Hydrogen Liberation from Gaseous 2-Bora-1,3-diazacycloalkanium Cations.

Evidence is presented for cyclization to yield 2-bora-1,3-diazacycloalkanium cations in the gas phase. While the neutral compounds in solution and solid phase are known to possess an acyclic structure (as revealed by X-ray diffraction), the gaseous cations (from which borohydride BH4- ion has been expelled) have a cyclic structure, as revealed by InfraRed Multiple Photon Dissociation (IRMPD) spectroscopy and collisionally activated decomposition (CAD). The IRMPD decomposition of the monocyclic ions proceeds principally via H2 expulsion, although CAD experiments show additional pathways. Pyrolyses of solid monomeric salts and small oligomers produce higher polymers that are consistent with H2 expulsion as the major pathway. Deuterium labeling experiments show that scrambling occurs prior to IRMPD or CAD decomposition in the gas phase.

Low-Frequency CH Stretch Vibrations of Free Alkoxide Ions.

CH stretches in hydrocarbon cations often shift to lower frequencies relative to neutral molecules, because they do not have sufficient electrons to give every bond an electron pair. A parallel effect in negatively charged species has not been previously observed. Here we show that CH bond weakening occurs in alkoxide anions as a consequence of hyperconjugation. The reasoning differs somewhat from the case of positively charged ions, but the net effect is the same: to lower CH stretching frequencies by hundreds of wavenumbers.

Negative Hyperconjugation versus Electronegativity: Vibrational Spectra of Free Fluorinated Alkoxide Ions in the Gas Phase.

CO stretching frequencies of free, gaseous, fluorinated alkoxide ions shift substantially to the blue, relative to those of corresponding alcohols complexed with ammonia. Free α-fluorinated ions, pentafluoroethoxide and heptafluoroisopropoxide anions, display further blue shifts relative to cases with only ß-fluorination, providing experimental evidence for fluorine negative hyperconjugation. DFT analysis with the atoms in molecules (AIM) method confirms an increase in CO bond order for the α-fluorinated ions, demonstrating an increase in carbonyl character for the free ions.

Proton-bound dimers of 1-methylcytosine and its derivatives: vibrational and NMR spectroscopy.

Vibrational spectroscopy and NMR demonstrate that the proton-bound dimer of 1-methylcytosine, 1, has an unsymmetrical structure at room temperature. In the gas phase, investigation of isolated homodimer 1 reveals five fundamental NH vibrations by IR Multiple Photon Dissociation (IRMPD) action spectroscopy. The NH···N stretching vibration between the two ring nitrogens exhibits a frequency of 1570 cm(-1), as confirmed by examination of the proton-bound homodimers of 5-fluoro-1-methycytosine, 2, and of 1,5-dimethylcytosine, 3, which display absorptions in the same region that disappear upon deuterium substitution. (13)C, and (15)N NMR of the solid iodide salt of 1 confirm the nonequivalence of the two rings in the anhydrous proton-bound homodimer at room temperature. IRMPD spectra of the three possible heterodimers also show NH···N stretches in the same domain, and at least one of the heterodimers, the proton-bound dimer of 1,5-dimethylcytosine with 1-methylcytosine, exhibits two bands suggestive of the presence of two tautomers close in energy.

Proton-bridge motions in amine conjugate acid ions having intramolecular hydrogen bonds to hydroxyl and amine groups.

