Gas-phase chemistry of ionized and protonated GeF4: a joint experimental and theoretical study

The gas-phase ion chemistry of GeF(4) and of its mixtures with water, ammonia and hydrocarbons was investigated by ion trap mass spectrometry (ITMS) and ab initio calculations. Under ITMS conditions, the only fragment detected from ionized GeF(4) is GeF(3)(+). This cation is a strong Lewis acid, able to react with H(2)O, NH(3) and the unsaturated C(2)H(2), C(2)H(4) and C(6)H(6) by addition-HF elimination reactions to form F(2)Ge(XH)(+), FGe(XH)(2)(+), Ge(XH)(3)(+) (X = OH or NH(2)), F(2)GeC(2)H(+), F(2)GeC(2)H(3)(+) and F(2)GeC(6)H(5)(+). The structure, stability and thermochemistry of these products and the mechanistic aspects of the exemplary reactions of GeF(3)(+) with H(2)O, NH(3) and C(6)H(6) were investigated by MP2 and coupled cluster calculations. The experimental proton affinity (PA) and gas basicity (GB) of GeF(4) were estimated as 121.5 ± 6.0 and 117.1 ± 6.0 kcal mol(-1), respectively, and GeF(4)H(+) was theoretically characterized as an ion-dipole complex between GeF(3)(+) and HF. Consistently, it reacts with simple inorganic and organic molecules to form GeF(3)(+)-L complexes (L = H(2)O, NH(3), C(2)H(2), C(2)H(4), C(6)H(6), CO(2), SO(2) and GeF(4)). The theoretical investigation of the stability of these ions with respect to GeF(3)(+) and L disclosed nearly linear correlations between their dissociation enthalpies and free energies and the PA and GB of L. Comparing the behavior of GeF(3)(+) with the previously investigated CF(3)(+) and SiF(3)(+) revealed a periodically reversed order of reactivity CF(3)(+) < GeF(3)(+) < SiF(3)(+). This parallels the order of the Lewis acidities of the three cations.     

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.     

Thermodynamics of apoplastocyanin folding: comparison between experimental and theoretical results

It has been experimentally shown that the folding of apoplastocyanin (apoPC) accompanies a very large enthalpic loss [N. Baden et al., J. Chem. Phys. 127, 175103 (2007)]. This implies that an even larger entropic gain occurs in stabilizing the folded structure to overcome the enthalpic loss. Here, we calculate the water-entropy gain upon the folding of apoPC using the angle-dependent integral equation theory combined with the multipolar water model and the recently developed morphometric approach. It is demonstrated that the calculated value is in quantitatively good accord with the value estimated from the experimental data by accounting for the conformational-entropy loss. According to a prevailing view, the water adjacent to a hydrophobic group is unstable especially in terms of the rotational entropy and the folding is driven primarily by the release of such unfavorable water to the bulk through the burial of nonpolar side chains. We show, however, that the resultant entropic gain is too small to elucidate the experimental result. The great entropic gain observed is ascribed to the reduction in the restriction for the translational motion of water molecules in the whole system.     

Gas-phase reactivity and molecular modeling studies on triply protonated dodecapeptides that contain four basic residues

Gas-phase deprotonation and hydrogen/deuterium (H/D) exchange reactions for ions from three model dodecapeptides were studied by Fourier transform ion cyclotron resonance mass spectrometry. Molecular dynamics calculations were employed to provide information on conformations and Coulomb energies. The peptides, (KGG)₄, (K₂G₄)₂, and K₄G₈, each contain four high basicity lysine residues and eight low basicity glycine residues; however, in the present work only three lysine residues were protonated. Proton transfer reactions with a series of reference amines revealed apparent gas-phase acidities in a narrow range of 207. 3–209. 6 kcal/mol, with deprotonation efficiencies following the order [K₄G₈+3H]³⁺ > [(KGG)₄+3H]³⁺ > [(K₂G₄)₂+3H]³⁺. The three ions also react similarly with d ₄-methanol: each exchanged a maximum of 23–25 of their 25 labile hydrogens, with the first 15–17 exchanges occurring at rate constants of (1. 6–2. 6) × 10^?11 cm³ molecule^?1 s^?1. The experimental results agree with molecular modeling findings of similar conformations and Coulomb energies for the three peptide ions. The [M+3H]³⁺ data are compared to data obtained previously in our laboratory for the “fully” protonated [M+4H]⁴⁺ (Zhang, X.; Ewing, N. P.; Cassady, C. J. Int. J. Mass Spectrom. Ion Phys., in press). For (KGG)₄ and (K₂G₄)₂, there is a marked difference in H/D exchange reactivity between 3+ ions and 4+ ions. The 4+ ions, which have diffuse conformations, slowly exchange only 14 hydrogens, whereas their more compact 3+ counterparts exchange 23–25 hydrogens at a 5-times greater rate. In contrast, the 3+ and 4+ ions of K₄G₈ have similar compact conformations and exchange reactivity. The results indicate that a multiply hydrogen-bonded intermediate between the deuterating reagent and the peptide ion is necessary for facile H/D exchange. The slower, incomplete H/D exchange of [(KGG)₄+4H]⁴⁺ and [(K₂G₄)₂+4H]⁴⁺ is attributed to the inability of their protonated lysine n-butylamino groups (which extend away from the peptide backbone) to form this intermediate.     

