Perturbation of Pyridinium CIVP Spectra by N2 and H2 Tags: An Experimental and BOMD Study

Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B12 Derivatives?

Aryl corrins represent a novel class of designed B12 derivatives with biological properties of "antivitamins B12". In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born-Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both "static" DFT calculations and "dynamic" BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made.

Increasing Complexity in a Conformer Space Step-by-Step: Weighing London Dispersion against Cation-π Interactions

We report an evaluation of the importance of London dispersion in moderately large (up to 36 heavy atoms) organic molecules by means of a molecular torsion balance whose conformations "weigh" one interaction against another in the absence of solvents. The experimental study, with gas-phase cryogenic ion vibrational predissociation (CIVP) spectroscopy, solid-state Fourier transfer infrared (FT-IR), and single-crystal X-ray crystallography, is accompanied by density functional theory calculations, including an extensive search and analysis of accessible conformations. We begin with the unsubstituted molecular torsion balance, and then step up the complexity systematically by adding alkyl groups incrementally as dispersion energy donors (DEDs) to achieve a degree of chemical complexity comparable to what is typically found in transition states for many regio- and stereoselective reactions in organic and organometallic chemistry. We find clear evidence for the small attractive contribution by DEDs, as had been reported in other studies, but we also find that small individual contributions by London dispersion, when they operate in opposition to other weak noncovalent interactions, produce composite effects on the structure that are difficult to predict intuitively, or by modern quantum chemical calculations. The experimentally observed structures, together with a reasonable value for a reference cation-π interaction, indicate that the pairwise interaction between two tert-butyl groups, in the best case, is modest. Moreover, the visualization of the conformational space, and comparison to spectroscopic indicators of the structure, as one steps up the complexity of the manifold of noncovalent interactions, makes clear that in silico predictive ability for the structure of moderately large, flexible, organic molecules falters sooner than one might have expected.

Comment on "Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy"

This Viewpoint presents a re-examination of the conclusions of a study reported in The Journal of Physical Chemistry Letters (Saparbaev, et al. 2021, 12, 907) that compared the structure of microsolvated ions formed by electrospray ionization to those formed in the gas-phase via a previously published cryogenic ion trap approach. We conducted additional experiments that clearly show that most of the observed differences in the IR spectra can be accounted for by considering the different spectroscopic action schemes used to obtain them. In particular, the presence of the D₂-tag induces shifts in some of the N-H and O-H peaks which need to be carefully considered before comparing spectra. Once these spectral effects are taken into account, we show that both clustering approaches yield similar cluster structures for the small GlyH⁺(H₂O)_n species. Using unimolecular reaction rate theory, we also show that for the small complexes considered here, only the gas-phase equilibrium distribution of conformers should be expected in both experimental approaches. In addition, the barrier heights necessary to kinetically trap high-energy conformers at 298 K is explored using a series of model polyalanine chains.

Application of continuous wave quantum cascade laser in combination with CIVP spectroscopy for investigation of large organic and organometallic ions

Rapidly developing mid-infrared quantum cascade laser (QCL) technology gives easy access to broadly tunable mid-IR laser radiation at a modest cost. Despite several applications of QCL in the industry, its usage for spectroscopic investigation of synthetically relevant organic compounds has been limited. Here, we report the application of an external cavity, continuous wave, mid-IR QCL to cryogenic ion vibrational predissociation spectroscopy to analyze a set of large organic molecules, organometallic complexes, and isotopically labeled compounds. The obtained spectra of test molecules are characterized by a high signal-to-noise ratio and low full width at half-maximum-values, allowing the assignment of two compounds with just a few wavenumber difference. Data generated by cw-QCL and spectra produced by another standard Nd:YAG difference-frequency generation system are compared and discussed.