Proton-bound Complex Research Articles

Investigation of the Proton-Bound Dimer of Dihydrogen Phosphate and Formate Using Infrared Spectroscopy in Helium Droplets.

Understanding the structural and dynamic properties of proton-bound complexes is crucial for elucidating fundamental aspects of chemical reactivity and molecular interactions. In this work, the proton-bound complex between dihydrogen phosphate and formate, and its deuterated counterparts, is investigated using IR action spectroscopy in helium droplets. Contrary to the initial expectation that the stronger phosphoric acid would donate a proton to formate, both experiment and theory show that all exchangeable protons are located in the phosphate moiety. The experimental spectra show good agreement with both scaled harmonic and VPT2 anharmonic calculations, indicating that anharmonic effects are small. Some H-bending modes of the nondeuterated complex are found to be sensitive to the helium environment. In the case of the partially deuterated complexes, the experiments indicate that internal dynamics leads to isomeric interconversion upon IR excitation.

UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban.

Two ion populations of protonated Rivaroxaban, [C19H18ClN3O5S + H]+, are separated under pure N2 conditions using differential mobility spectrometry prior to characterization in a hybrid triple quadrupole linear ion trap mass spectrometer. These populations are attributed to bare protonated Rivaroxaban and to a proton-bound Rivaroxaban-ammonia complex, which dissociates prior to mass-selecting the parent ion. Ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) studies indicate that both protonated Rivaroxaban ion populations are comprised of the computed global minimum prototropic isomer. Two ion populations are also observed when the collision environment is modified with 1.5% (v/v) acetonitrile. In this case, the protonated Rivaroxaban ion populations are produced by the dissociation of the ammonium complex and by the dissociation of a proton-bound Rivaroxaban-acetonitrile complex prior to mass selection. Again, both populations exhibit a similar CID behavior; however, UVPD spectra indicate that the two ion populations are associated with different prototropic isomers. The experimentally acquired spectra are compared with computed spectra and are assigned to two prototropic isomers that exhibit proton sharing between distal oxygen centers.

Solvation of HeH+ in neon atoms: Proton-bound complexes of mixed He and Ne

Abstract The proton-bound complexes of the structure Ne X HeH+, with x ranging from one to four, are explored to investigate the effect of additional neon atoms on binding energies and bright vibrational modes of complexes involving HeH+. The first chemistry that occurred within the universe took place between helium and hydrogen, producing HeH+, which has been shown to solvate successfully with neon to form NeHeH+. CCSD(T)/aug-cc-pVTZ computations show that additional neon atoms in the complex are bound more loosely but still destabilize the existing He–H bond. Additionally, as more neon atoms are added, the harmonic frequencies of the species begin to converge to approximately 1580 cm−1, roughly 60 cm−1 less than the NeHeH+ proton-bound complex. Neon destabilizes the HeH+ structure in every instance, no matter the amount of neons added or whether additional heliums are added.

Mechanisms of sequential ion-molecule reactions in protonated methanol using mass spectrometry, ab initio methods, and statistical modeling

We present mass spectrometry results for reactions of protonated methanol clusters, (CH3OH)nH+. Mass spectra indicate a preference for association over condensation at our experimental conditions and are used in conjunction with computational methods to probe the reaction mechanisms involved. We find that the reaction for the protonated monomer with neutral methanol consists of two entrance complexes that are in equilibrium due to a very small barrier between them. Statistical modeling indicates that competition between proton transfer, condensation, and association are dictated by the depth of the proton-bound complex and the height of the SN2 transition state. For the reaction of the protonated dimer we determine condensation is not energetically favorable at thermal energies as a solvation effect raises the SN2 barrier. Geometries for protonated methanol clusters (CH3OH)nH+ up to n = 6 are also provided, which allow us to examine the role of entropy and hydrogen bonding in these structures.

Supercharging Proteins: How Many Charges Can a Protein Carry?

Very highly charged proteins, so-called "supercharged" ions, can lose (excess) protons to background gases like N2 . It is remarkable that such extremely acidic species can be generated in electrospray ionization, in the presence of not just N2 but also much higher-basicity solvents. What mechanism(s) can explain such high charging, and what is the ultimate limit?

