Unraveling the Catalytic Mechanism of β-Cyclodextrin in the Vitamin D Formation

Previous experimental studies have shown that the isomerization reaction of previtamin D3 (PreD3) to vitamin D3 (VitD3) is accelerated 40-fold when it takes place within a β-cyclodextrin dimer, in comparison to the reaction occurring in conventional isotropic solutions. In this study, we employ quantum mechanics-based molecular dynamics (MD) simulations and statistical multistructural variational transition state theory to unveil the origin of this acceleration. We find that the conformational landscape in the PreD3 isomerization is highly dependent on whether the system is encapsulated. In isotropic media, the triene moiety of the PreD3 exhibits a rich torsional flexibility. However, when encapsulated, such a flexibility is limited to a more confined conformational space. In both scenarios, our calculated rate constants are in close agreement with experimental results and allow us to identify the PreD3 flexibility restriction as the primary catalytic factor. These findings enhance our understanding of VitD3 isomerization and underscore the significance of MD and environmental factors in biochemical modeling.

Combined DFT and Kinetic Monte Carlo Study of UiO-66 Catalysts for γ-Valerolactone Production

Zr-based metal-organic frameworks (MOFs) are excellent heterogeneous porous catalysts due to their thermal stability. Their tunability via node and linker modifications makes them amenable for theoretical studies on catalyst design. However, detailed benchmarks on MOF-based reaction mechanisms combined with kinetics analysis are still scarce. Thus, we here evaluate different computational models and density functional theory (DFT) methods followed by kinetic Monte Carlo studies for a case reaction relevant in biomass upgrading, i.e., the conversion of methyl levulinate to γ-valerolactone catalyzed by UiO-66. We show the impact of cluster versus periodic models, the importance of the DF of choice, and the direct comparison to experimental data via simulated kinetics data. Overall, we found that Perdew-Burke-Ernzerhof (PBE), a widely employed method in plane-wave periodic calculations, greatly overestimates reaction rates, while M06 with cluster models better fits the available experimental data and is recommended whenever possible.

Correction: An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers

Correction for 'An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers' by David Ferro-Costas et al., Phys. Chem. Chem. Phys., 2022, DOI: 10.1039/d1cp03928h.

An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers

This work presents a protocol designed to study hydrogen abstraction reactions by atomic hydrogen in molecules with multiple conformations.

TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids

In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in TorsiFlex combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. TorsiFlex operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed TorsiFlex to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. TorsiFlex has produced a number of conformers that roughly doubles the amount of the most complete work to date.

Chemical reactivity from the vibrational ground-state level. The role of the tunneling path in the tautomerization of urea and derivatives

Recent developments of low-temperature techniques are providing valuable knowledge about chemical processes that manifest in the quantum regimen. The tunneling effect from the vibrational ground-state is the main mechanism of these reactions, which usually involves the motion or transfer of hydrogen atoms. Theoretical methods can enrich the information supplied by these experimental methods through an insightful analysis of the tunneling process. In this context, canonical variational transition state theory with multidimensional tunneling corrections (CVT/MT) can handle this type of reaction, and it has been applied to several systems within the small-curvature approximation for tunneling (SCT). This method is of proven reliability for polyatomic reactions occurring at room temperature and above, but no tests have been performed to check its performance when only the lowest energy level is populated. In this work, we compare SCT against the least-action tunneling (LAT) method to study the tautomerization and cis-trans interconversion reactions in the enol forms of urea, thiourea, and selenourea. To the best of our knowledge, this is the first time that the LAT method is applied to a polyatomic reaction occurring in the deep-tunneling region. The theoretical results indicate that the reaction mechanisms are controlled by tunneling. The SCT and LAT tautomerization reaction times are in good agreement with the experimental values; however, LAT seems superior to SCT for reactions (tautomerizations) that involve moderate reaction path curvature, whereas the opposite is true for reactions with small curvature (interconversions). These results led us to introduce and recommend the microcanonically optimized tunneling path that selects the tunneling probability as the maximum between the SCT and LAT tunneling probabilities.

A Combined Systematic-Stochastic Algorithm for the Conformational Search in Flexible Acyclic Molecules

We propose an algorithm that is a combination of systematic variation of the torsions and Monte Carlo (or stochastic) search. It starts with a trial geometry in internal coordinates and with a set of preconditioned torsional angles, i.e., torsional angles at which minima are expected according to the chemical knowledge. Firstly, the optimization of those preconditioned geometries is carried out at a low electronic structure level, generating an initial set of conformers. Secondly, random points in the torsional space are generated outside the “area of influence” of the previously optimized minima (i.e., outside a hypercube about each minima). These random points are used to build the trial structure, which is optimized by an electronic structure software. The optimized structure may correspond to a new conformer (which would be stored) or to an already existing one. Initial torsional angles (and also final ones if a new conformer is found) are stored to prevent visiting the same region of the torsional space twice. The stochastic search can be repeated as many times as desired. Finally, the low-level geometries are recovered and used as the starting point for the high-level optimizations. The algorithm has been employed in the calculation of multi-structural quasi harmonic and multi-structural torsional anharmonic partition functions for a series of alcohols ranging from n-propanol to n-heptanol. It was also tested for the amino acid L-serine.

