Ion-dipole Complex Research Articles

Mechanism of Thiolate-Disulfide Exchange: Addition–Elimination or Effectively SN2? Effect of a Shallow Intermediate in Gas-Phase Direct Dynamics Simulations

Direct dynamics trajectory simulations were performed for two examples of the thiolate-disulfide exchange reaction, that is, HS(-) + HSSH and CH(3)S(-) + CH(3)SSCH(3). The trajectories were computed for the PBE0/6-31+G(d) potential energy surface using both classical microcanonical sampling at the ion-dipole complex and quasi-classical Boltzmann sampling (T = 300 K) at the central transition state. The potential energy surface for these reactions involves a hypercoordinate sulfur intermediate. Despite the fact that the intermediate resides in a shallow well (less than 5 kcal/mol), very few trajectories follow a direct substitution path (the S(N)2 pathway). Rather, the mechanism is addition-elimination, with several trajectories sampling the intermediate for long times, up to 15 ps or longer.

Complexation of divalent metal ions with diols in the presence of anion auxiliary ligands: zinc‐induced oxidation of ethylene glycol to glycolaldehyde by consecutive hydride ion and proton shifts

Ternary complexes of the type AH•••M(2+)•••L(-) (AH = diol, including diethylene and triethylene glycol, M = Ca, Mn, Fe, Co, Ni, Cu and Zn and auxiliary anion ligand L(-) = CH(3)COO(-), HCOO(-) and Cl(-)) have been generated in the gas phase by MALDI and ESI, and their dissociation characteristics have been obtained. Use of the auxiliary ligands enables the complexation of AH with the divalent metal ion without AH becoming deprotonated, although A(-)•••M(2+) is often also generated in the ion source or after MS/MS. For M = Ca, dissociation occurs to AH + M(2+)•••L(-) and/or to A(-)•••M(2+) + LH, the latter being produced from the H-shifted isomer A(-) •••M(2+)•••LH. For a given ligand L(-), the intensity ratio of these processes can be interpreted (barring reverse energy barriers) in terms of the quantity PA(A(-)) - Ca(aff) (A(-)), where PA is the proton affinity and Ca(aff) is the calcium ion affinity. Deuterium labeling shows that the complex ion HOCH(2)CH(2) OH•••Zn(2+)•••(-)OOCCH(3), in addition to losing acetic acid (60 Da), also eliminates glycolaldehyde (HOCH(2)CH=O, also 60 Da); it is proposed that these reactions commence with a hydride ion shift to produce the ion-dipole complex HOCH(2)CHOH(+)••• HZnOOCCH(3), which then undergoes proton transfer and dissociation to HOCH(2)CH=O + HZn(+)•••O = C(OH)CH(3). In this reaction, ethylene glycol is oxidized by consecutive hydride ion and proton shifts. A minor process leads to loss of the isomeric species HOCH=CHOH.

Novel Fragmentation Pathways of Anionic Adducts of Steroids Formed by Electrospray Anion Attachment Involving Regioselective Attachment, Regiospecific Decompositions, Charge-Induced Pathways, and Ion–Dipole Complex Intermediates

The analysis of several bifunctional neutral steroids, 5-α-pregnane diol (5-α-pregnane-3α-20βdiol), estradiol (3,17α-dihydroxy-1,3,5(10)-estratriene), progesterone (4-pregnene-3,20-dione), lupeol (3β-hydroxy-20(29)-lupene), pregnenolone (5-pregnen-3β-ol-20-one), and pregnenolone acetate (5-pregnen-3β-ol-20-one acetate) was accomplished by negative ion electrospray mass spectrometry (ESI-MS) employing adduct formation with various anions: fluoride, bicarbonate, acetate, and chloride. Fluoride yielded higher abundances of anionic adducts and more substantial abundances of deprotonated molecules compared with other investigated anions. Collision-induced dissociation (CID) of precursor [M + anion](-) adducts of these steroids revealed that fluoride adduct [M + F](-) precursors first lose HF to produce [M - H](-) and then undergo consecutive decompositions to yield higher abundances of structurally-informative product ions than the other tested anions. In addition to charge-remote fragmentations, the majority of CID pathways of estradiol are deduced to occur via charge-induced fragmentation. Most interestingly, certain anions exhibit preferential attachment to a specific site on these bifunctional steroid molecules, which we are calling "regioselective anion attachment." Regioselective anion attachment is evidenced by subsequent regiospecific decomposition. Regioselective attachment of fluoride (and acetate) anions to low (and moderate) acidity functional groups of pregnenolone, respectively, is demonstrated using deuterated compounds. Moreover, the formation of unique intermediate ion-dipole complexes leading to novel fragmentation pathways of fluoride adducts of pregnenolone acetate, and bicarbonate adducts of d(4)-pregnenolone, are also discussed.