Gas-phase dissociation reactions of protonated saxitoxin and neosaxitoxin

The aim of this study was to investigate the behavior of the protonated paralytic shellfish poisons saxitoxin (STX) and neosaxitoxin (NEO) in the gas-phase after ion activation using different tandem mass spectrometry techniques. STX and NEO belong to a group of neurotoxins produced by several strains of marine dinoflagellates. Their chemical structures are based on a tetrahydropurine skeleton to which a 5-membered ring is fused. STX and NEO only vary in their substituent at N-1, with STX carrying hydrogen and NEO having a hydroxyl group at this position. The collision-induced dissociation (CID) spectra exhibited an unusually rich variety and abundance of species due to the large number of functional groups within the small skeletal structures. Starting with triple-quadrupole CID spectra as templates, linked ion-trap MSn data were added to provide tentative dissociation schemes. Subsequent high-resolution FTICR experiments gave exact mass data for product ions formed via infrared multiphoton dissociation (IRMPD) from which elemental formulas were derived. Calculations of proton affinities of STX and NEO suggested that protonation took place at the guanidinium group in the pyrimidine ring for both molecules. Most of the observed parallel and consecutive fragmentations could be rationalized through neutral losses of H2O, NH3, CO, CO2, CH2O and different isocyanate, ketenimine and diimine species, many of which were similar for STX and NEO. Several exceptions, however, were noted and differences could be readily correlated with reactions involving NEO's additional hydroxyl group. A few interesting variations between CID and IRMPD spectra are also highlighted in this paper.     

Infrared spectroscopy and theoretical studies on gas-phase protonated leu-enkephalin and its fragments: direct experimental evidence for the mobile proton

The gas-phase structures of the protonated pentapeptide Leu-enkephalin and its main collision-induced dissociation (CID) product ions, b4 and a4, are investigated by means of infrared multiple-photon dissociation (IR-MPD) spectroscopy and detailed molecular mechanics and density functional theory (DFT) calculations. Our combined experimental and theoretical approach allows accurate structural probing of the site of protonation and the rearrangement reactions that have taken place in CID. It is shown that the singly protonated Leu-enkephalin precursor is protonated on the N-terminus. The b4 fragment ion forms two types of structures: linear isomers with a C-terminal oxazolone ring, as well as cyclic peptide structures. For the former structure, two sites of proton attachment are observed, on the N-terminus and on the oxazolone ring nitrogen, as shown in a previous communication (Polfer, N. C.; Oomens, J.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2005, 127, 17154-17155). Upon leaving the ions for longer radiative cooling delays in the ion cyclotron resonance (ICR) cell prior to IR spectroscopic investigation, one observes a gradual decrease in the relative population of oxazolone-protonated b4 and a corresponding increase in N-terminal-protonated b4. This experimentally demonstrates that the mobile proton is transferred between two sites in a gas-phase peptide ion and allows one to rationalize how the proton moves around the molecule in the dissociation process. The a4 fragment, which is predominantly formed via b4, is also confirmed to adopt two types of structures: linear imine-type structures, and cyclic structures; the former isomers are exclusively protonated on the N-terminus in sharp contrast to b4, where a mixture of protonation sites was found. The presence of cyclic b4 and a4 fragment ions is the first direct experimental proof that fully cyclic structures are formed in CID. These results suggest that their presence is significant, thus lending strong support to the recently discovered peptide fragmentation pathways (Harrison, A. G.; Young, A. B.; Bleiholder, B.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2006, 128, 10364-10365) that result in scrambling of the amino acid sequence upon CID.     

