ANN-QSAR, Molecular Docking, ADMET Predictions, and Molecular Dynamics Studies of Isothiazole Derivatives to Design New and Selective Inhibitors of HCV Polymerase NS5B.

RNA polymerase (NS5B), serves as a crucial target for pharmaceutical interventions aimed at combating the hepatitis C virus (HCV), which poses significant health challenges worldwide. The present research endeavors to explore and implement a variety of advanced molecular modeling techniques that aim to create and identify innovative and highly effective inhibitors that specifically target the RNA polymerase enzyme. In this study, a QSAR investigation was carried out on a set of thirty-eight isothiazole derivatives targeting NS5B inhibition and thus hepatitis C virus (HCV) treatment.

SF Negative Ion Formation in Charge Transfer Experiments.

In the present work, we report an update and extension of the previous ion-pair formation study of Hubers, M.M.; Los, J.

DFT mechanistic study of the chemical fixation of CO by aziridine derivatives.

Using density functional theory (DFT), we treat the reaction of coupling of CO with aziridine in gas phase, in the presence of water and of a green catalyst (NaBr). Computations show that, in gas phase, this ring-opening conversions to oxazolidinones initiates by coordinating a CO molecule to the nitrogen atom of the aziridine. Then, a nucleophilic interaction between one oxygen atom of the coordinated CO and the carbon atom of the aziridine occurs.

Towards the generation of potential energy surfaces of weakly bound medium-sized molecular systems: the case of benzonitrile-He complex.

Currently, the explicitly correlated coupled cluster method is used routinely to generate the multi-dimensional potential energy surfaces (mD-PESs) of van der Waals complexes of small molecular systems relevant for atmospheric, astrophysical and industrial applications. Although very accurate, this method is computationally prohibitive for medium and large molecules containing clusters. For instance, the recent detections of complex organic molecules (COMs) in the interstellar medium, such as benzonitrile, revealed the need to establish an accurate enough electronic structure approach to map the mD-PESs of these species interacting with the surrounding gases.

Accurate Prediction of Adiabatic Ionization Energies for PAHs and Substituted Analogues.

The accurate calculation of adiabatic ionization energies (AIEs) for polycyclic aromatic hydrocarbons (PAHs) and their substituted analogues is essential for understanding their electronic properties, reactivity, stability, and environmental/health implications. This study demonstrates that the M06-2X density functional theory method excels in predicting the AIEs of polycyclic aromatic hydrocarbons and related molecules, rivaling the (R)CCSD(T)-F12 method in terms of accuracy. These findings suggest that M06-2X, coupled with an appropriate basis set, represents a reliable and efficient method for studying polycyclic aromatic hydrocarbons and related molecules, aligning well with the experimental techniques.

Doubly ionized OCS bond rearrangement upon fragmentation - experiment and theory.

The dissociation of OCS ions formed by photoionization of the neutral molecule at 40.81 eV is examined using threefold and fourfold electron-ion coincidence spectroscopy combined with high level quantum chemical calculations on isomeric structures and their potential energy surfaces. The dominant dissociation channel of [OCS] is charge separation forming CO + S ion pairs, found here to be formed with low intensity at a lower-energy onset and with a correspondingly smaller kinetic energy release than in the more intense higher energy channel previously reported.

Theoretical Spectroscopic Study of Two Ketones of Atmospheric Interest: Methyl Glyoxal (CHCOCHO) and Methyl Vinyl Ketone (CHCOCH═CH).

Two ketones of atmospheric interest, methyl glyoxal and methyl vinyl ketone, are studied using explicitly correlated coupled cluster theory and core-valence correlation-consistent basis sets. The work focuses on the far-infrared region. At the employed level of theory, the rotational constants can be determined to within a few megahertz of the experimental data.

Unsymmetrical aromatic disulfides as SARS-CoV-2 Mpro inhibitors: Molecular docking, molecular dynamics, and ADME scoring investigations.

