Hypervalent Ammonium Radicals. Effects of Alkyl Groups and Aromatic Substituents

Organohypervalent heterocycles

This review summarizes the structural and synthetic aspects of heterocyclic molecules incorporating an atom of a hypervalent main-group element. The term "hypervalent" has been suggested for derivatives of main-group elements with more than eight valence electrons, and the concept of hypervalency is commonly used despite some criticism from theoretical chemists. The significantly higher thermal stability of hypervalent heterocycles compared to their acyclic analogs adds special features to their chemistry, particularly for bromine and iodine. Heterocyclic compounds of elements with double bonds are not categorized as hypervalent molecules owing to the zwitterionic nature of these bonds, resulting in the conventional 8-electron species. This review is focused on hypervalent heterocyclic derivatives of nonmetal main-group elements, such as boron, silicon, nitrogen, carbon, phosphorus, sulfur, selenium, bromine, chlorine, iodine(III) and iodine(V).

Synthesis and properties of hypervalent electron-rich pentacoordinate nitrogen compounds

Isolation and structural characterization of hypervalent electron-rich pentacoordinate nitrogen species have not been achieved despite continuous attempts for over a century. Herein we report the first synthesis and isolation of air stable hypervalent electron-rich pentacoordinate nitrogen cationic radical (11-N-5) species from oxidation of their corresponding neutral (12-N-5) species. In the cationic radical species, the nitrogen centers adopt a trigonal bipyramidal geometry featuring a 3-center-5-electron hypervalent attractive interaction. The combination of single crystal X-ray diffraction analysis and computational studies revealed weak N-O interactions between the central nitrogen cation and oxygen atoms. This successful design strategy and isolation of air-stable pentacoordinate hypervalent nitrogen species allow further investigations on reactivity and properties resulting from these unusually weakly coordinating interactions in nitrogen compounds.

Stereospecific control of peptide gas-phase ion chemistry with cis and trans cyclo ornithine residues

We report non-chiral amino acid residues cis- and trans-1,4-diaminocyclohexane-1-carboxylic acid (cyclo-ornithine, cO) that exhibit unprecedented stereospecific control of backbone dissociations of singly charged peptide cations and hydrogen-rich cation radicals produced by electron-transfer dissociation. Upon collision-induced dissociation (CID) in the slow heating regime, peptide cations containing trans-cO residues undergo facile backbone cleavages of amide bonds C-terminal to trans-cO. By contrast, peptides with cis-cO residues undergo dissociations at several amide bonds along the peptide ion backbone. Diastereoisomeric cO-containing peptides thus provide remarkably distinct tandem mass spectra. The stereospecific effect in CID of the trans-cO residue is explained by syn-facially directed proton transfer from the 4-ammonium group at cO to the C-terminal amide followed by neighboring group participation in the cleavage of the CO-NH bond, analogous to the aspartic acid and ornithine effects. Backbone dissociations of diastereoisomeric cO-containing peptide ions generate distinct [b_n ]⁺ -type fragment ions that were characterized by CID-MS³ spectra. Stereospecific control is also reported for electron-transfer dissociation of cis- and trans-cO containing doubly charged peptide ions. The stereospecific effect upon electron transfer is related to the different conformations of doubly charged peptide ions that affect the electron attachment sites and ensuing N-C_α bond dissociations.

Electron predators are hydrogen atom traps. Effects of aryl groups on N-C(α) bond dissociations of peptide radicals

