Rate coefficients for the O + H2 and O + D2 reactions: how well ring polymer molecular dynamics accounts for tunelling.

We present here extensive calculations of the O(3P) + H2 and O(3P) + D2 reaction dynamics spanning the temperature range from 200 K to 2500 K. The calculations have been carried out using fully converged time-independent quantum mechanics (TI QM), quasiclassical trajectories (QCT) and ring polymer molecular dynamics (RPMD) on the two lowest lying adiabatic potential energy surfaces (PESs), 13A' and 13A'', calculated by Zanchet et al. [J. Chem. Phys., 2019, 151, 094307]. TI QM rate coefficients were determined using the cumulative reaction probability formalism on each PES including all of the total angular momenta and the Coriolis coupling and can be considered to be essentially exact within the Born-Oppenheimer approximation. The agreement between the rate coefficients calculated by using QM and RPMD is excellent for the reaction with D2 in almost the whole temperature range. For the reaction with H2, although the agreement is very good above 500 K, the deviations are significant at lower temperatures. In contrast, the QCT calculations largely underestimate the rate coefficients for the two isotopic variants due to their inability to account for tunelling. The differences found in the disagreements between RPMD and QM rate coefficients for the reactions for both the isotopologues are indicative of the ability of the RPMD method to accurately describe systems where tunelling plays a relevant role. Considering that both reactions are dominated by tunelling below 500 K, the present results show that RPMD is a very powerful tool for determining rate coefficients. The present QM rate coefficients calculated on adiabatic PESs slightly underestimate the best global fits of the experimental measurements, which we attribute to the intersystem crossing with the singlet 11A' PES.

Stereodynamical control of cold HD + D2 collisions.

We report full-dimensional quantum calculations of stereodynamic control of HD(v = 1, j = 2) + D2 collisions that has been probed experimentally by Perreault et al. using the Stark-induced adiabatic Raman passage (SARP) technique. Computations were performed on two highly accurate full-dimensional H4 potential energy surfaces. It is found that for both potential surfaces, rotational quenching of HD from with concurrent rotational excitation of D2 from is the dominant transition with cross sections four times larger than that of elastically scattered D2 for the same quenching transition in HD. This process was not considered in the original analysis of the SARP experiments that probed ΔjHD = -2 transitions in HD(vHD = 1, jHD = 2) + D2 collisions. Cross sections are characterized by an l = 3 resonance for ortho-D2(jD2 = 0) collisions, while both l = 1 and l = 3 resonances are observed for the para-D2(jD2 = 1) partner. While our results are in excellent agreement with prior measurements of elastic and inelastic differential cross sections, the agreement is less satisfactory with the SARP experiments, in particular for the transition for which the theoretical calculations indicate that D2 rotational excitation channel is the dominant inelastic process.

Stereodynamical Control of Cold Collisions between Two Aligned D_{2} Molecules.

Resonant scattering of optically state-prepared and aligned molecules in the cold regime allows the most detailed interrogation and control of bimolecular collisions. This technique has recently been applied to collisions of two aligned ortho-D_{2} molecules prepared in the j=2 rotational level of the v=2 vibrational manifold using the Stark-induced adiabatic Raman passage technique. Here, we develop the theoretical formalism for describing four-vector correlations in collisions of two aligned molecules and apply our approach to state-prepared D_{2}(v=2,j=2)+D_{2}(v=2,j=2)→D_{2}(v=2,j=2)+D_{2}(v=2,j=0) collisions, making possible the simulations of the experimental results from first principles. Key features of the experimental angular distributions are reproduced and attributed primarily to a partial wave resonance with orbital angular momentum ℓ=4.

Li + HF and Li + HCl Reactions Revisited I: QCT Calculations and Simulation of Experimental Results.

