Insights into the mechanism of [3+2] cycloaddition reactions between N-benzyl fluoro nitrone and maleimides, its selectivity and solvent effects.

We present a theoretical study of the [3+2] cycloaddition (32CA) reactions of N-benzyl fluoro nitrone with a series of maleimides producing isoxazolidines. We use the Molecular Electron Density Theory at the MPWB1K/6-311G(d) level. We focus on the reaction mechanism, selectivity, solvent, and temperature effects. In addition, we perform topological analyses at the minimal and transition states to identify the intermolecular interactions. Electron Localization Function approach classifies the N-benzyl fluoro nitrone as zwitterionic (zw-) three-atom components (TACs), associated with a high energy barrier. The low polar character of the reaction is evaluated using the Conceptual Density Functional Theory analysis of the reactants, confirmed by the low global electron density transfer computed at the transition states. Computations show that these 32CA reactions follow a one-step mechanism under kinetic control, with highly asynchronous bond formation and no new covalent bond is formed at the TS. Besides, the potential energy surfaces along the reaction pathways in gas phase and in solvent are mapped. The corresponding Gibbs free energy profiles reveal that the exo-cycloadducts are kinetically and thermodynamically more favored than endo-cycloadducts, in agreement with the exo-selectivity observed experimentally. In particular, we found that solvent and temperature did not affect this selectivity and mainly influence the activation energies and the exothermic character of these 32CA reactions.

Temperature-Dependent Line-Broadening Effects in CO2 Caused by Ar.

This computational study of line-broadening effects is based on an accurate, analytical representation of the intermonomer potential energy surface (PES) of the CO2 ⋅ Ar van der Waals (vdW) complex. The PES is employed to compute collisional broadening coefficients for rovibrational lines of CO2 perturbed by Ar. The semiclassical computations are performed using the modified Robert-Bonamy approach, including real and imaginary terms, and the exact trajectory model. The lines investigated are in the 10001←00011, 01101←00001, 00011←00001, and 00031←00001 vibrational bands and the computations are repeated at multiple temperatures. The computed results are in good agreement with the available experimental values, validating both the intermonomer PES developed and the methodology used. For lines in the 01101←00001 band of CO2 , temperature-dependent Ar-broadening coefficients are reported for the first time. The parameters presented should prove useful, among other applications, for the accurate experimental determination of CO2 and Ar abundances in planetary atmospheres.

Formation of Eigen or Zundel Features at Protonated Water Cluster-Aromatic Interfaces.

Interfacial interactions of protonated water clusters adsorbed at aromatic surfaces play an important role in biology, and in atmospheric, chemical and materials sciences. Here, we investigate the interaction of protonated water clusters ((H+ H2 O)n (where n=1-3)) with benzene (Bz), coronene (Cor) and dodecabenzocoronene (Dbc)). To study the structure, stability and spectral features of these complexes, computations are done using DFT-PBE0(+D3) and SAPT0 methods. These interactions are probed by AIM electron density topography and non-covalent interactions index (NCI) analyses. We suggest that the excess proton plays a crucial role in the stability of these model interfaces through strong inductive effects and the formation of Eigen or Zundel features. Also, computations reveal that the extension of the π-aromatic system and the increase of the number of water molecules in the H-bounded water network led to a strengthening of the interactions between the corresponding aromatic compound and protonated water molecules, except when a Zundel ion is formed. The present findings may serve to understand in-depth the role of proton localized at aqueous medium interacting with large aromatic surfaces such as graphene interacting with acidic liquid water. Besides, we give the IR and UV-Vis spectra of these complexes, which may help for their identification in laboratory.

Collision excitation of c-C3H-(X1A1) by He.

Accurate modeling of anionic abundances in the interstellar and circumstellar media requires calculations of collisional data with the most abundant species that are usually He atoms and H2 molecules. In this paper, we focus on smaller cyclic molecular anion, c-C3H-, an astrophysical candidate, following the detection of larger CnH- carbon chains. From a new three-dimensional potential energy surface, the rotational (de-)excitation of the c-C3H-(X1A1) anion by collision with He is investigated. The surface is obtained in the supermolecular approach at the CCSD(T)-F12/aug-cc-pVTZ level of theory. Fully quantum close-coupling calculations of inelastic integral cross sections are performed on a grid of collisional energies large enough to ensure the convergence of the state-to-state rate coefficients for the 34 first rotational levels up to jKa,Kc = 77,0 of c-C3H- and temperatures ranging from 5 to 100 K. For this collisional system, rate coefficients exhibit a strong dominance in favor of 21,2 → l1,1 downward transition. This transition was previously used for the detection of the cyclic parent c-C3H. The c-C3H--He rate coefficients (∼10-11 cm3 s-1) are of the same order of magnitude as those of the detected anions CnH- (as C2H-, C4H-, and C6H-) in collision with He and one order of magnitude smaller than those with H2. The critical densities of H2 were also estimated, and a discussion on the validity of the local thermodynamic equilibrium conditions is carried out. This work represents the contribution to understanding and modeling abundances and chemistry of hydrocarbon radicals, CnH, in astrophysical media.

