Proton Scrambling Research Articles

Low-energy H+ + H2 reactive collisions

An overview of the results of theoretical treatments of the reactive H+ + H2 system in the interval of collision energies Ec = (1 − 500) meV is presented. The inelastic and reactive processes occur via scrambling of protons and formation of a long-lived collision complex, allowing for the application of various statistical theories. The first systematic theoretical treatment has been based on the "most dynamically biased" (MDB) statistical theory. Recently, the numerically exact (converged) time-independent quantum mechanical (TIQM) calculations have been compared with the statistical quantum mechanical (SQM) model. Our recent results have demonstrated, within the mean-potential statistical (MPS) model, the importance of a proper incorporation of the permutation symmetry of equivalent protons taking part in the collision. We present detailed comparisons of the calculated cross sections and thermal rate coefficients obtained by using our MPS model with MDB, SQM and TIQM results.

The role of large-amplitude motions in the spectroscopy and dynamics of ${\rm H}_5^+$H5+

Protonated hydrogen dimer, H₅⁺, is the intermediate in the astrochemically important proton transfer reaction between H₃⁺ and H2. To understand the mechanism for this process, we focus on how large amplitude motions in H₅⁺ result in scrambling of the five hydrogen atoms in the collision complex. To this end, the one-dimensional zero-point corrected potential surfaces were mapped out as functions of reaction coordinates for the H₃⁺ + H2 collision using minimized energy path diffusion Monte Carlo [C. E. Hinkle and A. B. McCoy, J. Phys. Chem. Lett. 1, 562 (2010)]. In this study, the previously developed approach was extended to allow for the investigation of selected excited states that are expected to be involved in the proton scrambling dynamics. Specifically, excited states in the shared proton motion between the two H2 groups, and in the outer H2 bending motions were investigated. Of particular interest is the minimum distance between H₃⁺ and H2 at which all five hydrogen atoms become free to exchange. In addition, this diffusion Monte Carlo-based approach was used to determine the zero-point energy E0, the dissociation energy D0, and excitation energies associated with the vibrational motions that were investigated. The evolution of the wave functions was also studied, with a focus on how the intramolecular vibrations in H₅⁺ evolve into motions of H₃⁺ or H2. In the case of the proton scrambling, we find that the relevant transition states become fully accessible at separations between H₃⁺ and H2 of approximately 2.15 Å, a distance that is accessed by the excited states of H₅⁺ with two or more quanta in the shared proton stretch. The implications of this finding on the vibrational spectroscopy of H₅⁺ are also discussed.

Evidence for an Intermediate in the Methylation of CB11 H12 - with Methyl Triflate: Comparison of Electrophilic Substitution in Cage Boranes and in Arenes.

The trideuteriomethylation of BH vertices in CB11 H12 - and its derivatives with CD3 OTf (OTf=triflate, trifluoromethanesulfonate) yields a mixture of BCD3 and BCHD2 substitution products, thus demonstrating the intermediacy of a species with a long enough lifetime for hydrogen scrambling between the boron vertex and the methyl substituent. No such scrambling is observed if CD3 OTf is used to methylate toluene. According to density functional theory calculations, the intermediate in BH vertex methylation is a three-center bonded σ adduct of a methyl cation to the BH bond and the proton scrambling occurs via a transition structure containing a distorted square-pyramidal methane attached axially to a "naked" boron vertex. The subsequent proton or deuteron loss is presently not understood in detail. A general comparison of electrophilic substitution on closo-boranes and arenes is provided and similarities as well as differences are discussed. A recalculation of the optimized geometry of the CB11 Me12 . radical produced a second Jahn-Teller distorted minimum and resulted in a somewhat improved agreement between calculated and measured proton hyperfine coupling constants.

