Aspartic acid side chain effect—Experimental and theoretical insight

Gas-phase H/D exchange and density functional theory study of the Asp and Glu side-chain carboxylic group intrinsic reactivity is reported. H/D exchange site specific treatment and some additional theoretical calculations showed that a side-chain carboxylic group may initiate proton transfer along with bond formation to one of its oxygens, i.e., possibility to initiate selective of cleavage peptide bond ("aspartic acid effect"). That finding is used to select aspartic acid cleavage mechanisms (side-chain proton transfer either to backbone carbonyl or to amide nitrogen) for further computational study. B3LYP/6-31G(d) and G3(MP2)//B3LYP potential energy profiles of both mechanisms on a model system CH3CO-Asp-NHCH3 were constructed. Although energy employed in low-energy collision induced dissociation suffices for both mechanisms thresholds, energy transferred to specific modes suggests a complex one-step mechanism of proton transfer (from the side-chain carboxylic group to the backbone amide group), bond formation (between deprotonated carboxylic group and carbon atom of the backbone carbonyl), and peptide bond cleavage as favorable.     

Cα-Cβ and Cα-N bond cleavage in the dissociation of protonated N-benzyllactams: dissociative proton transfer and intramolecular proton-transport catalysis

In mass spectrometry of protonated N-benzylbutyrolactams, the added proton is initially localized on the carbonyl oxygen, which is the thermodynamically preferred protonation site. Upon collisional activation, dissociative proton transfer takes place leading to the occurrence of fragmentation reactions. The major fragmentations observed are the cleavages of C(α)-C(β) and C(α)-N bonds on the two sides of the methylene linker, which is different to the cleavage of the amide bond itself seen in most amide cases. Theoretical calculations and isotopic labeling experiments demonstrate that the phenyl ring regulates the proton transfer reactions. The proton directly migrates to the C(β) position via a 1,5-H shift leading to the efficient loss of benzene, while it stepwise migrates to the amide nitrogen resulting in the formation of a benzyl cation. The stepwise proton transfer is achieved via intramolecular proton-transport catalysis. The C(γ) position accepts the proton from the carbonyl oxygen via a 1,6-H shift, and then donates it to the amide nitrogen via a 1,4-H shift. The general 1,3-H shift from the carbonyl oxygen to the amide nitrogen can be excluded in this case due to its significant energy barrier. The substituent effects are also applied to explore the reaction mechanism, and it proves that both C(β) and C(γ) are involved in the dissociative proton transfer processes. For monosubstituted N-benzylbutyrolactams, the abundance ratios of the two competing product ions are well correlated with the nature of the substituents.     

How Strong is Hydrogen Bonding to Amide Nitrogen?

The protonation of the carboxamide nitrogen atom is an essential part of in vivo and in vitro processes (cis-trans isomerization, amides hydrolysis etc). This phenomenon is well studied in geometrically strongly distorted amides, although there is little data concerning the protonation of undistorted amides. In the latter case, the participation of amide nitrogen in hydrogen bonding (which can be regarded as the incipient state of a proton transfer process) is less well-studied. Thus, it would be a worthy goal to investigate the enthalpy of this interaction. We prepared and investigated a set of peri-substituted naphthalenes containing the protonated dimethylamino group next to the amide nitrogen atom (“amide proton sponges”), which could serve as models for the study of an intramolecular hydrogen bond with the amide nitrogen atom. X-Ray analysis, NMR spectra, basicity values as well as quantum chemical calculations revealed the existence of a hydrogen bond with the amide nitrogen, that should be attributed to the borderline between moderate and weak intramolecular hydrogen bonds (2–7 kcal ⋅ mol⁻¹).     

