Constrained dipole moment density functional theory for charge distributions in force fields for the study of molecular fluids

ADCHα-I population analysis and constrained dipole moment density functional theory in force fields for molecular simulations

A new population analysis, ADCHα-I, based on the interpolation between the Hirshfeld (H) and the iterative Hirshfeld (H-I) methods through a parameter α and on the atomic dipole moment corrected Hirshfeld (ADCH) methodology is proposed, in combination with the constrained dipole moment density functional theory (CD-DFT) previously developed, to determine the charge distributions of force fields. Following this approach, the electronic density of the isolated molecule is determined for the value of the dipole moment that reproduces the experimental dielectric constant, in order to incorporate through this property the effects of the surrounding molecules in the liquid, and to carry on this information to the molecular simulation, the new population analysis is built to obtain the set of charges that reproduces this dipole moment. By selecting α = 1/2, one is led to charges that are larger than the ones obtained through H and ADCH and smaller than those of H-I and that incorporate, at the local level, information about the response of isolated atoms to donate or to accept charge, which is not considered in ADCH. The results obtained for several liquid properties indicate that the combination of CD-DFT with this population analysis leads to a good description of the charge distributions in force fields used in molecular simulations.

The use of constrained methods to analyze the molecular reactivity and to define a new type of pseudo atoms

CONTEXT

Constrained methods in electronic structure methodologies add terms to the variational equations and generate solutions that represent distorted electronic distributions. In some cases, the new solutions can be used to study the chemical reactivity of parts of the molecule. Additionally, this contribution presents the use of population constraints to define pseudo atoms in a molecule. The effects of the pseudo atom on the molecular properties are analyzed. The pseudo atoms are used to simulate the inductive effect of the substituent in a group of carbonyl molecules and their effect on the stability of the complexes between these organic species and one molecule of water. A discussion on the assumptions involved in the present definition of pseudo atoms is also included.

METHOD

The constrained RHF computations are done in a modified Hartree-Fock code for Gaussian basis sets. The selected basis set is STO-6 G.

Simulating Electron Transfer Reactions in Solution: Radical-Polar Crossover

Single-electron transfer (SET) promotes a wide variety of interesting chemical transformations, but modeling of SET requires a careful treatment of electronic and solvent effects to give meaningful insight. Therefore, a combined constrained density functional theory and molecular mechanics (CDFT/MM) tool is introduced specifically for SET-initiated reactions. Mechanisms for two radical-polar crossover reactions involving the organic electron donors tetrakis(dimethylamino)ethylene (TDAE) and tetrathiafulvalene (TTF) were studied with the new tool. An unexpected tertiary radical intermediate within the TDAE system was identified, relationships between kinetics and substitution in the TTF system were explained, and the impact of the solvent environments on the TDAE and TTF reactions were examined. The results highlight the need for including solvent dynamics when quantifying SET kinetics and thermodynamics, as a free energy difference of >20 kcal/mol was observed. Overall, the new method informs mechanistic analysis of SET-initiated reactions and therefore is envisioned to be useful for studying reactions in the condensed phase.

Synthesis, characterization, and theoretical investigation of 4-chloro-6(phenylamino)-1,3,5-triazin-2-yl)asmino-4-(2,4-dichlorophenyl)thiazol-5-yl-diazenyl)phenyl as potential SARS-CoV-2 agent

The synthesis of 4-chloro-6(phenylamino)-1,3,5-triazin-2-yl)amino-4-(2,4 dichlorophenyl)thiazol-5-yl-diazenyl)phenyl is reported in this work with a detailed structural and molecular docking study on two SARS-COV-2 proteins: 3TNT and 6LU7. The studied compound has been synthesized by the condensation of cyanuric chloride with aniline and characterized with various spectroscopic techniques. The experimentally obtained spectroscopic data has been compared with theoretical calculated results achieved using high-level density functional theory (DFT) method. Stability, nature of bonding, and reactivity of the studied compound was evaluated at DFT/B3LYP/6-31 + (d) level of theory. Hyper-conjugative interaction persisting within the molecules which accounts for the bio-activity of the compound was evaluated from natural bond orbital (NBO) analysis. Adsorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties of the experimentally synthesized compound was studied to evaluate the pharmacological as well as in silico molecular docking against SARS-CoV-2 receptors. The molecular docking result revealed that the investigated compound exhibited binding affinity of −9.3 and −8.8 for protein 3TNT and 6LU7 respectively. In conclusion, protein 3TNT with the best binding affinity for the ligand is the most suitable for treatment of SARS-CoV-2.