Experimental Collision-induced Dissociation Research Articles

Quantitative collision induced mass spectrometry of substituted piperazines – A correlative analysis between theory and experiment

The present paper deals with quantitative kinetics and thermodynamics of collision induced dissociation (CID) reactions of piperazines under different experimental conditions together with a systematic description of effect of counter-ions on common MS fragment reactions of piperazines; and intra-molecular effect of quaternary cyclization of substituted piperazines yielding to quaternary salts. There are discussed quantitative model equations of rate constants as well as free Gibbs energies of series of m–independent CID fragment processes in GP, which have been evidenced experimentally. Both kinetic and thermodynamic parameters are also predicted by computational density functional theory (DFT) and ab initio both static and dynamic methods. The paper examines validity of Maxwell–Boltzmann distribution to non–Boltzmann CID processes in quantitatively as well. The experiments conducted within the latter framework yield to an excellent correspondence with theoretical quantum chemical modeling. The important property of presented model equations of reaction kinetics is the applicability in predicting unknown and assigning of known mass spectrometric (MS) patterns. The nature of “GP” continuum of CID–MS coupled scheme of measurements with electrospray ionization (ESI) source is discussed, performing parallel computations in gas–phase (GP) and polar continuum at different temperatures and ionic strengths. The effect of pressure is presented. The study contributes significantly to methodological and phenomenological developments of CID–MS and its analytical implementations for quantitative and structural analyses. It also demonstrates great prospective of a complementary application of experimental CID–MS and computational quantum chemistry studying chemical reactivity, among others. To a considerable extend this work underlies the place of computational quantum chemistry to the field of experimental analytical chemistry in particular highlighting the structural analysis.

Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration, and proton affinity causes surprising compensation effects among the various energy terms. It appears that this work provides the most detailed account to date of the mechanism whereby noncovalent protein complexes disassemble during CID.

Artificial neural network for charge prediction in metabolite identification by mass spectrometry.

Collision-induced dissociation (CID) is widely used in mass spectrometry to identify biologically important molecules by gaining information about their internal structure. Interpretation of experimental CID spectra always involves some form of in silico spectra of potential candidate molecules. Knowledge of how charge is distributed among fragments is an important part of CID simulations that generate in silico spectra from the chemical structure of the precursor ions entering the collision chamber. In this chapter we describe a method to obtain this knowledge by machine learning.

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations

In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.

Collision-induced dissociation of MO + and MO 2+ (M = Ta and W): Metal oxide and dioxide cation bond energies

The collision-induced dissociation (CID) of TaO +, WO +, TaO 2 +, and WO 2 + with Xe along with reactions of TaO + and WO + with O 2 are studied as a function of kinetic energy using guided ion beam tandem mass spectrometry in order to elucidate the thermochemistry of the MO 2 + species. The kinetic energy dependences for the CID reactions show endothermic behavior, whereas the MO ++O 2 → MO 2 + + O reactions proceed near the collision limit indicating exothermic processes. Analyses of the endothermic CID reaction cross sections yield 0 K threshold energies in eV of E 0(Ta +–O) = 7.01 ± 0.12, E 0(W +–O) = 6.72 ± 0.10, E 0(OTa +–O) = 6.08 ± 0.12, and E 0(OW +–O) = 5.49 ± 0.09. The nature of the bonding in MO + and MO 2 + is discussed and compared for Ta and W and analyzed using theoretical calculations at the B3LYP/HW+/6-311 + G(3df) level of theory. Bond energies for all MO + and MO 2 + species are calculated using geometries calculated at this level as well as BHLYP and CCSD(T) levels and the Stuttgart–Dresden (SDD) and the Def2TZVPP basis sets. Reasonable agreement between the theoretical bond energies and experimental CID threshold energies for TaO +, WO +, TaO 2 +, and WO 2 + is found. Potential energy surfaces for the reaction of the metal cations with O 2 are also calculated at the B3LYP level of theory and reveal additional information about the reaction mechanisms.

Mass Spectral Metabonomics beyond Elemental Formula: Chemical Database Querying by Matching Experimental with Computational Fragmentation Spectra

Despite recent advances in NMR and mass spectrometry, the structural identification of organic compounds in complex biofluids remains a significant analytical challenge. For mass spectroscopy applications, chemical identification is generally limited to determination of elemental formula. Here we test the hypothesis that unknown chemical structures can be determined by matching their experimental collision-induced dissociation (CID) fragmentation spectra with computational fragmentation spectra of compounds retrieved from chemical databases. The monoisotopic molecular weights (MIMW +/- 10 ppm) of 102 "test" compounds were used to download 102 "bins" from the PubChem database. Each bin contained the corresponding test compound and, on average, 272 other candidate compounds, including 158 compounds having the same elemental formula as the test compound. Commercially available software was used to generate fragmentation spectra for all compounds in each of the 102 bins. Experimental CID spectra for each of the 102 test compounds were then compared to the computational spectra in order to rank candidate compounds based on number of fragment MIMW matches. This method returned the test compound as the highest ranking (or tied with the highest ranking) compound for 65 of the 102 bins. The test compound was ranked within the top 20 candidate compounds for 87 bins. In addition, the correct elemental formula was ranked first for 98 of 102 bins. Thus, matching experimental with computational fragmentation spectra is a valid method for rapidly discriminating among compounds having the same elemental formula and provides a novel approach for querying chemical databases for structural information.