Theoretical spectroscopic characterization at low temperatures of methyl hydroperoxide and three S-analogs

9 pags.; 3 figs.; 6 tabs.© 2015 AIP Publishing LLC. The low temperature spectra of the detectable species methyl hydroperoxide (CH3OOH) and three sulfur analogs, the two isomers of methanesulfenic acid (CH3SOH and CH3OSH) and the methyl hydrogen disulfide (CH3SSH), are predicted from highly correlated ab initio methods (CCSD(T) and CCSD(T)-F12). Rotational parameters, anharmonic frequencies, torsional energy barriers, torsional energy levels, and their splittings are provided. Our computed parameters should help for the characterization and the identification of these organic compounds in laboratory and in the interstellar medium.This research was supported by the MINECO of Spain Grant No. FIS2013-40626-P and by a Marie Curie International Research Staff Exchange Scheme Fellowship within the 7th European Community Framework Program under Grant No. PIRSES-GA-2012-31754. The authors acknowledge the COST Actions CM1002 CODECS and CM1401 “Our Astrochemical History.” The authors acknowledge the CTI (CSIC) and CESGA for computing facilities.Peer Reviewe

DFT and Molecular docking study of natural molecules proposed for COVID-19 treatment

AbstractEmergence and spread of corona virus disease 2019 (COVID-19), caused by severe respiratory syndrome coronavirus, is considered a public health emergency threatening global health systems, as of June, 2020, It caused a cumulative total of 9,033,423 confirmed cases and more than 469,539 deaths across 215 countries, person to-person transmission has being identified as the route for spreading. So far, the lack of effective vaccines for the treatment or prevention of Covid-19 has further worsened the situation. In this context, the present study aims to assess whether naturally occurring components have an antiviral effect via a computational modeling approach. Density Functional theory (DFT) was performed to estimate the kinetic parameters, frontier molecular orbitals, molecular electrostatic potential as well as chemical reactivity descriptors of various ligands. The results revealed that Crocin and Digitoxigenin exhibited a potential applicant with the lowest resistance to electronic charge transfer with a chemical hardness of 2.19eV and 2.96eV respectively, as well as the lowest HOMO-LUMO difference. In addition to the DFT calculation, a docking simulation study was conducted on the SARS-CoV-2 base protease (PDB: 6LU7) to determine the binding affinity of ligands. The findings show that Crocin exhibits the lowest binding energy of -8.1 Kcal/mol and may be a good inhibitor of CoV-2-SARS compared to hydroxychloroquine and chloroquine, which have a binding affinity of -5.4 and -4.9 Kcal/mol, respectively. The high binding affinity of L3 was assigned to the existence of 14 hydrogen bonds connecting the ligand to the critical amino acid residues of the receptor

Structural and spectroscopic characterization of methyl isocyanate, methyl cyanate, methyl fulminate, and acetonitrile N-oxide using highly correlated ab initio methods

10 pags.,3 figs., 7 tabs.Various astrophysical relevant molecules obeying the empirical formula CHNO are characterized using explicitly correlated coupled cluster methods (CCSD(T)-F12). Rotational and rovibrational parameters are provided for four isomers: methyl isocyanate (CHNCO), methyl cyanate (CHOCN), methyl fulminate (CHONC), and acetonitrile N-oxide (CHCNO). A CHCON transition state is inspected. A variational procedure is employed to explore the far infrared region because some species present non-rigidity. Second order perturbation theory is used for the determination of anharmonic frequencies, rovibrational constants, and to predict Fermi resonances. Three species, methyl cyanate, methyl fulminate, and CHCON, show a unique methyl torsion hindered by energy barriers. In methyl isocyanate, the methyl group barrier is so low that the internal top can be considered a free rotor. On the other hand, acetonitrile N-oxide presents a linear skeleton, C symmetry, and free internal rotation. Its equilibrium geometry depends strongly on electron correlation. The remaining isomers present a bend skeleton. Divergences between theoretical rotational constants and previous parameters fitted from observed lines for methyl isocyanate are discussed on the basis of the relevant rovibrational interaction and the quasi-linearity of the molecular skeleton. Published by AIP PublishingThis research was supported by a Marie Curie International Research Staff Exchange Scheme Fellowship within the 7th European Community Framework Program under Grant No. PIRSES-GA-2012-31754 and the FIS2013- 40626-P project of the MINECO, Spain. The authors also acknowledge the COST Actions 1401 and 1405. S.D. acknowledges MAEC-ACID (Spain) for the grant.Peer Reviewe

