Non-Covalent Interactions Atlas Benchmark Data Sets 5: London Dispersion in an Extended Chemical Space

The Non-Covalent Interactions Atlas (www.nciatlas.org) has been extended with two data sets of benchmark interaction energies in complexes dominated by London dispersion. The D1200 data set of equilibrium geometries provides a thorough sampling of an extended chemical space, while the D442×10 set features dissociation curves for selected complexes. In total, they provide 5,178 new CCSD(T)/CBS data points of the highest quality. The new data have been combined with previous NCIA data sets in a comprehensive test of dispersion-corrected DFT methods, identifying the ones that achieve high accuracy in all types of non-covalent interactions in a broad chemical space. Additional tests of dispersion-corrected MP2 and semiempirical QM methods are also reported.

Theoretical investigation of five-coordinated manganese(III) oxophlorin with different axial ligands at various spin states using different DFT methods

The Mn(III)-oxophlorin complexes with imidazole, pyridine and t-butylcyanide as axial ligands have been studied using B3LYP, Bv86p, and M06-2X methods. All of the possible optimized geometries are specified, while the M06-2X is employed. Results obtained show that the isomers of Mn(III)-oxophlorin with imidazole or pyridine are the most stable at quintet state, compared to singlet and triplet spin states. Besides, there are two and four [Formula: see text]-electrons on manganese in each of these complexes at triplet and quintet states, respectively. Also, Mn(III)-oxophlorin with t-butylcyanide as axial ligand is only stable at singlet state. Non-specific solvent effects show that dispersion and London forces have the basic role in stability of complexes in a solvent. Note that latter interactions can occur in medium with dielectric constant ([Formula: see text]) of [Formula: see text]8, such as [Formula: see text] for position of oxophlorin in heme oxygenase enzyme. NBO analysis show that there is no degeneracy between d orbitals of Mn in the five-coordinated Mn(III)-oxophlorin at singlet and triplet spin states, but two d orbitals of manganese are degenerated in latter complexes at quintet state. Such degeneracy of d orbitals is observed in a complex with square pyramid structure. Then five-coordinated Mn(III)-oxophlorin with imidazole or pyridine is the most stable at quintet spin state, because of its geometry corresponding to square pyramid configuration of atoms. Also, nonbounding interaction between Mn and the ring of oxophlorin or Mn and ligand are more effective in Mn(III)-oxophlorin with imidazole as axial ligand, compared to pyridine and t-butylcyanide.

Excited States Computation of Models of Phenylalanine Protein Chains: TD-DFT and Composite CC2/TD-DFT Protocols

The present benchmark calculations testify to the validity of time-dependent density functional theory (TD-DFT) when exploring the low-lying excited states potential energy surfaces of models of phenylalanine protein chains. Among three functionals suitable for systems exhibiting charge-transfer excited states, LC-ωPBE, CAM-B3LYP, and ωB97X-D, which were tested on a reference peptide system, we selected the ωB97X-D functional, which gave the best results compared to the approximate coupled-cluster singles and doubles (CC2) method. A quantitative agreement for both the geometrical parameters and the vibrational frequencies was obtained for the lowest singlet excited state (a ππ* state) of the series of capped peptides. In contrast, only a qualitative agreement was met for the corresponding adiabatic zero-point vibrational energy (ZPVE)-corrected excitation energies. Two composite protocols combining CC2 and DFT/TD-DFT methods were then developed to improve these calculations. Both protocols substantially reduced the error compared to CC2 and experiment, and the best of both even led to results of CC2 quality at a lower cost, thus providing a reliable alternative to this method for very large systems.