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.

Cationic noble gas hydrides-2: A theoretical investigation on HNgHNgH+ (Ng = Ar, Kr, Xe)

The linear, centrosymmetric HNgHNgH+ (Ng=Ar, Kr, Xe) were characterized as true energy minima at the MP2, CCSD(T), and B3LYP levels of theory. The optimized geometries, atomic charges, AIM bond topologies, and harmonic frequencies point to ion–dipole complexes between a hydride anion and two covalent NgH+ cations, best formulated as (H–Ng+)2H−. The xenon cation HXeHXeH+ resulted thermochemically stable with respect to dissociation into XeHXe+ and 2H, and protected by a barrier of ca. 17–22kcalmol−1 with respect to the largely exothermic extrusion of a Xe atom so to form XeH+ and H2. On the other hand, both HArHArH+ and HKrHKrH+, even though kinetically stable by ca. 5–15 and 12–19kcalmol−1 with respect to dissociation into NgH+, Ng, and H2, are however largely unstable with respect to the loss of two H atoms and formation of NgHNg+. Therefore, they are predicted to be unstable even at the lowest temperatures. The HNgHNgH+ cations (Ng=Ar, Kr, Xe) are also considerably less stable than the isomeric clusters (Ng)2–H3+, recently proposed as intermediates in the sequestration of noble gases by H3+ in protoplanetary objects. In any case, our calculations invite the theoretical investigation of the stability of these clusters with respect to dissociation into the low-energy fragments NgHNg+ and H2.

Cationic Noble Gas Hydrides: A Theoretical Investigation of Dinuclear HNgFNgH+(Ng = He−Xe)

Theoretical calculations at the B3LYP, MP2, and CCSD(T) levels of theory disclose the conceivable existence of cationic noble gas hydrides containing two Ng atoms. These species have a general formula of HNgFNgH(+) (Ng = He-Xe), and are the cationic counterparts of the neutral HNgF. The optimized geometries, harmonic frequencies, and bonding properties point to ion-dipole complexes between a fluoride anion and two covalent H-Ng(+) cations, best formulated as (H-Ng(+))(2)F(-). The HXeFXeH(+) is also isoelectronic with the recently experimentally observed HXeOXeH (Khriachtchev et al. J. Am. Chem. Soc. 2008, 130, 6114-6118). The resulting HNgFNgH(+) are thermochemically stable with respect to dissociation into HNg(+) + HNgF and HNg(+) + H + Ng + F, but are largely unstable with respect to both the loss of HF (with formation of HNg(+) + Ng) and H(2)F(+) (with formation of two Ng atoms). These decompositions pass through bent transition structures, and only the heaviest HArFArH(+), HKrFKrH(+), and HXeFXeH(+) are protected by energy barriers large enough (ca. 10-15 kcal mol(-1)) to support their conceivable metastability. In line with other series of noble gas compounds, the neon cation HNeFNeH(+) is the least stable among the various HNgFNgH(+).

