Pablo Garcia Jambrina

Certain oxidases and oxygenases catalyze the spin-forbidden incorporation of O2 into organic substrates without requiring a cofactor. A general mechanism for this reaction remains elusive; intriguingly, these enzymes accomplish this without relying on specialized catalytic machinery. Here, we report nonadiabatic quantum scattering calculations on a simplified model to investigate the nuclear quantum effects governing these processes. Our model includes six singlet and three triplet states, explicitly accounting for spin–orbit coupling. Our results indicate that the degree of spin-forbiddenness corresponds to a kinetic hindrance of only ≈2.45 kcal/mol at room temperature, slightly lower than the value predicted by nonadiabatic transition state theory (NA-TST). However, the discrepancy between the scattering results and NA-TST predictions is minor, validating the use of NA-TST for this class of reactions. Furthermore, our calculations account for the possible formation of singlet O2, a reactive oxygen species (ROS). We find that once this channel opens, singlet O2 is produced with significant probability, suggesting that ROS could be generated via the stabilization of singlet O2 within the protein cavity.

Phosphates are essential for life in all organisms, playing key roles in nucleic acids, signaling, energy transfer, and biosynthesis. We conducted a quantitative analysis of nucleoside triphosphate (NTP) processing enzymes across all enzymatic reactions, revealing their dominance in phosphate reactivity with ATP as the most prevalent substrate. Two main reaction types occur predominantly: cleavage resulting in pyrophosphate release or phosphate release/transfer. The large majority of NTP processing enzymes require divalent Mg²⁺ ions in a mechanistically analogous manner. However, the catalytically competent metal-ion coordination remains unclear for many NTP-processing enzymes. By examining a vast data set of crystallographic structures, we identified a universal "Mg-pinch" motif, confirming our structural hypothesis for almost all NTP processing enzymes. We hypothesized and subsequently confirmed that the catalytic Mg²⁺ typically coordinates the two phosphate groups between which the P-O bond is cleaved. We present a comprehensive analysis of NTP processing superfamilies across all species, determining distinct enzyme active site structures. We highlight exceptional cases and propose challenging superfamilies that lack sufficient structural data to determine precise active site coordination. DFT-based QM/MM calculations with full electrostatic embedding support a mechanistic interpretation in which appropriately coordinated Mg²⁺ ions contribute to catalysis by electrostatic preorganization and polarization of the reacting phosphate groups. The Mg-pinch motif provides a mechanistic framework for understanding the catalytic role of metal ions in NTP processing. Our findings offer insights into enzyme evolution, provide a basis for rational enzyme engineering, and could inform the development of novel therapeutics targeting NTP processing enzymes.

Cold collisions can be achieved experimentally by co-propagating colliding partners of similar mass within a single molecular beam. This technique, combined with Stark-induced adiabatic Raman passage (SARP), makes it possible to measure the angular distributions for different molecular axis alignments of the incoming molecules, thus probing the stereodynamics of the collisions at very low energies. Reproducing SARP experiments is a very stringent test for theory, even though the systems under study involve closed-shell atoms and molecules with very few electrons for which exact quantum scattering calculations on highly accurate potential energy surfaces are computationally feasible. While simulations of some experimental results using first-principles theoretical calculations have been satisfactory, theory has been unable to reproduce the experimental angular distributions for He + D2 inelastic collisions. Furthermore, an ℓ = 1 partial-wave resonance predicted by theory came at variance with the ℓ = 2 resonance obtained by fitting the experimental results. Here, we demonstrate how theory and experiment can be reconciled by the explicit consideration of the divergence of the molecular beam. While the effect of the divergence is almost irrelevant for collision energies higher than 0.5 K, at lower collision energies, it can produce significantly different results. Our simulations show that signatures of an ℓ = 2 resonance obtained through fitting of the experimental angular distribution ignoring beam divergence is, in fact, an ℓ = 1 resonance observed in the scattering calculations. These results indicate that the combination of theory and experiment is necessary for the analysis and interpretation of complex molecular beam experiments.