On the spectroscopic constants, first electronic state, vibrational frequencies, and isomerization of hydroxymethylene (HCOH[formula omitted

The hydroxymethylene cation (HCOH+) is believed to be chemically independent of the more stable formaldehyde cation isomer in interstellar chemistry and may likely be a precursor to methanol in chemical reaction networks. Previous work is corroborated here showing that the trans conformer of HCOH+ is 3.48 kcal/mol lower than the cis on the potential energy surface. The small energy difference between the conformers and the much larger dipole moment of cis-HCOH+ (2.73 D) make this conformer more likely to be observed than trans-HCOH+ via telescopic rotational spectroscopy. A strong adiabatic shift is also predicted in the first electronic excitation into the 1 2A′′/2 2A state out of either conformer into a C1 structure reducing the excitation wavelength from the near-ultraviolet all the way into the near-infrared. The full set of fundamental vibrational frequencies are also computed here at high-level. The 3306.0 cm−1 and 3225.3 cm−1 hydroxide stretches, respective of bare trans- and cis-HCOH+, are in agreement with previous theory but are significantly higher than the frequencies determined from previous experiment utilizing argon tagging techniques. This shift is likely because the proton-bound complex created with the argon tag reduces the experimental frequencies. Lower-level computations including the argon tag bring the hydroxide stretches much closer to the experimental frequencies indicating that the predicted frequencies for bare HCOH+ are likely well-described.

TOWARD THE ASTRONOMICAL DETECTION OF THE PROTON-BOUND COMPLEX NN–HCO+: IMPLICATIONS FOR THE SPECTRA OF PROTOPLANETARY DISKS

ABSTRACT Proton-bound complexes have been hypothesized as further means of detecting the nitrogen molecule in the interstellar medium. The study of such complexes has largely been hindered by the necessary experimental setups utilized or by their difficulty in producing and/or analyzing computed potential energy surfaces. Here the NN–HCO+ proton-bound complex is analyzed via quartic force fields (QFFs). While QFFs have produced meaningful results for other proton-bound complexes, they have been hindered by double-well potentials or flat potential surfaces. NN–HCO+ is not affected by these constraints. This strongly dipolar (3.63 D) molecule can be observed rotationally unlike the more heavily analyzed OCHCO+ and NNHNN+ proton-bound complexes. Additionally, the large absorption feature corresponding to the proton motion, a hallmark of proton-bound complexes, is much higher in frequency at 2547.1 cm−1, changing the range of experimental observation for the bright frequency. NN–HCO+ is hypothesized to be present in protoplanetary disks where N2H+ and CO are known. As such, it may help to influence the nitrogen budget of planet-forming astronomical regions.

Ion-molecule reactions involving HCO+and N2H+: Isotopologue equilibria from new theoretical calculations and consequences for interstellar isotope fractionation

$Aims$: We revisit with new augmented accuracy the theoretical dynamics of basic isotope exchange reactions involved in the $^{12}$C/$^{13}$C, $^{16}$O/$^{18}$O, and $^{14}$N/$^{15}$N balance because these reactions have already been studied experimentally in great detail. $Methods$: Electronic structure methods were employed to explore potential energy surfaces, full-dimensional rovibrational calculations to compute rovibrational energy levels that are numerically exact, and chemical network models to estimate the abundance ratios under interstellar conditions. $Results$: New exothermicities, derived for HCO$^+$ reacting with CO, provide rate coefficients markedly different from previous theoretical values in particular at low temperatures, resulting in new abundance ratios relevant for carbon chemistry networks. In concrete terms, we obtain a reduction in the abundance of H$^{12}$C$^{18}$O$^+$ and an increase in the abundance of H$^{13}$C$^{16}$O$^+$ and D$^{13}$C$^{16}$O$^+$. In all studied cases, the reaction of the ion with a neutral polarizable molecule proceeds through the intermediate proton-bound complex found to be very stable. For the complexes OCH$^+$...CO, OCH$^+$...OC, COHOC$^+$, N$_2$...HCO$^+$, N$_2$H$^+$...OC, and N$_2$HN$_2^+$, we also calculated vibrational frequencies and dissociation energies. $Conclusions$: The linear proton-bound complexes possess sizeable dipole moments, which may facilitate their detection.