First-principle computations of rotational-vibrational transition probabilities

International audienceThe theoretical calculations of dipole moments provide reliable compact information required for the evaluation of radiative transition probabilities in the electronic states of small molecular ions. The comparison of the computed line intensities and dipole derivatives with available experimental data in neutral molecules demonstrates that they can be calculated ab initio with a precision of a few percent, hence with an accuracy sufficient for most of the experimental applications

Large amplitude motions of pyruvic acid (CH3-CO-COOH)

ATMOS 2022 International Winter School on Atmospheric Chemistry Greenhouse gases and Pollutants Rabat, February 21-26, 2022Peer reviewe

Solvation effects and stabilization of multicharged ions: a case study of ArmBeOq+ complexes

International audienceUsing first-principle methods, we characterized ArmBeOq+ (0 <= m <= 3 and 0 <= q <= 2) and BeOq+ (3 <= q <= 5) multicharged ions (MCIs). This includes their structural parameters, relative stabilities and vibrational wavenumbers. Our calculations confirm the existence of the ArBeO complex. In addition, we found (meta-) stable neutral and ionic complexes such as ArBeO+, ArBeO2+, Ar2BeO, Ar2BeO+, Ar2BeO2+, Ar3BeO, Ar3BeO+ and Ar3BeO2+. The analysis of the structural parameters and of the electron density differences shows that a strong perturbation in the electronic structure of the BeOq+ (q = 1,2) moiety occurs upon complexation, resulting in a major increase in covalency of these multicharged ions (MCIs). The consequences of solvation of MCIs in argon matrices are pointed out. More generally, the effects on the spectroscopy of MCIs trapped on cold matrices are discussed

Highly correlated ab initio calculations of various Monosubstituted Isotopologues of Acetone (CH3-CO-CH3)

ATMOS 2022 International Winter School on Atmospheric Chemistry Greenhouse gases and Pollutants Rabat, February 21-26, 2022Peer reviewe

Atmospheric pollutants; CO2 Capture

CAPZEO-2014, Faculté Des Sciences-Université Mohammed V-Agdal, Rabat (Morocco), 9-12 June 2014Peer Reviewe

The absorption wavelengths of sulfur chromophors of ultramarines calculated by time-dependent density functional theory

International audienc

Stability of van der Waals complexes of the greenhouse effect gases NH3, SO2 and CO with imidazole in gas mixtures containing CO2

The NH, SO and CO van der Waals complexes with imidazole are characterized using highly correlated ab initio methods. The aim is to compare the behavior of greenhouse effect gases and pollutants in the presence of imidazole for predicting the ability of new materials, such as Zeolite Imidazolate Frameworks (ZIF's), for CO capture, storage and gas filters. Imidazole is considered as the simplest model to study the nature of host-guest interactions in ZIF's. Hydrogen bonding plays an important role in these polar gas capture processes, leading to three equilibrium structures of the imidazole + NH, five of the imidazole + SO, and twelve of the imidazole + CO. Real harmonic frequencies confirm the minimum energy character of these geometries. The complexation processes carry out important changes in the charge distribution of the ring. Binding energies calculated with CCSD(T)-F12 theory predict a favored adsorption of ammonia with respect to CO. In this case, the formation of intramolecular bonds involving the unprotonated nitrogen is clearly favored energetically. The binding energy corresponding to the most stable structure I1A of SO is approximately twice of the corresponding value of CO. Carbon monoxide presents the largest number of possible equilibrium structures which assure its capture by solid ZIF's although binding energies are relatively low.This research was supported by a Marie Curie International Research Staff Exchange Scheme Fellowship within the 7th European Community Framework Program under grant n PIRSES-GA- 2012-31754, the FIS2013-40626-P and FIS2016-76418-P projects of the MINECO, Spain. The authors also acknowledge the COST Actions 1401 and 1405. S.D. acknowledges MAEC-ACID (Spain) for the grant.Peer Reviewe