Double-resonance versus pulsed Fourier transform two-dimensional infrared spectroscopy: an experimental and theoretical comparison

In this study we focus on the differences and analogies of two experimental implementations of two-dimensional infrared (2D-IR) spectroscopy: double-resonance or dynamic hole burning 2D-IR spectroscopy and pulsed Fourier transform or heterodyne detected photon echo spectroscopy. A comparison is done theoretically as well as experimentally by contrasting data obtained from both methods. As an example we have studied the strongly coupled asymmetric and symmetric carbonyl stretching vibrations of dicarbonylacetylacetonato rhodium dissolved in hexane. Both methods yield the same peaks in a 2D-IR spectrum. Within certain approximations we derive an analytic expression which shows that the 2D-IR spectra are broadened in one frequency dimension in the double-resonance experiment by convolution with the pump pulse spectral width, while the spectral resolution in the other frequency direction is the same in both cases.     

Nonlinear chromatography Recent theoretical and experimental results

The theory of nonlinear chromatography has been advanced by the incorporation of recent results obtained by the theory of partial differential equations. The system of equations of the ideal model has been solved analytically in the case of a single component for which the equilibrium isotherm between the mobile and the stationary phases is given by a Langmuir equation. A series of computer programs has been written which permits the calculation of numerical solutions of the semi-ideal model. The properties of the solutions obtained are described and discussed for a one-component system (profile of high concentration bands of a pure compound eluted by a pure solvent), several two-component systems (elution of a pure compound band by a binary mobile phase, separation of a binary mixture eluted by a pure mobile phase), and three-component systems (separation of a binary mixture eluted by a binary solvent, displacement and separation of a binary mixture). Experimental results are reported which validate the conclusions derived from the numerical integration of the model. The conclusions of the work apply to all high-performance chromatographic procedures, i.e., to those where the kinetics of mass transfer are fast enough for the mobile and stationary phases always to be near equilibrium. More specifically, the contribution from the kinetics of the retention mechanism to the mass transfer resistance must itself be negligible. This clearly excludes affinity chromatography.     

Gas-phase kinetics and mechanism of the reactions of protonated hydrazine with carbonyl compounds. Gas-phase hydrazone formation: kinetics and mechanism

The gas-phase reactions of protonated hydrazine (hydrazinium) with organic compounds were studied in a selected ion flow tube-chemical ionization mass spectrometer (SIFT-CIMS) at 0.5 Torr pressure and approximately 300 K and with hybrid density functional calculations. Carbonyl and other polar organic compounds react to form adducts, e.g., N(2)H(5)(+)(CH(3)CH(2)CHO). In the presence of neutral hydrazine, aldehyde adducts react further to form protonated hydrazones, e.g., CH(3)CH(2)CH[double bond]HNNH(2)(+) from propanal. Using deuterated hydrazine (N(2)D(4)) and butanal, we demonstrate that the gas-phase ion chemistry of hydrazinium and carbonyls operates by the same mechanisms postulated for the reactions in solution. Calculations provide insight into specific steps and transition states in the reaction mechanism and aid in understanding the likely reaction process upon chemical or translational activation. For most carbonyls, rate coefficients for adduct formation approach the predicted maximum collisional rate coefficients, k approximately 10(-9) cm(3) molecule(-1) s(-1). Formaldehyde is an exception (k approximately 2 x 10(-11) cm(3) molecule(-1) s(-1)) due to the shorter lifetime of its collision complex. Following adduct formation, the process of hydrazone formation may be rate limiting at thermal energies. The combination of fast reaction rates and unique chemistry shows that protonated hydrazine can serve as a useful chemical-ionization reagent for quantifying atmospheric carbonyl compounds via CIMS. Mechanistic studies provide information that will aid in optimizing reaction conditions for this application.     

