Proton-bound Heterodimers Research Articles

Impact of Ambient Vapors on Spectra of 4-Nitroaniline Recorded under Atmospheric Solids Analysis Probe (ASAP) Mass Spectrometric Conditions.

Thermally desorbed 4-nitroaniline (4-NA), upon atmospheric pressure chemical ionization (APCI), generates gaseous ions for its protonated species. The APCI mass spectrum recorded under mild in-source ion-activating conditions from 4-NA showed a peak at m/z 139, whereas that acquired under high ion-activating conditions showed two additional peaks at m/z 122 (•OH loss) and 92 (•NO loss). The spectrum changed instantaneously when acetonitrile vapor was introduced to the source. In the new spectrum, both m/z 122 and 92 peaks were absent, while a new peak appeared at m/z 93. Ion-mobility separation carried out with the m/z 139 ion revealed that the initial ion represented the thermodynamically favored nitro-protonated tautomer. The ion population changed to an ensemble dominated by the less-favored amino-protomer when acetonitrile vapor was introduced to the ion source. The amino-protomer, upon collisional activation, loses •NO2 to generate an m/z 93 ion, which was confirmed to be the 4-dehydroanilinium ion. Ion mobility provided a practical way to monitor the changes secured by acetonitrile vapor because the two protomers showed different arrival times. Under spray-ionization conditions, the formation of the thermodynamically less favored protomer has been attributed to kinetic trapping. Our study demonstrated that the less favored amino-protomer could be generated by introducing acetonitrile vapor under nonspray conditions. Apparently, under APCI conditions, protonated water vapor attaches to the nitro group to generate a proton-bound heterodimer, which upon activation dissociates to yield the nitro-protomer. In contrast, protonated acetonitrile makes a tighter complex preferentially with the amino group, which upon activation breaks to the amino-protomer.

Non-contact vapor detection of illicit drugs via atmospheric flow tube-mass spectrometry

Real-time, non-contact detection of illicit drugs is a desirable goal for the interdiction of these controlled substances, but the relatively low vapor pressures of such species present a challenge for trace vapor detection technologies. The introduction of atmospheric flow tube-mass spectrometry (AFT-MS), which has previously been demonstrated to detect gas-phase analytes at low parts-per-quadrillion levels for explosives and organophosphorus compounds, also enables the potential for non-contact drug detection. With AFT-MS, direct vapor detection of cocaine and methamphetamine from ∼5 μg residues at room temperature is demonstrated herein. Furthermore, thermal desorption of low- to sub-picogram levels of cocaine, methamphetamine, fentanyl, and heroin is observed via AFT-MS using a carrier flow rate of several L min-1 of air. These low levels can permit non-contact sampling through collection of vapor, effectively preconcentrating the analyte before desorption and analysis. Quantitative evaluation of the thermal desorption approach has yielded limits of detection (LODs) on the order of 10 fg for cocaine and fentanyl, 100 fg for methamphetamine, and 1.6 pg for heroin. The LOD for heroin was lowered to 300 fg by using tributyl phosphate as a dopant to form a proton-bound heterodimer with heroin. When used with AFT-MS, the intentional formation of specific drug-dopant adducts has the potential to enhance detection limits and selectivity of additional drug species. Species that are prone to form adducts present a challenge to analysis, but that difficulty can be overcome by the intentional addition of a dopant. Molecules unlikely to form adducts will remain essentially unimpacted, but the adduct-forming species will interact with the dopant to compress the analyte signal into a single peak. This approach would be valuable in the application of non-contact screening for illicit substances via vapor collection followed by thermal desorption for analysis.

Deducing Proton-Bound Heterodimer Association Energies from Shifts in Ion Mobility Arrival Time Distributions.