Structural and spectroscopic study of the linear proton-bound complex of PN with HNP+

This work reports the results of high level ab initio calculations of the PN-HNP(+) complex and the corresponding hydrogen migration transition state. The geometries, rotational constants, harmonic vibrational frequencies, and energetics of each species involved in the complex are reported. A reduced dimensional 2D and 4D potential energy surface is constructed and used to obtain 2D and 4D vibrational states. The results of this study show excellent correlation to available experimental data for PN. The presented results can facilitate both laboratory and interstellar observations of this novel and strongly interacting linear proton-bound complex.

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.

Proton Transfer and Dissociation of GlyLysH+ following O–H and N–H Stretching Mode Excitations: Dynamics Simulations

Proton transfer and dissociation processes following excitation of the OH or NH stretching modes of the proton-bound complex GlyLysH(+) are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are sampled to correspond to the v=1 excited state of the OH or NH stretching modes. Five different conformers of the complex are studied as initial structures. The main findings are (1) Photoinduced proton transfer is on the picosecond time scale. (2) Proton transfer is much faster than the processes of dissociation. (3) Proton transfer involves different sites. Most trajectories show sequences of two proton transfer events. (4) The proton transfer events show high selectivity with regard to the initially excited vibration and the initial structure. (5) Photodissociation of the complex occurs on a typical time scale of 100 ps. (6) Conformational transitions are found to be often faster than proton transfer. These results have implications for the mass spectrometry of complexes, for dynamics of proton wires, and for proton migration in proteins.

Fragmentation characteristics of bn (n = 2–15) ions from protonated peptides

The fragmentation reactions of protonated oligoalanines (trialanine, tetraalanine and pentaalanine) and the fragments present in the electrospray ionization (ESI) mass spectrum of polyalanine have been studied by collisionally activated dissociation (CAD) mass spectrometry (MS(2) and MS(3) experiments). The MS(n) experiments provided strong evidence that the m/z 71n+1 ion series in the ESI mass spectrum of polyalanine is a b(n) series. These ions are formed via the b(n) -y(m) pathway of amide bond cleavage, which results in the formation of a proton-bound complex of an oxazolone and a peptide/amino acid. Also, the MS(2) spectra of the b(n) series from polyalanine revealed that the chain length of b(n) ions influences significantly the dissociations taking place. For example, b(n) ions start losing H(2)O at n ≥5 and the losses of CO and CO+NH(3) decrease in intensity from b(2) to b(15). The elimination of H(2)O+NH(3) and the elimination of 61 mass (HN=C=O+H(2)O) commence with b(6); their abundances initially increase up to ~ b(8)-b(9) and then gradually decrease until b(15) (largest fragment studied). The tandem mass spectrometry experiments help to elucidate the dissociation mechanisms of the observed structures of biopolymer fragments.

Aromatic Nucleophilic Substitution (S NAr) Reactions of 1,2- and 1,4-Halonitrobenzenes and 1,4-Dinitrobenzene with Carbanions in the Gas Phase

In the gas-phase reactions of halonitro- and dinitrophenide anions with X (X = F, Cl, Br, NO(2)) and NO(2) groups in ortho or para position to each other with selected C-H acids: CH(3)CN, CH(3)COCH(3), and CH(3)NO(2), products of the S(N)Ar-type reaction are formed. Nitrophenide anions are generated by decarboxylation of the respective nitrobenzenecarboxylate anions in ESI ion source and the S(N)Ar reaction takes place either in the medium-pressure zone of the ion source or in the collision chamber of the triple quadrupole mass spectrometer. In the case of F, Cl, and NO(2) derivatives, the main ionic product is the respective [NO(2)-Ph-CHR](-) anion (R = CN, COCH(3), NO(2)). In the case of Br derivatives, the main ionic product is Br(-) ion because it has lower proton affinity than the [NO(2)-Ph-CHR](-) anion (for R = CN, COCH(3)). For some halonitrophenide anion C-H acid pairs of reactants, the S(N)Ar reaction is competed by the formation of halophenolate anions. This reaction can be rationalized by the single electron-transfer mechanism or by homolytic C-H bond cleavage in the proton-bound complex, both resulting in the formation of the halonitrobenzene radical anion, which in turn undergoes -NO(2) to -ONO rearrangement followed by the NO(.) elimination.