The Li + HF and Li + HCl reactions share some common features. They have the same kinematics, relatively small barrier heights, bent transition states, and are both exothermic when the zero point energy is considered. Nevertheless, the pioneering crossed beam experiments by Lee and co-workers in the 80s (Becker et al., J. Chem. Phys. 1980, 73, 2833) revealed that the dynamics of the two reactions differ significantly, especially at low collision energies. In this work, we present theoretical simulations of their results in the laboratory frame (LAB), based on quasiclassical trajectories and obtained using accurate potential energy surfaces. The calculated LAB angular distributions and time-of-flight spectra agree well with the raw experimental data, although our simulations do not reproduce the experimentally derived center-of-mass (CM) differential cross section and velocity distributions. The latter were derived by forward convolution fitting under the questionable assumption that the CM recoil velocity and scattering angle distribution were uncoupled, while our results show that the coupling between them is relevant. Some important insights into the reaction mechanism discussed in the article by Becker et al. had not been contrasted with those that can be extracted from the theoretical results. Among them, the correlation between the angular momenta involved in the reactions has also been examined. Given the kinematics of both systems, the reagent orbital angular momentum, l, is almost completely transformed into the rotation of the product diatom, j'. However, contrary to the coplanar mechanism proposed in the original paper, we find that the initial and final relative orbital angular momenta are not necessarily parallel. Both reactions are found to be essentially direct, although about 15% of the LiFH complexes live longer than 200 fs.

Cold Collisions of Ro-Vibrationally Excited D2 Molecules.

The H2 + H2 system has long been considered a benchmark system for ro-vibrational energy transfer in bimolecular collisions. However, most studies thus far have focused on collisions involving H2 molecules in the ground vibrational level or in the first excited vibrational state. While H2 + H2/HD collisions have received wide attention due to the important role they play in astrophysics, D2 + D2 collisions have received much less attention. Recently, Zhou et al. [ Nat. Chem. 2022, 14, 658-663, DOI: 10.1038/s41557-022-00926-z] examined stereodynamic aspects of rotational energy transfer in collisions of two aligned D2 molecules prepared in the v = 2 vibrational level and j = 2 rotational level. Here, we report quantum calculations of rotational and vibrational energy transfer in collisions of two D2 molecules prepared in vibrational levels up to v = 2 and identify key resonance features that contribute to the angular distribution in the experimental results of Zhou et al. The quantum scattering calculations were performed in full dimensionality and using the rigid-rotor approximation using a recently developed highly accurate six-dimensional potential energy surface for the H4 system that allows descriptions of collisions involving highly vibrationally excited H2 and its isotopologues.

Spin-Forbidden Addition of Molecular Oxygen to Stable Enol Intermediates-Decarboxylation of 2-Methyl-1-tetralone-2-carboxylic Acid.

The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O2 to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. Nevertheless, the spin-forbidden addition of O2 to uncharged ligands has also been observed in the laboratory, and the detailed mechanism of how the system circumvents the spin-forbiddenness of the reaction is still unknown. One of these examples is the cofactorless peroxidation of 2-methyl-3,4-dihydro-1-naphthol, which will be studied computationally using single and multi-reference electronic structure calculations. Our results show that the preferred mechanism is that in which O2 picks a proton from the substrate in the triplet state, and subsequently hops to the singlet state in which the product is stable. For this reaction, the formation of the radical pair is associated with a higher barrier than that associated with the intersystem crossing, even though the absence of the negative charge leads to relatively small values of the spin-orbit coupling.

DpgC-Catalyzed Peroxidation of 3,5-Dihydroxyphenylacetyl-CoA (DPA-CoA): Insights into the Spin-Forbidden Transition and Charge Transfer Mechanisms*.

Despite being a very strong oxidizing agent, most organic molecules are not oxidized in the presence of O2 at room temperature because O2 is a diradical whereas most organic molecules are closed-shell. Oxidation then requires a change in the spin state of the system, which is forbidden according to non-relativistic quantum theory. To overcome this limitation, oxygenases usually rely on metal or redox cofactors to catalyze the incorporation of, at least, one oxygen atom into an organic substrate. However, some oxygenases do not require any cofactor, and the detailed mechanism followed by these enzymes remains elusive. To fill this gap, here the mechanism for the enzymatic cofactor-independent oxidation of 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) is studied by combining multireference calculations on a model system with QM/MM calculations. Our results reveal that intersystem crossing takes place without requiring the previous protonation of molecular oxygen. The characterization of the electronic states reveals that electron transfer is concomitant with the triplet-singlet transition. The enzyme plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. The results show that the stabilization of the singlet radical-pair between dioxygen and enolate is enough to promote spin-forbidden reaction without the need for neither metal cofactors nor basic residues in the active site.

