Gastroprotective role of a flavonoid-rich subfraction from Fridericia chica (Bonpl.) L. G. Lohmann: a medicinal plant used in the Amazon region.

Fridericia chica is an Amazonian plant used to treat stomach disorders. However, the pharmacological activity of flavonoids in the extract has yet to be investigated. Therefore, we considered that a flavonoid-rich F. chica subfraction (FRS) has gastroprotective functions. For this, before the induction of gastric ulcers with ethanol or piroxicam, the rats received vehicle (water), omeprazole (30 mg/kg), or FRS (30 mg/kg), and the ulcer area was measured macro and microscopically, and the antisecretory action was investigated in pylorus-ligated rats. In addition, the roles of nitric oxide (NO) and nonprotein sulfhydryl compounds (NP-SH) in the gastroprotective effects of FRS were studied. FRS reduced ethanol- and piroxicam-induced ulcerations by 81% and 77%, respectively, as confirmed histologically. Antioxidant effects were observed for FRS through the maintenance of GSH and LPO levels, and the SOD and CAT activity similar to those found in the nonulcerated group. Moreover, FRS avoided the increase in MPO activity and TNF, IL-6, IL-4 and IL-10 levels. Moreover, mucin staining increased in ulcerated rats receiving FRS, and the pharmacological mechanism gastroprotective seems to involve the NO and NP-SH in addition to antisecretory actions. The chemical study by mass spectrometry confirmed the presence of flavonoids in FRS, and molecular docking studies have shown that these compounds interact with cyclooxygenase-1 and NO synthase. Furthermore, there was no indication that FRS had cytotoxic effects. Our results support the popular use of F. chica, and we conclude that the gastroprotection effect promoted by FRS can be attributed to the combined effect of the flavonoids.

Crystallization-induced diastereomer transformation assists the diastereoselective synthesis of 4-nitroisoxazolidine scaffolds.

This communication describes a solution to the vexing problem of synthesis of 4-nitroisoxazolidine rings from cyclic nitrones and ß-nitrostyrenes. The trans-endo adduct 2 is quantitatively synthesised from E-ß-nitrostyrene under mild conditions avoiding purification, while the trans-exo adduct 4 is obtained at higher temperatures. Furthermore, a Crystallization-Induced Diastereomer Transformation (CIDT) process was used to epimerise the NO2 bond from 2 to the cis-exo adduct 3 with total conversion assisted by the para-halogen substitution of the aromatic ring without any additives. By combining these approaches, we can establish a simple synthetic methodology that allows the diastereoselective synthesis of three diastereoisomers, overcoming the previous problems described in the literature.

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.

New Full-Dimensional Reactive Potential Energy Surface for the H4 System.

As the most abundant molecule in the universe, collisions involving H2 have important implications in astrochemistry. Collisions between hydrogen molecules also represent a prototype for assessing various dynamic methods for understanding fundamental few-body processes. In this work, we develop a new and highly accurate full-dimensional potential energy surface (PES) covering all reactive channels of the H2 + H2 system, which extends our previously reported H2 + H2 nonreactive PES [J. Chem. Theory Comput., 2021, 17, 6747] by adding 39,538 additional ab initio points calculated at the MRCI/AV5Z level in the reactive channels. The global PES is represented with high fidelity (RMSE = 0.6 meV for a total of 79,000 points) by a permutation invariant polynomial neural network (PIP-NN) and is suitable for studying collision-induced dissociation, single-exchange, as well as four-center exchange reactions. Preliminary quasi-classical trajectory studies on the new PIP-NN PES reveal strong vibrational enhancement of all reaction channels.

Quantum stereodynamics of cold molecular collisions.

Advances in quantum state preparations combined with molecular cooling and trapping technologies have enabled unprecedented control of molecular collision dynamics. This progress, achieved over the last two decades, has dramatically improved our understanding of molecular phenomena in the extreme quantum regime characterized by translational temperatures well below a kelvin. In this regime, collision outcomes are dominated by isolated partial waves, quantum threshold and quantum statistics effects, tiny energy splitting at the spin and hyperfine levels, and long-range forces. Collision outcomes are influenced not only by the quantum state preparation of the initial molecular states but also by the polarization of their rotational angular momentum, i.e., stereodynamics of molecular collisions. The Stark-induced adiabatic Raman passage technique developed in the last several years has become a versatile tool to study the stereodynamics of light molecular collisions in which alignment of the molecular bond axis relative to initial collision velocity can be fully controlled. Landmark experiments reported by Zare and coworkers have motivated new theoretical developments, including formalisms to describe four-vector correlations in molecular collisions that are revealed by the experiments. In this Feature article, we provide an overview of recent theoretical developments for the description of stereodynamics of cold molecular collisions and their implications to cold controlled chemistry.

Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the α/ß-hydrolase fold.

Protein fold adaptation to novel enzymatic reactions is a fundamental evolutionary process. Cofactor-independent oxygenases degrading N-heteroaromatic substrates belong to the α/ß-hydrolase (ABH) fold superfamily that typically does not catalyze oxygenation reactions. Here, we have integrated crystallographic analyses under normoxic and hyperoxic conditions with molecular dynamics and quantum mechanical calculations to investigate its prototypic 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) member. O2 localization to the "oxyanion hole", where catalysis occurs, is an unfavorable event and the direct competition between dioxygen and water for this site is modulated by the "nucleophilic elbow" residue. A hydrophobic pocket that overlaps with the organic substrate binding site can act as a proximal dioxygen reservoir. Freeze-trap pressurization allowed the structure of the ternary complex with a substrate analogue and O2 bound at the oxyanion hole to be determined. Theoretical calculations reveal that O2 orientation is coupled to the charge of the bound organic ligand. When 1-H-3-hydroxy-4-oxoquinaldine is uncharged, O2 binds with its molecular axis along the ligand's C2-C4 direction in full agreement with the crystal structure. Substrate activation triggered by deprotonation of its 3-OH group by the His-Asp dyad, rotates O2 by approximately 60°. This geometry maximizes the charge transfer between the substrate and O2, thus weakening the double bond of the latter. Electron density transfer to the O2(π*) orbital promotes the formation of the peroxide intermediate via intersystem crossing that is rate-determining. Our work provides a detailed picture of how evolution has repurposed the ABH-fold architecture and its simple catalytic machinery to accomplish metal-independent oxygenation.

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.

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.

Improving Properties of Podophyllic Aldehyde-Derived Cyclolignans: Design, Synthesis and Evaluation of Novel Lignohydroquinones, Dual-Selective Hybrids against Colorectal Cancer Cells.

New lignohydroquinone conjugates (L-HQs) were designed and synthesized using the hybridization strategy, and evaluated as cytotoxics against several cancer cell lines. The L-HQs were obtained from the natural product podophyllotoxin and some semisynthetic terpenylnaphthohydroquinones, prepared from natural terpenoids. Both entities of the conjugates were connected through different aliphatic or aromatic linkers. Among the evaluated hybrids, the L-HQ with the aromatic spacer clearly displayed the in vitro dual cytotoxic effect derived from each starting component, retaining the selectivity and showing a high cytotoxicity at short (24 h) and long (72 h) incubation times (4.12 and 0.0450 µM, respectively) against colorectal cancer cells. In addition, the cell cycle blockade observed by flow cytometry studies, molecular dynamics, and tubulin interaction studies demonstrated the interest of this kind of hybrids, which docked adequately into the colchicine binding site of tubulin despite their large size. These results prove the validity of the hybridization strategy and encourage further research on non-lactonic cyclolignans.

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.

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.

Role of Low Energy Resonances in the Stereodynamics of Cold He + D2 Collisions.

In recent experiments using the Stark-induced adiabatic Raman passage technique, Zhou et al. ( J. Chem. Phys. 2021, 154, 104309; Science 2021, 374, 960-964) measured the product's angular distribution for the collisions between He and aligned D2 molecules at cold collision energies. The signatures of the angular distributions were attributed to an [Formula: see text] = 2 resonance that governs scattering at low energies. A first-principles quantum mechanical treatment of this problem is presented here using a highly accurate interaction potential for the He-H2 system. Our results predict a very intense [Formula: see text] = 1 resonance at low energies, leading to angular distributions that differ from those measured in the experiment. A good agreement with the experiment is achieved only when the [Formula: see text] = 1 resonance is artificially removed, for example, by excluding the lowest energies present in the experimental velocity distribution. Our analysis revealed that neither the position nor the intensity of the [Formula: see text] = 1 resonance significantly changes when the interaction potential is modified within its predicted uncertainties. Energy-resolved measurements may help to resolve the discrepancy.

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.

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.

Controlling the Spin-Orbit Branching Fraction in Molecular Collisions.

The collision geometry, that is, the relative orientation of reactants before interaction, can have a large effect on how a collision or reaction proceeds. Certain geometries may prevent access to a given product channel, while others might enhance it. In this Letter, we demonstrate how the initial orientation of NO molecules relative to approaching Ar atoms determines the branching between the spin-orbit changing and the spin-orbit conserving rotational product channels. We use a recently developed quantum treatment to calculate differential and integral branching fractions, at any arbitrary orientation, from theoretical and experimental data points. Our results show that a substantial degree of control over the final spin-orbit state of the scattering products can be achieved by tuning the initial collision geometry.

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.