Effects of substituted aryl groups on dissociations of peptide aminoketyl radicals were studied computationally for model tetrapeptide intermediates GXD(•) G where X was a cysteine residue that was derivatized by S-(3-nitrobenzyl), S-(3-cyanobenzyl), S-(3,5-dicyanobenzyl), S-(2,3,4,5,6-pentafluorobenzyl), and S-benzyl groups. The aminoketyl radical was placed within the Asp amide group. Aminoketyl radicals having the S-(3-nitrobenzyl) group were found to undergo spontaneous and highly exothermic migration of the hydroxyl hydrogen atom onto the nitro group in conformers allowing interaction between these groups. Competing reaction channels were investigated for aminoketyl radicals having the S-(3-cyanobenzyl) and S-(3,5-dicyanobenzyl) groups, e.g. H-atom migration to the C and N atoms of the C≡N group, migration to the C-4 position of the phenyl ring, and dissociation of the radical-activated NC(α) bond between the Asp and Gly residues. RRKM kinetic analysis on the combined B3LYP and ROMP2/6-311++G(2d,p) potential energy surface indicated > 99% H-atom transfer to the C≡N group forming a stable iminyl intermediate. The NC(α) bond dissociation was negligible. In contrast, peptides with the S-(2,3,4,5,6-pentafluorobenzyl) and S-benzyl groups showed preferential NC(α) bond dissociation that outcompeted H-atom migration to the C-4 position and fluorine substituents in the phenyl ring. These computational results are used to suggest an alternative mechanism for the quenching effect on electron-based peptide backbone dissociations of benzyl groups with electron-withdrawing substitutents, as reported recently.

Transition metals as electron traps. I. Structures, energetics, electron capture, and electron-transfer-induced dissociations of ternary copper-peptide complexes in the gas phase

Electron-induced dissociations of gas-phase ternary copper-2,2'-bipyridine complexes of Gly-Gly-Gly and Gly-Gly-Leu were studied on a time scale ranging from 130 ns to several milliseconds using a combination of charge-reversal ((+)CR(-)) and electron-capture-induced dissociation (ECID) measured on a beam instrument and electron capture dissociation (ECD) measured in a Penning trap. Charge-reduced intermediates were observed on the short time scale in the (+)CR(-) and ECID experiments but not in ECD. Ion dissociations following electron transfer or capture mostly occurred by competitive bpy or peptide ligand loss, whereas peptide backbone fragmentations were suppressed in the presence of the ligated metal ion. Extensive electron structure theory calculations using density functional theory and large basis sets provided optimized structures and energies for the precursor ions, charge-reduced intermediates, and dissociation products. The Cu complexes underwent substantial structure changes upon electron capture. Cu was calculated to be pentacoordinated in the most stable singly charged complexes of the [Cu(peptide-H)bpy](+*) type where it carried a approximately +1 atomic charge. Cu coordination in charge-reduced [Cu(peptide-H)bpy] intermediates depended on the spin state. The themodynamically more stable singlet states had tricoordinated Cu, whereas triplet states had a tetracoordinated Cu. Cu was tricoordinated in stable [Cu(peptide-H)bpy](-*) products of electron transfer. [Cu(peptide)bpy](2+*) complexes contained the peptide ligand in a zwitterionic form while Cu was tetracoordinated. Upon electron capture, Cu was tri- or tetracoordinated in the [Cu(peptide)bpy](+) charge-reduced analogs and the peptide ligands underwent prototropic isomerization to canonical forms. The role of excited singlet and triplet electronic states is assessed.

Probing the mechanism of electron capture and electron transfer dissociation using tags with variable electron affinity

Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of doubly protonated electron affinity (EA)-tuned peptides were studied to further illuminate the mechanism of these processes. The model peptide FQpSEEQQQTEDELQDK, containing a phosphoserine residue, was converted to EA-tuned peptides via beta-elimination and Michael addition of various thiol compounds. These include propanyl, benzyl, 4-cyanobenzyl, perfluorobenzyl, 3,5-dicyanobenzyl, 3-nitrobenzyl, and 3,5-dinitrobenzyl structural moieties, having a range of EA from -1.15 to +1.65 eV, excluding the propanyl group. Typical ECD or ETD backbone fragmentations are completely inhibited in peptides with substituent tags having EA over 1.00 eV, which are referred to as electron predators in this work. Nearly identical rates of electron capture by the dications substituted by the benzyl (EA = -1.15 eV) and 3-nitrobenzyl (EA = 1.00 eV) moieties are observed, which indicates the similarity of electron capture cross sections for the two derivatized peptides. This observation leads to the inference that electron capture kinetics are governed by the long-range electron-dication interaction and are not affected by side chain derivatives with positive EA. Once an electron is captured to high-n Rydberg states, however, through-space or through-bond electron transfer to the EA-tuning tags or low-n Rydberg states via potential curve crossing occurs in competition with transfer to the amide pi* orbital. The energetics of these processes are evaluated using time-dependent density functional theory with a series of reduced model systems. The intramolecular electron transfer process is modulated by structure-dependent hydrogen bonds and is heavily affected by the presence and type of electron-withdrawing groups in the EA-tuning tag. The anion radicals formed by electron predators have high proton affinities (approximately 1400 kJ/mol for the 3-nitrobenzyl anion radical) in comparison to other basic sites in the model peptide dication, facilitating exothermic proton transfer from one of the two sites of protonation. This interrupts the normal sequence of events in ECD or ETD, leading to backbone fragmentation by forming a stable radical intermediate. The implications which these results have for previously proposed ECD and ETD mechanisms are discussed.

The effect of radical trap moieties on electron capture dissociation spectra of substance P

To further test the hypothesis that electron capture dissociation (ECD) involves long-lived radical intermediates and radical migration occurs within these intermediates before fragmentation, radical trap moieties were attached to peptides with the assumption that they would reduce fragmentation by decreasing the mobility of the radical. Coumarin labels were chosen for the radical traps, and unlabeled, singly-labeled, and doubly-labeled Substance P were analyzed by ECD. The results demonstrated a correlation between the number and position of tags on the peptide and the intensity of side-chain cleavages observed, as well as an inverse correlation between the number of tags on the peptide and the intensity of backbone cleavages. Addition of radical traps to the peptide inhibits backbone cleavages, suggesting that either radical mobility is required for these cleavages, or new noncovalent interactions prevent separation of backbone cleavage fragments. The enhancement of side-chain cleavages and the observation of new side-chain cleavages associated with aromatic groups suggest that the gas-phase conformation of this peptide is substantially distorted from untagged Substance P and involves previously unobserved interactions between the coumarin tags and the phenylalanine residues. Furthermore, the use of a double resonance (DR)-ECD experiment showed that these side-chain losses are all products of long-lived radical intermediate species, which suggests that steric hindrance prevents the coumarin-localized radical from interacting with the backbone while simultaneously increasing the radical rearrangements with the side chains.

Study of a bisquaternary ammonium salt by atmospheric pressure photoionization mass spectrometry

A comprehensive atmospheric pressure photoionization (APPI) mass spectrometry investigation of hexamethonium bromide is reported. This bisquaternary ammonium salt is a model system for the investigation of multiply charged species and elucidation of ion formation processes. It has been used to elucidate the physicochemical phenomenon occurring when photoionization is carried out at atmospheric pressure. First, the in-source fragmentations were studied for aqueous solutions of the salt with the photoionization lamp switched off, i.e. under thermospray conditions. It is shown that, in this mode of operation, fragmentations are minor and may be classified into two classes, namely dequaternization and charge separation, arising from the two precursors, M2+ and [M+Br]+. Second, the fragmentation patterns have been monitored in dopant- assisted APPI for different dopants (toluene, toluene-d8, anisole and hexafluorobenzene) at various amounts. At low dopant flow rates, the [M+Br]+ and M2+ ions are still observed. As the flow rate is increased, these precursor ions lose intensity and are finally suppressed for all three dopants. Comparison of toluene and toluene-d8 reveals that H atoms may be transferred from the dopant to the molecular ions, very likely mediated by the solvent. The role of the solvent (water) was also investigated by using heavy water. Apart from the thermospray fragmentations, which are also observed in APPI, several fragmentation pathways appear to be specific to the photoionization process. Photoionization efficiencies are measured by determination of the relative photoionization cross sections with respect to toluene. It is found that, when the ionization efficiencies are taken into account, the depletion of the precursors as a function of the dopant flow rates is the same for all three dopant molecules. This result shows that the precursor ions are depleted by reactions with the photoelectrons released from the dopant. Three additional mechanisms are proposed to account for this effect: electron transfer or H atom transfer from negatively charged water nanodroplets and H atom transfer from the dopant.