Nuclear-Spin Selection Rules in the Chemistry of Interstellar Nitrogen Hydrides

Nitrogen hydrides are at the root of the nitrogen chemistry in interstellar space. The detailed modeling of their gas phase formation, however, requires the knowledge of nuclear-spin branching ratios for chemical reactions involving multiprotonated species. We investigate in this work the nuclear-spin selection rules in both exothermic and near thermoneutral ion–molecule reactions involved in the synthesis of ammonia, assuming full scrambling of protons in the reaction complexes. The formalism of Oka [ J. Mol. Spectrosc. 2004, 228, 635] is employed for highly exothermic ion–molecule and dissociative recombination reactions. For thermoneutral reactions, a simple state-to-state statistical approach is suggested, which is in qualitative agreement with both quantum scattering and microcanonical statistical calculations. This model is applied to the seven atom reaction NH4(+) + H2, of possible importance in the nuclear-spin thermalization of ammonia.

The influence glutamic acid in protonated b3 → b2 formation from VGEIG and related analogs

A direct pathway for the fragmentation of peptide b3 fragment ions to b2 ions has, until now, not been identified. Experimental evidence for the formation of a b3 anhydride structure and isomerization to an extended macrocycle is demonstrated here by comparison of the completely different fragmentation patterns of the b3 ions generated from protonated VGEIG and its methyl ester. In particular, the absence of a b2 ion in the fragmentation spectrum of the methyl ester b3 indicates that facile fragmentation of an anhydride-type b3 is responsible for virtually all b2 ions formed. The stability of this b3 structure and the ease with which it fragments to the b2 may be responsible for the relatively high abundance of the b3 and b2 ions. IRMPD action spectroscopy measurements indicate the presence of a ring protonated oxazolone in the b2 population. VGEIG and three related analogs, VAlEIG, VAdEIG, and V(Aib)EIG were studied by QCID-HDX-SORI experiments in an FT-ICR instrument, and provide significant evidence for extensive alpha proton scrambling in an ion–molecule complex formed between the b2 and neutral loss fragment following formation of the b2. MS3 and HDX of VG(2,2-d2)EIG indicate that the scrambled b2 ions have the same structure as the unscrambled b2. Based on these data and with the support of molecular modeling, we propose a new mechanism for this scrambling, in which the alpha protons are transferred in a multi-step pathway during an ion–molecule complex formed between the b2 and amino-terminated anhydride ring neutral loss component.

Online H/D exchange liquid chromatography as a support for the mass spectrometric identification of the oxidation products of melatonin

The hydrogen-deuterium exchange of protonated melatonin and its in vitro oxidation end-products have been examined by liquid chromatography coupled with ion-trap mass spectrometry. Specific H/D scrambling of protons in the C2 and C4 positions of the indole ring during gas-phase fragmentation process was observed for both melatonin and its oxidation products. Collision-induced dissociation spectra showed losses of variably deuterated NH(3), H(2)O and CH(3)CONH(2). In addition, a similar H/D scrambling behaviour was observed for the oxidation products, obtained from the opening of the indole ring by oxidative attack. Fragmentation pathways are proposed and H/D scrambling has been employed as a fingerprint, allowing identification of N(1)-acetyl-5-methoxykynurenin (AMK), N(1)-acetyl-N(2)-formyl-5-methoxykynurenin (AFMK), dehydro-AFMK and hydroxymelatonin as the oxidation products of melatonin in vitro.

Microcanonical statistical study of ortho-para conversion in the reaction H3++H2→(H5+)*→H3++H2 at very low energies

The ortho-para conversion of H(3) (+) and H(2) in the reaction H(3) (+)+H(2)-->(H(5) (+))(*)-->H(3) (+)+H(2) in interstellar space is possible by scrambling the five protons via (H(5) (+))(*) complex formation. The product distribution of the ortho-para conversion reaction can be given by ratios of cumulative reaction probabilities (CRP) calculated by microcanonical statistical theory with conservation of energy, motional angular momentum, nuclear spin, and parity. A statistical method to calculate the state-to-state reaction probabilities for given initial nuclear spin species, rotational states, and collision energies is developed using a simple semiclassical approximation of tunneling and above-barrier reflection. A new calculation method of branching ratios for given total nuclear spins and scrambling mechanisms is also developed. The anisotropic long-range electrostatic interaction potential of H(2) in the Coulomb field of H(3) (+) is taken into account using the first-order perturbation theory in forming the complex. The CRPs and the product distribution of the ortho-para conversion reaction at very low energies with reactants in their ground vibronic and lowest rotational states for given initial nuclear spin species are presented as a function of collision energy assuming complete proton scrambling or incomplete proton scrambling. The authors show that the product distribution at very low energies (or very low temperatures) differs substantially from the high energy (or high temperature) limit branching ratios.

