Jongcheol Seo

Protomers of Benzocaine: Solvent and Permittivity Dependence

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid that finds an application as a local anesthetic, is found to adopt in its protonated form at least two populations of distinct structures in the gas phase, and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization process. Here, we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry to yield gas-phase IR spectra of simultaneously m/z and drift-time-resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species: the N- and O-protonated forms. Density functional theory calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution-phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation have been suggested.

Rules and trends of metal cation driven hydride-transfer mechanisms in metal amidoboranes.

Group I and II metal amidoboranes have been identified as one of the promising families of materials for efficient H(2) storage. However, the underlying mechanism of the dehydrogenation of these materials is not well understood. Thus, the mechanisms and kinetics of H(2) release in metal amidoboranes are investigated using high level ab initio calculations and kinetic simulations. The metal plays the role of catalyst for the hydride transfer with formation of a metal hydride intermediate towards the dehydrogenation. In this process, with increasing ionic character of the metal hydride bond in the intermediate, the stability of the intermediate decreases, while the dehydrogenation process involving ionic recombination of the hydridic H with the protic H proceeds with a reduced barrier. Such correlations lead directly to a U-shaped relationship between the activation energy barrier for H(2) elimination and the ionicity of metal hydride bond. Oligomerized intermediates are formed by the chain reaction of the size-driven catalytic effects of metals, competing with the non-oligomerization pathway. The kinetic rates at low temperatures are determined by the maximum barrier height in the pathway (a Lambda-shaped relation), while those at moderately high temperatures are determined by most of multiple-barriers. This requires kinetic simulations. At the operating temperatures of proton exchange membrane fuel cells, the metal amidoboranes with lithium and sodium release H(2) along both oligomerization and non-oligomerization paths. The sodium amidoboranes show the most accelerated rates, while others release H(2) at similar rates. In addition, we predict that the novel metal amidoborane-based adducts and mixtures would release H(2) with accelerated rates as well as with enhanced reversibility. This comprehensive study is useful for further developments of active metal-based better hydrogen storage materials.

Host–Guest Chemistry from Solution to the Gas Phase: An Essential Role of Direct Interaction with Water for High-Affinity Binding of Cucurbit[n]urils

An investigation of the host-guest chemistry of cucurbit[n]uril (CB[n], n = 6 and 7) with α,ω-alkyldiammonium guests (H2N(CH2)xNH2, x = 4, 6, 8, 10, and 12) both in solution and in the gas phase elucidates their intrinsic host-guest properties and the contribution of solvent water. Isothermal titration calorimetry and nuclear magnetic resonance measurements indicate that all alkyldiammonium cations have inclusion interactions with CB[n] except for the CB[7]-tetramethylenediamine complex in aqueous solution. The electrospray ionization of mixtures of CB[n] and the alkyldiammonium guests reflects their solution phase binding constants. Low-energy collision-induced dissociations indicate that, after the transfer of the CB[n]-alkyldiammonium complex to the gas phase, its stability is no longer correlated with the binding properties in solution. Gas phase structures obtained from density functional theory calculations, which support the results from the ion mobility measurements, and molecular dynamics simulated structures in water provide a detailed understanding of the solvated complexes. In the gas phase, the binding properties of complexation mostly depend on the ion-dipole interactions. However, the ion-dipole integrity is strongly affected by hydrogen bonding with water molecules in the aqueous condition. Upon the inclusion of water molecules, the intrinsic characteristics of the host-guest binding are dominated by entropic-driven thermodynamics.

An infrared spectroscopy approach to follow β-sheet formation in peptide amyloid assemblies

Amyloidogenic peptides and proteins play a crucial role in a variety of neurodegenerative disorders such as Alzheimers and Parkinsons disease. These proteins undergo a spontaneous transition from a soluble, often partially folded form, into insoluble amyloid fibrils that are rich in β-sheets. Increasing evidence suggests that highly dynamic, polydisperse folding intermediates, which occur during fibril formation, are the toxic species in the amyloid-related diseases. Traditional condensed-phase methods are of limited use for characterizing these states because they typically only provide ensemble averages rather than information about individual oligomers. Here we report the first direct secondary-structure analysis of individual amyloid intermediates using a combination of ion mobility spectrometry-mass spectrometry and gas-phase infrared spectroscopy. Our data reveal that oligomers of the fibril-forming peptide segments VEALYL and YVEALL, which consist of 4-9 peptide strands, can contain a significant amount of β-sheet. In addition, our data show that the more-extended variants of each oligomer generally exhibit increased β-sheet content.

