Pulsed-ionization High Pressure Mass Spectrometry Research Articles

Gas-phase solvation of protonated amino acids by methanol.

The enthalpy and entropy changes for the formation of the 1:1 complexes of methanol with various gaseous protonated amino acids have been measured using pulsed-ionization high-pressure mass spectrometry. The enthalpy changes for formation of the clusters Gly(MeOH)H(+), Ala(MeOH)H(+), Val(MeOH)H(+), Leu(MeOH)H(+), Ile(MeOH)H(+), and Pro(MeOH)H(+) have been determined to be -92.0, -83.3, -82.4, -79.5, -78.7, and -73.6 kJ mol(-1), respectively. These values agree very well with the energetic values computed at the MP2(full)/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level of theory for the lowest energy adducts in each system. Both experimental observations and computational determinations of the potential energy surface for the glycine system suggest that a mixture of low-lying isomers may be present for each of the cluster systems examined. The primary structural motif for these clusters is the coordination of the methanol molecule to the ammonium group of the protonated amino acid via a strong ionic hydrogen bond. For the amino acids studied here, computational results reveal that one methanol molecule does not sufficiently stabilize any zwitterionic structure such that no appreciable extent of proton transfer from the amino acid to methanol was observed.

Stabilization of Zwitterionic Structures of Amino Acids (Gly, Ala, Val, Leu, Ile, Ser and Pro) by Ammonium Ions in the Gas Phase

The thermochemistry of gas-phase ion-molecule interactions and structures of a variety of clusters formed between protonated amino acids and either ammonia or amines have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. The enthalpy changes for the association reactions of protonated Gly, Ala, Val, Leu, Ile, Ser, and Pro with ammonia have been measured as -23.2, -21.9, -21.0, -20.8, -20.6, -22.6, and -20.4 kcal mol(-1), respectively. A very good linear relationship exists between the enthalpy changes and the proton affinities (PAs) of the amino acids, with an exception of Ser, where the hydroxyl substituent forms an extra hydrogen bond with ammonia. For the association reaction of protonated proline and methylamine, the measured enthalpy and entropy changes are -26.6 kcal mol(-1) and -30.1 cal mol(-1) K(-1), respectively. The experimental and calculated results indicate that the zwitterionic structure of proline may be well stabilized by CH3NH3(+). For the first time, the interaction strengths between these amino acids and NH4(+) have been obtained, and comparison with Na+ is discussed. Stabilization of zwitterionic structures of a series of amino acids (Gly, Ala, Val, Ser, and Pro) by various ammonium ions (NH4(+), CH3NH3(+), (CH3)2NH2(+), and (CH3)3NH+) has been investigated systematically. Energy decomposition analysis has been performed so that the salt bridge interaction strengths between zwitterionic amino acids and ammonium ions have been obtained. Some generalizations with respect to the relative stability of zwitterionic structures may be drawn. First, as the PA of an amino acid increases, within a series of Gly, Ala, Val, the zwitterionic structure becomes more energetically favorable relative to a non-zwitterionic isomer. Second, as the PA of an amine increases, the zwitterionic structure of a given amino acid within the complex becomes gradually less favorable. Third, compared to the other amino acids, Pro, the only secondary amine among the 20 naturally occurring amino acids, has a much more pronounced tendency to form the zwitterionic structure, which has been confirmed by the experimental results. Finally, substituents on the amino acid backbone that may participate in additional hydrogen bond interactions in non-zwitterionic isomer may render it more stable, as seen in Ser. These organic ammonium ions are found to be able to very effectively stabilize the zwitterionic structure of amino acids, even more effectively than metal ions, which aids significantly in the understanding of why zwitterionic structures exist extensively in biological systems.

Investigation of Proton Transport Tautomerism in Clusters of Protonated Nucleic Acid Bases (Cytosine, Uracil, Thymine, and Adenine) and Ammonia by High-Pressure Mass Spectrometry and Ab Initio Calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.