Through vapor modification of the counter-current drift gas in an atmospheric pressure drift tube ion mobility spectrometer (IMS), we demonstrate measurement of gas-phase association enthalpies and entropies for select proton-bound heterodimers formed from a phosphonic acid with 2-propanol. Previous efforts to determine gas-phase association thermodynamic properties have relied largely upon lower pressure systems and inference of the relative concentrations of m/ z isolated species. In contrast, the drift tube IMS based approach developed and applied in this study leverages the explicit gas-phase equilibrium that is established within an ion mobility drift cell. The inferred enthalpies and entropies of association are based solely upon monitoring a shift in the arrival time of an ion at different temperatures (and not on the signal intensity or on external instrument drift time calibration). We specifically report the gas-phase Gibbs free energy, enthalpy, and entropy changes for the association of 2-propanol with protonated methyl, ethyl, and propyl phosphonic acid ions (MPA, EPA, PPA) across the 100-175 °C temperature range. For all of these proton-bound heterodimers, the standard enthalpies and entropies of 2-propanol association were negative and positive, respectively. These data indicate that proton-bound heterodimer formation is both enthalpically and entropically favorable, though we find that the magnitude of the standard enthalpy change for vapor association is small (near 1 kcal/mol for all examined heterodimers). Though many prior results (largely obtained with high pressure mass-spectrometry) for other proton-bound organic heterodimer complexes show larger enthalpic favorability and an entropic barrier, our results qualitatively conform to the bulk Kelvin-Thomson-Raoult (KTR) model, which is commonly utilized in describing ion-induced nucleation of a vapor onto a soluble, nanometer scale ion. The KTR model suggests that heterodimer formation due to vapor binding to an ion should be slightly enthalpically favored (due to a larger Thomson effect than the Kelvin effect) and entropically favored because of ion solvation (Raoult's effect). The method presented in this study can be applied to any static-field ion mobility spectrometer and to a wide variety of heterodimers. Due to the ease of implementation and broad applicability, this approach may find consistent use in determining the thermodynamic properties of weakly bound gas-phase heterodimer complexes which are difficult to probe via alternative techniques. Moreover, this renewed implementation of the IMS experiment is directly compatible with soft ionization sources which will enable the characterization of vapor modifier-induced mobility shift experiments for larger molecular complexes.

Proton Transfer Accounting for Anomalous Collision-Induced Dissociation of Proton-Bound Hoogsteen Base Pair of Cytosine and Guanine.

To understand the anomalous collision-induced dissociation (CID) behavior of the proton-bound Hoogsteen base pair of cytosine (C) and guanine (G), C:H+∙∙∙G, we investigated CID of a homologue series of proton-bound heterodimers of C, 1-methylcytosine, and 5-methylcytosine with G as a common base partner. The CID experiments were performed in an energy-resolved way (ER-CID) under both multiple and near-single collision conditions. The relative stabilities of the protonated complexes examined by ER-CID suggested that the proton-bound complexes produced by electrospray ionization in this study are proton-bound Hoogsteen base pairs. On the other hand, in contrast to the other base pairs, CID of C:H+∙∙∙G exhibited more abundant productions of C:H+, the fragment protonated on the moiety with a smaller proton affinity, than that of G:H+. This appeared to contradict general prediction based on the kinetic method. However, further theoretical exploration of potential energy surfaces found that there can be facile proton transfers in the proton-bound Hoogsteen base pairs during the CID process, which makes the process accessible to an additional product state of O-protonated C for C:H+ fragments. The presence of an additional dissociation channel, which in other words corresponds to twofold degeneracy in the transition state leading to C:H+ fragments, effectively doubles the apparent reaction rate for production of C:H+. In this way, the process gives rise to the anomaly, the observed pronounced formation of C:H+ in the CID of the proton-bound Hoogsteen base pair, C:H+∙∙∙G. Graphical Abstract ᅟ.

Selective Reagent Ions for the Direct Vapor Detection of Organophosphorus Compounds Below Parts-per-Trillion Levels.