Bonding along a linear B...N...B triad

The synthesis of tris(2,6-dihydroxyphenyl)amine diborate, 4, is reported. This compound contains a linear B...N...B array for which a symmetrical three-center two-electron (3c-2e) bond is possible. The X-ray crystal structure of 4 shows that 3c-2e bonding is, in fact, absent. Rather, the B-N-B array of 4 is unsymmetrical, having a 2c-2e B-N dative bond with the remaining boron pyramidalized outward and bonded to the oxygen of THF, i.e., 4 x THF. In THF solution, 4 displays temperature-dependent 13C NMR spectra from which a DeltaG++ of 11.6 kcal/mol at 262 K may be calculated. The dynamic process observed in solution corresponds to a bond-switching equilibrium in which the B-N bond oscillates between the two borons ("bell clapper"). Ab initio calculations indicate that the most likely pathway for the bond switch does not involve a 3c-2e B...N...B bond, but rather occurs by nucleophilic attack of THF on the datively bonded boron to generate 4 x (THF)2, lacking any B-N interactions, followed by loss of one THF. The B-N-B system of 4 sans the perturbing effect of solvent was also investigated computationally. The form of 4 containing a 3c-2e bond is found to be a transition state in the solvent-free bond-switch reaction of 4, lying 2.66 kcal/mol above 4. The stability of three-center bonds to in-line distortion (viz., X...Y...X --> X-Y.........X) is discussed from the point of view of the second-order Jahn-Teller effect.

Toward a general mechanism of electron capture dissociation

The effects of positive charge on the properties of ammonium and amide radicals were investigated by ab initio and density functional theory calculations with the goal of elucidating the energetics of electron capture dissociation (ECD) of multiply charged peptide ions. The electronic properties of the amide group in N-methylacetamide (NMA) are greatly affected by the presence of a remote charge in the form of a point charge, methylammonium, or guanidinium cations. The common effect of the remote charge is an increase of the electron affinity of the amide group, resulting in exothermic electron capture. The N-Calpha bond dissociation and transition state energies in charge-stabilized NMA anions are 20-50 kJ mol(-1) greater than in the hydrogen atom adduct. The zwitterions formed by electron capture have proton affinities that were calculated as 1030-1350 kJ mol(-1), and are sufficiently basic for the amide carbonyl to exothermically abstract a proton from the ammonium, guanidinium and imidazolium groups in protonated lysine, arginine, and histidine residues, respectively. A new mechanism is proposed for ECD of multiply charged peptide and protein cations in which the electron enters a charge-stabilized electronic state delocalized over the amide group, which is a superbase that abstracts a proton from a sterically proximate amino acid residue to form a labile aminoketyl radical that dissociates by N-Calpha bond cleavage. This mechanism explains the low selectivity of N-Calpha bond dissociations induced by electron capture, and is applicable to dissociations of peptide ions in which the charge carriers are metal ions or quaternary ammonium groups. The new amide superbase and the previously proposed mechanisms of ECD can be uniformly viewed as being triggered by intramolecular proton transfer in charge-reduced amide cation-radicals. In contrast, remote charge affects N-H bond dissociation in weakly bound ground electronic states of hypervalent ammonium radicals, as represented by methylammonium, CH3NH3*, but has a negligible effect on the N-H bond dissociation in the strongly bound excited electronic states. This refutes previous speculations that loss of "hot hydrogen" can occur from an excited state of an ammonium radical.