Electronic Structure Theory Study of the F− + CH3I → FCH3 + I− Potential Energy Surface

MP2 and DFT electronic structure theories, with the functionals OPBE, OLYP, HCTH407, BhandH, and B97-1 for the latter, were used to investigate stationary point properties on the F(-) + CH(3)I → FCH(3) + I(-) potential energy surface (PES). The aug-cc-pVDZ and aug-cc-pVTZ basis sets for C, H, and F, with Wadt and Hay's 3s3p valence basis and an effective core potential (ECP) for iodine, were employed for both MP2 and DFT. Single-point CCSD(T) calculations were also performed to obtain the complete basis set (CBS) limit for the stationary point energies. The CCSD(T)/CBS reaction exothermicity is only 5.0 kJ/mol different than the experimental value. MP2 and DFT do not predict the same stationary points on the PES. MP2 predicts the C(3v) F(-)-CH(3)I and FCH(3)-I(-) ion-dipole complexes and traditional [F-CH(3)-I](-) central barrier as stationary points, as well as a C(s) hydrogen-bonded F(-)-HCH(2)I complex and a [F-HCH(2)-I](-) transition state connecting this latter complex to the F(-)-CH(3)I complex. A CCSD(T)/CBS relaxed potential energy curve, calculated for the MP2 structures, shows that going from the F(-)-CH(3)I complex to the [F-CH(3)-I](-) TS is a barrierless process, indicating these two structures are not stationary points. This is also suggested by the DFT calculations. The structures and frequencies for CH(3)I and CH(3)Cl given by MP2 and DFT are in overall good agreement with experiment. The calculations reported here indicate that the DFT/B97-1 functional gives the overall best agreement with the CCSD(T) energies, with a largest difference of only 7.5 kJ/mol for the FCH(3)-I(-) complex.

Proton transfer reactions of halogenated compounds: Using gas chromatography/Fourier transform ion cyclotron resonance mass spectrometry (GC/FT-ICR MS) and ab initio calculations

We combine modern GC mass spectrometric techniques (GC/FT-ICR MS) and ab initio molecular orbital calculations at G2, G3, and MP2/6-31+G** levels for characterization of disinfection byproducts (DBPs) present in treated drinking water samples. We introduce an additional dimension to GC/MS analysis that utilizes theoretically calculated proton affinities (PAs) and gas-phase basicities (GBs) to elucidate reaction mechanisms. The observed species at m/ z = 100.9 ( i.e., CH 3OCl 2 +) in our GC/MS experiments is an ion-dipole complex (CHCl 2 +⋯OH 2), formally corresponding to protonated dichloromethanol (G3 calculated P A C H 2 OC l 2 ∼ 163.3 kcal mo l − 1 ) produced in the gas phase either by the association of a water molecule with a CHCl 2 + fragment ion from chloroform (present in the treated drinking water sample) or by the elimination of HCl in a condensation reaction between chloroform and protonated water. The calculated PA of chloroform at the G3 level ( P A CHC l 3 ∼ 157.8 kcal mo l − 1 ) as well as entropy considerations indicate that a non-dissociative proton transfer (PT) reaction from H 3O + to CHCl 3 would be inefficient; however, the observed dissociative PT product ions ( e.g., CHCl 2 +) can be explained by considering the reaction entropy (Δ S). The overall dissociative PT reaction is unfavorable at 298 K and marginally exoergic (“entropy driven”) under our experimental conditions at 360 K. Besides DBPs, we report the presence of the Zundel cation H 5O 2 + in our mass spectrum. We speculate that the Zundel cation is formed by multiple ion-molecule reactions involving water in the presence of helium carrier gas and GC eluting compounds.

Block-Localized Density Functional Theory (BLDFT), Diabatic Coupling, and Their Use in Valence Bond Theory for Representing Reactive Potential Energy Surfaces.