Real-time low to sub parts-per-trillion (pptv) vapor detection of some organophosphorous compounds (OPCs) is demonstrated with an atmospheric flow tube-mass spectrometer. The chemical species investigated included dimethyl methylphosphonate, triethyl phosphate, and tributylphosphate. The atmospheric flow tube provides ambient chemical ionization with up to several seconds of ionization time. With sensitivities in the parts-per-quadrillion (ppqv) range, there are many background contaminants competing for charge with the target analytes. Initially, the OPCs were not observable in direct room air analysis, presumably due to other trace components possessing higher proton affinities. However, the addition of a trialkylamine as a dopant chemical served to provide a single reagent ion that also formed a proton-bound heterodimer with the OPCs. These asymmetric proton-bound dimers had sufficiently high hydrogen bond energy to allow the cluster to remain intact during the analysis time of several seconds. Changes in stability were observed for some of these asymmetric proton-bound dimers with a shorter half-life for adducts with a larger proton affinity differences between the amine and the OPC. Detection levels approaching low pptv to high ppqv were correlated by three different methods, including use of a permeation tube, direct injection of a fixed mass into the sample air flow, and calculations based upon signal intensity ratios, reaction time, and an estimated reaction rate constant. A practical demonstration showed real-time monitoring of a laboratory environment initially with low pptv levels of vapor observed to decay exponentially over about an hour while returning to baseline levels.

Theoretical exploration of gas-phase conformers of proton-bound non-covalent heterodimers of guanine and cytosine rare tautomers: structures and energies

Due to complexity arising from the presence of various rare tautomers and multiple protonation sites, little is known of the proton-bound heterodimers of guanine (G) and cytosine (C) that may exist in the gas phase. We extensively explored structures and energies of the heterodimers by density functional theory using the B3LYP functional, wherein rare tautomers of G and C that were predicted to be energetically accessible were considered in possible heterodimer structures. This extensive search found more than 90 stable structures for the proton-bound heterodimers, where various types of base-pairings were observed. For the six lowest energy structures that lie within 3 kcal/mol in energy from the most stable structure, ionic hydrogen bonding was found to be involved in base-pairing. The non-covalent complexation energies of the heterodimers were found to be quite strong at 40–50 kcal/mol. Some pairs of the heterodimers were connected by simple proton transfer in the ionic hydrogen bond as well. In addition, a Hoogsteen base pair was predicted to be the most stable conformer in the gas phase with a more than 90% population. Solvent field effects also suggested that the Hoogsteen base pair is one of the most stable conformers in an aqueous environment. Thus, we suggest that the Hoogsteen base pair is the most predominant form of the proton-bound heterodimers of G and C that may exist in the gas phase.

The structures of proton-bound dimers of glycine with phenylalanine and pentafluorophenylalanine

Infrared multiple photon dissociation spectra of the proton-bound heterodimers of phenylalanine/glycine (Phe·H+·Gly) and pentafluorophenylalanine/glycine (F5-Phe·H+·Gly) have been acquired in the 975–1975cm−1 region. Exhaustive basin hopping molecular dynamics searches and subsequent DFT calculations predict four low energy intermolecular binding motifs. The spectrum of F5-Phe·H+·Gly is assigned predominantly to isomers exhibiting a NH+⋯O intermolecular interaction between nitrogen-protonated Gly and the carbonyl oxygen atom of F5-Phe. In contrast, the spectrum Phe·H+·Gly is found to consist of a mixture of isomers exhibiting the NH+⋯O between nitrogen-protonated Gly and the carbonyl oxygen of neutral Phe, and isomers exhibiting a NH+⋯N interaction between nitrogen-protonated Phe and the neutral Gly moiety. Cation-π effects also seem to influence the cluster geometries, especially in the case of the Phe·H+·Gly global minimum structure where the phenyl ring orients with the site of protonation so as to maximize charge-quadrupole interactions.

Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif.

(CCG)(n)•(CGG)(n) trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)(n)•(CGG)(n) repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C(+)•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.