Stereodynamic control of cold rotationally inelastic CO + HD collisions.

Quantum control of molecular collision dynamics is an exciting emerging area of cold collisions. Co-expansion of collision partners in a supersonic molecular beam combined with precise control of their quantum states and alignment/orientation using Stark-induced Adiabatic Raman Passage allows exquisite stereodynamic control of the collision outcome. This approach has recently been demonstrated for rotational quenching of HD in collisions with H2, D2, and He and D2 by He. Here we illustrate this approach for HD(v = 0, j = 2) + CO(v = 0, j = 0) → HD(v' = 0, j') + CO(v' = 0, j') collisions through full-dimensional quantum scattering calculations at collision energies near 1 K. It is shown that the collision dynamics at energies between 0.01-1 K are controlled by an interplay of L = 1 and L = 2 partial wave resonances depending on the final rotational levels of the two molecules. Polarized cross sections resolved into magnetic sub-levels of the initial and final rotational quantum numbers of the two molecules also reveal a significant stereodynamic effect in the cold energy regime. Overall, the stereodynamic effect is controlled by both geometric and dynamical factors, with parity conservation playing an important role in modulating these contributions depending on the particular final state.

Probing the location of the unpaired electron in spin-orbit changing collisions of NO with Ar.

Understanding the molecular forces that drive a reaction or scattering process lies at the heart of molecular dynamics. Here, we present a combined experimental and theoretical study of the spin-orbit changing scattering dynamics of oriented NO molecules with Ar atoms. Using our crossed molecular beam apparatus, we have recorded velocity-map ion images and extracted differential and integral cross sections of the scattering process in the side-on geometry. We observe an overall preference for collisions close to the N atom in the spin-orbit changing manifold, which is a direct consequence of the location of the unpaired electron on the potential energy surface. In addition, a prominent forward scattered feature is observed for intermediate, even rotational transitions when the atom approaches the molecule from the O-end. The appearance of this peak originates from an attractive well on the A' potential energy surface, which efficiently directs high impact parameter trajectories towards the region of high unpaired electron density near the N-end of the molecule. The ability to orient molecules prior to collision, both experimentally and theoretically, allows us to sample different regions of the potential energy surface(s) and unveil the associated collision pathways.

Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations.

Proton pumping A-type cytochrome c oxidase (CcO) terminates the respiratory chains of mitochondria and many bacteria. Three possible proton transfer pathways (D, K, and H channels) have been identified based on structural, functional, and mutational data. Whereas the D channel provides the route for all pumped protons in bacterial A-type CcOs, studies of bovine mitochondrial CcO have led to suggestions that its H channel instead provides this route. Here, we have studied H-channel function by performing atomistic molecular dynamics simulations on the entire, as well as core, structure of bovine CcO in a lipid-solvent environment. The majority of residues in the H channel do not undergo large conformational fluctuations. Its upper and middle regions have adequate hydration and H-bonding residues to form potential proton-conducting channels, and Asp51 exhibits conformational fluctuations that have been observed crystallographically. In contrast, throughout the simulations, we do not observe transient water networks that could support proton transfer from the N phase toward heme a via neutral His413, regardless of a labile H bond between Ser382 and the hydroxyethylfarnesyl group of heme a In fact, the region around His413 only became sufficiently hydrated when His413 was fixed in its protonated imidazolium state, but its calculated pKa is too low for this to provide the means to create a proton transfer pathway. Our simulations show that the electric dipole moment of residues around heme a changes with the redox state, hence suggesting that the H channel could play a more general role as a dielectric well.

A Novel Cytotoxic Conjugate Derived from the Natural Product Podophyllotoxin as a Direct-Target Protein Dual Inhibitor.