Role of Microsolvation and Quantum Effects in the Accurate Prediction of Kinetic Isotope Effects: The Case of Hydrogen Atom Abstraction in Ethanol by Atomic Hydrogen in Aqueous Solution

Hydrogen abstraction from ethanol by atomic hydrogen in aqueous solution is studied using two theoretical approaches: the multipath variational transition state theory (MP-VTST) and a path-integral formalism in combination with free-energy perturbation and umbrella sampling (PI-FEP/UM). The performance of the models is compared to experimental values of H kinetic isotope effects (KIE). Solvation models used in this study ranged from purely implicit, via mixed–microsolvation treated quantum mechanically via the density functional theory (DFT) to fully explicit representation of the solvent, which was incorporated using a combined quantum mechanical-molecular mechanical (QM/MM) potential. The effects of the transition state conformation and the position of microsolvating water molecules interacting with the solute on the KIE are discussed. The KIEs are in good agreement with experiment when MP-VTST is used together with a model that includes microsolvation of the polar part of ethanol by five or six water molecules, emphasizing the importance of explicit solvation in KIE calculations. Both, MP-VTST and PI-FEP/UM enable detailed characterization of nuclear quantum effects accompanying the hydrogen atom transfer reaction in aqueous solution.

Reply to the 'Comment on "Methanol dimer formation drastically enhances hydrogen abstraction from methanol by OH at low temperature"' by D. Heard, R. Shannon, J. Gomez Martin, R. Caravan, M. Blitz, J. Plane, M. Antiñolo, M. Agundez, E. Jimenez, B. Ballesteros, A. Canosa, G. El Dib, J. Albaladejo and J. Cernicharo, Phys. Chem. Chem. Phys., 2018, 20, DOI: 10.1039/C7CP04561A

In this Reply we answer the two main arguments raised in the Comment. The first argument is related to the binding energy of the methanol dimer and its influence on the dimerization rate constant. We show that the dimerization rate constants calculated in the Comment are unphysically low. We report values that are about two orders of magnitude higher than the values of the Comment, which confirm the conclusions of the original article that dimers can be present in a small amount. The second argument based on the dependence of the pseudo-first order rates on the methanol concentration was already explained in detail in the Supporting Information of the original article.

How Electronic Excitation Can be Used to Inhibit Some Mechanisms Associated to Substituent Effects

Despite the fact that transferability and chemistry go hand in hand, transferability studies in electronically excited states (EESs) are normally omitted, although these states are becoming extremely important in modern processes and applications. In this work, it is shown that this kind of studies can be used to understand how substituent effects can be modified in EESs. Thus, for example, the analysis of the carbonyl oxygen transferability in different HCO-R molecules allowed us to find that the nO→πCO* excitation can be used to break the π conjugation associated to the resonance substituent effect. Moreover, as a direct consequence, the oxygen transferability is enhanced in the first electronically excited state.

Revisiting Lewis dot structure weightings: a pair density perspective

A method based on a real space partitioning to measure the importance of Lewis structures is proposed in this work. A matrix containing diverse QTAIM atomic and diatomic properties endowed with significance within a Lewis structure framework is expanded in terms of what we call Lewis-structure matrices. Each of these matrices flawlessly describes an individual resonance structure and its associated linear expansion coefficient (Q-ALE coefficient) indicates the importance or convenience of the given Lewis structure. These coefficients were inspected looking at their evolution in a series of usual chemical issues. Among all the results, we find of interest that σ resonance structures in systems with π electrons are more important than normally expected, which justifies why the qualitative predictions arising from the application of the resonance model and the quantitative results based on QTAIM properties are sometimes discrepant. Likewise, we observe that the variation of the dielectric constant of the medium affects the π resonance to a greater extent than it does the σ one. Other interesting results in this manuscript are connected to homolytic dissociation of diatomic molecules, periodic trends in hydrogen compounds, and polarization of aromatic systems as a consequence of their interaction with electric fields and with diverse ions.

Excluding hyperconjugation from the Z conformational preference and investigating its origin: formic acid and beyond

A scheme indicating that the preference for the Z conformer in proteins is chemically equivalent to that of amides. Other compounds, such as carboxylic acids, also exhibit the same conformational trend.

Revisiting the carbonyl n → π* electronic excitation through topological eyes: expanding, enriching and enhancing the chemical language using electron number distribution functions and domain averaged Fermi holes

Interpretations of the S₀ → S₁ transition in formaldehyde arising from the DAFH analysis.

Beyond the molecular orbital conception of electronically excited states through the quantum theory of atoms in molecules

Application of QTAIM electron density analysis and energy partitioning based on it provide quantitative support for qualitative predictions derived from the MO paradigm, as well as further descriptions for electron density rearrangements in electronically excited states.

Influence of the O-protonation in the O═C-O-Me Z preference. A QTAIM study

One of the three O-protonations of methyl formate (MF) gives rise to a system where the Z preference is switched off and the E conformer becomes the most stable arrangement. The quantum theory of atoms in molecules scheme for splitting the physical space of a molecule into atomic subspaces has been employed to analyze this trend, as well as the effect of the protonation in MF. The most important changes in energy and electron density upon protonation do not take place when MF reorganizes its nuclei, but when the proton is introduced explicitly. The same trend is observed when the H attached to the carbonyl C is replaced by electron donating and withdrawing groups (CN, F, OH, CH(3), and CF(3)). The origin of the inversion in the conformational preference relies in the changes experienced by two interactions: (i) the methyl group with the proton and (ii) that between the atoms of the ether C-O bond.