Mechanisms of nucleophilic reactions of carbonyl compounds in the gas phase and in a solution

The effect of substituents on nucleophilic addition at the C=O bond, which occurs by the mechanism of intramolecular proton transfer, has been studied by the quantum-chemical MNDO/H method. The effect of nucleophiles and substituents at the carbonyl C atom in the gas phase is opposite to that in solution. Strengthening of the bond between the nucleophile and the carbonyl compound as the result of the transfer of electron density to the carbonyl C atom results in the stabilization of the tetrahedral bipolar adduct. In the formation of an adduct with a strong nucleophile the geometry of the transition state (TS) is closer to that of the reaction product, whereas in the case of a weak nucleophile it is similar to that of the initial reagents. Attack by a weak nucleophile and electron-donating groups at the carbonyl C atom favor the situation in which the reaction system achieves a TS earlier and proton transfer occurs with a low activation barrier.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 227–230, February, 1994.     

On the structure of protonated methane

Results of a Fourier transform-ion cyclotron resonance study are reported concerning the reactivity of protonated perdeuteromethane and deuteronated methane, generated under varying pressure conditions in an external chemical ionization ion source, toward ammonia. The competition between proton and deuteron transfer from both protonated perdeuteromethane and deuteronated methane to ammonia exhibits chemically distinguishable hydrogens. The chemical behavior of protonated methane appears to be compatible with the theoretically predicted stable structure with C_S symmetry, involving a three-center two-electron bond associating two hydrogens and the carbon atom. Interconversion of this structure due to exchange between one of these hydrogens and one of the three remaining hydrogens appears to be a fast process that is induced by interactions with the chemical ionization gas.     

Concomitant hydride and proton transfer: an essay on competing and consecutive key reactions occurring in gaseousion/neutral complexes

The interplay of proton transfer and hydride transfer reactions in alkylbenzenium ions and related protonated di- and oligophenylalkanes is presented and discussed. While intra- and interannular proton exchange has been recognised to be an ubiquitous feature in protonated arenes, hydride abstraction is much less obvious but can become a dominating fragmentation channel in metastable ions of tert-butyl-substituted alkylbenzenium ions and related carbocations. In such cases, proton-induced release of the tert-butyl cation gives rise to ion/neutral complexes as reactive intermediates, for example, [(CH(3))(3)C(+)...arylCH(2)(α)(CH(2))(n)CH(2)(ω)aryl '] with n ≥ 0, and highly regioselective intra-complex hydride transfer occurs from all of the benzylic methylene hydride ion donor groups (α-CH(2) and ω-CH(2)) to the tert-butyl cation acting as a Lewis acid. Substituent effects on the individual contributions to the overall hydride transfer from different donor sites, including ortho-methyl groups, in particular, and the concomitant intra- complex proton transfer from the tert-butyl cation to the neutral diarylalkane constituent corroborate the view of "bisolvated" complexes as the central intermediates, in which the carbenium ion is coordinated to both of the aromatic π-electron systems. The role of cyclisation processes converting the benzylic, [M - H](+) type, ions into the isomeric benzenium, [M + H](+)-type, ions prior to fragmentation is demonstrated for several cases. This overall scenario, consisting of consecutive and/or competing intra-complex hydride abstraction and proton transfer, intraannular proton shifts (H+ ring walk) and interannular proton transfer, hydrogen exchange ("scrambling") processes, and cyclisation and other electrophilic substitution reactions, is of general importance in this field of gas-phase ion chemistry, and more recent examples concerning protonated ethers, benzylpyridinium and benzylammmonium ions are discussed in which these recurring features play central and concerted mechanistic roles as well.     

Modeling of protonation processes in acetohydroxamic acid

This work presents a theoretical study of acetohydroxamic acid and its protonation processes using ab initio methodology at the MP2(FC)/cc-pdVZ level. We find the amide form more stable than the imidic tautomer by less than 1.0 kcal mol(-)(1). For comparison with the experimental data, a three-dimensional conformational study is performed on the most stable tautomer (amide). From this study, the different barriers to rotation and inversion are determined and the intramolecular hydrogen bond between the OH group and the carbonyl oxygen is characterized. The electrostatic potential distribution shows three possible sites for electrophilic attack, but it is shown that only two of them, the carbonyl oxygen and the nitrogen atoms, are actual protonation sites. The protonation energy (proton affinity) is obtained from the results of the neutral and charged species. Proton affinities for the species charged on the carbonyl oxygen and the nitrogen atoms are estimated to be 203.4 and 194.5 kcal mol(-)(1), respectively. The development of a statistical model permits the quantification of DeltaG (gas-phase basicity) for the two protonation processes. In this way, the carbonyl oxygen protonated form is found to be more stable than that of the nitrogen atoms by 8.3 kcal mol(-)(1) at 1 atm and 298.15 K, due to the enthalpic contribution. As temperature increases, the proportion of the nitrogen protonated form increases slightly.     