A multistate density functional theory in the framework of the valence bond model is described. The method is based on a block-localized density functional theory (BLDFT) for the construction of valence-bond-like diabatic electronic states and is suitable for the study of electron transfer reactions and for the representation of reactive potential energy surfaces. The method is equivalent to a valence bond theory with the treatment of the localized configurations by using density functional theory (VBDFT). In VBDFT, the electron densities and energies of the valence bond states are determined by BLDFT. A functional estimate of the off-diagonal matrix elements of the VB Hamiltonian is proposed, making use of the overlap integral between Kohn-Sham determinants and the exchange-correlation functional for the ground state substituted with the transition (exchange) density. In addition, we describe an approximate approach, in which the off-diagonal matrix element is computed by wave function theory using block-localized Kohn-Sham orbitals. The key feature is that the electron density of the adiabatic ground state is not directly computed nor used to obtain the ground-state energy; the energy is determined by diagonalization of the multistate valence bond Hamiltonian. This represents a departure from the standard single-determinant Kohn-Sham density functional theory. The multistate VBDFT method is illustrated by the bond dissociation of H2+ and a set of three nucleophilic substitution reactions in the DBH24 database. In the dissociation of H2+, the VBDFT method yields the correct asymptotic behavior as the two protons stretch to infinity, whereas approximate functionals fail badly. For the S(N)2 nucleophilic substitution reactions, the hybrid functional B3LYP severely underestimates the barrier heights, while the approximate two-state VBDFT method overcomes the self-interaction error, and overestimates the barrier heights. Inclusion of the ionic state in a three-state model, VBDFT(3), significantly improves the computed barrier heights, which are found to be in accord with accurate results. The BLDFT method is a versatile theory that can be used to analyze conventional DFT results to gain insight into chemical bonding properties, and it is illustrated by examining the intricate energy contributions to the ion-dipole complex stabilization.

Survey of the Reactivity of O2(a 1Δg) with Negative Ions

The reactivity of O(2)(a (1)Delta(g)) was studied with a series of anions, including (-)CH(2)CN, (-)CH(2)NO(2), (-)CH(2)C(O)H, CH(3)C(O)CH(2)(-), C(2)H(5)O(-), (CH(3))(2)CHO(-), CF(3)CH(2)O(-), CF(3)(-), HC(2)(-), HCCO(-), HC(O)O(-), CH(3)C(O)O(-), CH(3)OC(O)CH(2)(-), and HS(-). Reaction rate constants and product ion branching ratios were measured. All of the carbanions react through a common pathway to produce their major products. O(2)(a) adds across a bond at the site of the negative charge, resulting in the cleavage of this bond and the O=O bond. Oxyanions react through a hydride transfer to produce their major products. Proton transfer within these product ion-dipole complexes can occur, where the final branching ratios reflect the basicity of the resulting anions. Several of these anions (CF(3)(-), HC(2)(-), CH(3)OC(O)CH(2)(-)) were also found to undergo several sequential reactions within a single encounter. These three basic types of mechanisms are supported by calculations; a potential energy diagram for each type of reaction has been calculated. Additionally, six of these reactions had been qualitatively studied before; our results are in agreement with previous data.

Theoretical study of the interaction of a proton with the O, F and Cl atoms of enflurane (CHFCl–CF 2–O–CHF 2)

Ab initio MP2 and density functional B3LYP calculations were performed to investigate the interaction of a proton with the O, F and Cl atoms of enflurane (CHFCl–CF 2–O–CHF 2) in the gas phase. The study included the optimized structures, proton affinities, interactions energies and thermodynamic properties of protonated enflurane. The proton affinities (PAs) of the O and Cl atoms are 154.5 and 139.8 kcal mol −1, respectively, whereas PAs of five of the fluorine atoms are between 143.6 and 165.5 kcal mol −1 (MP2 results). In contrast to protonation at the O and Cl atoms, protonation at each of the F atoms of enflurane reveals a striking result, it leads to a cleavage of the C–F bond and formation of an ion–dipole complex between the enfluranyl cation and neutral hydrogen fluoride. The [(enfluranyl) +⋯FH] complexes are weakly bound, the SAPT-calculated interaction energy varies between −12.5 and −11.7 kcal mol −1. The long range attraction in these complexes is dominated by the electrostatic term (70%), whereas the induction and dispersion components contribute by about 15% each. Protonation at the chlorine atom of enflurane does not lead to a cleavage of the C–Cl bond. For the O-protonated enflurane the results from the natural bond orbital analysis (NBO) are discussed in details.