Base-Pairing Energies of Proton-Bound Heterodimers of Cytosine and Modified Cytosines: Implications for the Stability of DNA i-Motif Conformations

The DNA i-motif conformation was discovered in (CCG)•(CGG)n trinucleotide repeats, which are associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The DNA i-motif is a four-stranded structure whose strands are held together by proton-bound dimers of cytosine (C(+)•C). The stronger base-pairing interactions in C(+)•C proton-bound dimers as compared to Watson-Crick G•C base pairs are the major forces responsible for stabilization of i-motif conformations. Methylation of cytosine results in silencing of the FMR1 gene and causes fragile X syndrome. However, the influence of methylation or other modifications such as halogenation of cytosine on the base-pairing energies (BPEs) in the i-motif remains elusive. To address this, proton-bound heterodimers of cytosine and 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, and 5-iodocytosine are probed in detail. Experimentally, the BPEs of proton-bound heterodimers of cytosine and modified cytosines are determined using threshold collision-induced dissociation (TCID) techniques. All modifications at the 5-position of cytosine are found to lower the BPE and therefore would tend to destabilize DNA i-motif conformations. However, the BPEs in these proton-bound heterodimers still significantly exceed those of the Watson-Crick G•C and neutral C•C base pairs, suggesting that C(+)•C mismatches are still energetically favored such that i-motif conformations are preserved. Excellent agreement between TCID measured BPEs and B3LYP calculated values is found with the def2-TZVPPD and 6-311+G(2d,2p) basis sets, suggesting that calculations at these levels of theory can be employed to provide reliable energetic predictions for related systems.

Infrared Multiple Photon Dissociation Action Spectroscopy of Proton-Bound Dimers of Cytosine and Modified Cytosines: Effects of Modifications on Gas-Phase Conformations

The gas-phase structures of proton-bound dimers of cytosine and modified cytosines and their d6-analogues generated by electrospray ionization are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. The modified cytosines examined include the 5-methyl-, 5-fluoro-, and 5-bromo-substituted species. IRMPD action spectra of seven proton-bound dimers exhibit both similar and distinctive spectral features over the range of ∼2600-3700 cm(-1). The IRMPD spectra of all of these proton-bound dimers are relatively simple, but exhibit obvious shifts in the positions of several bands that correlate with the properties of the substituent. The measured IRMPD spectra are compared to linear IR spectra calculated for the stable low-energy tautomeric conformations, determined at the B3LYP/6-31G* level of theory, to identify the conformations accessed in the experiments. Comparison of the measured IRMPD and calculated IR spectra indicates that only a single conformation, the ground-state structure, is accessed for all proton-bound homodimers, whereas the ground-state and a small population of the first-excited tautomeric conformations are accessed for all proton-bound heterodimers. In all cases, three hydrogen-bonding interactions in which the nucleobases are aligned in an antiparallel fashion analogous to that of the DNA i-motif are responsible for stabilizing the base pairing. Thus, base modifications such as 5-methyl- and 5-halo-substitution of cytosine should not alter the structure of the DNA i-motif.

Role of 2‐oxo and 2‐thioxo modifications on the proton affinity of histidine and fragmentation reactions of protonated histidine

A combination of electrospray ionisation (ESI), multistage and high-resolution mass spectrometry experiments was used to compare the gas-phase chemistry of the amino acids histidine (1), 2-oxo-histidine (2), and 2-thioxo-histidine (3). Collision-induced dissociation (CID) of all three different proton-bound heterodimers of these amino acids led to the relative gas-phase proton affinity order of: histidine >2-thioxo-histidine >2-oxo-histidine. Density functional theory (DFT) calculations confirm this order, with the lower proton affinities of the oxidised histidine derivatives arising from their ability to adopt the more stable keto/thioketo tautomeric forms. All protonated amino acids predominately fragment via the combined loss of H(2)O and CO to yield a(1) ions. Protonated 2 and 3 also undergo other small molecule losses including NH(3) and the imine HN=CHCO(2)H. The observed differences in the fragmentation pathways are rationalised through DFT calculations, which reveal that while modification of histidine via the introduction of the oxygen atom in 2 or the sulfur atom in 3 does not affect the barriers against the loss of H(2)O+CO, barriers against the losses of NH(3) and HN=CHCO(2)H are lowered relative to protonated histidine.