Dissociation of the N-C(alpha) bond and competitive formation of the [z(n) - H](+) and [c(n) + 2H](+) product ions in radical peptide ions containing tyrosine and tryptophan: the influence of proton affinities on product formation

Dissociations at the N-C_α bond of tryptophan and tyrosine residues are the prevalent pathways in the fragmentations of radical cations of tripeptides that contain such as residues. This process involves a proton transfer from the β-carbon of the tryptophan or tyrosine residue to the carbonyl oxygen of the amide group, followed by cleavage of the N-C_α bond, generating low-lying proton-bound dimers that dissociate to give each an ionic and a neutral product. Formation of the [z _n −H]^∢+ or [c _n +2H]⁺ ion is a competition between the two incipient fragments for the proton in a dissociating proton-bound dimer.     

Fragmentation of protonated amides through intermediate ion-neutral complexes: Neighboring group participation

It has been shown that neighboring group participation plays an important role in the fragmentation of protonated amides; the attachment of an adjacent functional group capable of accepting a proton provides alternative pathways of low energy for the formation of the inevitable N-protonated species in the fragmentation of the amide bond. Under methane chemical ionization (CI) conditions, protonated aniline (m/z 94) is only 1. 6% of the base peak MH⁺ ion for acetanilide; the abundance of the m/z 94 ion is increased to 15% for acetoacetanilide and protonated o-methoxyaniline reaches a relative intensity of 49% for N-acetyl-o-methoxyaniline. A more striking difference in ease of the formation of protonated anilines is found for acetanilides bearing a nitro group at different positions. Protonated nitroaniline (m/z 139) is the base peak in the methane CI spectrum of N-acetyl-o-nitroaniline; the m/z 139 ion drops to only 0.7% for the para isomer, and this ion is increased to 31.5% in the spectrum of N-acetoaceto-p-nitroaniline. By employing low energy collision-induced dissociation, it has been found that the fragmentation of protonated amides proceeds by way of ion-neutral complexes. In the case of acetanilide, for example, the cleavage of the amide bond gives rise to an acetylium ion and neutral aniline, which are bound together as a complex. An α-hydrogen of the acetylium ion, which is activated by the positive charge, is captured by aniline due to its higher proton affinity as compared with ketene. For those compounds having mobile protons other than the amidic hydrogen, it is indicated that such proton has the priority to be transferred in the reaction. Thus, the proton on the free carboxyl group of N-phenyl succinic and maleic monoamides is transferred in the fragmentation, leading to anhydrides as the neutral species in the formation of protonated aniline.     

Mechanism and energetics of intramolecular hydrogen transfer in amide and peptide radicals and cation-radicals

Intramolecular hydrogen transfer in five model amide and peptide radicals and cation-radicals was investigated by combined B3LYP-MP2 calculations. Hypervalent ammonium radicals produced by electron capture in protonated peptides undergo competitive elimination of ammonia, H-atom loss, and H-atom migration to neighboring amide carbonyls. The calculated transition state energies for H-atom migration are slightly but uniformly lower than those for H-atom loss. Transition state theory calculations with inclusion of quantum tunneling effects predict k(H migration)/k(H loss) branching ratios that increase with the ring size of the cyclic transition state for the migration. Intramolecular hydrogen-atom migration in amide and peptide radicals can be described by the proton-coupled electron transfer mechanism. The migrating hydrogen atom shows a negligible spin density and substantial positive charge that are typical of a proton migration. Electron transfer occurs through a pi-orbital system and proceeds in the same (clockwise) or opposite (counterclockwise) direction as the proton motion, depending on the electronic properties of the chain connecting the ammonium group and the amide bond.     