Theoretical Studies of the Nucleophilic Substitution of Halides and Amine at a Sulfonyl Center

Gas-phase nucleophilic substitution reactions, F(-) + CH(3)SO(2)F, Cl(-) + CH(3)SO(2)Cl, Cl(-) + CH(3)SO(2)F, and NH(3) + CH(3)SO(2)Cl, have been investigated at the B3LYP/6-311+G** and MP2/6-31+G* levels of theory. A very shallow well for the reaction intermediate in a triple-well potential energy surface (PES) was observed for the identity fluoride exchange, but double well PESs were obtained for the other three reactions with three different PES profiles. NBO analyses of the transition states showed substantial charge transfer interactions in all cases which provided a much larger amount of stabilization energy compared with the corresponding species at the carbon center of methyl halides. This difference is primarily caused by the strong electropositive nature of the sulfur center. The F-S-F axial linkage in the distorted TBP type intermediate in the identity fluoride exchange reaction exhibited a weak three-center, four-electron omega-bonding, which is considered to provide stability of the intermediate. All the reactant (RC) and product complexes (PC) have Cs symmetry. The symmetry plane bisects angles HCH (of methyl group), OSO (of sulfonyl group), and HNH (of ammonia). Vicinal charge transfer interactions between the two out-of-plane C-H, S-O, and N-H bonds provide extra stabilization to the ion-dipole complexes together with H-bond formation of in-plane H atom with the nucleophile and/or leaving group.

Reactions of α-Nucleophiles with Alkyl Chlorides: Competition between SN2 and E2 Mechanisms and the Gas-Phase α-Effect

Reaction rate constants and deuterium kinetic isotope effects for the reactions of BrO(-) with RCl (R = methyl, ethyl, isopropyl, and tert-butyl) were measured using a tandem flowing afterglow-selected ion flow tube instrument. These results provide qualitative insight into the competition between two classical organic mechanisms, nucleophilic substitution (S(N)2) and base-induced elimination (E2). As the extent of substitution in the neutral reactants increases, the kinetic isotope effects become increasingly more normal, consistent with the gradual onset of the E2 channel. These results are in excellent agreement with previously reported trends for the analogous reactions of ClO(-) with RCl. [Villano et al. J. Am. Chem. Soc. 2006, 128, 728.] However, the reactions of BrO(-) and ClO(-) with methyl chloride, ethyl chloride, and isopropyl chloride were found to occur by an additional reaction pathway, which has not previously been reported. This reaction likely proceeds initially through a traditional S(N)2 transition state, followed by an elimination step in the S(N)2 product ion-dipole complex. Furthermore, the controversial alpha-nucleophilic character of these two anions and of the HO(2)(-) anion is examined. No enhanced reactivity is displayed. These results suggest that the alpha-effect is not due to an intrinsic property of the anion but instead due to a solvent effect.

Protonated MF 3 (M = N–Bi): Structure, stability, and thermochemistry of the H–MF 3+ and HF–MF 2+ isomers

The structure, stability, and thermochemistry of the H(MF 3) + isomers (M = N–Bi) have been investigated by MP2 and coupled cluster calculations. All the HF–MF 2 + revealed weakly bound ion–dipole complexes between MF 2 + and HF. For M = N, As, Sb, and Bi they are more stable than the H–MF 3 + covalent structures (free energy differences) by 6.3, 14.3, 32.1, and 73.5 kcal mol −1, respectively. H–PF 3 + is instead more stable than HF–PF 2 + by 21.8 kcal mol −1. The proton affinities (PAs) of MF 3 at the M atom range from 91.9 kcal mol −1 (M = Bi) to 156.5 kcal mol −1 (M = P), and follow the irregular periodic trend BiF 3 < SbF 3 < AsF 3 < NF 3 < PF 3. The PAs at the F atom range instead from 131.9 kcal mol −1 (M = P) to 164.9 kcal mol −1 (M = Bi), and increase in the more regular order PF 3 ≈ NF 3 < AsF 3 < SbF 3 < BiF 3. This trend parallels the fluoride-ion affinities of the MF 2 + cations. For protonated NF 3 and PF 3, the calculations are in good agreement with the available experimental results. As for protonated AsF 3, they support the formation of HF–AsF 2 + rather than the previously proposed H–AsF 3 +. The calculations indicate also that the still elusive H(SbF 3) + and H(BiF 3) + should be viable species in the gas phase, exothermically obtainable by various protonating agents.