Gas-phase tautomers of protonated 1-methylcytosine. Preparation, energetics, and dissociation mechanisms

Tautomers of 1-methylcytosine that are protonated at N-3 (1+) and C-5 (2+) have been specifically synthesized in the gas phase and characterized by tandem mass spectrometry and quantum chemical calculations. Ion 1+ is the most stable tautomer in aqueous and methanol solution and is likely to be formed by electrospray ionization of 1-methylcytosine and transferred in the gas phase. Gas-phase protonation of 1-methylcytosine produces a mixture of 1+ and the O-2-protonated tautomer (3+), which are nearly isoenergetic. Dissociative ionization of 6-ethyl-5,6-dihydro-1-methylcytosine selectively forms isomer 2+. Upon collisional activation, ions 1+ and 3+ dissociate by loss of ammonia and [C,H,N,O], whose mechanisms have been established by deuterium labeling and ab initio calculations. The main dissociations of 2+ following collisional activation are losses of CH2=C=NH and HN=C=O. The mechanisms of these dissociations have been elucidated by deuterium labeling and theoretical calculations.     

Gas-phase reactions of nitronium ions with acetylene and ethylene: an experimental and theoretical study

A comparative study of the gas-phase reactions of NO2+ with acetylene and ethylene was performed by using FT-ICR, MIKE, CAD, and NfR/ CA mass spectrometric techniques, in conjunction with ab initio calculations at the MP2/6-31+G* level of theory. Both reactions proceed according to the same mechanism, that is, 1,3-dipolar cycloaddition, but yield products of different stability. The C2H2NO2+ adduct from acetylene has an aromatic character and hence is highly stabilized with respect to the C2H4NO2+ adduct from ethylene. Both cycloadducts tend to isomerize into O-nitroso derivatives, that is, nitrosated ketene and nitrosated acetaldehyde, which represent the thermodynamically most stable products from the addition of NO2+ to acetylene and ethylene, respectively. As prototypal examples of the reactivity of free nitronium ions with most simple pi systems, the reactions investigated are useful starting points to model the mechanism of aromatic nitration.     

Time-resolved and steady-state fluorescence spectroscopic studies of the human lens with comparison to argpyrimidine,pentosidine and 3-OH-kynurenine

The intrinsic fluorescence from the human lens on excitation in the UV region, referred to as blue lens autofluorescence, increases with age or in the presence of diabetes. The present study reveals that the relative contribution of compounds responsible for the blue autofluorescence appears to be a constant with age. Three potential candidates for the blue fluorescence were also studied with respect to fluorescence spectroscopic properties. These were argpyrimidine and pentosidine, both advanced glycation end products, and 3-hydroxykynurenine (3-OH-kynurenine), a photooxidative derivative of tryptophan. It was shown that the spectral properties of argpyrimidine and pentosidine are compatible with the observed blue fluorescence of the human lens, whereas the fluorescence from 3-OH-kynurenine is negligible.     

Insulator-based dielectrophoresis of microorganisms: theoretical and experimental results

Dielectrophoresis (DEP) is the motion of particles due to polarization effects in nonuniform electric fields. DEP has great potential for handling cells and is a non-destructive phenomenon. It has been utilized for different cell analysis, from viability assessments to concentration enrichment and separation. Insulator-based DEP (iDEP) provides an attractive alternative to conventional electrode-based systems; in iDEP, insulating structures are used to generate nonuniform electric fields, resulting in simpler and more robust devices. Despite the rapid development of iDEP microdevices for applications with cells, the fundamentals behind the dielectrophoretic behavior of cells has not been fully elucidated. Understanding the theory behind iDEP is necessary to continue the progress in this field. This work presents the manipulation and separation of bacterial and yeast cells with iDEP. A computational model in COMSOL Multiphysics was employed to predict the effect of direct current-iDEP on cells suspended in a microchannel containing an array of insulating structures. The model allowed predicting particle behavior, pathlines and the regions where dielectrophoretic immobilization should occur. Experimental work was performed at the same operating conditions employed with the model and results were compared, obtaining good agreement. This is the first report on the mathematical modeling of the dielectrophoretic response of yeast and bacterial cells in a DC-iDEP microdevice.     