Dissociative protonation sites: reactive centers in protonated molecules leading to fragmentation in mass spectrometry

It is often found in mass spectrometry that when a molecule is protonated at the thermodynamically most favorable site, no fragmentation occurs, but a major reaction is observed when the proton migrates to a different position. For benzophenones, acetophenones, and dibenzyl ether, which are all preferentially protonated at the oxygen, deacylation or dealkylation was observed in the collision-induced dissociation of the protonated molecules. For para-monosubstituted benzophenones, electron-withdrawing substituents favor the formation of RC6H4CO+ (R = substituent), whereas electron-releasing groups favor the competing reaction leading to C6H5CO+. The ln[(RC6H4CO+)/(C6H5CO+)] values are well-correlated with the sigmap+ substituent constants. In the fragmentation of protonated acetophenones, deacetylation proceeds to give an intermediate proton-bound dimeric complex of ketene and benzene. The distribution of the product ions was found to depend on the proton affinities of ketene and substituted benzenes, and the kinetic method was applied in identifying the reaction intermediate. Protonated dibenzyl ether loses formaldehyde upon dealkylation, via an ion-neutral complex of the benzyloxymethyl cation and neutral benzene. These gas-phase retro-Friedel-Crafts reactions occurred as a result of the attack of the proton at the carbon atom to which the carbonyl or the methylene group is attached on the aromatic ring, which is described as the dissociative protonation site.     

Electrochemical oxidation of amides of type Ph2CHCONHAr

Anodic oxidation of N-aryl-2,2-diphenylacetamides in acetonitrile undergoes three types of bond-cleavage, one between the benzylic carbon and the carbonyl group, the second between a carbonyl and 'N', and the third between the 'N' atom and aryl group. The selectivity of the cleavage and nature of emerged products is highly dependent on the nature of substituent attached to the aryl group. For example, electron-withdrawing groups direct the benzyl-carbonyl bond-breaking whereas electron-donating substituents favor the N-aryl bond cleavage. The type of products obtained involve benzophenone, 2,2-diphenylacetamide, N-(diphenylmethylene)acetamide, N-(diphenylmethyl)acetamide, α-lactam (1-acetyl-3,3-diphenylaziridin-2-one, as a 1 : 1 complex with 2,4-dinitroaniline) and aniline derivatives.     

Migration of trimethylsilyl group in the reaction of sodium bis(trimethylsilyl)amide with bromobenzene

The reaction of sodium bis(trimethylsilyl)amide with bromobenzene gave a mixture of N,N-bis-(trimethylsilyl)aniline and N,2-bis(trimethylsilyl)aniline, the latter being a rearrangement product formed via 1,3-migration of trimethylsilyl group from the nitrogen atom to the ortho-carbon atom in the benzene ring.     

Do amines react with protonated peptides in the gas phase via transacylation reactions to induce peptide bond cleavage?

The proposal that protonated peptides react with NH(3) in the gas phase via transacylation reactions (Tabet et al., Spectros. Int. J. 5: 253 1987) has been investigated by studying the reactions of the fixed charge derivatives [RC(O)NMe(2)CH(2)CO(2)H](+) (R=Me and Ph) with pyridine and triethylamine and the reactions of protonated glycine oligomers and leucine enkenphalin with butylamine. Under the near thermal conditions of the quadrupole ion trap, both the fixed charge derivatives as well as the protonated peptides react with the amines via either proton transfer or proton bound dimer formation. Collision induced dissociation of protonated peptides in the presence of butylamine yields b(n) and y(n) sequence ions as well as [b(n) + BuNH(2)](+) and [y(n) + BuNH(2)](+) ions. MS(3) experiments reveal that a major route to these [b(n) + BuNH(2)](+) and [y(n) + BuNH(2)](+) ions involves ion-molecule reactions between the b(n) and y(n) sequence ions and butylamine. MS(4) experiments, carried out to determine the nature of the [b(n) + BuNH(2)](+) ions, reveal that they correspond to a mixture of hydrogen bonded (i.e. proton bound dimer) and covalent amide bond structures.     