Retention of Native Protein Structures in the Absence of Solvent: A Coupled Ion Mobility and Spectroscopic Study

Abstract Can the structures of small to medium‐sized proteins be conserved after transfer from the solution phase to the gas phase? A large number of studies have been devoted to this topic, however the answer has not been unambiguously determined to date. A clarification of this problem is important since it would allow very sensitive native mass spectrometry techniques to be used to address problems relevant to structural biology. A combination of ion‐mobility mass spectrometry with infrared spectroscopy was used to investigate the secondary and tertiary structure of proteins carefully transferred from solution to the gas phase. The two proteins investigated are myoglobin and β‐lactoglobulin, which are prototypical examples of helical and β‐sheet proteins, respectively. The results show that for low charge states under gentle conditions, aspects of the native secondary and tertiary structure can be conserved.

The impact of environment and resonance effects on the site of protonation of aminobenzoic acid derivatives

The charge distribution in a molecule is crucial in determining its physical and chemical properties. Aminobenzoic acid derivatives are biologically active small molecules, which have two possible protonation sites: the amine (N-protonation) and the carbonyl oxygen (O-protonation). Here, we employ gas-phase infrared spectroscopy in combination with ion mobility-mass spectrometry and density functional theory calculations to unambiguously determine the preferred protonation sites of p-, m-, and o-isomers of aminobenzoic acids as well as their ethyl esters. The results show that the site of protonation does not only depend on the intrinsic molecular properties such as resonance effects, but also critically on the environment of the molecules. In an aqueous environment, N-protonation is expected to be lowest in energy for all species investigated here. In the gas phase, O-protonation can be preferred, and in those cases, both N- and O-protonated species are observed. To shed light on a possible proton migration pathway, the protonated molecule-solvent complex as well as proton-bound dimers are investigated.

Mass-Balanced 1H/2H Isotope Dipeptide Tag for Simultaneous Protein Quantitation and Identification

Mass-balanced (1)H/(2)H isotope dipeptide tags (MBITs) are presented for simultaneous protein quantitation and identification. MBIT is derived from N-acetyl-Ala-Ala dipeptide and conjugated to primary amines of target peptides. (1)H/(2)H isotopes are encoded in the methyl groups of N-acetylated dipeptide: one tag deuterated on the N-acetyl group and another on the C-terminal alanine. MBIT-linked peptides comigrate in reversed-phase liquid chromatography without significant (1)H/(2)H isotope effects and provide 2-plex quantitation signals at 114 and 117 Th as well as peptide sequence information upon MS/MS analysis with MALDI TOF/TOF. MBIT shows good quantitation linearity in a concentration range of 20-250 fmol. The performance of MBIT on protein quantitation and identification is further tested with yeast heat-shock protein (Hsp82p) obtained from three different physiological states. MBIT using nanogram-scale samples produces the relative abundance ratios comparable to those obtained from optical imaging of microgram-scale samples visualized with SYPRO Ruby stain. The MBIT strategy is a simple and low-cost alternative for 2-plex quantitation of proteins and offers possibilities of tuning the 2-plex signal mass window by replacing the N-terminal alanine with other amino acid residues.

