M. Mogren Al-Mogren

Accurate spectroscopic characterization of ethyl mercaptan and dimethyl sulfide isotopologues: a route toward their astrophysical detection

Using state-of-the-art computational methodologies, we predict a set of reliable rotational and torsional parameters for ethyl mercaptan and dimethyl sulfide monosubstituted isotopologues. This includes rotational, quartic, and sextic centrifugal-distortion constants, torsional levels, and torsional splittings. The accuracy of the present data was assessed from a comparison to the available experimental data. Generally, our computed parameters should help in the characterization and the identification of these organo-sulfur molecules in laboratory settings and in the interstellar medium.

Characterization and reactivity of the weakly bound complexes of the [H, N, S](-) anionic system with astrophysical and biological implications.

We investigate the lowest electronic states of doublet and quartet spin multiplicity states of HNS(-) and HSN(-) together with their parent neutral triatomic molecules. Computations were performed using highly accurate ab initio methods with a large basis set. One-dimensional cuts of the full-dimensional potential energy surfaces (PESs) along the interatomic distances and bending angle are presented for each isomer. Results show that the ground anionic states are stable with respect to the electron detachment process and that the long range parts of the PESs correlating to the SH(-) + N, SN(-) + H, SN + H(-), NH + S(-), and NH(-) + S are bound. In addition, we predict the existence of long-lived weakly bound anionic complexes that can be formed after cold collisions between SN(-) and H or SH(-) and N. The implications for the reactivity of these species are discussed; specifically, it is shown that the reactions involving SH(-), SN(-), and NH(-) lead either to the formation of HNS(-) or HSN(-) in their electronic ground states or to autodetachment processes. Thus, providing an explanation for why the anions, SH(-), SN(-), and NH(-), have limiting detectability in astrophysical media despite the observation of their corresponding neutral species. In a biological context, we suggest that HSN(-) and HNS(-) should be incorporated into H2S-assisted heme-catalyzed reduction mechanism of nitrites in vivo.

Role of size and shape selectivity in interaction between gold nanoclusters and imidazole: a theoretical study

AbstractWe present a theoretical study on the structure, stability, spectra and electronic properties of imidazole (Im) adsorbed on gold nanoclusters (Aun, n = 2, 4, 6, 8, 10, and 20). These computations were performed using various density functional theories with and without inclusion of Grimme’s (D3) dispersion correction. For small clusters, we also carried out wavefunction-based ab initio (MP2 and SCS-MP2) computations for comparison. Vibrational, atoms in molecules (AIM) and natural bond orbital (NBO) analyses clearly reveal the occurrence of charge transfer (CT) through covalent (N1–Au) and noncovalent interactions that play important roles in the stability of the Im@Aun complexes with anchor assisted H-bonds (Cα–H · Au). Therefore, gold clusters can act as H-bond acceptors with biomolecules for development of new materials and applications. Our study establishes also the ability and reliability of PBE0 and M05-2X functionals compared to B3LYP and PBE for an accurate description of covalent and noncovalent interactions between Im and gold clusters since they lead to close agreement with MP2. Finally, we show that the Au8 cluster may be viewed as large enough to mimic the 3D gold surface. Graphical AbstractImidazole@gold nanoclusters

Theoretical characterization of C7, C7−, and C7+

We present a theoretical investigation of neutral and ionic C7 molecules. Since carbon chains present isomerism and the number of possible structures increases fast with the number of carbon atoms, a B3LYP∕aug-cc-pVTZ search of stationary points has been achieved. For C7, we found twelve minimal structures. Among these forms, eleven C7 isomers are located into the lowest singlet hyper potential energy surface. The most stable form of C7 is linear and possesses a (1)Σg(+) symmetry species. For C7(-), we characterized fifteen stable forms, where twelve are of doublet spin-multiplicity. The global minimum of C7(-) is a (2)Πg doubly degenerate Renner-Teller structure. For C7(+) cation, we found eleven doublet and three quartet isomers with a 7-atom cycle, C7(+) (X(2)A1) ground state. For the most stable forms, explicitly correlated (R)CCSD(T)-F12 calculations have been performed for the determination of equilibrium geometries and for the spectroscopic characterization of C7, C7(-), and C7(+), providing accurate rotational constants and harmonic frequencies. Vertical excitation energies to the lowest electronic states have been computed at the CASSCF∕MRCI∕aug-cc-pVTZ level. Thirty five electronic states of C7, suitable of being involved in reactive processes, lie below 7 eV. Fourteen metastable electronic states of C7(-) have been found below 3.5 eV. For linear-C7, we compute the electron affinity and the ionization energy to be 3.38 eV and 10.42 eV, respectively.

