Gilles Ohanessian

Fragmentation mechanisms of α-amino acids protonated under electrospray ionization: a collisional activation and ab initio theoretical study

Abstract The ionic complexes formed by electrospray of methanol/water solutions of all the α amino acids (AA) were studied by collisional activation in a triple quadrupole mass spectrometer. The fragmentation common to all protonated AA, except tryptophan, lysine, and arginine, is the well known sequential loss of H2O and CO yielding an immonium ion. For GlyH+ it is argued that formation of CH2NH2+ involves the most stable N-protonated form from which a proton is transferred to the hydroxy group. For the amino acids bearing a functional group on their side chain, formation of the immonium ion is in competition either with the loss of ammonia from the amino terminus or with the loss of a small molecule from the side chain. Extensive ab initio calculations at the MP2/6-31G∗ level have been carried out to determine the various fragmentation pathways of SerH+ and CysH+. These calculations are further used to validate an empirical determination of thermochemical data based on experimental heats of formation and Benson increments. Such approximate data are used to interpret the fragmentations of protonated Met, Thr, Asn, Asp, Gln, and Glu. They are in agreement with an initial protonation at the N terminus of these amino acids. On the other hand, side chain protonation is expected to occur for His, Trp, Lys, and Arg. With increasing collision energy, proton transfer to less basic sites X (X = SH, SCH3, OH, NH2 … ) can occur. All primary fragmentations start with an elongation of the C–+XH bond. This elongation may be assisted by a cyclisation stabilizing the incoming carbocation. The competitive fragmentations of each protonated amino acid are governed by a combination of enthalpic factors [bond dissociation energies (BDE) of the various C–+XH bonds and the energy of the final states associated with each HX loss] and activation barriers associated with rearrangements.

INTERACTION OF ALKALI METAL CATIONS (LI+-CS+) WITH GLYCINE IN THE GAS PHASE : A THEORETICAL STUDY

The complexes formed by alkali metal cations (Cat(+)) and glycine (Gly) were studied by means of ab initio quantum chemical methods. Seven types of Gly-Cat(+) interaction were considered in each case. It was found that in the most stable forms of Gly-Li+ and Gly-Na+ the metal ion is chelated between the carbonyl oxygen and nitrogen ends of glycine. For Gly-K+ an isomer involving complexation with both oxygens of the carboxylic function is found to be degenerate with the above chelate, and becomes slightly more stable for Gly-Rb+ and Gly-Cs+. In all cases, interaction of the ion with the carboxylate group of zwitterionic glycine is also low in energy. Computed binding energies (Delta H-298, kcal mol(-1)) are 54.5 (Gly-Li+), 36.3 (Gly-Na+), 26.5 (Gly-K+), 24.1 (Gly-Rb+) and 21.4 (Gly-Cs+). The values for Gly-Na+ and Gly-K+ are in good agreement with recent experimental determinations. For Gly-Li+, a revised experimental value of 54.0 kcal mol(-1) is obtained, based on the computed complexation enthalpy and entropy of Li+ with N,N-dimethylformamide (51.7 kcal mol(-1) and 23.8 cal mol(-1) K-1, respectively). Three isomers among the most stable of the lithiated dimer Gly-Li+-Gly have been determined and found to involve local Gly-Li+ interactions analogous to those in the monomer However, the relative energies of the various isomers show nonnegligible differences between the monomer and the dimer, implying that the kinetic method must be used with care for the determination of cation affinities of larger molecules. Finally, the fluxionality of the Gly-Na+ complex has been considered by locating the transition states for interconversion of the lowest energy isomers. In particular it is found that the lowest isomer can be transformed into the one involving zwitterionic Gly with a rate-determining barrier of 20.4 kcal mol(-1).

An Experimental and Ab Initio Study of the Nature of the Binding in Gas‐Phase Complexes of Sodium Ions

Fourier transform ion cyclotron resonance (FT-ICR) ligand exchange equilibrium experiments have been used to establish a relative scale of sodium binding free energies of about fifty organic molecules. Ab initio calculations yield accurate enthalpies and entropies of complexation for a new set of 30 molecules. These calculations establish an absolute basis for the relative experimental free energy scale. In addition, they provide structural information for the complexes which permits considerable insight into the nature of sodium ion binding. We found that when the binding site is a first row atom, the sodium ion aligns with the molecular dipole axis in order to maximize charge-dipole electrostatic interactions. Strong deviations from this behavior occur when the ion is attached to a heavier atom such as sulfur, chlorine or bromine. For flexible molecules such as the isomers of butyl chloride, there are several isomers of low energy, and differences exist between the enthalpy and free energy orders of stability. Finally, sodium ion affinities have been obtained for several aromatic molecules which lend support to the importance of charge-quadrupole interactions in such cation-pi complexes.