The proton-bound complex Cl −⋯H-CCl 3: A high-level theoretical study

Large-scale coupled cluster calculations within variant CCSD(T) have been employed to study major portions of the potential energy and electric dipole moment surfaces for the hydrogen-bonded anionic complex Cl −⋯H-CCl 3. The recommended dissociation energy D 0 is 6280 cm −1 or 75.1 kJ mol −1, with an estimated error of ca. 1%. Upon complex formation, the weak CH stretching vibration ( ν 1) of free HCCl 3 experiences an intensity enhancement by four orders of magnitude, with anharmonicity effects playing an important role. The band origins of the ν 1 bands of 35Cl −⋯H-C 35Cl 3 and 35Cl −⋯H-D 35Cl 3 are calculated at 2553 and 1949 cm −1, respectively.

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.

Collision-Induced Dissociation of HS-(HCN): Unsymmetrical Hydrogen Bonding in a Proton-Bound Dimer Anion

The energy-resolved competitive collision-induced dissociation of the proton-bound complex [HS.H.CN](-) is studied in a guided ion beam tandem mass spectrometer. H(2)S and HCN have nearly identical gas-phase acidities, and therefore, the HS(-) + HCN and the CN(-) + H(2)S product channels exhibit nearly the same threshold energies, as expected. However, the HS(-) + HCN channel has a cross section up to a factor of 50 larger than CN(-) + H(2)S at higher energies. The cross sections are modeled using RRKM theory and phase space theory. The complex dissociates to HS(-)+ HCN via a loose transition state, and it dissociates to CN(-) + H(2)S via a tight transition state. Theoretical calculations show that the proton-transfer potential energy surface has a single minimum and that the hydrogen bonding in the complex is strongly unsymmetrical, with an ion-molecule complex of the form HS(-)..HCN rather than CN(-)..H(2)S or an intermediate structure. The requirement for proton transfer before dissociation and curvature along the reaction path impedes the CN(-) + H(2)S product channel.

Fragmentation of protonated oligoalanines: Amide bond cleavage and beyond

The fragmentation reactions of the singly-protonated oligoalanines trialanine to hexaalanine have been studied using energy-resolved mass spectrometry in MS(2) and MS(3) experiments. The primary fragmentation reactions are rationalized in terms of the b(x)-y(z) pathway of amide bond cleavage which results in formation of a proton-bound complex of an oxazolone and a peptide/amino acid; on decomposition of this complex the species of higher proton affinity preferentially retains the proton. For protonated pentaalanine and protonated hexaalanine the major primary fragmentation reaction involves cleavage of the C-terminal amide bond to form the appropriate b ion. The lower mass b ions originate largely, if not completely, by further fragmentation of the initially formed b ion. MS(3) energy-resolved experiments clearly show the fragmentation sequence b(n) --> b(n-1) --> b(n-2). A more minor pathway for the alanines involves the sequence b(n) --> a(n) --> b(n-1) --> b(n-2). The a(5) ion formed from hexaalanine loses, in part, NH(3) to begin the sequence of fragmentation reactions a(5) --> a(5)* --> a(4)* --> a(3)* where a(n)* = a(n) - NH(3). The a(3)* ion also is formed from the b(3) ion by the sequence b(3) --> a(3) --> a(3)* with the final step being sufficiently facile that the a(3) ion is not observed with significant intensity in CID mass spectra. A cyclic structure is proposed for the a(3)* ion.