Vibrational spectra of two gaseous cations having NH···O intramolecular ionic hydrogen bonds and of nine protonated di- and polyamines having NH···N internal proton bridges, recorded using IR Multiple Photon Dissociation (IRMPD) of mass-selected ions, are reported. The band positions of hydroxyl stretching frequencies do not shift when a protonated amine becomes hydrogen bonded to oxygen. In three protonated diamines, lower frequency bands (550-650 cm(-1)) disappear upon isotopic substitution, as well as several bands in the 1100-1350 cm(-1) region. By treating the internal proton bridge as a linear triatomic, theory assigns the lowest frequency bands to N-H···N asymmetric stretches. A 2-dimensional model, based on quantization on a surface fit to points calculated using a double hybrid functional B2-P3LYP/cc-pVTZ//B3LYP/6-31G**, predicts their positions accurately. In at least one case, the conjugate acid of 1,5-cis-bis(dimethylamino)cyclooctane, a N-H···N bend shows up in the domain predicted by DFT normal mode calculations, but in most other cases the observed bands have frequencies 20-25% lower than expected for bending vibrations. Protonated Me(2)NCH(2)CMe(2)CH(2)CH(2)CH(2)NMe(2) shows three well-resolved bands at 620, 1200, and 1320 cm(-1), of which the lowest can be assigned to the asymmetric stretch. Other ions observed include doubly protonated 1,2,4,5-(Me(2)NCH(2))(4)-benzene and 1,2,4-(Me(2)NCH(2))(3)-benzene-5-CH(2)OH. Apart from the aforementioned rigid ion derived from the alicyclic diamine, the other ions enjoy greater conformational mobility, and coupling to low-frequency C-C bond torsions may account for the shift of vibrations with N-H···N character to lower frequencies. Low-barrier hydrogen bonding (LBHB) accounts for the fact that N-H···N asymmetric stretching vibrations of near linear proton bridges occur at frequencies below 650 cm(-1).

Vibrations of a chelated proton in a protonated tertiary diamine.

Vibrational spectra of the conjugate acid of Me(2)NCH(2)CH(2)CH(2)CH(2)NMe(2) (N,N,N',N'-tetramethylputrescine) have been examined in the gaseous and crystalline phases using Infrared Multiple Photon Dissociation (IRMPD) spectroscopy, Inelastic Neutron Scattering (INS), and high pressure Raman spectroscopy. A band observed near 530 cm(-1) is assigned to the asymmetric stretch of the bridging proton between the two nitrogens, based on deuterium substitution and pressure dependence. The NN distance measured by X-ray crystallography gives a good match to DFT calculations, and the experimental band position agrees with the value predicted from theory using a 2-dimensional potential energy surface. The reduced dimensionality potential energy surface, which treats the ion as though it possesses a linear NHN geometry, shows low barriers to proton transit from one nitrogen to the other, with zero point levels close to the barrier tops. In contrast, two other related systems containing strong hydrogen bonds do not exhibit the same spectroscopic signature of a low barrier hydrogen bond (LBHB). On the one hand, the IRMPD spectra of the conjugate acid ions of the amino acid N,N,N',N'-tetramethylornithine (in which the two nitrogens have different basicities) show fewer bands and no comparable isotopic shifts in the low frequency domain. On the other hand, the IRMPD spectrum of the shorter homologue Me(2)NCH(2)CH(2)CH(2)NMe(2) (N,N,N',N'-tetramethyl-1,3-propanediamine), for which the NHN bond angle deviates substantially from linearity, displays more than one band in the 1100-1400 cm(-1) domain, which vanish as a consequence of deuteration.

IR spectra of boron-stabilized anions in the gas phase.

Action spectroscopy of gaseous Me(3)BF(-) and Me(2)BCH(2)(-), determined using IR multiple photon dissociation (IRMPD), exhibits experimental peak positions in good agreement with those predicted by anharmonic DFT calculations at the B3LYP/aug-cc-pVTZ level. Comparing spring constants among boron-carbon bonds and consideration of isoelectronic systems reveals that the anions have B-CH(3) bonds a factor of 1.3-1.4 weaker than those in neutral trimethylboron, suggesting a greater role for hyperconjugation in B(CH(3))(3) than inferred from previous vibrational spectroscopic studies.

Structures of products from positive ion-molecule reactions by means of vibrational spectroscopy.