Vibrational signatures of protonated, phosphorylated amino acids in the gas phase.

Structural characterization of protonated phosphorylated serine, threonine, and tyrosine was performed using mid-infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. The ions were generated and analyzed by an external electrospray source coupled to a Paul ion-trap type mass spectrometer. Their fragmentation was induced by the resonant absorption of multiple photons from a tunable free electron laser (FEL) beam. IRMPD spectra were recorded in the 900-1850 cm(-1) energy range and compared to the corresponding computed IR spectra. On the basis of the frequency and intensity of two independent bands in the 900-1400 cm(-1) energy range, it is possible to identify the phosphorylated residue. IRMPD spectra for a 12-residue fragment of stathmin in its phosphorylated and nonphosphorylated forms were also recorded in the 800-1400 cm(-1) energy range. The lack of spectral congestion in the 900-1300 cm(-1) region makes their distinction facile. Our results show that IRMPD spectroscopy may became a valuable tool for structural characterization of small phosphorylated peptides.

Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations

The interaction of Zn2+ with glycine (Gly) in the gas phase is studied by a combination of ab initio and molecular mechanics techniques. The structures and energetics of the various isomers of the Gly–Zn2+ complex are first established via high‐level ab initio calculations. Two low‐energy isomers are characterized: one in which the metal ion interacts with the carboxylate end of zwitterionic glycine, and another in which it chelates the amino nitrogen and the carbonyl oygen of neutral glycine. These calculations lead to the first accurate value of the gas‐phase affinity of glycine for Zn2+. Ab initio calculations were also used to evaluate the performance of various implementations of the SIBFA force field. To assess the extent of transferability of the distributed multipoles and polarizabilities used in the SIBFA computations, two approaches are followed. In the first, approach (a), these quantities are extracted from the ab initio Hartree–Fock wave functions of glycine or its zwitterion in its entirety, and for each individual Zn2+‐binding conformation. In the second, approach (b), they are assembled from the appropriate constitutive fragments, namely methylamine and formic acid for neutral glycine, and protonated methylamine and formate for the zwitterion; they undergo the appropriate vector or matrix rotation to be assembled in the conformation studied. The values of the Zn2+–glycine interaction energies are compared to those resulting from ab initio SCF and MP2 computations using both the all‐electron 6‐311+G(2d,2p) basis set and an effective core potential together with the valence CEP 4‐31G(2d) basis set. Approach (a) values closely reproduce the ab initio ones, both in terms of the total interaction energies and of the individual components. Approach (b) can provide a similar match to ab initio interaction energies as does approach (a), provided that the two constitutive Gly building blocks are considered as separate entities having mutual interactions that are computed simultaneously with those occurring with Zn2+. Thus, the supermolecule is treated as a three‐body rather than a two‐body system. These results indicate that the current implementation of the SIBFA force field should be adequate to undertake accurate studies on zinc metallopeptides.

Alkali Metal Ion Binding to Amino Acids Versus Their Methyl Esters: Affinity Trends and Structural Changes in the Gas Phase

The relative alkali metal ion (M(+)) affinities (binding energies) between seventeen different amino acids (AA) and the corresponding methyl esters (AAOMe) were determined in the gas phase by the kinetic method based on the dissociation of AA-M(+)-AAOMe heterodimers (M=Li, Na, K, Cs). With the exception of proline, the Li(+), Na(+), and K(+) affinities of the other aliphatic amino acids increase in the order AA<AAOMe, while their Cs(+) affinities generally decrease in this direction. For aliphatic beta-amino acids, which are particularly basic molecules, the order AA>AAOMe is already observed for K(+). Proline binds more strongly than its methyl ester to all M(+) except Li(+). Ab initio calculations on the M(+) complexes of alanine, beta-aminoisobutyric acid, proline, glycine methyl ester, alanine methyl ester, and proline methyl ester show that their energetically most favorable complexes result from charge solvation, except for proline which forms salt bridges. The most stable mode of charge solvation depends on the ligand (AA or AAOMe) and, for AA, it gradually changes with metal ion size. Esters chelate all M(+) ions through the amine and carbonyl groups. Amino acids coordinate Li(+) and Na(+) ions through the amine and carbonyl groups as well, but K(+) and Cs(+) ions are coordinated by the O atoms of the carboxyl group. Upon consideration of these differences in favored binding geometries, the theoretically derived relative M(+) affinities between aliphatic AA and AAOMe are in good overall agreement with the above given experimental trends. The majority of side chain functionalized amino acids studied show experimentally the affinity order AA<AAOMe for all M(+) ions, which is consistent with charge solvation. Deviations are only observed with the most basic amino acids lysine and arginine, whose K(+) (for arginine) and Cs(+) complexes (for both) follow the affinity order AA>AAOMe. The latter ranking is attributed to salt bridge formation.