Investigations of the clustering reactions of protonated amino acid esters by high pressure mass spectrometry and quantum chemical calculations

The equilibria involved in the formation of the proton-bound dimers of the three simplest amino acid methyl esters (glycine, alanine and valine methyl esters) were characterized by means of pulsed ionization high pressure mass spectrometry (PHPMS) experiments and density functional theory (DFT) calculations. Our results would indicate that, within the temperature range employed in these experiments, the most stable proton-bound dimer conformers are formed in the case of glycine and alanine whereas a more entropically favoured isomer would dominate in the case of valine. Various possible isomers of each of the proton-bound dimer species have been investigated computationally each exhibiting a combination of inter- and intramolecular hydrogen bonding. A system of nomenclature for these various species is proposed. The possibility of structures exhibiting 'salt-bridge’ interactions have also been explored, recognizing that such structures would necessarily result from highly energetic structural rearrangements.

Gas Phase SN2 Reactions of Halide Ions with Trifluoromethyl Halides: Front- and Back-Side Attack vs. Complex Formation

Density functional theory computations and pulsed-ionization high-pressure mass spectrometry experiments have been used to explore the potential energy surfaces for gas-phase S(N)2 reactions between halide ions and trifluoromethyl halides, X(-) + CF(3)Y --> Y(-) + CF(3)X. Structures of neutrals, ion-molecule complexes, and transition states show the possibility of two mechanisms: back- and front-side attack. From pulsed-ionization high-pressure mass spectrometry, enthalpy and entropy changes for the equilibrium clustering reactions for the formation of Cl(-)(BrCF(3)) (-16.5 +/- 0.2 kcal mol(-1) and -24.5 +/- 1 cal mol(-1) K(-1)), Cl(-)(ICF(3)) (-23.6 +/- 0.2 kcal mol(-1)), and Br(-)(BrCF(3)) (-13.9 +/- 0.2 kcal mol(-1) and -22.2 +/- 1 cal mol(-1) K(-1)) have been determined. These are in good to excellent agreement with computations at the B3LYP/6-311+G(3df)//B3LYP/6-311+G(d) level of theory. It is shown that complex formation takes place by a front-side attack complex, while the lowest energy S(N)2 reaction proceeds through a back-side attack transition state. This latter mechanism involves a potential energy profile which closely resembles a condensed phase S(N)2 reaction energy profile. It is also shown that the Cl(-) + CF(3)Br --> Br(-) + CF(3)Cl S(N)2 reaction can be interpreted using Marcus theory, in which case the reaction is described as being initiated by electron transfer. A potential energy surface at the B3LYP/6-311+G(d) level of theory confirms that the F(-) + CF(3)Br --> Br(-) + CF(4) S(N)2 reaction proceeds through a Walden inversion transition state.

A high‐pressure mass spectrometric and density functional theory investigation of the thermochemical properties and structure of protonated dimers and trimers of glycine

A new modification of pulsed-ionization high-pressure mass spectrometry (PHPMS) has been used to perform equilibrium thermochemical studies for relatively nonvolatile biomolecules such as amino acids. Binding enthalpy and entropy changes have been measured for proton-bound clusters of glycine, which are in good agreement with both theoretical (DFT) results of this work and a previous blackbody infrared dissociation experiment. Experimental data indicate that a number of conformers of the proton-bound dimer of glycine may coexist in the explored temperature range (360-460 K). Several new, conceptually different isomers (two of them zwitterionic) have been found by DFT calculations, one of which is 7 kJ mol(-1) lower in energy than the structure previously reported to be the energy minimum.

Potential Energy Surfaces for Gas-Phase SN2 Reactions Involving Nitriles and Substituted Nitriles

The stationary points on the potential energy surfaces for a number of gas-phase S(N)2 reactions have been determined using a combination of pulsed ionization high-pressure mass spectrometry. MP2/6-311++G**//B3LYP/6-311+G** calculations are shown to provide excellent agreement with the experimentally determined values, providing confidence for the use of this computational method to predict values that are not available experimentally. The binding in the halide/nitrile complexes has been described in the past as either hydrogen bonding or electrostatic bonding. The trends in the binding energies observed here, though, cannot be rationalized in terms of simply hydrogen bonding or ion-dipole bonding but a mixture of the two. The computed structures support the description of binding as a mixture of hydrogen bonding and ion-dipole bonding.