A study of the elimination of water from lithium‐cationized tripeptide methyl esters by means of tandem mass spectrometry and isotope labeling

Extensive isotope labeling (2H, 13C and 15N), collision-induced dissociation (CID) and multiple-stage tandem mass spectrometry were used to investigate the elimination of H2O from a series of model, metal-cationized tripeptide methyl esters. The present results corroborate our earlier suggestion that loss of water from lithiated peptides is initiated by a nucleophilic attack from the N-terminal side upon an amide carbonyl carbon atom to form a five-membered ring as an intermediate followed by 1,2-elimination of water. We show that the nucleophilic atom is the oxygen atom of the N-terminal amide group in the fragmentation of [AcGGGOMe+Li]+ as well as [GGGOMe+Li]+. However, the subsequent fragmentation is markedly different in the two cases as a result of the absence and presence of a free amino group. In particular, extensive scrambling of protons in the alpha-positions of GGGOMe is observed, presumably as a consequence of intervention of the basic amino group.

Investigation of intramolecular proton migration in a series of model, metal‐cationized tripeptides using in situ generation of an isotope label

In this study we used an isotope label, generated in situ, to investigate intramolecular proton migration or scrambling during formation of [b(2)+17+Li](+) products by collision-induced dissociation (CID) of Li(+)-cationized tripeptides. To generate the isotope label, we used a McLafferty-type rearrangement of N-terminally acetylated, C-terminal peptide tert-butyl esters in which all amide positions were exchanged with deuterium. Using a set of small, model peptides, we show that intramolecular proton scrambling occurs during CID, particularly amongst adjacent sites along a peptide backbone, on the time scales employed for low-energy collisional activation in an ion-trap mass spectrometer.

Insignificance of P−H···P Hydrogen Bonding: Structural Chemistry of Neutral and Protonated 1,8-Di(phosphinyl)naphthalene

While there is extensive information on 1,8-di(amino)naphthalene (i.e., the parent compound of the "proton sponge" series), the corresponding phosphorus compound has not been described. A high-yield synthesis of 1,8-di(phosphinyl)naphthalene (9) and the 1-naphthylphosphine reference compound (4) is now reported. Thermal decomposition of 9 leads to intramolecular dehydrogenative P-P coupling to afford 1,2-dihydro-1,2-diphosphaacenaphthene (10). Protonation of 9 and 4 with CF(3)SO(3)H gives quantitative yields of the monophosphonium salts 11 and 5, respectively. With excess acid and traces of moisture, the hydronium salt [C(10)H(6)(PH(2))(PH(3))](+)[H(3)O](+)2[CF(3)SO(3)](-) (13) is obtained. The structures of 9, 11, and 13 have been determined. Molecules of 9 have a planar naphthalene skeleton, C(10)H(6)P(2), with the two -PH(2) groups in a transoid conformation. The molecules form loose dimers in the crystal, the individual chiral enantiomers of which are related by a center of inversion. In contrast to the situation for the amino analogue, and despite the proximity of the two -PH(2) functions, there is no intra- or intermolecular hydrogen bonding. Solutions of 9 (in CD(2)Cl(2)) show equivalent P-bound hydrogen atoms due to conformational fluctionality. By analysis of the ABCD(2)XX'D'(2)C'B'A' spin system, it was shown that, in 9, there are strong through-space pericouplings [(n)J(P(X)P(X)(')) = 221.6 Hz, (n)J(P(X)H(D)(')) = 31.7 Hz, (n)J(H(D)H(D)(')) = 3.9 Hz]. In the cations of 11, the C(10)H(6)P(2) skeleton is also planar (by C(s) symmetry), with the -PH(2) and -PH(3)(+) groups in a conformation which rules out any P-H...P hydrogen bonding. The hydronium cation and the two triflate anions in 13 are associated into an anionic network through extensive hydrogen bonding surrounding stacks of the phosphonium cations. In solution, the cations of 11 and 13 show separate (31)P resonances for the two phosphorus atoms with fully resolved (1)J(PH) couplings, which indicate that there is no intra- or intercationic proton exchange. By contrast, the NMR spectra of solutions of [C(10)H(6)(NH(2))(NH(3))](+)X(-) salts show proton scrambling equilibrating all five N-bound hydrogen atoms, and in the crystal, the conformations of the cations feature intramolecular N-H...N hydrogen bonding.