Structures and fragmentations of zinc(II) complexes of amino acids in the gas phase. I. Electrosprayed ions which are structurally different from their liquid phase precursors

Abstract Zinc complexes of deprotonated amino acids (AA), denoted [AA − H + Zn]+, are readily formed in the gas phase by electrospray. Their fragmentations can be studied by low energy collisional activation, yielding structural information about the gaseous ions. In this article we show that such ions may not have a structure similar to that of their liquid phase precursors. The simple case of the deprotonated methanol complex [ZnOCH3]+ is first studied in detail. The precursor of this ion in the desolvation process is [(CH3OH)ZnOCH3]+. Accurate ab initio calculations show that the direct desolvation of this ion via methanol evaporation is a costly reaction, while rearrangement via β − H transfer to [(CH3OH)ZnH(OCH2)]+ is much more favorable. Competitive evaporation of either methanol or methanal from the rearranged ion is also more favorable. Thus the [Zn, O, C, H3]+ ion observed corresponds to a two-ligand, hydride complex [ZnH(OCH2)]+. These computational results are fully consistent with experiments, either direct source or collision induced dissociation (CID) spectra. Analogous observations hold for the zinc complex of deprotonated glycine [Gly − H + Zn]+. Detailed computations of the various possible structures of [Gly-H+Zn]+ and its precursor are consistent with the formation of rearranged structures, which are more stable than those of the initially formed species in solution. These structures are also adequate for explaining the low energy CID spectrum of [(Gly − H)Zn]+. It is concluded that for electrosprayed ions in general, whenever the last desolvation steps are energetically costly, rearrangements may occur before evaporation of the last solvent molecule. The common wisdom that electrospray ionization is a gentle process which produces faithful images of solution phase structures is shown not to apply to certain categories of metal ions.

COMPLEXATION OF SMALL ORGANIC MOLECULES BY CU

Abstract The structure and binding energetics have been computed for the complexes of Cu + with water, hydrogen sulfide, ammonia, formaldehyde, formimine, methanol, methanethiol, methylamine, formic acid and formamide, using ab initio and density functional methods. The use of extended basis sets and correlated wavefunctions is mandatory to reduce basis set superposition error and describe properly the energetically significant s/d σ hybridization and electron transfer to the metal ion. Complexation energies at 298 K have been found to range from 35.9 kcal/mol for H 2 O to 56.1 kcal/mol for methylamine.

Structures and fragmentations of zinc(II) complexes of amino acids in the gas phase. III. Rearrangement versus desolvation in the electrospray formation of the glycine-zinc complex

Abstract The zinc complex of deprotonated glycine (Gly), denoted [Gly−H+Zn] + , is readily formed in the gas phase by electrospray ionization. Low energy collisional activation of [Gly−H+Zn] + leads to three primary fragments, resulting from the losses of CO 2 , H 2 O+CO, and CO. Previous work has shown that the first two reactions require isomerization of the glycinate to nonclassical structures before the last desolvation step, and that loss of CO can only occur from a N-deprotonated glycine complex. It is shown herein, using accurate ab initio calculations, that such a structure does not pre-exist in solution, and that it is also formed in the electrospray process, during one of the last desolvation steps. Solvent molecules participate in this mechanism as proton relays between the two functional groups of Gly. These results provide a complete picture of the fragmentation of gaseous [Gly−H+Zn] + : each of the primary fragmentations arises from a specific precursor, none of which is the parent structure formed in solution.

Structure of Sodiated Octa-Glycine: IRMPD Spectroscopy and Molecular Modeling

The structure of the sodiated peptide GGGGGGGG-Na+ or G8-Na+ was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N—H/O—H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N—Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G8-Na+ is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G8-Na+ at room temperature.