A nitrogen-15 NMR study of hydrogen bonding in 1-alkyl-4-imino-1,4-dihydro-3-quinolinecarboxylic acids and related compounds

The title compounds contain groups (amine, amide, imine, carboxylic acid) that are capable of forming intramolecular hydrogen bonds involving a six-membered ring. In compounds where the two interacting functional groups are imine and carboxylic acid, the imine is protonated to give a zwitterion; where the two groups are imine and amide, the amide remains intact and forms a hydrogen bond to the imine nitrogen. The former is confirmed by the iminium 15N signal, which shows the coupling of 1J(15N,1H) -85 to -86.8 Hz and 3J(1H,1H) 3.7-4.2 Hz between the iminium proton and the methine proton of a cyclopropyl substituent on the iminium nitrogen. Hydrogen bonding of the amide is confirmed by its high 1H chemical shift and by coupling of the amide hydrogen to (amide) nitrogen [(1J(15N,1H) -84.7 to -90.7 Hz)] and to ortho carbons of a phenyl substituent. Data obtained from N,N-dimethylanthranilic acid show 15N-1H coupling of (-)8.2 Hz at 223 K (increasing to (-)5.3 Hz at 243 K) consistent with the presence of a N... H-O hydrogen bond.     

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.     

A DFT study of the ambiphilic nature of arylpalladium species in intramolecular cyclization reactions

The remarkable structure-dependent reactivity observed in the cyclization of (2-haloanilino)-ketones with Pd-catalysts has been studied computationally within the density functional theory framework. The experimental reaction products ratio may be explained through the formation of a common palladaaminocyclobutane intermediate which can undergo a nucleophilic addition reaction and/or an enolate α-arilation process. The evolution of this metallacycle to the final products depends on two factors, the length of the tether joining the amino and the carbonyl groups, and the electronic nature of the substituent directly attached to the nitrogen atom. Thus, shorter chains (2 CH(2)) facilitate the nucleophic addition reaction by approximating the reactive aryl and Pd-coordinated carbonyl groups whereas longer chains (3 CH(2)) favor the enolate α-arylation proccess. For electron-withdrawing groups attached to the aniline nitrogen atom, the nucleophilic addition pathway becomes slightly disfavored, mainly due to the electron-withdrawing effect of the CO(2)Me group which avoids the delocation of the LP in the π-system, thus decreasing the nucleophilicity of the reactive arylic carbon atom. In contrast, the enolate α-arylation reaction is facilitated by the CO(2)Me group. This is translated into a small computed barrier energy difference of these competitive reaction pathways which should lead to a mixture of reaction products as experimentally found.     

Gas phase retro‐Michael reaction resulting from dissociative protonation: fragmentation of protonated warfarin in mass spectrometry

A mass spectrometric study of protonated warfarin and its derivatives (compounds 1 to 5) has been performed. Losses of a substituted benzylideneacetone and a 4‐hydroxycoumarin have been observed as a result of retro‐Michael reaction. The added proton is initially localized between the two carbonyl oxygens through hydrogen bonding in the most thermodynamically favorable tautomer. Upon collisional activation, the added proton migrates to the C‐3 of 4‐hydroxycoumarin, which is called the dissociative protonation site, leading to the formation of the intermediate ion‐neutral complex (INC). Within the INC, further proton transfer gives rise to a proton‐bound complex. The cleavage of one hydrogen bond of the proton‐bound complex produces the protonated 4‐hydroxycoumarin, while the separation of the other hydrogen bond gives rise to the protonated benzylideneacetone. Theoretical calculations indicate that the 1, 5‐proton transfer pathway is most thermodynamically favorable and support the existence of the INC. Both substituent effect and the kinetic method were utilized for explaining the relative abundances of protonated 4‐hydroxycoumarin and protonated benzylideneacetone derivative. For monosubstituted warfarins, the electron‐donating substituents favor the generation of protonated substituted benzylideneacetone, whereas the electron‐withdrawing groups favor the formation of protonated 4‐hydroxycoumarin. Copyright © 2012 John Wiley & Sons, Ltd.     