Thermochemistry and structures of solvated S N2 complexes and transition states in the gas phase: experiment and theory

The standard enthalpy and entropy changes (Δ H° and Δ S°) for the formation of solvated S N2 complexes (S)X −(RY) (X, Y = Cl, Br; R = (CH 3) 2CH; S = CH 3OH, CH 3CN, (CH 3) 2CO, CH 3CF 2H) have been determined by pulsed-ionization high pressure mass spectrometry. Not surprisingly, solvent effects are evident even at this mono-salvation level. Structures of solvated S N2 complexes and transition states for the Cl −(S) + CH 3Cl S N2 reaction (S = H 2O, H 2S, NH 3, PH 3, SO 2) have also been determined at the MP2/6-31+G(d) level of theory. A large variety of solvent dependent structures have been obtained, showing solvent reorganization upon going from the complex to the transition state. Standard binding and activation enthalpies ( Δ H 298 ∘ and Δ H 298 ‡ ) were determined at the MP2/6-311+G(3df,2p)//MP2/6-31+G(d,p) level of theory. For the Cl −(H 2O) + CH 3Br and Br −(H 2O) + CH 3Cl reactions, structures and enthalpies were calculated at the MP2/[6-31+G(d)/LanL2DZ(spd)] and MP2/[6-311+G(3df,2p)/LanL2DZ(spdf)]//MP2/[6-31+G(d)/LanL2DZ(spd)] level of theory. For the Cl − + CH 3Br and Cl −(H 2O) + CH 3Br reactions potential energy surface scans were performed at the MP2/[6-31+G(d)/LanL2DZ(spd)] level of theory. Formation of the two possible sets of solvated products, Br −(H 2O) + CH 3Cl and Br − + (CH 3Cl)(H 2O) proceeds through two different surfaces. Water transfer to the leaving group can be facilitated by rotation of the Br −(CH 3Cl) part in the exit channel Br −(CH 3Cl)(H 2O) complex. Finally, for the Cl − + CH 3Cl reactions in the condensed phase, complexation and activation energies (Δ E( ɛ) and Δ E ‡( ɛ)) were determined for a variety of solvents at the MP2/6-31+G(d) level of theory using the isodensity polarized continuum model. A linear correlation between −Δ E( ɛ) and Δ E ‡( ɛ) was obtained, and a similar correlation exists for the mono-solvated gas phase S N2 reaction, indicating that mono-solvation already exhibits some features of the condensed phase reaction.

Structures, thermochemistry, and infrared spectra of chloride ion–fluorinated acetone complexes and neutral fluorinated acetones in the gas phase: experiment and theory

The thermochemistry of chloride ion clustering onto acetone and four fluorinated acetones (CH 3C(O)CH 2F, CF 3C(O)CH 3, CF 3C(O)CF 2H, and CF 3C(O)CF 3) under thermal equilibrium conditions has been determined by pulsed-ionization high pressure mass spectrometry (PHPMS). The standard enthalpy (Δ H°) and entropy (Δ S°) changes obtained indicate a variety of different types of bonding in these complexes. Ab initio computational methods have been used to obtain more insight into the structures and energetics. Surprisingly, in the Cl −(CF 3C(O)CF 2H) complex the chloride ion is not linearly hydrogen bonded, despite the presence of a very acidic CF 2H bond. Instead, coordination with the carbonyl group carbon atom seems to be more pronounced, as found for the Cl −(CF 3C(O)CF 3) complex. For the Cl −(CF 3C(O)CF 3) clustering equilibrium a Δ S° value of −37.6 cal mol −1 K −1 has been measured, indicating that one or both CF 3 group rotations will be hindered upon complex formation. Excellent agreement between Δ H° 298 values calculated at the MP2/[6-311++G(3df,3pd)/6-311+G(2df,p)]//MP2/[6-31+G(d)/6-31G(d)] level of theory and experimental Δ H° values has been obtained. In addition, Δ acid H° 298 values for a set of small to medium sized organic and inorganic acids, and the fluorinated acetones have been determined at the G3 and G3(MP2) levels of theory. Good to excellent agreement was obtained compared to experimental data, indicating that these composite methods perform well for the determination of reliable Δ acid H° 298 results for medium sized molecules containing up to eight second row atoms. No linear correlation between clustering Δ H° 298 and Δ acid H° 298 values was found, indicating that most likely ion–dipole and ion-induced dipole interactions are determining the observed thermochemical trends. Finally, gas phase FT-IR spectra of CH 3C(O)CH 2F, CF 3C(O)CH 3, CF 3C(O)CF 2H, and CF 3C(O)CF 3 have been obtained, and the normal mode vibrational frequencies compared to results from calculations at the HF/6-31G(d) level of theory, scaled by 0.8953, and the B3LYP/6-311++G(3d,3p) level of theory. For the Cl −(CF 3C(O)CF 3) complex some large shifts in frequencies and IR absorption intensities are observed relative to CF 3C(O)CF 3, especially for the CO stretch.