Synthesis of Nucleoside-like Molecules from a Pyrolysis Product of Cellulose and Their Computational Prediction as Potential SARS-CoV-2 RNA-Dependent RNA Polymerase Inhibitors

(1R,5S)-1-Hydroxy-3,6-dioxa-bicyclo[3.2.1]octan-2-one, available by an efficient catalytic pyrolysis of cellulose, has been applied as a chiral building block in the synthesis of seven new nucleoside analogues, with structural modifications on the nucleobase moiety and on the carboxyl- derived unit. The inverted configuration by Mitsunobu reaction used in their synthesis was verified by 2D-NOESY correlations, supported by the optimized structure employing the DFT methods. An in silico screening of these compounds as inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase has been carried out in comparison with both remdesivir, a mono-phosphoramidate prodrug recently approved for COVID-19 treatment, and its ribonucleoside metabolite GS-441524. Drug-likeness prediction and data by docking calculation indicated compound 6 [=(3S,5S)-methyl 5-(hydroxymethyl)-3-(6-(4-methylpiperazin-1-yl)-9H-purin-9-yl)tetrahydrofuran-3-carboxylate] as the best candidate. Furthermore, molecular dynamics simulation showed a stable interaction of structure 6 in RNA-dependent RNA polymerase (RdRp) complex and a lower average atomic fluctuation than GS-441524, suggesting a well accommodation in the RdRp binding pocket.

Anti-Corrosion Mechanism of Parsley Extract and Synergistic Iodide as Novel Corrosion Inhibitors for Carbon Steel-Q235 in Acidic Medium by Electrochemical, XPS and DFT Methods

The parsley extract (PLE) was prepared using absolute ethyl alcohol. The PLE and synergistic iodide were firstly utilized as efficacious corrosion inhibitors to slow down the corrosion rate of carbon steel-Q235 in 0.5 mol/L H2SO4 solution. The anti-corrosion performance was researched by weight loss method, electrochemical tests, surface analysis and quantum chemistry calculation. Results of electrochemical and weight loss tests show that the synergetic PLE and I− exhibit the optimal corrosion inhibition efficiency 99%. The combined inhibitor displays the favorable long-term corrosion inhibition effect, and the inhibition efficiency can maintain more than 90% after 144 h immersion. The introduction of I− makes carbon steel surface with higher negative charge amount, which could be beneficial to the interaction between corrosion inhibitor and Fe atoms. The adsorption behavior obeys the Langmuir isotherm adsorption, and involves chemical and physical adsorption. On the basis of electrochemical consequences and theoretical calculation, the adsorption process and anti-corrosion mechanisms are further explored.

Exploration of Luteolin as Potential Anti-COVID19 agent: Molecular Docking, Molecular Dynamic Simulation, ADMET and DFT analysis

Background: Recently, coronavirus disease-2019 (COVID-19) has become a pandemic disease of the respiratory tract having mild to severe symptoms of pneumonia. No clinical antiviral agent is available so far, however, several repurposing drugs and vaccine are being given to individuals or in clinical trials against SARS-CoV-2 Objective: The aim of this study is to uncover the potential effects of Luteolin (Lut) as an inhibitor of SARS-CoV2 encoded proteins via utilizing computational tools Method: Molecular modelling to unfold the anti-SARS-CoV2 potential of Lut along with reference drugs namely remdesivir and nafamostat was performed by the use of molecular docking, molecular dynamic (MD) simulation, absorption, distribution, metabolism, excretion, toxicity (ADMET) and density functional theory (DFT) methods against the five different SARS-CoV-2 encoded key proteins and one human receptor protein. The chemical reactivity of Luteolin is done through prediction of HOMO-LUMO gap energy and other chemical descriptors analysis Results: In the present study, Lut binds effectively in the binding pockets of spike glycoprotein (6VSB), ADP phosphatase of NSP3 (6W02), and RNA dependent RNA polymerase (7AAP) protein receptors with significant values of docking scores -7.00, -7.25, and -6.46 respectively as compared to reference drugs remdesivir and nafamostat. Conclusion:: Thus, Lut can act as therapeutic agent and is orally safe for human consumption as predicted by molecular modelling against SARS-CoV-2 in the treatment of COVID-19