Combined docking methods and molecular dynamics to identify effective antiviral 2, 5-diaminobenzophenonederivatives against SARS-CoV-2.

The aim of this work is to contribute to the research in finding lead compounds for clinical use, to identify new drugs that target the SARS-CoV-2 virus main protease (Mpro). In this study, we used molecular docking strategies to analyze 2.5-diaminobenzophenone compounds against Malaria and to compare results with the Nelfinavir as a FDA-approved HIV-1 protease inhibitor recommended for the treatment of COVID-19. These efforts identified the potential compounds against SAR-COV-2 Mpro with the docking scores ranges from -6.1 to -7.75 kcal/mol, which exhibited better interactions than the Nelfinavir. Among thirty-six studied, compounds 20c, 24c, 30c, 34c, 35c and 36c showed the highest affinity and involved in forming hydrophobic interactions with Glu166, Thr24, Thr25, and Thr26 residues and forming H-bonding interactions with Gln189, Cys145, and His41residues. Pharmacokinetic properties and toxicity (ADMET) were also determined for identified compounds. This study result in the identification of two compounds 35 and 36 having high binding affinity, good pharmacokinetics properties and lowest toxicity. The structural stability and dynamics of lead compounds within the active site of 3CLpro was also examined using molecular dynamics (MD) simulation. Essential dynamics demonstrated that the two complexes remain stable during the entire duration of simulation. We have shown that these two lead molecules would have the potential to act as promising drug-candidates and would be of interest as starting point for designing compounds against the SARS-CoV-2.

The first microsolvation step for furans: New experiments and benchmarking strategies.

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring. Contrasting comparison strategies, which emphasize either the experimental or the theoretical input, are explored. Within the harmonic approximation, only a few composite computational approaches are able to achieve a satisfactory performance. Deuteration experiments suggest that the harmonic treatment itself is largely justified for the zero-point energy, likely and by design due to the systematic cancellation of important anharmonic contributions between the docking variants. Therefore, discrepancies between experiment and theory for the isomer abundance are tentatively assigned to electronic structure deficiencies, but uncertainties remain on the nuclear dynamics side. Attempts to include anharmonic contributions indicate that for systems of this size, a uniform treatment of anharmonicity with systematically improved performance is not yet in sight.

Characterization of the electronic states of the biological relevant SSNO molecule.

Using configuration interaction ab initio methods, we investigate the lowest electronic states of doublet and quartet spin multiplicities of SSNO where the one-dimensional cuts of the six-dimensional potential energy surfaces of these electronic states along the stretching and bending coordinates are computed. Mainly, these electronic states are found to be repulsive along the central SN distance. A high density of electronic states is computed even at low excitation energies that may favor their couplings. Therefore, the dynamics of the SSNO electronic states is expected to be very complex. We also characterized the bound electronic states spectroscopically where we derived their equilibrium structures and vibrational frequencies. Our calculations show the importance of taking into account of dynamical correlation, in addition to static correlation, for the accurate description of SSNO electronic excited states and more generally for those of R-NO molecular species. Finally, we highlighted the potential role of SSNO in light-induced NO delivery from SSNO related species in biological media.

On the role of HNS and HSN as light-sensitive NO-donors for delivery in biological media.

Results are presented that suggest that thiazyl hydride (HSN)/thionitrosyl hydride (sulfimide, HNS) can be used as light-sensitive compounds for NO-delivery in biological media, as well as markers for the possible detection of intermediates in nitrites + H2S reactions at the cellular level. They are expected to be more efficient than the HNO/HON isovalent species and hence they should be considered instead. A set of characteristic spectroscopic features are identified that could aid in the possible detection of these species in the gas phase or in biological environments. The possibility of intramolecular dynamical processes involving excited states that are capable of interconverting HNS and its isomeric form HSN is examined.