Threshold Collision-Induced Dissociation of Hydrogen-Bonded Dimers of Carboxylic Acids

Energy-resolved competitive collision-induced dissociation is used to investigate the proton-bound heterodimer anions of a series of carboxylic acids (formic, acetic, and benzoic acid) and nitrous acid with their conjugate bases. The dissociation reactions of the complexes [CH3COO.H.OOCH]-, [CH3COO.H.ONO]-, [HCOO.H. ONO]-, [C6H5COO.H.OOCH]-, and [C6H5COO.H.ONO]- are investigated using a guided ion beam tandem mass spectrometer. Cross sections of the two dissociation channels are measured as a function of the collision energy between the complex ions and xenon target gas. Apparent relative gas-phase acidities are found by modeling the cross sections near the dissociation thresholds using statistical rate theory. Internal inconsistencies are found in the resulting relative acidities. These deviations apparently result from the formation of higher-energy conformers of the acids within the complex ions induced by double hydrogen bonding, which impedes the kinetics of dissociation to ground-state product acid conformations.

Proton affinity ladder for uridine and analogs: influence of the hydroxyl group on the sugar ring conformation

A ladder of relative proton affinities (PA) for a series of modified uridines (e.g. araU, ddU, 5BrU, 5BrdU and 5IU) was established from competitive dissociations of proton-bound heterodimers using Cooks and co-workers' kinetic method. The studied heterodimers are constituted of a modified nucleoside and either an amino acid or a nucleoside with known PA value. These non-covalent heterodimers were prepared under electrospray conditions to be selected and dissociated into the ion-trap analyzer. These results allowed our PA ladder of uridine and deoxyuridine analogs substituted at the C-5 position in the uracil ring to be extended. From this scale, it was showed that the substitution of hydrogen atom at the C-2' position in the sugar ring by a hydroxyl group involves a decrease of about 7 kJ mol(-1). The experimental values for U, 5MeU, dU, 5MedU, ddU and araU are consistent with those obtained by DFT calculations (B3P86/6-31+G//B3LYP/6-31G(.)). Several neutral and protonated conformations of these compounds were considered, in particular the ring conformation of furanose and the orientation of the base with respect to the sugar ring. These calculated results showed the influence of sugar substituent on the conformation of the neutral form of theses nucleosides. However, the most stable protonated structure is the same for all the studied nucleosides except for araU, where the position of the anti 2'-OH group imposes a specific conformation.

A comprehensive evaluation of the kinetic method applied in the determination of the proton affinity of the nucleic acid molecules

The determination of proton affinity (PA) of 2′-deoxyadenosine (dA) is used as a case study for the evaluation of possible drawbacks in the determination of the PA of the nucleic acid molecules by the kinetic method. The observed ΔPA among the different values obtain for dA by applying this procedure in its different extensions was 0.64 Kcal/mol, which is within the uncertainties of any theoretical or experimental approach. It was demonstrated that nucleosides can be generally used as reference compounds to measure the PA of an unknown nucleoside. The evaluation of ΔΔS value for two competing reaction channels taken by proton-bound heterodimers formed by two nucleosides provides clear information on the reference base which has to be discarded from the set of reference compounds used for the estimation of an unknown PA. The PA of dA obtained with the most elaborated kinetic method (237.00 ± 0.07 kcal/mol) is consistent with the value of 237.0 kcal/mol obtained by a simple treatment of the relative intensities of the product ions generated by two couples of the proton bound dimers formed by the nucleoside and two reference amines. The kinetic method can be, therefore, confidently used to assess the proton affinity of the multifunctional molecules such as nucleosides and nucleobases.

Self-assembling of cytosine nucleoside into triply-bound dimers in acid media. a comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, x-rays diffractometry, and theoretical calculations

Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.