Influence of fluorine substitution on the structures and thermochemistry of chloride ion–ether complexes in the gas phase

The thermochemistry of the chloride ion clustering onto dimethyl ether, diethyl ether, and three fluorinated ethers (CH3OCF3, (CF2H)2O, and CF3OCF2H) under thermal equilibrium conditions has been determined using pulsed-ionization high pressure mass spectrometry. The standard enthalpy (ΔH°) and entropy change (ΔS°) values obtained indicate a variety of different types of bonding in these complexes. The mode of binding is mainly determined by the number of fluorine atoms present and by the substitution pattern. In addition ab initio computational methods have been used to obtain more insight into the structures and energetics. ΔH°298 value calculated at the MP2/[6-311 ++ G(3df,3pd)/6-311 + G(2df,p)]//MP2/[6-31 + G(d)/6-31G(d)] level of theory show excellent agreement with the experimentally obtained ΔH° values.

Stepwise solvation of halides by alcohol molecules in the gas phase

The gas phase equilibrium clustering reactions X −(ROH) n + ROH ⇌ X −(ROH) n+1 (X = F, Cl, Br, I; R = CH 3, CH 3CH 2, (CH 3) 2CH, (CH 3) 3C; n = 0, 1, 2) have been investigated by using pulsed-ionization high pressure mass spectrometry (PHPMS). From the corresponding van’t Hoff plots the standard enthalpies (Δ H n, n+1 O ) and entropies (Δ S n, n+1 O ) were obtained, which are discussed in terms of the radii of the halides, the geometry of the alcohol molecules, the number of alcohol molecules, and molecular properties such as polarizability and gas phase acidity. The observed enthalpy trends can be explained on the basis of ion-dipole, ion-induced dipole, and dipole-dipole interactions within the clusters. The observed entropy trends are qualitatively discussed in terms of hindered rotations and low frequency intermolecular vibrations. In general, where available, there is good agreement between the present data and literature values obtained by various experimental techniques. In addition to the experiments, both density functional theory (DFT) calculations at the B3LYP/6–311+G( d, p) level of theory and G2 level calculations have been performed on a number of selected systems to test these methods for obtaining energetic data and to gain more insight into the structures of the investigated clusters.

Generation of Covalent and Electrostatic Complexes in Association Reactions of tert-Butyl Cation with Small Organics

Pulsed ionization High-Pressure Mass Spectrometry (PHPMS) has been used to investigate the thermochemistry of the association reactions of t-C4H9+ with various neutral molecules in the gas phase. The behavior of the logarithm of the association equilibrium constant as a function of inverse reaction temperature (a van't Hoff plot) has been examined over a broad temperature range to yield accurate thermochemical data for the enthalpy and entropy of association. All of the systems investigated show either a pronounced break or a subtle curvature in the van't Hoff plot. This behavior is consistent with two coexisting isomeric forms of the association adduct, viz, (i) a low-temperature, covalently bound isomer characterized by larger −ΔH° and −ΔS° values and (ii) a high-temperature, electrostatically bound isomer of lower −ΔH° and −ΔS° values. Experimental thermochemical data for the association reactions are reported. From the low-temperature data, proton affinities (PA) of t-C4H9OCH3 (205.1 kcal/mol) and t-C...