Gas-phase reactivities of charged platinum dimers with ammonia: A combined experimental/theoretical study

Computational and experimental studies of with ammonia are reported. While ammonia is dehydrogenated with either cluster type, the reaction efficiencies are quite different with  = 0.27 for [K. Koszinowski, D. Schröder, H. Schwarz, J. Phys. Chem. A 107 (2003) 4999.] and  = 0.0033 for . DFT-based relativistic calculations are consistent with this distinct behavior, with maximum energies along the reaction path of −13.3 kcal/mol for the cationic and +1.4 kcal/mol for the anionic clusters relative to the reactants. The recently proposed mechanism for the system [D. Xu. X.-Y. Chen, S.-G. Wang, Int, J. Quant. Chem. 107 (2007) 1985.] needs to be modified to account for the experimental findings.     

Characterization of the arc cathode attachment by emission spectroscopy and comparison to theoretical predictions

Emission spectroscopic diagnostics of electron temperature distribution and electron number density distribution in the cathode region have been carried out employing an OMA/spectrometer system. Single color and two color pyrometry of cathode temperature distributions have also been performed. The experimental results are compared with results of a theoretical model formulated previously to study the arc cathode interaction.The results show that the plasma in the cathode region strongly deviates from LTE. Thermionic cooling is the major cooling mechanism of cathodes at high arc currents. The work function of 2% thoriated tungsten cathodes increases during arcing due to fast evaporation of thorium from 2% thoriated tungsten cathodes.     

Gas-phase thermolysis reaction of formaldehyde diperoxide. Kinetic study and theoretical mechanisms

Gas-phase thermolysis reaction of formaldehyde diperoxide (1,2,4,5-tetroxane) was performed in an injection chamber of a gas chromatograph at a range of 463-503 K. The average Arrhenius activation energy and pre-exponential factor were 29.3 ± 0.8 kcal/mol and 5.2 × 10¹³ s⁻¹, respectively. Critical points and reaction paths of the ground singlet and first triplet potential energy surfaces (PES) were calculated, using DFT method at BHANDHLYP/6-311+G^∗∗ level of the theory. Also, G3 calculations were performed on the reactant and products. Reaction by the ground-singlet and first-triplet states turned out to be endothermic and exothermic, respectively. The mechanism in three steps seemed to be the most probable one. An electronically non-adiabatic process appeared, in which a crossing, at an open diradical structure, from the singlet to the triplet state PES occurred, due to a spin-orbit coupling, yielding an exothermic reaction. Theoretical kinetic constant coming from the non- adiabatic transition from the singlet to the triplet state agrees with the experimental values.     

Gas-phase infrared photodissociation spectroscopy of tetravanadiumoxo and oxo-methoxo cluster anions.

The infrared spectra of the binary vanadium oxide cluster anions V(4)O(9)(-) and V(4)O(10)(-) and of the related methoxo clusters V(4)O(9)(OCH(3))(-) and V(4)O(8)(OCH(3))(2)(-) are recorded in the gas phase by photodissociation of the mass-selected ions using an infrared laser. For the oxide clusters V(4)O(9)(-) and V(4)O(10)(-), the bands of the terminal vanadyl oxygen atoms, nu(V-O(t)), and of the bridging oxygen atoms, nu(V-O(b)-V), are identified clearly. The clusters in which one or two of the oxo groups are replaced by methoxo ligands show additional absorptions which are assigned to the C-O stretch, nu(C-O). Density functional calculations are used as a complement for the experimental studies and the interpretation of the infrared spectra. The results depend in an unusual way on the functional employed (BLYP versus B3LYP), which is due to the presence of both V-O(CH(3)) single and V=O double bonds as terminal bonds and to the strong multireference character of the latter.     

Problems in the comparison of theoretical and experimental hyperpolarizabilities revisited

The relationship between nonlinear susceptibilities and hyperpolarizabilities defined using different conventions is reexamined. In previous work [Willetts et al., J. Chem. Phys. 97, 7590 (1992)], relations between different conventions for microscopic hyperpolarizabilities have been derived, but the application of the corresponding conversion factors led to several inconsistencies. It is shown that different conventions for macroscopic susceptibilities have to be taken into account, too, in order to arrive at consistently comparable values. The complete set of conversion factors between several conventions are given for second harmonic generation, electric field induced second harmonic (EFISH) generation, and third harmonic generation. As an illustration, experimental EFISH and hyper-Rayleigh scattering results of p-nitroaniline are compared with each other and with recent results of ab initio computations including solvation effects. Several problems in the comparison of computational and experimental values are also discussed.