Examples of various approaches to determining gaseous ion structures are described. Two cases are presented in which infrared multiple photon dissociation (IRMPD) spectroscopy provides characteristic information. Comparison with DFT-calculated normal modes differentiates isomers. The IRMPD spectrum of the even-electron C(8)D(8)F(+) product ion from the ion-molecule reaction of CF(3)(+) with perdeuterated acetophenone exhibits a degree of resolution sufficient to identify C(6)D(5)CFCD(3)(+) and rule out ring-fluorinated isomers. The dimerization of phenylacetylene with its molecular ion has been explored, with the conclusion that a mixture of product ions is formed. The best match to the experimental spectrum is achieved by superimposing the bands calculated for ionized 1-phenylazulene and ionized 1,2-diphenylcyclobutadiene.

Evidence of strong hydrogen bonding by 8-aminoguanine.

DNA oligonucleotides containing 8-aminodeoxyguanosine residues form a pH-dependent self-structure with strong hydrogen bonds.

Chelation of a proton by an aliphatic tertiary diamine.

A series of monoprotonated aliphatic diamines has been examined, which crystallize in three general motifs: salt-bridged, cyclic, or clustered. The monoprotonated triflic acid salt of Me2N(CH2)4NMe2 forms a proton-bridged cyclic cation. The internal N-N distance is 2.66 A, with the bridging proton in the middle, having an NHN angle >/=172 degrees. The triflate oxygens lie more than 4 A away from the midpoint between the nitrogen atoms, indicating that a salt bridge does not form. The average NH distance in a solid sample was determined by measuring the 15N-H dipolar coupling in the triflic acid salt of the completely deuterated diamine (CD3)2N(CD2)4N(CD3)2. The value of the dipolar coupling constant, 5250 +/- 90 Hz, corresponds to an average NH distance of 1.32 A, nearly half-the NN distance. That result agrees with DFT calculations, which give a double-well potential minimum for proton transit between the two amino groups, having a zero-point vibrational level close to the barrier top. Theory predicts that the maximum value of the zero point vibrational wave function is almost coincident with a local potential energy maximum, consistent with the experimental findings.

Stereochemical preferences in 4-center syn-eliminations from gaseous ions.

Concerted unimolecular eliminations from ionized sec-alkyl aryl ethers (ROAr (+*)) display a preference for producing double bonds with trans geometry. This preference can be assessed quantitatively, provided that a regioselective variant can be found. Expulsion of neutral alkenes via syn-elimination to give ionized ArOH does not exhibit a pronounced preference with regard to the direction of elimination. By contrast, ionized 2-hexyl p-trifluoromethylphenyl ether eliminates neutral ArOH regioselectively, giving ionized 2-hexenes rather than ionized 1-hexene. Vicinally monodeuterated 2-hexyl and 3-hexyl ethers were prepared as pure diastereomers. Metastable ion decompositions of their gaseous radical cations are compared over two different time windows. The regioselectivity for the 2-hexyl ether allows the geometric preference for the double bonds to be estimated based on the difference between the erythro and threo monodeuterated diastereomers ( trans/ cis = 2.0 for producing ionized 2-hexene from parent ions with the lowest internal energies). The 3-hexyl ethers and ionized 2- and 3-phenoxyoctanes also undergo stereoselective elimination but give experimental values that reflect their lack of regioselectivity. Examination of erythro/ threo combinations shows that GC/MS/MS has the ability to quantitate stereochemistry in mixtures containing both positional and stereoisomers.

Structure, vibrational spectra, and unimolecular dissociation of gaseous 1-fluoro-1-phenethyl cations.

