Performances of DFT methods implemented in G09 for simulations of the dispersion-dominated CH-π in ligand–protein complex: A case study with glycerol-GDH

QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin

Intermolecular interaction between key residue N501 of the epitope on SARS-CoV-2 RBD and screening antibody B38 was studied using the QM/MM and QM approach. The QM/MM optimized geometry shows that angle X-H---Y is 165° for O-H---O between mAb light chain S30 and RBD N501. High level MP2 calculations indicated the interaction between RBD N501 and S30 of B38 Fab light chain provide a relatively strong attractive force of - 3.32 kcal/mol, whereas the hydrogen bond between RBD Q498 and S30 was quantified as 0.10 kcal/mol. The decrease in ESP partial charge on hydrogen atom of hydroxyl group on S30 drops from 0.38 a.u. to 0.31 a.u., exhibiting the sharing of 0.07 a.u. from the lone pair electron oxygen of N501 due to hydrogen bond formation. The NBO occupancy of hydrogen atom also decreases from 25.79 % to 22.93 % in the hydroxyl H-O NBO bond of S30. However, the minor change of NBO hybridization of hydroxyl oxygen of S30 from sp3.00 to sp3.05 implies the rigidity of hydrogen bond tetrahedral geometry in the relative dynamic protein complex. The O-H---O angle is 165° which is close but not exactly linear. The structural requirement for sp3 hybridization of oxygen for hydroxyl group on S30 and dimension of protein likely prevent O-H---O from adopting linear geometry. The hydrogen bond strengths were also calculated using a variety of DFT methods, and the result of - 3.33 kcal/mol from the M06L method is the closest to that of the MP2 calculation. Results of this work may aid in the COVID-19 vaccine and drug screening.

Interaction of glyphosate in matrices of cellulose and diethylaminoethyl cellulose biopolymers: theoretical viewpoint of the adsorption process

Glyphosate is an herbicide widely used in agricultural activities causing contamination of soils and bodies of water and damage to the biodiversity of ecosystems. In this context, the present study aimed to theoretically study the adsorption potential of the biopolymer cellulose (CE) and its diethylaminoethyl cellulose derivative (DEAEC) with the herbicide glyphosate (GLY). Theoretical calculations were performed using the density functional theory. Molecular electrostatic potential and frontier molecular orbital analyses were performed, which allowed identifying the possible sites of interaction of biopolymers that were in the functional groups -OH and O- of cellulose and in the groups -O- and -NH+(CH2CH3)2 of the DEAEC. Reactivity indices chemical softness and hardness showed that both adsorbents could interact with adsorbate. Simulated IR indicated that the interactions could be evinced in experimental measurements by changes in the bands of glyphosate (ν(P = O), δ(P-O-H), δ(C-N-H)) or in the bands of CE and DEAEC (ν(C-O), ν(C-H), ν(N-H)). The binding energies showed that the GLY interacts more effectively with CE than DEAEC. The ΔH prove that all processes are exothermic and the CE-GLY1 interaction showed value of ΔG < 0. The topological results showed a greater number of interactions with electrostatic nature. The results found in the study show that the theoretical data provides useful information to support the use of biopolymers as matrices for glyphosate adsorption or other contaminants.

Structure-based screening and validation of potential dengue virus inhibitors through classical and QM/MM affinity estimation

The recurrent outbreaks of dengue virus around the globe represent a huge challenge for governments and public health organizations. With the rapid growth and ease of transportation, dengue disease continues to spread, placing more of the world population under constant threat. Despite decades of research efforts, no effective small molecule antivirals are available against dengue virus. With the efficacy of the recently developed vaccine to be determined, there is an urgent unmet need for small molecule dengue virus treatments. In the current study, we employed state-of-the-art molecular modelling simulations to identify novel inhibitors of the dengue virus envelope protein. The binding modes of all compounds within the conserved β-OctylGlucoside (β-OG) pocket were studied using a combination of docking, molecular dynamics simulations and binding free energy calculations. Here, we describe ten new compounds that significantly reduce production of dengue virus as determined using standard cell-based virological assays. Moreover, we present a comprehensive structural analysis of the identified hits, focusing on their electrostatic and lipophilic binding energy contributions. Finally, we highlight the effect of the desolvation penalty in limiting the activity of some of these compounds. The data presented here paves the way toward rationally designing selective and potent novel inhibitors against dengue virus.

Variable segment roles: modulation of the packing modes, nanocrystal morphologies and optical emissions

Three isomers were prepared by covalently grafting carbazole (Cz) onto spiro[fluorene-9,9'-xanthene] (SFX) at different positions. Due to the complicated and variable roles of molecular segments, an evolution of the corresponding molecular packing mode was realized, accompanied by the change of nanocrystal morphology and photoluminescence properties.

Evaluating dispersion forces for optimization of van der Waals complexes using a non-empirical functional

Modelling dispersion interactions with traditional density functional theory (DFT) is a challenge that has been extensively addressed in the past decade. The exchange-dipole moment (XDM), among others, is a non-empirical add-on dispersion correction model in DFT. The functional PW86+PBE+XDM for exchange, correlation and dispersion, respectively, compromises an accurate functional for thermochemistry and for van der Waals (vdW) complexes at equilibrium and non-equilibrium geometries. To use this functional in optimizing vdW complexes, rather than computing single point energies, it is necessary to evaluate accurate forces. The purpose of this paper is to validate that, along the potential energy surface, the distance at which the energy is minimum is commensurate with the distance at which the forces vanish to zero. This test was validated for 10 rare gas diatomic molecules using various integration grids and different convergence criteria. It was found that the use of either convergence criterion, 10^-6 or 10^-8, in Gaussian09, does not affect the accuracy of computed optimal distances and binding energies. An ultra-fine grid needs to be used when computing accurate energies using generalized gradient approximation functionals.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Mechanism of Oxidation of Ethane to Ethanol at Iron(IV)-Oxo Sites in Magnesium-Diluted Fe2(dobdc)

The catalytic properties of the metal-organic framework Fe2(dobdc), containing open Fe(II) sites, include hydroxylation of phenol by pure Fe2(dobdc) and hydroxylation of ethane by its magnesium-diluted analogue, Fe0.1Mg1.9(dobdc). In earlier work, the latter reaction was proposed to occur through a redox mechanism involving the generation of an iron(IV)-oxo species, which is an intermediate that is also observed or postulated (depending on the case) in some heme and nonheme enzymes and their model complexes. In the present work, we present a detailed mechanism by which the catalytic material, Fe0.1Mg1.9(dobdc), activates the strong C-H bonds of ethane. Kohn-Sham density functional and multireference wave function calculations have been performed to characterize the electronic structure of key species. We show that the catalytic nonheme-Fe hydroxylation of the strong C-H bond of ethane proceeds by a quintet single-state σ-attack pathway after the formation of highly reactive iron-oxo intermediate. The mechanistic pathway involves three key transition states, with the highest activation barrier for the transfer of oxygen from N2O to the Fe(II) center. The uncatalyzed reaction, where nitrous oxide directly oxidizes ethane to ethanol is found to have an activation barrier of 280 kJ/mol, in contrast to 82 kJ/mol for the slowest step in the iron(IV)-oxo catalytic mechanism. The energetics of the C-H bond activation steps of ethane and methane are also compared. Dehydrogenation and dissociation pathways that can compete with the formation of ethanol were shown to involve higher barriers than the hydroxylation pathway.