Structure and protonation of the bis-ethylene adduct [Pt(micro-PBut2)(eta2-CH2=CH2)]2. Pt-H-P agostic interaction and proton scrambling.

The bis-ethylene derivative [Pt(micro-PBu(t)(2))(eta(2)-CH(2)=CH(2))](2) was prepared and characterized by X-ray diffraction; its protonation affords [Pt(2)(micro-PBu(t)(2))(micro-PBu(t)(2)H)(eta(2)-CH(2)=CH(2))(2)](CF(3)SO(3)), with a rarely observed P-H-M agostic proton in rapid exchange with those of the adjacent ethylene molecule.

Gas-phase reactions of protonated tryptophan

The gas phase reactions of protonated tryptophan have been examined in a quadrupole ion trap using a combination of collision induced dissociation, hydrogen–deuterium exchange, regiospecific deuterium labeling and molecular orbital calculations (at the B3LYP/6-31G* level of theory). The loss of ammonia from protonated tryptophan is observed as the primary fragmentation pathway, with concomitant formation of a [M + H − NH 3] + ion by nucleophilic attack from the C3 position of the indole side chain. Hydrogen–deuterium exchange and regiospecific deuterium labeling reveals that scrambling of protons in the C2 and C4 positions of the indole ring, via intramolecular proton transfer from the thermodynamically preferred site of protonation at the amino nitrogen, precedes ammonia loss. Molecular orbital calculations have been employed to demonstrate that the activation barriers to intramolecular proton transfer are lower than that for NH 3 loss.

5-Amino-3-imino-1,2,6,7-tetracyano-3H-pyrrolizine: characterization of the solvent-free solid phase and interaction with ammonia and water

The 5-amino-3-imino-1,2,6,7-tetracyano-3H-pyrrolizine (LH, C11H3N7), previously characterized as the 2:1 1-chloronaphthalene adduct, has been further investigated as a solvent-free solid phase. Strong intermolecular interactions take place in this phase, as revealed by the optical spectra of evaporated LH thin films (lambda;max=615 and 570 nm) compared to the optical spectrum of LH in solution (lambda;max=580 nm). 13C NMR spectra also support the occurrence of intermolecular attractive CN group interactions in the solid state. X-Ray diffraction patterns indicate that the controlled sublimation process of LH (Tsubl=200 °C, 10–6 mmHg) leads to films composed of highly oriented crystallites, with two main sets of diffracting planes parallel to the film surface. The refractive index of LH as an evaporated thin film has also been determined in the 400–800 nm spectral range (n=1–2). LH interacts with ammonia and/or water in the gas phase. In the first case the acid–base reaction (LH+NH3 ⇄L′·NH4+) occurs. The resulting L′ anion (L′C11H2N7–) is the 2-(5-amino-3,4-dicyano-2H-pyrrol-2-ylidene)-1,1,2-tricyanoethanide (A, lambda;max=525 nm) or the isomer 1,2,6,7-tetracyano-3,5-dihydro-3,5-diiminopyrrolizinide (B, lambda;max=680 nm), depending on the relative amount of water to ammonia in the gas phase. This reaction is driven by the hydrogen bonding of NH4+ to B and/or to water. In the second case a fast proton scrambling occurs.