The multiple CF bond character of PhCFMe (+) ions has been examined by means of theory, vibrational spectroscopy of the gaseous ions, and unimolecular decomposition chemistry. Atoms in Molecules analysis of DFT wave functions gives a CF bond order of n = 1.25 (as compared with n = 1.38 for Me 2CF (+), relative to n = 1 for fluoromethane and n = 2 for diatomic CF (+)), which is consistent with calculations of adiabatic CF stretching frequencies (nu CF). Experimental gas phase IR spectra, recorded by means of resonant multiphoton dissociation (IRMPD) using a free-electron laser connected to an FTICR mass spectrometer, show good agreement with predicted band positions for five deuterated isotopomers of PhCFMe (+). Metastable ion decompositions of deuterated analogues of PhCFMe (+) show the same HF/DF loss patterns as those produced by IRMPD. The evidence supports the conclusion that PhCFMe ions retain structural integrity until they become sufficiently excited to dissociate, whereupon they undergo intramolecular hydrogen scrambling that is competitive with HF/DF expulsion. Relative rates of hydrogen transposition and unimolecular dissociation are extracted from relative experimental fragment ion abundances. The predominant decomposition pathway is inferred to operate via a five-center transition state, as opposed to a four-center transition state for HF loss from gaseous Me 2CF (+).

Photoionization of 2,3-dimethyl-2-butanol (thexyl alcohol): interaction between the charged and expelled fragments.

Photoionization studies of (CH(3))(2)CHC(CH(3))(2)OH (tert-hexyl alcohol, also called thexyl alcohol) exhibit four fragmentations below 10 eV. As with other tertiary alcohols, no molecular ion is detected. The only ion observed at threshold corresponds to propane loss. Examination of a deuterated analogue, (CH(3))(2)CHC(CD(3))(2)OH, shows only loss of C(3)H(7)D, implying that the fragment ion has the structure of ionized acetone enol. There is no evidence for reversible deuterium transposition, as has been reported for isotopomers of the homologous secondary alcohol (CH(3))(2)CHCH(CH(3))OH. Propane loss from thexyl alcohol is attributed to intermediacy of ion-neutral complexes containing isopropyl radical and O-protonated acetone. Simple cleavage to give O-protonated acetone has an appearance energy 18 kJ mol(-1) higher than that of propane loss. Thermochemical estimates and ab initio calculations both predict that methyl loss should have a lower threshold than the fragmentation leading to isopropyl loss, but experiments show the appearance energy to be 6 kJ mol(-1) higher. This is consistent with previous reports of reverse activation barriers for methyl cleavages. Finally, formation of tert-hexyl cation, (CH(3))(2)CHC(CH(3))(2)(+), is observed with an appearance energy comparable to that of methyl loss, substantially below that predicted for OH radical expulsion from the molecular ion. The comparatively low threshold of this fragmentation is ascribed to ion-pair formation (concomitant with hydroxide ion) directly from an electronically excited neutral. Interactions between charged and neutral fragments (including energetics, bond orders <1, and electrical charges on molecular fragments) are explored using a combination of DFT and ab initio methods, along with topological analysis using the Atoms in Molecules approach.

Decomposition of protonated threonine, its stereoisomers, and its homologues in the gas phase: evidence for internal backside displacement.

Protonated threonine and its allo diastereomer exhibit different proportions of collisionally activated dissociation (CAD) product ions. N-Methylation attenuates these differences. Water loss from protonated allo-threonine gives protonated trans-3-methylaziridinecarboxylic acid via an internal S(N)2 pathway, rather than protonated vinylglycine.

cis-1,5-Diaminocyclooctane: the most basic gaseous primary amine?

The gas phase basicity of the title compound has been determined to be greater than that of putrescine, making it the most basic primary diamine measured to date.

Aldehyde and ketone adducts of the gaseous trifluoromethyl cation.

IR spectra of CF(3)(+) adduct ions are reported for the first time using infrared multiple photon dissociation (IRMPD). Carbonyl stretches of ketone conjugate acids shift less than do those of ions containing C═OCF(3)(+) groups. Carbonyl absorptions shift in proportion to the empirical softness of the corresponding neutrals. Anharmonic DFT fits band positions of C═OCF(3)(+) stretches for aliphatic ions, but unscaled harmonic calculations match O-CF(3) stretches more closely. Calculated O-CF(3) bond orders increase with gas phase CF(3)(+) affinities of the corresponding neutral carbonyl.

DFT energy surfaces for aminopurine homodimers and their conjugate acid ions.