First principle investigations of organobismuth palladium-catalyzed C–C coupling reaction: mechanism, chemoselectivity and solvent effects

A first principle study of the cross-coupling reaction between 3-chloro-6-iodopyridazine and triphenylbismuth under palladium catalysis has been carried out. The approach selected for this investigation is the density functional theory within the framework of the PBE0 and B3LYP hybrid exchange–correlation functionals, with and without including empirical corrections for the dispersion forces at the GD3 level. For this reaction, a three-step mechanism including an oxidative addition, a transmetalation and a reductive elimination has been proposed. All intermediates and transition states have been fully characterized. The energy profile is deduced in gas phase and in solvent. Calculations suggest that the oxidative addition is the rate-determining step for the entire cross-coupling reaction.

VUV photoionization and dissociative photoionization of the prebiotic molecule acetyl cyanide: theory and experiment.

The present combined theoretical and experimental investigation concerns the single photoionization of gas-phase acetyl cyanide and the fragmentation pathways of the resulting cation. Acetyl cyanide (AC) is inspired from both the chemistry of cyanoacetylene and the Strecker reaction which are thought to be at the origin of medium sized prebiotic molecules in the interstellar medium. AC can be formed by reaction from cyanoacetylene and water but also from acetaldehyde and HCN or the corresponding radicals. In view of the interpretation of vacuum ultraviolet (VUV) experimental data obtained using synchrotron radiation, we explored the ground potential energy surface (PES) of acetyl cyanide and of its cation using standard and recently implemented explicitly correlated methodologies. Our PES covers the regions of tautomerism (between keto and enol forms) and of the lowest fragmentation channels. This allowed us to deduce accurate thermochemical data for this astrobiologically relevant molecule. Unimolecular decomposition of the AC cation turns out to be very complex. The implications for the evolution of prebiotic molecules under VUV irradiation are discussed.

Insights on the interaction of Zn2 + cation with triazoles: Structures, bonding, electronic excitation and applications

At present, we investigate the structures, the stability, the bonding and the spectroscopy of the Zn2+-triazole complexes (Zn2+-Tz), which are subunits of triazolate based porous materials and Zn-enzymes. This theoretical work is performed using ab initio methods and density functional theory (DFT) where dispersion correction is included. Through these benchmarks, we establish the ability and reliability of M05-2X+D3 and PBE0+D3 functionals for the correct description of Zn2+-Tz bond since these DFTs lead to close agreement with post Hartree-Fock methods. Therefore, M05-2X+D3 and PBE0+D3 functionals are recommended for the characterization of larger organometallic complexes formed by Zn and N-rich linkers. For Zn2+-Tz, we found two stable σ-type complexes: (i) a planar structure where Zn2+ links to unprotonated nitrogen and (ii) an out-of-plane cluster where carbon interacts with Zn2+. The most stable isomers consist on a coordinated covalent bond between the lone pair of unprotonated nitrogen and the vacant 4s orbital of Zn2+. The roles of covalent interactions within these complexes are discussed after vibrational, NBO, NPA charges and orbital analyses. The bonding is dominated by charge transfer from Zn2+ to Tz and intramolecular charge transfer, which plays a vital role for the catalytic activity of these complexes. These findings are important to understand, at the microscopic level, the structure and the bonding within triazolate based macromolecular porous materials and Zn-enzymes.