Fragmentation reactions of protonated peptides containing glutamine or glutamic acid

A variety of protonated dipeptides and tripeptides containing glutamic acid or glutamine were prepared by electrospray ionization or by fast atom bombardment ionization and their fragmentation pathways elucidated using metastable ion studies, energy-resolved mass spectrometry and triple-stage mass spectrometry (MS(3)) experiments. Additional mechanistic information was obtained by exchanging the labile hydrogens for deuterium. Protonated H-Gln-Gly-OH fragments by loss of NH(3) and loss of H(2)O in metastable ion fragmentation; under collision-induced dissociation (CID) conditions loss of H-Gly-OH + CO from the [MH - NH(3)](+) ion forms the base peak C(4)H(6)NO(+) (m/z 84). Protonated dipeptides with an alpha-linkage, H-Glu-Xxx-OH, are characterized by elimination of H(2)O and by elimination of H-Xxx-OH plus CO to form the glutamic acid immonium ion of m/z 102. By contrast, protonated dipeptides with a gamma-linkage, H-Glu(Xxx-OH)-OH, do not show elimination of H(2)O or formation of m/z 102 but rather show elimination of NH(3), particularly in metastable ion fragmentation, and elimination of H-Xxx-OH to form m/z 130. Both the alpha- and gamma-dipeptides show formation of [H-Xxx-OH]H(+), with this reaction channel increasing in importance as the proton affinity (PA) of H-Xxx-OH increases. The characteristic loss of H(2)O and formation of m/z 102 are observed for the protonated alpha-tripeptide H-Glu-Gly-Phe-OH whereas the protonated gamma-tripeptide H-Glu(Gly-Gly-OH)-OH shows loss of NH(3) and formation of m/z 130 as observed for dipeptides with the gamma-linkage. Both tripeptides show abundant formation of the y(2)' ion under CID conditions, presumably because a stable anhydride neutral structure can be formed. Under metastable ion conditions protonated dipeptides of structure H-Xxx-Glu-OH show abundant elimination of H(2)O whereas those of structure H-Xxx-Gln-OH show abundant elimination of NH(3). The importance of these reaction channels is much reduced under CID conditions, the major fragmentation mode being cleavage of the amide bond to form either the a(1) ion or the y(1)' ion. Particularly when Xxx = Gly, under CID conditions the initial loss of NH(3) from the glutamine containing dipeptide is followed by elimination of a second NH(3) while the initial loss of H(2)O from the glutamic acid dipeptide is followed by elimination of NH(3). Isotopic labelling shows that predominantly labile hydrogens are lost in both steps. Although both [H-Gly-Glu-Gly-OH]H(+) and [H-Gly-Gln-Gly-OH]H(+) fragment mainly to form b(2) and a(2) ions, the latter also shows elimination of NH(3) plus a glycine residue and formation of protonated glycinamide. Isotopic labelling shows extensive mixing of labile and carbon-bonded hydrogens in the formation of protonated glycinamide.     

Synthesis of Fischer type-carbene complexes containing a coordinated thioimidate structural motif

This paper describes a tandem strategy to synthesize a series of new Fischer carbene complexes [(CO)(4)M[double bond, length as m-dash]C[N-(CH(2))(4)-]CH[double bond, length as m-dash]C(NRR')(SR'); M = Cr, W; R = Ar, R' = Me, -(CH(2))(2)-] with a thioimide or thiazoline fragment, in which the sulfur or nitrogen atom is coordinated to a metal center, depending on the nature of alkylating groups included as R'. We have trapped by protonation the proposed intermediate as the thioamide 12 [(CO)(5)W[double bond, length as m-dash]C[N-(CH(2))(4)-]CH(2)C(S)NHPh], which reveals the pathway of this reaction.