Ab Initio Study of the H2Elimination from CH2OH+, CH2NH2+, and CH2SH+

The potential energy surfaces (PESs) of H2CXHn+ (X = O, n = 1; X = N, n = 2; X = S, n = 1) systems were investigated by using the ab initio method at MP2/6-311+G** and QCISD/6-311+G** levels, and single-point calculations on the MP2 and the QCISD geometries were performed at the QCISD(T)/6-311+G(3df,2p) level. At the QCISD(T)/6-311+G(3df,2p)//MP2/6-311+G** level including ZPVE correction from MP2/6-311+G** unscaled frequencies, the proton affinities are 168.9, 207.2, and 182.9 kcal/mol for formaldehyde, formaldimine, and thioformaldehyde, respectively, while the energy barriers and reaction energies for hydrogen 1,2-elimination from the corresponding protonated systems are 79.3 and 22.0, 90.3 and 42.2, and 61.9 and 27.9 kcal/mol, respectively. Hydrogen 1,1-eliminations are not competitive compared with 1,2-eliminations. The reaction path for hydrogen 1,2-elimination from protonated formaldehyde goes through planar structures, whereas those from protonated formaldimine and thioformaldehyde involve rotation about the C−X double bond. The hydrogen 1,2-elimination takes place through a concerted mechanism for protonated formaldehyde and formaldimine, whereas for protonated thioformaldehyde a two-step mechanism was found on the electronic PES. By taking account of the ZPVE correction, a concerted mechanism results. For protonated thioformaldehyde a TS for proton scrambling was found about 5 kcal/mol more stable than the TS for hydrogen 1,2-elimination (this energy difference remains even at the QCISD(T)/6-311+G(3df,2p)//MP2/6-311+G(3df,2p) level). This result is in contrast with deuterium label experiments.

Benzenium Ion Chemistry on Solid Metal Halide Superacids: In Situ13C NMR Experiments and Theoretical Calculations

The benzenium, toluenium, and ethylbenzenium ions were synthesized on aluminum bromide by coadsorption of the precursors with either HBr or alkyl bromide. Principal components of the 13C chemical shift tensors for the ring carbons of these species were measured from magic angle spinning spectra. The benzenium ion was static at 77 K but underwent both proton scrambling and anisotropic rotation at 298 K as well as oligomerization at higher loadings. The para form of the toluenium ion was the dominant isomer at 77 K, but a temperature-dependent equilibrium between the para and ortho isomers was observed at 273 K. Observations of 1H−13C self-decoupling and loading-dependent 13C shifts for small amounts of toluene on high-purity AlBr3 demonstrate the existence of trace Bronsted sites on an important Friedel−Crafts catalyst. Geometries of the benzenium ions were optimized with both MP2/6-311+G* and density functional calculations at B3LYP/6-311+G*; these were in very good agreement with one another. Energy calc...

Competitive 1,2- and 1,3-hydride shifts and the possible role of protonated and methylated cyclopropane intermediates in alkyl group rearrangements accompanying the thermal decomposition of saturated alkyl chloroformates in the liquid phase

Deuterium labelling shows that the thermal decomposition of ethyl chloroformate in the liquid phase yields chloroethane without rearrangement of the ethyl group. Longer chain primary alkyl chloroformates yield rearrangement products which can be rationalised on the basis of two initial competitive pathways, one involving a 1,2-hydride shift and the other the formation of a corner-protonated cyclopropane intermediate. The latter may be captured to yield rearranged primary alkyl chloride (with considerable proton scrambling in the n-propyl case) or give rise to a 1,3-hydride shift in higher alkyl groups (Bun, n-pentyl, 3-methylbutyl, n-octyl) where rearrangement to a s- or t-alkyl cation is possible. Successive 1,2-hydride shifts are of minor significance unless the second of these leads to a t-alkyl cation. The 3,3-dimethylbutyl group affords products derived from successive 1,2-shifts of hydrogen and methyl and also a 1,2-t-butyl shift which is thought to involve the intermediacy of a methylated cyclopropane. s-Alkyl cations derived directly from s-alkyl chloroformates show less tendency to rearrangement than those derived by rearrangement from primary alkyl chloroformates. Evidence is presented which suggests that alk-1-enes are formed from primary alkyl chloroformates via carbocation intermediates in which rearrangement by 1,2- and/or 1,3-hydride shift has occurred.

Proton magnetic resonance study of proton exchange kinetics in molten ammonium hydrogen sulphate

1 H n.m.r. spectra of molten ammonium hydrogen sulphate indicate that proton scrambling occurs both between cations and between cations and anions; rate constants for both processes are determined by Abragam–Bloch analysis.