Quantum Chemical Calculations of the Cl− + CH3I → CH3Cl + I− Potential Energy Surface

Electronic structure theory calculations, using MP2 theory and the DFT functionals OPBE, OLYP, HCTH407, BhandH, and B97-1, were performed to characterize the structures, vibrational frequencies, and energies for stationary points on the Cl(-) + CH(3)I --> ClCH(3) + I(-) potential energy surface. The aug-cc-pVDZ and aug-cc-pVTZ basis sets, with an effective core potential (ECP) for iodine, were employed. Single-point CCSD(T) calculations were performed to obtain the complete basis set (CBS) limit for the reaction energies. DFT was found to give significantly longer halide ion/carbon atom bond lengths for the ion-dipole complexes and central barrier transition state than MP2. BhandH, with either the aug-cc-pVDZ or aug-cc-pVTZ basis sets, gives good agreement with the experimental structures for both CH(3)I and CH(3)Cl. The frequencies of CH(3)I and CH(3)Cl, obtained with the different levels of theory and basis sets, are in excellent agreement with experiment. The major difference between the MP2 and DFT frequencies is for the imaginary frequency of the central barrier. Using the aug-cc-pVTZ basis the MP2 value for this frequency ranges from 1.26 to 1.59 times larger than those for the DFT functionals. Thus, the MP2 and DFT theories have different PES shapes in the vicinity of the [Cl--CH(3)--I](-) central barrier. The CCSD(T)/CBS energies are in good agreement with experiments for the complexation energies and reaction exothermicity, with a small 1 kcal/mol difference for the latter. The CCSD(T)/CBS central barrier height is lower than values deduced by using statistical theoretical models to fit the Cl(-) + CH(3)I --> ClCH(3) + I(-) experimental rate constant, which is consistent with the expected nonstatistical dynamics for the reaction. The BhandH energies are in overall best agreement with the CCSD(T) values, with a largest difference of only 0.7 kcal/mol.

An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane.

An effective Hamiltonian mixed molecular orbital and valence bond (EH-MOVB) method is described to obtain an accurate potential energy surface for chemical reactions. Building upon previous results on the construction of diabatic and adiabatic potential surfaces using ab initio MOVB theory, we introduce a diabatic-coupling scaling factor to uniformly scale the ab initio off-diagonal matrix element H(12) such that the computed energy of reaction from the EH-MOVB method is in agreement with the target value. The scaling factor is very close to unity, resulting in minimal alteration of the potential energy surface of the original MOVB model. Furthermore, the relative energy between the reactant and product diabatic states in the EH-MOVB method can be improved to match the experimental energy of reaction. A key ingredient in the EH-MOVB theory is that the off-diagonal matrix elements are functions of all degrees of freedom of the system and the overlap matrix is explicitly evaluated. The EH-MOVB method has been applied to the nucleophilic substitution reaction between hydrosulfide and chloromethane to illustrate the methodology and the results were matched to reproduce the results from ab initio valence bond self-consistent valence bond (VBSCF) calculations. The diabatic coupling (the off-diagonal matrix element in the generalized secular equation) has small variations along the minimum energy reaction path in the EH-MOVB model, whereas it shows a maximum value at the transition state and has nearly zero values in the regions of the ion-dipole complexes from VBSCF calculations. The difference in the diabatic coupling stabilization is attributed to the large overlap integral in the computationally efficient MOVB method.

Inverse Temperature Dependent Lifetimes of Transient SN2 Ion-Dipole Complexes

The association and collisional stabilization of the S(N)2 entrance channel complex [Cl(-)...CH3Cl]* is studied in a low-temperature radiofrequency ion trap. The temperature dependence of the ternary rate coefficient is measured and a much stronger inverse temperature dependence than expected from a simple statistical calculation is found. From these data the lifetime of the transient S(N)2 complex has been derived as a function of temperature. It is suggested that the inverse temperature dependent rates of nonsymmetric S(N)2 reactions are related to the observed inverse temperature dependence of the transient ion-dipole complexes.