Dimers of free nucleobases with their conjugate acid ions can be assigned to either of two categories: protonated dimers or proton-bound dimers. In the former, the extra proton attaches to a lone pair of a neutral dimer. In the latter, the extra proton is situated between two lone pairs and participates in a proton bridge. In general, proton-bound dimers are found to be more tightly held together than protonated dimers. While neutral adenine and its isomer 8-aminopurine (C(5)H(5)N(5)) are substantially more stable than their 7H tautomers, their conjugate acid ions and those of their respective 7H tautomers have nearly the same heats of formation. Correspondingly, the most stable (C(5)H(5)N(5))2H+ structures contain 7H tautomers as the neutral partner. Proton transit from one partner to the other within the most stable protonated dimer of 8-aminopurine has a low barrier (6 kJ mol(-1)). The potential energy curve for the NH stretch in that case is better fitted as a double minimum rather than as a harmonic potential. Purine-purine mismatches have been observed in nucleic acids, to which calculated (C(5)H(5)N(5))2H+ dimer geometries appear nearly isosteric.

Activation barriers for addition of methyl radicals to oxygen-stabilized carbocations.

Activation barriers (DeltaHMe(double dagger)) for adding methyl radicals to ions of the general formula CH3CR=OCH3+ have been measured by looking at the threshold energies for the reverse reaction, dissociative photoionization of ethers of the general formula RC(CH3)2OCH3. Dissociation by loss of a methyl radical has more favorable thermochemistry than loss of R*, yet the onset of R* loss occurs at lower energies than loss of CH3*. In other words, the more endothermic dissociation exhibits a lower appearance energy. Contrathermodynamic ordering of appearance energies is observed for R = Et, nPr, iPr, tBu, and neopentyl. The sum of the appearance energy difference, DeltaAE, and the thermochemical difference (DeltaDeltaH, calculated using G3 theory) gives a lower bound for the barrier for adding methyl radical to CH3CR=OCH3+. More specifically, the difference between that activation barrier and the one for adding R* to (CH3)2C=OCH3+, DeltaHMe(double dagger)-DeltaHR(double dagger), equals DeltaAE + DeltaDeltaH and has values in the range 20-24 kJ mol(-1) for the homologous series investigated. There is no systematic trend with the steric bulk of R, and available evidence suggests that DeltaHR(double dagger) does not have a value >5 kJ mol(-1). The difference in barrier heights, DeltaHMe(double dagger)-DeltaHiPr(double dagger) for CH3* plus iPrC(CH3)=OX+ vs iPr* + (CH3)2C=OX+, has the same value, regardless of whether X = H or CH3. Mixing of higher energy electronic configurations provides a qualitative theoretical explanation for some (but not all) observed trends in barrier heights.

Mass spectrometric differentiation of linear peptides composed of L-amino acids from isomers containing one D-amino acid residue.

MS/MS of electrosprayed ions is shown to have the capacity to discriminate between peptides that differ by configuration about their alpha-carbons. It is not necessary for the peptides to possess tertiary structures that are affected by stereochemistry, since five epimers of the pentapeptide, H2N-Gly-Leu-Ser-Phe-Ala-OH (GLSFA) all display different collisionally activated dissociation (CAD) patterns of their protonated parent ions. The figure of merit, r, is a ratio of ratios of fragment ion abundances between stereoisomers, where r = 1 corresponds to no stereochemical effect. Values of r as high as 3.8 are seen for diastereomer pairs. Stereochemical effects are also seen for the diprotonated dodecapeptide H2N-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-OH (LVFFAEDVGSNK), a tryptic fragment from the amyloid beta-protein. Triply charged complexes of the protonated dodecapeptide with cobalt(II) ions undergo CAD at lower collision energies than do doubly protonated LVFFAEDVGSNK ions. Statistically significant (p < 0.01) differences between the all-L-dodecapeptide and the ones containing a d-serine or a D-aspartic acid are observed.