β-Cyclodextrin and 5-Methoxytryptammonium Ion Host-Guest Association in vacuo: Simulation of Non-Covalent Inclusion by Molecular Dynamics

The structure of gaseous charged host-guest adducts ofcyclodextrins (CDs) generated by mass spectrometry (MS) still requires to be addressed correctly,as these adducts could be true inclusion complexes or non-specific proton bound heterodimers(PBHs). The present theoretical study of inclusion complex vs. PBH of 5-methoxytryptammonium ion(5-MTA+) with β-CD in vacuo by energy minimisation and moleculardynamics proved that the most stable forms of β-CD/5-MTA+ non-covalent associationare inclusion complexes. PBHs evolved to genuine inclusion complexes with two differenthost-guest arrangements during MD runs.

Entropy effect in the evaluation of the proton affinity of N-3-benzoyl-2-deoxycytidines by the kinetic method

The kinetic method has been applied, in its extended form, to the evaluation of the entropy effect in the determination of the proton affinity (PAN) of N-3-para substituted benzoyl 2′-deoxycytidines. The latter, mixed with nucleosides of known PA, afforded the appropriate proton-bound heterodimers when subjected to electrospray ionization. Their collisional induced dissociations were studied in a QqTOF hybrid instrument as a function of both the gas pressure and the collision energy of the dimers entering q. The value of ΔS for each reaction was evaluated and correlated with the effect of the substituent at the para position of the benzoyl group. For each reaction, a Hammett plot of ΔPAN vs. σ values of the substituents on the benzoyl group shows that the carbonyl group participates, in the transition state, to the stabilization/destabilization of the N-3-protonated species. In the cases examined, one can rule out that the formation of intramolecular hydrogen bonds occurs under thermodynamic control. The activation energy for the back reaction can, therefore, be neglected. [See chart on next page.]

Gas-phase basicities for ions from bradykinin and its des-arginine analogues.

Apparent gas-phase basicities (GB(app)s) for [M + H]+ of bradykinin, des-Arg1-bradykinin and des-Arg9-bradykinin have been assigned by deprotonation reactions of [M + 2H]2+ in a Fourier transform ion cyclotron resonance mass spectrometer. With a GB(app) of 225.8 +/- 4.2 kcal x mol(-1), bradykinin [M + H]+ is the most basic of the ions studied. Ions from des-Arg1-bradykinin and des-Arg9-bradykinin have GB(app) values of 222.8 +/- 4.3 kcal x mol(-1) and 214.9 +/- 2.3 kcal x mol(-1), respectively. One purpose of this work was to determine a suitable reaction efficiency 'break point' for assigning GB(app) values to peptide ions using the bracketing method. An efficiency value of 0.1 (i.e. approximately 10% of all collisions resulting in a deprotonation reaction) was used to assign GB(app)s. Support for this criterion is provided by the fact that our GB(app) values for des-Arg1-bradykinin and des-Arg9-bradykinin are identical, within experimental error, to literature values obtained using a modified kinetic method. However, the GB(app)s for bradykinin ions from the two studies differ by 10.3 kcal x mol(-1). The reason for this is not clear, but may involve conformation differences produced by experimental conditions. The results may be influenced by salt-bridge conformers and/or by conformational changes caused by the use of a proton-bound heterodimer in the kinetic method. Factors affecting the basicities of these peptide ions are also discussed, and molecular modeling is used to provide information on protonation sites and conformations. The presence of two highly basic arginine residues on bradykinin results in its high GB(app), while the basicity of des-Arg1-bradykinin ions is increased by the presence of two proline residues at the N-terminus. The proline residue in the second position folds the peptide chain in a manner that increases intramolecular hydrogen bonding to the protonated N-terminal amino group of the proline at the first position.