COVID-19 pandemic caused by very severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) agent is an ongoing major global health concern. The disease has caused more than 452 million affected cases and more than 6 million death worldwide. Hence, there is an urgency to search for possible medications and drug treatments.

Ab Initio Study of the Large Amplitude Motions of Various Monosubstituted Isotopologues of Methylamine (CH-NH).

CCSD(T)-F12 theory is applied to determine electronic ground state spectroscopic parameters of various isotopologues of methylamine (CH-NH) containing cosmological abundant elements, such as D, C and N. Special attention is given to the far infrared region. The studied isotopologues can be classified in the G, G and G molecular symmetry groups.

Optically Pumped Intensive Light Amplification from a Blue Oligomer.

We demonstrated the time-resolved dynamics of laser action from the conductive oligomer (CO) 1,4-Bis(9-ethyl-3-carbazo-vinylene)-9,9-dihexyl-fluorene (BECV-DHF). Absorption and fluorescence spectra were studied for BECV-DHF in different solvents under a wide range of concentrations. The Fourier-transform infrared spectroscopy (FTIR) spectrum was measured using simulation and experiments.

A novel nanocomposite with superior electrocatalytic activity: A magnetic property based ZnFeO nanocubes embellished with reduced graphene oxide by facile ultrasonic approach.

Herein, a novel Zinc Ferrite nanocubes (ZnFeO NCs) decorated reduced graphene oxide (rGO) nanocomposite have been designed through a sonochemical method. After then, as-synthesized ZnFeO NCs/rGO was characterized by XPS, XRD, HRTEM and EIS. Furthermore, the ZnFeO NCs/rGO nanocomposite modified GCE (glassy carbon electrode) shows excellent electrochemical sensing performance towards biomarker of 4-nitroquinoline N-oxide (4-NQ) with fast detection.

Mechanistic study of the photoexcitation, photoconversion, and photodissociation of CS.

Carbon disulfide is a prototype molecular system for studies of photophysical processes in molecules at different time scales and is also relevant to astrophysics. Here, reliable molecular properties are computed for linear SCS, bent CS, and linear CSS forms using highly correlated post Hartree-Fock methods in conjunction with large basis sets. Structures are identified using explicitly correlated and standard coupled cluster techniques.

Unveiling the complex vibronic structure of the canonical adenine cation.

Adenine, a DNA base, exists as several tautomers and isomers that are closely lying in energy and that may form a mixture upon vaporization of solid adenine. Indeed, it is challenging to bring adenine into the gas phase, especially as a unique tautomer. The experimental conditions were tuned to prepare a jet-cooled canonical adenine (9H-adenine).

Electronic and Vibrational Spectroscopy of CsS.

Using multi configurational ab initio methodologies, we compute the potential energy curves (PECs) of the lowest electronic states of the diatomic CsS. These computations are performed using internally contracted multireference interaction configuration including Davidson correction (MRCI+Q) with and without considering spin-orbit effects. The shapes of the PECs are governed by the interactions between the two ionic states, Σ and Π, correlating at large internuclear separations ( R) to the first ionic dissociation limit and the other electronic states correlating to the three lowest neutral dissociation limits.

Identification of Key Intermediates during the NO and HS Crosstalk Signaling Pathways.

The stable isomers and electronic states of [S,S,N,O] species are investigated with a special focus on the most relevant isomers that could be involved in the NO/HS cross-talk pathways in biological media. This work identifies eight stable anions, among which are the already known cis-SSNO and trans-SSNO molecules and a new NO-like anionic species, NSO. Our computations show that the previously determined structure in lab experiment is trans-SSNO, which is not relevant for biological activity in vivo.

Electronic and spectroscopic characterizations of SNP isomers.

High-level ab initio electronic structure calculations were performed to characterize SNP isomers. In addition to the known linear SNP, cyc-PSN, and linear SPN isomers, we identified a fourth isomer, linear PSN, which is located ∼2.4 eV above the linear SNP isomer.

The furan microsolvation blind challenge for quantum chemical methods: First steps.

Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion.

Benchmark study of the structural and spectroscopic parameters of the hydroxymethyl peroxy (HOCHOO) radical and its decomposition reaction to HO and HCO.

The hydroxymethyl peroxy (HMOO) radical is a product of the oxidation of non-methane hydrocarbons. The present study provides the first accurate computational determination of critical spectroscopic features of the title radical that should aid in its experimental characterization. Structure, energetics, vibrational frequencies, and rotational parameters are reported for the three stable isomers on the ground electronic state of HMOO.

Identifying Cytosine-Specific Isomers via High-Accuracy Single Photon Ionization.

Biological entities, such as DNA bases or proteins, possess numerous tautomers and isomers that lie close in energy, making the experimental characterization of a unique tautomer challenging. We apply VUV synchrotron-based experiments combined with state-of-the-art ab initio methodology to determine the adiabatic ionization energies (AIEs) of specific gas-phase cytosine tautomers produced in a molecular beam. The structures and energetics of neutral and cationic cytosine tautomers were determined using explicitly correlated methods.

HNS(+) and HSN(+) cations: Electronic states, spin-rovibronic spectroscopy with planetary and biological implications.

Ab initio methods in conjunction with a large basis set are used to compute the potential energy surfaces of the 12 lowest electronic states of the HNS(+) and HSN(+) isomeric forms. These potentials are used in discussions of the metastability of these cations and plausible mechanisms for the H(+)/H + SN(+)/SN, S/S(+) + NH(+)/NH, N/N(+) + SH(+)/SH ion-molecule reactions. Interestingly, the low rovibrational levels of HSN(+)(1(2)A″) and HNS(+)(1(2)A″) electronically excited ions are predicted to be long-lived.

Toward the laboratory identification of [O,N,S,S] isomers: Implications for biological NO chemistry.

Benchmark ab initio calculations are performed to investigate the stable isomers of [O,N,S,S]. These computations are carried out using coupled cluster (RCCSD(T)) and explicitly correlated coupled cluster methods (RCCSD(T)-F12). In addition to the already known cis isomer of SSNO, nine other stable forms are predicted.

Ab Initio and DFT Studies on CO2 Interacting with Zn(q+)-Imidazole (q=0, 1, 2) Complexes: Prediction of Charge Transfer through σ- or π-Type Models.

Using first-principles methodologies, the equilibrium structures and the relative stability of CO2 @[Zn(q+) Im] (where q=0, 1, 2; Im=imidazole) complexes are studied to understand the nature of the interactions between the CO2 and Zn(q+) -imidazole entities. These complexes are considered as prototype models mimicking the interactions of CO2 with these subunits of zeolitic imidazolate frameworks or Zn enzymes. These computations are performed using both ab initio calculations and density functional theory.

State-to-state vacuum ultraviolet photodissociation study of CO2 on the formation of state-correlated CO(X(1)Σ(+); v) with O((1)D) and O((1)S) photoproducts at 11.95-12.22 eV.

The state-to-state photodissociation of CO2 is investigated in the VUV range of 11.94-12.20 eV by using two independently tunable vacuum ultraviolet (VUV) lasers and the time-sliced velocity-map-imaging-photoion (VMI-PI) method.

Vibrationally resolved photoelectron spectroscopy of electronic excited states of DNA bases: application to the ã state of thymine cation.

For fully understanding the light-molecule interaction dynamics at short time scales, recent theoretical and experimental studies proved the importance of accurate characterizations not only of the ground (D0) but also of the electronic excited states (e.g., D1) of molecules.

Theoretical and Experimental Photoelectron Spectroscopy Characterization of the Ground State of Thymine Cation.

We report on the vibronic structure of the ground state X̃(2)A″ of the thymine cation, which has been measured using a threshold photoelectron photoion coincidence technique and vacuum ultraviolet synchrotron radiation. The threshold photoelectron spectrum, recorded over ∼0.7 eV above the ionization potential (i.