Scattering resonances are quantum phenomena arising from the decay of metastable collision complexes trapped by a centrifugal barrier or supported by a closed channel that is coupled to a scattering state. As such, resonances can provide significant insights into the scattering process and serve as a sensitive probe of the interaction potential. In this article, we present a detailed analysis of a cluster of shape resonances associated with the orbital angular momentum L = 5 in the j = 2 → j′ = 0 rotational transition in Ne + D2 collisions for vibrational levels v = 0, 1, and 4. The energies and lifetimes of the resonances arising from different values of the total angular momentum quantum number J were analyzed through numerical fitting of the scattering matrix and employing a one-dimensional model based on an effective potential. We further investigated the sensitivity of the resonances to changes in the alignment of the D2 internuclear axis with respect to the initial relative velocity. Our results show that resonances can be exquisitely controlled by carefully selecting the initial alignment of the D2 molecule. In particular, not only the intensity of the resonance can be modulated but also the shape of the overall resonance profile can be altered, depending on the stereodynamical preferences of the individual resonances that contribute to the cluster.

Context. C₂O molecules are very good probes of oxygen chemistry in interstellar molecular clouds. The accurate derivation of their abundance requires non-local thermodynamic equilibrium (LTE) modeling of their emission spectra. Aims. This study aims to provide highly accurate fine-structure resolved excitation rate coefficients of C₂O induced by collisions with He, enabling the improvement of the modeling of C₂O emission spectra in (cold) molecular clouds. Methods. A new potential energy surface for the C₂O–He system was calculated using the spin-restricted coupled-cluster method together with a complete atomic basis set extrapolation. Quantum scattering calculations were performed using the exact close-coupling approach, explicitly accounting for the fine structure of C₂O. Excitation calculations using a radiative transfer model were conducted in order to interpret observations of C₂O in TMC-1. Results. Rate coefficients for transitions up to the rotational state N = 20 and temperatures up to 70 K were obtained. The analysis of the excitation calculations revealed non-LTE effects of C₂O emission lines at typical densities of TMC-1 (n(H₂)∼10⁴ cm⁻³), reflecting a balance between collisional excitation and radiative relaxation. These effects significantly influence the derived physical conditions. The column density of C₂O in TMC-1 was estimated to be NC₂O ≈ 9 · 10¹¹ cm⁻². This refined value, derived using the newly calculated rate coefficients, highlights the limitations of previous LTE-based estimates and underscores the importance of non-LTE modeling. Conclusions. The new accurate collisional data enable a more confident modeling of C₂O excitation in interstellar clouds and improve the interpretation of C₂O emission spectra in molecular clouds, highlighting again the necessity of having accurate molecular data in astrochemical studies.

Phosphates are essential for all forms of life, playing key roles in DNA/RNA, signaling, energy storage and transfer, and biosynthetic processes. We conducted a quantitative analysis of nucleoside triphosphate (NTP) processing enzymes across all enzymatic reactions, revealing their dominance in phosphate reactivity with ATP as the most prevalent substrate. Two main reaction types occur predominantly: cleavage resulting in (i) pyrophosphate or (ii) phosphate release/transfer. The large majority of NTP processing enzymes require divalent Mg2+ ions in a mechanistically analogous manner. Despite their importance, the precise coordination of metal ions in the catalytically competent active site structure in many NTP processing enzymes remains elusive. We hypothesized that efficient phosphate processing requires specific metal ion coordination, facilitating the catalytic reaction. By examining a vast dataset of crystallographic structures, we identified a universal "Mg-pinch" motif, confirming our structural hypothesis for almost all NTP processing enzymes. We postulated that the Mg2+ ion should coordinate both phosphates that are involved in the cleaved P-O bond. We present a comprehensive analysis of NTP processing superfamilies across all species, determining distinct enzyme active site structures. We highlight exceptional cases and propose challenging superfamilies that lack sufficient structural data to determine precise active site coordination. Our quantum mechanical calculations based on DFT-based QM/MM with full electrostatic embedding revealed the essential electrostatic polarization effects of the Mg²⁺ ion as key determinants of their role in the enzyme catalysis. The Mg-pinch motif provides a mechanistic framework for understanding the catalytic role of metal ions in NTP processing. Our findings offer insights into enzyme evolution, provide a basis for rational enzyme engineering, and could inform the development of novel therapeutics targeting NTP processing enzymes.