Natural products are the ideal basis for the design of novel efficient molecular entities. Podophyllotoxin, a naturally occurring cyclolignan, is an example of natural product which displays a high versatility from a biological activity point of view. Based on its unique chemical structure, different derivatives have been synthesized presenting the original antitumoral properties associated with the compound, i.e., the tubulin polymerization inhibition and arising anti-topoisomerase II activity from structural modifications on the cyclolignan skeleton. In this report, we present a novel conjugate or hybrid which chemically combines both biological activities in one single molecule. Chemical design has been planned based in our lead compound, podophyllic aldehyde, as an inhibitor of tubulin polymerization, and in etoposide, an approved antitumoral drug targeting topoisomerase II. The cytotoxicity and selectivity of the novel synthetized hybrid has been evaluated in several cell lines of different solid tumors. In addition, these dual functional effects of the novel compound have been also evaluated by molecular docking approaches.

Stereodynamical Control of a Quantum Scattering Resonance in Cold Molecular Collisions.

Cold collisions of light molecules are often dominated by a single partial wave resonance. For the rotational quenching of HD (v=1, j=2) by collisions with ground state para-H_{2}, the process is dominated by a single L=2 partial wave resonance centered around 0.1 K. Here, we show that this resonance can be switched on or off simply by appropriate alignment of the HD rotational angular momentum relative to the initial velocity vector, thereby enabling complete control of the collision outcome.

Kinetics Of The H + CH2 → CH + H2 Reaction At Low Temperature.

A quasiclassical trajectory study of the kinetics of the title astrochemical reaction in a range of temperatures varying from 5 to 1000 K (corresponding to both the outer and the inner regions of the protostar and the circumstellar envelopes) was carried out and a clear dependence of the rate coefficient on the temperature is given, in contrast with the constant value adopted in kinetics astrochemical databases. Levering the massive nature of the performed calculations and of the detailed dynamical investigation of the reactive process, a rationalization of the temperature dependence of the released translational energy and of the rovibrational population of the CH and H2 diatomic products is also provided. Furthermore, the effect of the initial rovibrational energy of CH2 on the state-specific rate coefficients and cross sections is analyzed in order to single out the role played by the different regions of the potential energy surface on the dynamical outcomes and on the modeling the temperature dependence of the reactive efficiency of the investigated process. This led to a parametrization of the computed rate in terms of the following double Arrhenius expression (in cm3 s-1), k(T) = 2.50 × 10-10 exp(- 1.67/T) + 5.98 × 10-11 exp(- 280.5/T), alternative to the piecewise formulation into the three subintervals of temperature in which the overall 5-1000 K interval can be divided.

Competing Dynamical Mechanisms in Inelastic Collisions of H + HF.

The dynamics of inelastic collisions between HF and H has been investigated in detail by means of time-independent quantum mechanical calculations on the LWA-78 potential energy surface ( Li , G. ; et al. J. Chem. Phys. 2007 , 127 , 174302 ). Reaction probabilities, differential cross sections, and three-vector correlations have been calculated and analyzed. Our results show that there are two competing collision mechanisms that correlate with low and high impact parameters and show very different stereodynamical preferences. The mechanism promoted by high impact parameters is the only one present at low collision energies. We also observe the presence of an apparent threshold in the inelastic cross section for relatively high initial HF rotational quantum numbers, which is associated with the larger energy difference between adjacent rotational quantum states with increasing rotation.

Steric Effects in the Inelastic Scattering of NO(X) + Ar: Side-on Orientation.

The rotationally inelastic collisions of NO(X) with Ar, in which the NO bond-axis is oriented side-on (i.e., perpendicular) to the incoming collision partner, are investigated experimentally and theoretically. The NO(X) molecules are selected in the |j = 0.5, Ω = 0.5, ε = -1, f⟩ state prior to bond-axis orientation in a static electric field. The scattered NO products are then state selectively detected using velocity-map ion imaging. The experimental bond-axis orientation resolved differential cross sections and integral steric asymmetries are compared with quantum mechanical calculations, and are shown to be in good agreement. The strength of the orientation field is shown to affect the structure observed in the differential cross sections, and to some extent also the steric preference, depending on the ratio of the initial e and f Λ-doublets in the superposition determined by the orientation field. Classical and quantum calculations are compared and used to rationalize the structures observed in the differential cross sections. It is found that these structures are due to quantum mechanical interference effects, which differ for the two possible orientations of the NO molecule due to the anisotropy of the potential energy surface probed in the side-on orientation. Side-on collisions are shown to maximize and afford a high degree of control over the scattering intensity at small scattering angles (θ < 90°), while end-on collisions are predicted to dominate in the backward scattered region (θ > 90°).