Formation of iminium ions by fragmentation of a2 ions.

Tandem mass spectrometric experiments have been carried out on the protonated amides H-Gly-Ala-NH2, H-Ala-Gly-NH2, H-Ala-Val-NH2, H-Val-Ala-pNA, H-Leu-Phe-NH2, H-Phe-Leu-NH2, H-Phe-Tyr-NH2 and H-Tyr-Phe-NH2 with particular emphasis on the fragmentation of the isomeric a2 ions derived therefrom. Primary fragmentation reactions of the protonated amides involve formation of the y1" and b2 ions with further fragmentation of the b2 ion to form the a2 ion which fragments to form iminium ions. Collision-induced dissociation studies of the mass-selected a2 ions were carried out. For the Gly-Ala, Ala-Gly and Val-Ala a2 ions, weak signals were observed corresponding to loss of CO from the a2 ion. With the exception of the Gly-Ala, Ala-Gly and Val-Ala a2 ions, both possible iminium ions (a1 and the internal iminium ion) are observed with the most abundant being that formed by proton attachment to the imine of higher proton affinity. The results provide strong support for the recently proposed (El Aribi et al. J. Am. Chem. Soc. 2003; 125: 9229) mechanism of fragmentation of a2 ions which involves elimination of CO from the a2 ion to form a proton-bound complex of two imines. Based on this mechanism ab initio calculations of the total energies of the a2 ions and the transition states for fragmentation have been carried out giving the energy barrier for fragmentation of each a2 ion. The experimental results are interpreted in terms of these energetics data, unimolecular rate constants calculated by using the RRKM theory, and the imine proton affinities.

In-source H/D exchange and ion-molecule reactions using matrix assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry with pulsed collision and reaction gases

Controlled in-source ion-molecule reactions are performed for the first time in an external matrix assisted laser desorption ionization (MALDI) source of a Fourier transform ion cyclotron resonance mass spectrometer. The MALDI source with a hexapole ion guide that was originally designed to incorporate pulsed gas to collisionally cool ions (Baykut, G.; Jertz, R.; Witt, M. Rapid Commun. Mass Spectrom. 2000, 14, 1238–1247) has been modified to allow the study of in-source ion-molecule reactions. Upon laser desorption, a reaction gas was introduced through a second inlet and allowed to interact with the MALDI-generated ions trapped in the hexapole ion guide. Performing ion-molecule reactions in the high pressure range of the ion source prior to analysis in the ion cyclotron resonance (ICR) cell allows to maintain the ultra high vacuum in the cell which is crucial for high mass resolution measurements. In addition, due to the reaction gas pressure in the hexapole product ion formation is much faster than would be otherwise possible in the ICR cell. H/D exchange reactions with different peptides are investigated, as are proton-bound complex formations. A typical experimental sequence would be ion accumulation in the hexapole ion guide from multiple laser shots, addition of cooling gas during ion formation, addition of reaction gas, varied time delays for the ion-molecule reactions, and transmission of the product ions into the ICR cell for mass analysis. In this MALDI source H/D exchange reactions for different protonated peptides are investigated, as well as proton-bound complex formations with the reaction gas triethylamine. Amino acid sequence, structural flexibility and folding state of the peptides can be seen to play a part in the reactivity of such ions.

Gas-phase acidity and C–H bond energy of diacetylene

Threshold energies for the proton transfer reaction C 4H −+C 2H 2 → C 4H 2+C 2H − and for competitive collision-induced dissociation of the proton-bound complex of diacetylide and acetaldehyde, [HC 4··H··CH 2CHO] −, are measured using guided ion beam tandem mass spectrometry. From the bimolecular proton transfer threshold, the gas-phase acidity of diacetylene is Δ acid H 0(C 4H 2)≥1500±8 kJ/mol as a lower limit. The competitive dissociation is modeled using RRKM theory, yielding Δ acid H 0(C 4H 2)=1508±12 kJ/mol. Using the literature electron affinity of C 4H, the derived bond dissociation energy of diacetylene is D 0(HC 4–H)=539±12 kJ/mol.