Cycloreversion and other gas-phase reactions of neutral and cationic pyrrolidine-fused chlorins and isobacteriochlorins under ion bombardment and electrospray

Neutral and cationic pyrrolidine-fused chlorins and isobacteriochlorins derived from meso-tetrakis(pentafluorophenyl)porphyrin undergo cycloreversion reactions in the gas phase, either when desorbed from a liquid matrix by ion bombardment or when electrosprayed. Cycloreversion occurs through loss of either neutral or charged moieties, with and without hydrogen and methyl radical migration, and both as high- and low-energy collision processes. For the doubly charged isobacteriochlorin, one-electron reduction with methyl loss occurs under ion bombardment and electrospray, through hypervalent pyrrolidinium radical formation.

Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation-radicals and dications corresponding to hydrogen atom adducts to N-terminus-protonated N(alpha)-glycylphenylalanine amide (Gly-Phe-NH(2)) are studied by combined density functional theory and Møller-Plesset perturbational computations (B3-MP2) as models for electron-capture dissociation of peptide bonds and elimination of side-chain groups in gas-phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation-radicals, and hydrogen-bonded ion-radicals, and ylid-cation-radical complexes. The hydrogen-bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N-C(alpha) bonds in aminoketyl cation-radicals are 18-47 kJ mol(-1) exothermic and require low activation energies to produce ion-radical complexes as stable intermediates. Loss of the side-chain benzyl group is calculated to be 44 kJ mol(-1) endothermic and requires 68 kJ mol(-1) activation energy. Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations of unimolecular rate constants predict fast preferential N-C(alpha) bond cleavage resulting in isomerization to ion-molecule complexes, while dissociation of the C(alpha)bond;CH(2)C(6)H(5) bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation-radicals that have thermal (298 K) energies and thus behave ergodically.

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.

Stereochemical interactions in ammonium dications, hypervalent diammonium cation-radicals and ammonium radicals. A B3-MP2 computational study

Hypervalent ammonium radicals and cation-radicals derived from cis and trans-cyclopentane-1,2-diamine have been studied computationally with the goal of elucidating intramolecular interactions between the ammonium and amine functional groups in a conformationally rigid model system. Hypervalent cis and trans-cyclopentane-1-ammonium-2-amine radicals are only marginally stable against dissociation by loss of an ammonium hydrogen atom and ammonia. The radicals are predicted to exhibit very similar dissociations originating from the ground and excited electronic states. The dissociation and transition state energies in bifunctional hypervalent ammonium radicals are analogous to those reported previously for monofunctional ammonium radicals. Stereochemical effects are predicted to occur in the formation and dissociations of hypervalent cis and trans-cyclopentane-1,2-diammonium cation-radicals. The cis-isomer is calculated to undergo very facile elimination of dihydrogen resulting from a dipolar H(+)....H(-) interaction between the ammonium groups. The trans-isomer is predicted to spontaneously dissociate to a complex of cyclopentene cation-radical and two ammonia molecules.

Silicon surfaces as electron acceptors: dative bonding of amines with Si(001) and Si(111) surfaces

The bonding of the trimethylamine (TMA) and dimethylamine (DMA) with crystalline silicon surfaces has been investigated using X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy, and density-functional computational methods. XPS spectra show that TMA forms stable dative-bonded adducts on both Si(001) and Si(111) surfaces that are characterized by very high N(1s) binding energies of 402.2 eV on Si(001) and 402.4 eV on Si(111). The highly ionic nature of these adducts is further evidenced by comparison with other charge-transfer complexes and through computational chemistry studies. The ability to form these highly ionic charge-transfer complexes between TMA and silicon surfaces stems from the ability to delocalize the donated electron density between different types of chemically distinct atoms within the surface unit cells. Corresponding studies of DMA on Si(001) show only dissociative adsorption via cleavage of the N-H bond. These results show that the unique geometric structures present on silicon surfaces permit silicon atoms to act as excellent electron acceptors.