New global potential energy surfaces of the ground 3A' and 3A″ states of the O(3P) + H2 system.

This paper presents two new adiabatic, global potential energy surfaces (PESs) for the two lowest 3A' and 3A″ electronic states of the O(3P) + H2 system. For each of these states, ab initio electronic energies were calculated for more than 5000 geometries using internally contracted multireference configuration interaction methods. The calculated points were then fitted using the ansatz by Aguado et al. [Comput. Phys. Commun. 108, 259 (1998)] leading to very accurate analytical potentials well adapted to perform reaction dynamics studies. Overall, the topographies of both PESs are in good agreement with the benchmark potentials of Rogers et al. [J. Phys. Chem. A 104, 2308 (2000)], but those presented in this work reproduce better the height and degeneracy of the two states at the saddle point. Moreover, the long range potential in the entrance channel does not require any cutoff. These features make the new PESs particularly suitable for a comparison of the dynamics on each of them. The new set of PESs was then used to perform quantum mechanics and quasiclassical trajectory calculations to determine differential and integral cross sections, which are compared to the experimental measurements by Garton et al. [J. Chem. Phys. 118, 1585 (2003)].

Λ-Doublet Propensities for Reactions on Competing A' and A″ Potential Energy Surfaces: O(3 P) + N2 and O(3 P) + HCl.

This work presents scattering calculations for the O(3 P) + N2(1Σ) → NO(2Π) + N(4S) and for the O(3 P) + HCl(1Σ) → OH(2Π) + Cl(2P) reactions with a focus on the prediction of the Λ-doublet populations in which NO and OH are produced. Both reactions can take place on two competing potential energy surfaces of symmetries 3 A' and 3 A″ that correlate reagents with products but with very distinct topographies. As a result, they exhibit very different dynamical behaviors and total reactivity. Using a method that relates the reaction yield on the two competing surfaces to the Λ-doublet populations through the explicit consideration of the stereodynamics of the reaction, we predict that the population of NO and OH on the two Λ-doublet sates is surprisingly similar for both systems. These results contradict the model that assumes that collisions on the 3 A' and 3 A″ would give rise to products in the Π( A') and Π( A″) states, respectively.

Light-Regulated Molecular Trafficking in a Synthetic Water-Soluble Host.

Cucurbit[8]uril (CB[8])-mediated complexation of a dicationic azobenzene in water allows for the light-controlled encapsulation of a variety of second guest compounds, including amino acids, dyes, and fragrance molecules. Such controlled guest sequestration inside the cavity of CB[8] enables the regulation of the thermally induced phase transition of poly(N-isopropylacrylamide)-which is not photosensitive-thus demonstrating the robustness and relevancy of the light-regulated CB[8] complexation.

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation.

RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N-terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC-helix and charged residues upstream of the NtA motif. Additionally, we show that the R-spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure-based mechanism for the auto-transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization-related drug resistance.

Molecular mechanisms of asymmetric RAF dimer activation.

Protein phosphorylation is one of the most common post-translational modifications in cell regulatory mechanisms. Dimerization plays also a crucial role in the kinase activity of many kinases, including RAF, CDK2 (cyclin-dependent kinase 2) and EGFR (epidermal growth factor receptor), with heterodimers often being the most active forms. However, the structural and mechanistic details of how phosphorylation affects the activity of homo- and hetero-dimers are largely unknown. Experimentally, synthesizing protein samples with fully specified and homogeneous phosphorylation states remains a challenge for structural biology and biochemical studies. Typically, multiple changes in phosphorylation lead to activation of the same protein, which makes structural determination methods particularly difficult. It is also not well understood how the occurrence of phosphorylation and dimerization processes synergize to affect kinase activities. In the present article, we review available structural data and discuss how MD simulations can be used to model conformational transitions of RAF kinase dimers, in both their phosphorylated and unphosphorylated forms.