Resonant scattering of highly vibrationally excited and aligned D2 in cold collisions with Ne has recently been probed experimentally using the Stark-induced adiabatic Raman passage technique [Perreault et al., J. Chem. Phys. 157, 144301 (2022)]. A partial-wave analysis and numerical fitting of the experimental data attributed the measured angular distribution to an l = 2 shape resonance near Ec/kB = 1 K (≈0.7 cm−1). Here, we report the computation of a new potential energy surface for the Ne–H2 interaction suitable for the study of collisions between highly vibrationally excited H2/D2 with Ne as well as quantum scattering calculations of stereodynamics of D2 (v = 4, j = 2) + Ne collisions probing Δj = −2 rotational transition in D2. Our results show that collisions are dominated by a strong l = 5 resonance near 3 K (≈2.09 cm−1) and a weaker l = 6 resonance near 8 K (≈5.56 cm−1) and not an l = 2 resonance, as suggested in the analysis of the experimental data. A reasonable agreement between our calculations and the experiments is obtained only when an artificial energy cutoff is applied to the integral over the collision energy to exclude contributions from the l = 5 resonance while retaining contributions from l = 0, 1, and 2. However, our calculations do not support the claim that the measured angular distributions are dominated by a single l = 2 partial-wave resonance characteristic of orbiting collisions.

One of the aims of the chemist is to obtain the greatest possible level of control over the outcome of a reaction. A factor that can influence such outcomes is the so-called steric effect. The underpinning idea of this effect is that the mutual orientation of the collision partners at the moment of collision may impact the nature of the products. The steric effect has been studied in a variety of ways, notably using optical methods, as well as making use of both magnetic and electric fields, to orient or align reactants. Here, we present a general framework for interpreting and evaluating steric effects in collisions of open shell linear molecules with an atom in the presence of an electric field. While in previous studies, the theory has been limited to the specific system of interest, such as for the end-on collisions of NO(X), this new formalism provides a fundamental basis for examining any system of this type. Some examples of the utility and power of this formalism are also provided. This theory may then be built on further in the future to provide greater insights into the stereodynamics of collisions and, hence, provide the foundation for deeper study into how the steric effect may be harnessed for control.

We present a comprehensive quantum mechanical study of stereodynamic control of HD + He and D2 + He collisions that have been probed experimentally by Perreault et al. [J. Phys. Chem. Lett. 13, 10912 (2022)] using Stark-induced adiabatic Raman passage (SARP) techniques. Our calculations utilize a highly accurate full-dimensional H2 + He interaction potential with diagonal Born–Oppenheimer correction appropriate for HD and D2 isotopomers. The results show that rotational quenching of HD from j = 2 → j′ = 0 in v = 2, j = 2 → j′ = 1 in v = 2 and v = 4, and j = 4 → j′ = 3 in v = 4 is dominated by an l = 1 shape resonance located between 0.1 and 1.0 cm−1. For collision energies less than 0.1 cm−1, isotropic scattering prevails. An l = 1 resonance centered around 0.02 cm−1 is also found to dominate the j = 2 → j′ = 0 and j = 4 → j′ = 2 transitions in v = 4 for He–D2 collisions consistent with our prior studies of Δj = −2 transition in He + D2(v = 2, j = 2) collisions. Our analysis does not support the hypothesis of Perreault et al. [J. Phys. Chem. Lett. 13, 10912 (2022)] that a strong l = 2 resonance controls the angular distribution for Δj = −2 transition for both systems. Despite improvements in the development of the potential energy surface, a good agreement with SARP experiments for v = 2 is achieved only when contributions from collision energies less than 1.0 cm−1 were excluded in the computation of velocity averaged differential rate coefficients for both systems. This could be due to some uncertainties in the velocity spread in the experiment that employs co-propagation of the collision partners and possibly, the neglect of transverse velocities in the simulation of the experiment.