Unimolecular Fragmentation Properties of Thermometer Ions from Chemical Dynamics Simulations

Heterobimetallic Complexes That Point to When Bond Dissociation Energies Deviate from Computational Expectations

Measurement of the formal, gas-phase, d8-d10 bond dissociation energy across a series of structurally homologous heterobimetallic complexes of Pd(II) with Cu(I), Ag(I), Au(I), and Zn(II), themselves models for the transition states for transmetalation in Sonogashira and Negishi couplings, finds large discrepancies relative to predictions by a commonly used dispersion-corrected density-functional theory method, DFT-D3(BJ), but not in all cases. Control studies on the threshold collision-induced dissociation (T-CID) of electrosprayed molecular ions, as well as the deconvolution of the bond energy from the experimentally measured energy-resolved cross sections, indicate that the experimentally determined bond dissociation energies are most likely correct, which raises the question of why the computational methods, while sometimes agreeing acceptably with experiment, can also sometimes disagree egregiously. While initial attempts to characterize the discrepancy focused on the metal-metal interaction, the most likely origin of the discrepancy appears to be an uneven treatment of nonbonded interactions, among them medium-ranged correlation effects and London dispersion, between the ligands on the two metal centers. The contribution of these effects to the formal bond dissociation energy is large enough to be chemically significant, but it appears to depend on the nature of the interacting groups, specifically the hybridization at carbon, and, more importantly, their relative orientation. Whereas face-to-face aryl-aryl interactions seem to be modeled well by PBE-D3(BJ), a representative DFT-D3 method, alkyl-aryl, and edge-to-face aryl-aryl interactions appear to be overestimated. The consequences for structure and stability in organic and organometallic molecules are discussed, especially with regard to relative energies of conformers and interconverting valence isomers.

Gas-phase reactivity of protonated oxazolone: Chemical dynamics simulations and graph theory-based analysis reveal the importance of ion-molecule complexes

This study delves into the fragmentation mechanisms of the oxazolone form (OXA) of protonated cyclo-di-glycine using chemical dynamics simulations at multiple internal energies. While we focus our in-depth analyses on a representative total energy of 178 kcal/mol, we also performed simulations over the 127-187 kcal/mol range. This broader energy sampling reveals how the population of states evolves with increasing internal energy, enabling us to compute rate constants and then effective energy thresholds using a previously introduced three-state model [Perez Mellor et al., J. Chem. Phys. 155, 124103 (2021)]. By transforming molecular geometries into graph representations, we systematically analyze fragmentation processes and identify key intermediates and ion-molecule complexes (IMCs) that play a crucial role in fragmentation dynamics. The study highlights the distinct isomerization landscapes of OXA, driven by IMC formation, which contrasts with the previously reported behavior of cyclic and linear forms [Perez Mellor et al., J. Chem. Phys. 155, 124103 (2021)]. The resulting fragmentation channels are characterized by their unique energetic thresholds and branching ratios and can provide a molecular explanation of what was observed experimentally. Thanks to an accurate analysis of the trajectories using our graph-theory-based tools, it was possible to point out the particular behavior of OXA fragmentation, which is different from other isomers. In particular, the important role of IMCs is shown, which has an impact on populating different isomeric structures.

Novel Ag-modified vanadate nanosheets for determination of small organic molecules with laser desorption ionization mass spectrometry

Laser desorption ionization mass spectrometry (LDI-MS) aroused intensive concerns for the merits of label-free and high-throughput analysis. Here, we designed a silver nanoparticles (AgNP)-modified indium vanadate nanosheets with doping samarium (AgNP@InVO4:Sm) nanosheets. The developed AgNP@InVO4:Sm nanosheets (AIVON) were synthesized based on the microemulsion-mediated solvothermal method and ultraviolet-assisted in situ formation of AgNP, then for the first time applied as a matrix in LDI-MS analysis. With the advantages including enhanced MS signal, little matrix-related background, high reproducibility, and good salt tolerance, AIVON exhibited much better prospect than non-modified indium vanadate nanosheets with doping samarium (IVON) and traditional organic matrix, thus allowing sensitive MS detection for a wide range of low-molecular-weight (LMW) molecules. Moreover, by coupling with headspace sampling thin-film microextraction (TFME), a kind of representative pollutant chlorophenols were identified and quantified via AIVON-assisted LDI-MS in environmental and biological samples. Volatile LMW pollutants could be preconcentrated after TFME, hence a sensitive and rapid assay with negligible sample matrix effect was realized by using AIVON-assisted LDI-MS. It is anticipated that this novel nano-matrix AIVON and the proposed TFME coupling detection strategy were of competitive merits for LDI-MS analysis in the fields of environment, biomedicine, and agriculture.

Quantum versus classical unimolecular fragmentation rate constants and activation energies at finite temperature from direct dynamics simulations

In the present work, we investigate how nuclear quantum effects modify the temperature dependent rate constants and, consequently, the activation energies in unimolecular reactions. In the reactions under study, nuclear quantum effects mainly stem from the presence of a large zero point energy. Thus, we investigate the behavior of methods compatible with direct dynamics simulations, the quantum thermal bath (QTB) and ring polymer molecular dynamics (RPMD). To this end, we first compare them with quantum reaction theory for a model Morse potential before extending this comparison to molecular models. Our results show that, in particular in the temperature range comparable with or lower than the zero point energy of the system, the RPMD method is able to correctly capture nuclear quantum effects on rate constants and activation energies. On the other hand, although the QTB provides a good description of equilibrium properties including zero-point energy effects, it largely overestimates the rate constants. The origin of the different behaviours is in the different distance distributions provided by the two methods and in particular how they differently describe the tails of such distributions. The comparison with transition state theory shows that RPMD can be used to study fragmentation of complex systems for which it may be difficult to determine the multiple reaction pathways and associated transition states.

Efficient and Accurate Description of Diels-Alder Reactions Using Density Functional Theory

Modeling chemical reactions using Quantum Chemistry is a widely used predictive strategy capable to complement experiments in order to understand the intrinsic mechanisms guiding the chemicals towards the most favorable reaction products. However, at this purpose, it is mandatory to use reliable and computationally tractable theoretical methods. In this work, we focus on six Diels-Alder reactions of increasing complexity and perform an extensive benchmark of middle- to low-cost computational approaches to predict the characteristic reactions energy barriers. We found that Density Functional Theory, using the ωB97XD, LC-ωPBE, CAM-B3LYP, M11 and MN12SX functionals, with empirical dispersion corrections coupled to an affordable 6-31G basis set, provides quality results for this class of reactions, at a small computational effort. Such efficient and reliable simulation protocol opens perspectives for hybrid QM/MM molecular dynamics simulations of Diels-Alder reactions including explicit solvation.