control.     

On the 6-exo atom transfer radical cyclization reactions of 3-butenyl 2-iodoalkanoates

Bis(tributyltin)-initiated atom transfer cyclization reactions of 3-butenyl iodoalkanoates in the presence of BF3.OEt2 as the catalyst afforded the 6-exo cyclization products as a mixture of 3,4-cis- and trans-substituted tetrahydro-2H-pyran-2-ones in 53-71% yield with the major isomers being the cis ones. Ab initio calculations at the B3LYP/6-31G level on the transition states of the radical cyclization and on the cyclized products revealed that the reactions are kinetically controlled and the transition states for the 6-exo radical cyclization are in boat conformations. Moreover, the cis-oriented transition states are of lower energy than the corresponding trans-oriented ones, which are in excellent agreement with experimental results.     

Mechanism of the transition-metal-catalyzed hydroarylation of bromo-alkynes revisited: hydrogen versus bromine migration

A comprehensive mechanistic study of the InCl(3)-, AuCl-, and PtCl(2)-catalyzed cycloisomerization of the 2-(haloethynyl)biphenyl derivatives of Fürstner et al. was carried out by DFT/M06 calculations to uncover the catalyst-dependent selectivity of the reactions. The results revealed that the 6-endo-dig cyclization is the most favorable pathway in both InCl(3)- and AuCl-catalyzed reactions. When AuCl is used, the 9-bromophenanthrene product could be formed by consecutive 1,2-H/1,2-Br migrations from the Wheland-type intermediate of the 6-endo-dig cyclization. However, in the InCl(3)-catalyzed reactions, the chloride-assisted intermolecular H-migrations between two Wheland-type intermediates are more favorable. These Cl-assisted H-migrations would eventually lead to 10-bromophenanthrene through proto-demetalation of the aryl indium intermediate with HCl. The cause of the poor selectivity of the PtCl(2) catalyst in the experiments by the Fürstner group was predicted. It was found that both the PtCl(2)-catalyzed alkyne-vinylidene rearrangement and the 5-exo-dig cyclization pathways have very close activation energies. Further calculations found the former pathway would lead eventually to both 9- and 10-bromophenanthrene products, as a result of the Cl-assisted H-migrations after the cyclization of the Pt-vinylidene intermediate. Alternatively, the intermediate from the 5-exo-dig cyclization would be transformed into a relatively stable Pt-carbene intermediate irreversibly, which could give rise to the 9-alkylidene fluorene product through a 1,2-H shift with a 28.1 kcal mol(-1) activation barrier. These findings shed new light on the complex product mixtures of the PtCl(2)-catalyzed reaction.     

Hydrolysis of 2',3'-O-methyleneadenos-5'-yl bis(2',5'-di-O-methylurid-3'-yl) phosphate, a sugar O-alkylated trinucleoside 3',3',5'-monophosphate: implications for the mechanism of large ribozymes

Hydrolytic reactions of 2',3'-O-methyleneadenos-5'-yl bis(2',5'-di-O-methylurid-3'-yl) phosphate (1), a sugar O-alkylated trinucleoside 3',3',5'-monophosphate, have been followed by RP HPLC over a wide pH range. Under neutral and mildly acidic conditions, the only reaction observed was a pH-independent cleavage of the O-C5' bond of the 5'-linked nucleoside. Under more alkaline conditions nucleophilic attack by hydroxide ion starts to compete. The reaction is first order in [OH(-)] and becomes predominant at pH 10. Each of the 3'-linked nucleosides is displaced 2.9 times as readily as the 5'-linked one. To determine the beta(lg) value for the hydroxide ion catalyzed hydrolysis of 1, two diesters (2a,b) having 2',3'-O-methyleneadenosine (7) and 2',5'-di-O-methyluridine (4) as leaving groups were hydrolyzed under alkaline conditions. Since the beta(lg) value for this reaction is known, DeltapK(a) between 4 and 7 could be calculated. The beta(lg) for the hydrolysis of 1 was estimated to be -0.5 with use of this information. The mechanisms of the partial reactions and the role of leaving group properties in ribozyme reactions of large ribozymes are discussed.     

Lewis acid-catalyzed atom transfer radical cyclization of unsaturated β-keto amides

The Lewis acid-catalyzed atom transfer radical cyclization reactions of olefinic -bromo β-keto amides were investigated. It was found Lewis acid Yb(OTf)₃ or Mg(ClO₄)₂ not only promoted the cyclization reactions, but also resulted in excellent trans stereocontrol in the cyclization products. With the catalysis of Lewis acid Yb(OTf)₃ or Mg(ClO₄)₂ at −78°C in the presence of Et₃B/O₂, the cyclization reactions of C-olefinic β-keto amides provided cyclic ketones, while the cyclization reactions of N-olefinic β-keto amides led to the formation of γ-lactams, which could be converted to 3-aza-bicyclo[3,1,0]hexan-2-ones.     

Chelation-control in the formal [3+3] cyclization of 1,3-bis-(silyloxy)-1,3-butadienes with 1-hydroxy-5-silyloxy-hex-4-en-3-ones. One-pot synthesis of 3-aryl-3,4-dihydroisocoumarins

The [3+3] cyclization of 1,3-bis(silyloxy)-1,3-butadienes with 1-hydroxy-5-silyloxy-hex-4-en-3-ones resulted in the one-pot formation of 3-aryl-3,4-dihydroisocoumarins. The reactions proceeded by regioselective cyclization to give 6-(2-aryl-2-chloroethyl)salicylates, which underwent a silica gel-mediated lactonization. The cyclizations of protected 1-amino-5-silyloxy-hex-4-en-3-ones proved to be not regioselective.     

Hydrogen/chlorine exchange reactions of gaseous carbanions

Gas-phase reactions of three typical carbanions CH(2)NO(2)(-), CH(2)CN(-), and CH(2)S(O)CH(3)(-) with the chloromethanes CH(2)Cl(2), CHCl(3), and CCl(4), examined by tandem mass spectrometry, show a novel hydrogen/chlorine exchange reaction. For example, reaction between the nitromethyl anion CH(2)NO(2)(-) and carbon tetrachloride CCl(4) forms the ion CHClNO(2)(-). The suggested reaction mechanism involves nucleophilic attack by CH(2)NO(2)(-) at the chlorine of CCl(4) followed by proton transfer within the resulting complex [CH(2)ClNO(2) + CCl(3)(-)] to form CHClNO(2)(-) and CHCl(3). Two other carbanions CH(2)CN(-) and CH(2)S(O)CH(3)(-) also undergo the novel hydrogen/chlorine exchange reactions with CCl(4) but to a much smaller extent, their higher nucleophilicities favoring competitive nucleophilic attack reactions. Proton abstraction is the exclusive pathway in the reactions of these carbanions with CHCl(3). While CH(2)CN(-) and CH(2)S(O)CH(3)(-) promote mainly proton abstraction and nucleophilic displacement in reactions with CH(2)Cl(2), CH(2)NO(2)(-) does not react.