Noncovalent Binding between Fullerenes and Protonated Porphyrins in the Gas Phase

Noncovalent interactions between protonated porphyrin and fullerenes (C₆₀ and C₇₀) were studied with five different meso-substituted porphyrins in the gas phase. The protonated porphyrin-fullerene complexes were generated by electrospray ionization of the porphyrin-fullerene mixture in 3:1 dichloromethane/methanol containing formic acid. All singly protonated porphyrins formed the 1:1 complexes, whereas porphyrins doubly protonated on the porphine center yielded no complexes. The complex ion was mass-selected and then characterized by collision-induced dissociation with Xe. Collisional activation exclusively led to a loss of neutral fullerene, indicating noncovalent binding of fullerene to protonated porphyrin. In addition, the dissociation yield was measured as a function of collision energy, and the energy inducing 50% dissociation was determined as a measure of binding energy. Experimental results show that C₇₀ binds to the protonated porphyrins more strongly than C₆₀, and electron-donating substituents at the meso positions increase the fullerene binding energy, whereas electron-withdrawing substituents decrease it. To gain insight into π-π interactions between protonated porphyrin and fullerene, we calculated the proton affinity and HOMO and LUMO energies of porphyrin using Hartree-Fock and configuration interaction singles theory and obtained the binding energy of the protonated porphyrin-fullerene complex using density functional theory. Theory suggests that the protonated porphyrin-fullerene complex is stabilized by π-π interactions where the protonated porphyrin accepts π-electrons from fullerene, and porphyrins carrying bulky substituents prefer the end-on binding of C₇₀ due to the steric hindrance, whereas those carrying less-bulky substituents favor the side-on binding of C₇₀.

The kinetics of competing multiple-barrier unimolecular dissociations of o-, m-, and p-chlorotoluene radical cations.

The kinetics of competing multiple-barrier unimolecular dissociations of o-, m-, and p-chlorotoluene radical cations to C7H7(+) (benzyl and tropylium) are studied by ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) calculations. This system presents a very intriguing kinetic example in which the conventional approach assuming a single-barrier or a double-well potential surface with one transition state cannot predict or explain the outcome. The molecular parameters obtained at the SCF level of theory with the DZP basis set are utilized for the evaluation of microcanonical RRKM rate constants with no adjustable parameters. First-principles calculations provide the microscopic details of the reaction kinetics along the two competing multiple-barrier reaction pathways: the rate-energy curves for all elementary steps; temporal variations of the reactants, the reaction intermediates, and the products; and the product yield as a function of energy. The rate constant for each channel is calculated as a function of the internal energy at 0 K. After the thermal correction, the calculated rate-energy curves for the benzyl channel agree well with the photoelectron photoion coincidence data obtained at room temperature for all three isomers. Close agreement between experiments and theory suggests that first-principles calculations taking the full sequence of kinetic steps into account offer a useful kinetic model capable of correctly predicting the outcome of competing multiple-barrier reactions. The slowest process is identified as [1,2] and [1,3] alpha-H migration at the entrance to the tropylium and benzyl channel, respectively. However, the overall rate is determined not by the slowest process, but by the combination of the slowest rate and the net flux toward the product, which is multiplicatively reduced with an increasing number of reaction intermediates. The product yield calculation confirms the benzyl cation as the predominant product. For all isomers, the thermodynamically most stable tropylium ion is produced much less than expected because a large fraction of flux coming into the tropylium channel goes back to the benzyl channel. The benzyl channel is kinetically favored because it involves a lower entrance barrier with fewer rearrangements than the tropylium channel.

From Compact to String—The Role of Secondary and Tertiary Structure in Charge-Induced Unzipping of Gas-Phase Proteins

AbstractIn the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS)-based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases, and finally form extended structures with presumably little or no defined structure when the charge state is high. However, with respect to the secondary structure, IM-MS methods are essentially blind. Infrared (IR) spectroscopy, on the other hand, is sensitive to such structural details and there is increasing evidence that helices as well as β-sheet-like structures can exist in the gas phase, especially for ions in low charge states. Very recently, we showed that also the fully extended form of highly charged protein ions can adopt a distinct type of secondary structure that features a characteristic C5-type hydrogen bond pattern. Here we use a combination of IM-MS and IR spectroscopy to further investigate the influence of the initial, native conformation on the formation of these structures. Our results indicate that when intramolecular Coulomb-repulsion is large enough to overcome the stabilization energies of the genuine secondary structure, all proteins, regardless of their sequence or native conformation, form C5-type hydrogen bond structures. Furthermore, our results suggest that in highly charged proteins the positioning of charges along the sequence is only marginally influenced by the basicity of individual residues.n Graphical Abstractᅟ