Mass spectrometric and quantum-chemical study on the structure, stability, and chirality of protonated serine dimers

Structure, energetics, and spectroscopy of the chromophores of HHe+n, H2He+n, and He+n clusters and their deuterated isotopologues

The linear molecular ions H₂He⁺, HHe+2, and He+3 are the central units (chromophores) of certain He-solvated complexes of the H₂He+n, HHe+n, and He+n families, respectively. These are complexes which do exist, according to mass-spectrometry studies, up to very high n values. Apparently, for some of the H₂He+n and He+n complexes, the linear symmetric tetratomic H₂He+2 and the diatomic He+2 cations, respectively, may also be the central units. In this study, definitive structures, relative energies, zero-point vibrational energies, and (an)harmonic vibrational fundamentals, and, in some cases, overtones and combination bands, are established mostly for the triatomic chromophores. The study is also extended to the deuterated isotopologues D₂He⁺, DHe+2, and D₂He+2. To facilitate and improve the electronic-structure computations performed, new atom-centered, fixed-exponent, Gaussian-type basis sets called MAX, with X = T(3), Q(4), P(5), and H(6), are designed for the H and He atoms. The focal-point-analysis (FPA) technique is employed to determine definitive relative energies with tight uncertainties for reactions involving the molecular ions. The FPA results determined include the 0 K proton and deuteron affinities of the ⁴He atom, 14 875(9) cm^-1 [177.95(11) kJ mol^-1] and 15 229(8) cm^-1 [182.18(10) kJ mol^-1], respectively, the dissociation energies of the He+2 → He⁺ + He, HHe+2 → HHe⁺ + He, and He+3 → He+2 + He reactions, 19 099(13) cm^-1 [228.48(16) kJ mol^-1], 3948(7) cm^-1 [47.23(8) kJ mol^-1], and 1401(12) cm^-1 [16.76(14) kJ mol^-1], respectively, the dissociation energy of the DHe+2 → DHe⁺ + He reaction, 4033(6) cm^-1 [48.25(7) kJ mol^-1], the isomerization energy between the two linear isomers of the [H, He, He]⁺ system, 3828(40) cm^-1 [45.79(48) kJ mol^-1], and the dissociation energies of the H₂He⁺ → H+2 + He and the H₂He+2 → H₂He⁺ + He reactions, 1789(4) cm^-1 [21.40(5) kJ mol^-1] and 435(6) cm^-1 [5.20(7) kJ mol^-1], respectively. The FPA estimates of the first dissociation energy of D₂He⁺ and D₂He+2 are 1986(4) cm^-1 [23.76(5) kJ mol^-1] and 474(5) cm^-1 [5.67(6) kJ mol^-1], respectively. Determining the vibrational fundamentals of the triatomic chromophores with second-order vibrational perturbation theory (VPT2) and vibrational configuration interaction (VCI) techniques, both built around the Eckart-Watson Hamiltonian, proved unusually challenging. For the species studied, VPT2 has difficulties yielding dependable results, in some cases even for the fundamentals of the H-containing molecular cations, while carefully executed VCI computations yield considerably improved spectroscopic results. In a few cases unusually large anharmonic corrections to the fundamentals, on the order of 15% of the harmonic value, have been observed.

Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case

The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)^MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm^-1, has been obtained by combining CCSD(T)/(CBS+CV)^MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.

Probing chirality recognition of protonated glutamic acid dimers by gas-phase vibrational spectroscopy and first-principles simulations

We characterize stereospecific aspects of homochiral and heterochiral dimers of glutamic acid by infrared spectroscopy and first-principles molecular dynamics simulations.

Quantum chemical mass spectrometry: ab initio prediction of electron ionization mass spectra and identification of new fragmentation pathways

The electron ionization mass spectra of four organic compounds are predicted based on the results of quantum chemical calculations at the DFT/B3LYP/6-311 + G* level of theory. This prediction is performed 'ab initio', i.e. without any prior knowledge of the thermodynamics or kinetics of the reactions under consideration. Using a set of rules determining which routes will be followed, the fragmentation of the molecules' bonds and the complete resulting fragmentation pathways are studied. The most likely fragmentation pathways are identified based on calculated reaction energies ΔE when bond cleavage is considered and on activation energies ΔE^‡ when rearrangements are taken into account; the final intensities of the peaks in the spectrum are estimated from these values. The main features observed in the experimental mass spectra are correctly predicted, as well as a number of minor peaks. In addition, the results of the calculations allow us to propose fragmentation pathways new to empirical mass spectrometry, which have been experimentally verified using tandem mass spectrometry measurements. Copyright © 2016 John Wiley & Sons, Ltd.

Conformational effects in protein electrospray-ionization mass spectrometry

Electrospray-ionization mass spectrometry (ESI-MS) is a key tool of structural biology, complementing the information delivered by conventional biochemical and biophysical methods. Yet, the mechanism behind the conformational effects in protein ESI-MS is an object of debate. Two parameters-solvent-accessible surface area (As) and apparent gas-phase basicity (GBapp)-are thought to play a role in controlling the extent of protein ionization during ESI-MS experiments. This review focuses on recent experimental and theoretical investigations concerning the influence of these parameters on ESI-MS results and the structural information that can be derived. The available evidence supports a unified model for the ionization mechanism of folded and unfolded proteins. These data indicate that charge-state distribution (CSD) analysis can provide valuable structural information on normally folded, as well as disordered structures.

On the zwitterionic nature of gas-phase peptides and protein ions

Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation.

Electrostatic chiral distinction: tetrahedral model dimers

Although chiral distinction plays a pervasive role in chemistry, a complete understanding of how this takes place is still lacking. In this work, we expand the earlier described minimal requirement of so called four-point interactions (vide infra). We focus on chiral point charge model systems as a means to aid in the dissection of the underlying, operative principles. We also construct models with defined symmetry characteristics. By considering extensive constellations of diastereomeric complexes, we are able to identify emerging principles for chiral distinction. As previously postulated, all the diastereomeric complexes, regardless of their nominal contact-points, possess a chiral distinction energy. In the comparison of complexes, we find that, contrary to chemical intuition, the magnitude of chiral distinction does not correlate with the stability of the complexes, i.e., consideration of low energy complexes may not be an effective way to evaluate chiral distinction. Similarly, we do not find a correlation between the number of contact-points and chiral distinction. Moreover, favorable interactions and facile chiral distinction appear to be unrelated. We also see some tendency for greater chiral distinction in less symmetric systems, although this may not be general. These studies can now form the basis to fold in higher levels of complexity into the models so as to gain further insights into the nature of chiral distinction.