Electron transfer vs. proton transfer within radical-cation clusters of guanosine and deoxyguanosine with substituted naphthalenes and sinapinic acid

Guanosine (G) and deoxyguanosine (dG) radical cations can be generated in the gas phase by single electron transfer (SET) within nucleoside-dimethoxynaphthalenes ( 1–2) electron-bound heterodimers produced by fast atom bombardment in a four sector mass spectrometer. The nucleobase guanine is much more easily oxidized when it is linked to a ribose moiety. The radical cation dimers formed by G and dG with sinapinic acid behave as proton-bound heterodimers. The experiments mimic to some extent the migration of radical sites within stacking bases which causes DNA damaging through depurination processes.

Effects of Internal Hydrogen Bonds between Amide Groups: Gas-Phase Basicity and Proton Affinity of Linear Aliphatic Dicarboxamides

The apparent gas-phase basicity GBapp and the proton affinity PA of aliphatic dicarboxamides has been determined by tandem mass spectrometry using the kinetic method. The diamides analyzed are primary maleic acid diamide (1a), fumaric acid diamide (2a) and trans, trans-muconic acid diamide (3a) and the tertiary N,N,N‘,N’-tetramethyl derivatives 2b and 3b, which have an almost fixed relative orientation of the terminal amide groups because of the C–C double bond(s) in the carbon skeleton, and the 1,n-dicarboxamides of succinic acid (4a) and (4b), of glutaric acid (5a) and (5b), of adipinic acid (6a) and (6b) and of sebacinic acid (7a) and (7b) containing a flexible –(CH2) n chain with n = 2, 3, 4 and 8. Very large differences are observed for GBapp derived from the dissociation of proton-bound heterodimers either as metastable ions or by CID for all diamides which are expected to form an internal proton bridge between the carbonyl-O atoms of the terminal amide groups in the protonated species. These effects indicate considerable conformational changes of the diamides by protonation and entropic effects accompanying the dissociation of their proton-bound heterodimers. To study the effect of collisional activation, which is believed to alter the effective temperature, Teff, of the proton-bound dimer ions, on their dissociation, separate experiments have been performed with thermalized proton bound heterodimers of 5a using Fourier transform ion cyclotron resonance (FT-ICR) spectrometry to control the collision energy. The evaluation of Teff from these experiments and the use of Teff in Van't Hoff plots to determine the PA of 5a shows a surprisingly good agreement with the results from tandem mass spectrometry, which supports the view that the kinetic method using different Teff can be used to determine the PA and the difference of the “apparent entropy” of protonation, Δ(Δ SH+) app, of the compound under study and the reference base of the proton bound heterodimer from GBapp even in the case of large entropy effects. The PA of maleic acid diamide 1a and its trans isomer 2a, not building an internal proton bridge by protonation, differ by 80 kJ mol−1. A value of −19 J mol−1 K is obtained for (Δ SH+) app (1a) while entropic effects are essentially absent in the case of 2a. The PA of linear dicarboxamides 4a–7a increases with the length of the –(CH2) n chain and exceeds that of monoamides of a comparable size by 60–100 kJ mol−1. This is attributed to the formation of an internal proton bridge and a release of constraints for the internal proton bridge for the longer chains. Δ(Δ SH+) app is practically constant for 5a–7a at a value of −41 ± 2 J mol−1 K, but only −19 J mol−1 K for 4a. This can be understood if the entropy loss during protonation of the diamides is mostly due to loss of internal rotations of the amide groups. In contrast to the primary amides, the tertiary dicarboxamides 4b–7b display identical PA independent of the length of the –(CH2) n chain, and the effect of formation of the internal proton bridge on the PA is distinctly less than for primary dicarboxamides. In addition, a constant value of only −16 ± 3 J mol−1 K is obtained for Δ(Δ SH+) app of 4b–7b. These results are interpreted by different types of the proton bridges of primary and tertiary diamides. Primary linear dicarboxamides generate a true proton bridge between the carbonyl-O atoms of the terminal amide groups as corroborated by ab initio calculations of their structures. In contrast, protonated tertiary dicarboxamides display properties of (internal) ion/dipole complexes in which the protonated amide group is “solvated” by the second one.