Infrared Multiple Photon Dissociation Spectra of Proton- and Sodium Ion-Bound Glycine Dimers in the N−H and O−H Stretching Region

The proton- and the sodium ion-bound glycine homodimers are studied by a combination of infrared multiple photon dissociation (IRMPD) spectroscopy in the N-H and O-H stretching region and electronic structure calculations. For the proton-bound glycine dimer, in the region above 3100 cm (-1), the present spectrum agrees well with one recorded previously. The present work also reveals a weak, broad absorption spanning the region from 2650 to 3300 cm (-1). This feature is assigned to the strongly hydrogen-bonded and anharmonic N-H and O-H stretching modes. As well, the shared proton stretch is observed at 2440 cm (-1). The IRMPD spectra for the proton-bound glycine dimer confirms that the lowest energy structure is an ion-dipole complex between N-protonated glycine and the carboxyl group of the second glycine. This spectrum also helps to eliminate the existence of any of the higher-energy structures considered. The IRMPD spectrum for the sodium ion-bound dimer is a much simpler spectrum consisting of three bands assigned to the O-H stretch and the asymmetric and symmetric NH 2 stretching modes. The positions of these bands are very similar to those observed for the proton-bound glycine dimer. Numerous structures were considered and the experimental spectrum agrees with the B3LYP/6-31+G(d,p) predicted spectrum for the lowest energy structure, two bidentate glycine molecules bound to Na (+). Though some of the structures cannot be completely ruled out by comparing the experimental and theoretical spectra, they are energetically disfavored by at least 20 kJ mol (-1).

Collision Induced Dissociation-Based Characterization of Nucleotide Peptides: Fragmentation Patterns of Microcin C7-C51, an Antimicrobial Peptide Produced by Escherichia coli

Covalent protein-nucleic acid conjugates form an original class of compounds that occur in nature or can be generated in vitro through cross-linking to investigate domains involved in protein/nucleic acid interactions. Their mass spectrometry fragmentation patterns are poorly characterized. We have used electrospray-ionization mass spectrometry (ESI-MS) combined with collision-induced dissociation (CID) to characterize microcin C7-C51, an antimicrobial nucleotide peptide that targets aspartyl-tRNA synthetase and inhibits translation. The fragments of microcin C7-C51 were analyzed in positive- and negative-ion modes and compared with those of the corresponding unmodified heptapeptide and to the derived aspartyl-adenylate. The positive- and negative-ion mode fragments of microcin C7-C51 provided information on both the nucleotide and peptide moieties. Accurate mass measurement obtained using an LTQ Orbitrap instrument was a key factor for a comprehensive interpretation of the fragments. The experimental results obtained permitted the proposal of stepwise fragmentation pathways involving ion-dipole complexes. The data provide a better understanding of nucleotide peptide fragmentation in the gas phase.

Gas-phase ion chemistry of NF 3/SO 2 mixtures: A mass spectrometric and theoretical investigation

The gas-phase ion chemistry of NF 3/SO 2 mixtures has been investigated by ion trap mass spectrometry and theoretical calculations. SO + and SO 2 + react efficiently with NF 3 giving F (SO) + and F (SO 2) +. CAD experiments and thermochemical considerations support the exclusive formation of the sulfur–fluorine cations F SO + and F SO 2 +. NF 2 + is unreactive toward SO 2, and NF 3 + undergoes exclusively the efficient charge transfer. On the other hand, NF + activates the OS O bond, with formation of SO + and NO +. DFT and coupled cluster calculations indicate that these ionic products arise from a SO +–(FNO) ion–dipole complex, which dissociates into SO + and FNO or NO + and FSO. This intermediate is more stable than NF + and SO 2 by nearly 60 kcal mol −1. We have also located a less stable sulfur–nitrogen complex FN SO 2 +, whose formation explains the less efficient observed charge transfer between NF + and SO 2. The only observed negative ion–molecule reaction is the formation of F SO 2 − from the reaction between SO 2 − and NF 3. Our investigated processes may be of interest for the plasma and the atmospheric chemistry of NF 3, one of the gaseous compounds most extensively used in the electronic industry to perform etching and cleaning processes.