Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

ON THE ELECTRONIC AND GEOMETRIC STRUCTURE OF GRAPHENE OXIDE IN THE FRAMEWORK OF THE HOFFMAN AND RESS MODELS

For the first time, the geometric and electronic structure of graphene oxide was calculated within the framework of the Hoffman and Ress models by the quantum-chemical method MNDO. Optimized structures of this compound are obtained. The acidic strength (pKa = 28 and pKa = 14) was theoretically estimated in the Hoffman and Ress model, respectively.

Weaving a web of reliable thermochemistry around lignin building blocks: phenol, benzaldehyde, and anisole

Substituted benzenes such as phenol, benzaldehyde, and anisole are the simplest fragments from the lignin separation feedstocks. We have collected available primary experimental results on vapour pressures, enthalpies of phase transition, and enthalpies of combustion of phenol, benzaldehyde, and anisole. The resulting data on the gas-phase standard molar enthalpies of formation were validated using the quantum chemical method G4. The consistent sets of evaluated thermodynamic data are essential for calculating the energy balances of lignin conversion in the value-added chemicals and materials. Graphic abstract

QUANTUM-CHEMICAL CALCULATION OF THE GRAPHENE OXIDE MOLECULE IN THE FRAMEWORK OF THE NAKAJIMA-MATSUO AND LERFA-KLINOVSKY

Using the classical semi-empirical quantum-chemical method МNDO, for the first time the calculation of graphene oxide molecules was performed within the framework of the Nakajima-Matsuo and Lerf-Klinovsky models. The acidic strength of these models and the Hartree energy are theoretically estimated. It was found that the studied graphene oxides belong to dielectrics and to the class of intermediate Bronsted acids (pKa = 9-14).

Revisiting stacking interactions in tetrathiafulvalene and selected derivatives using tight-binding quantum chemical calculations and local coupled-cluster method

The engineering of supramolecular architectures needs accurate descriptions of the intermolecular interactions in crystal structures. Tetrathiafulvalene (TTF) is an effective building block used in the construction of promising functional materials. The parallel packing of the neutral TTF–TTF system was studied previously using the high-level quantum chemical method, advancing it as a valuable model system. The recently developed tight-binding quantum chemical method GFN2-xTB and local coupled-cluster method DLPNO-CCSD(T) were used to investigate the stacking interactions of TTF and selected derivatives deposited in the Cambridge Structural Database. Using the interaction energy of the TTF–TTF dimer calculated at the CCSD(T)/CBS level as the reference, the accuracies of the two methods are investigated. The energy decomposition analysis within the DLPNO-CCSD(T) framework reveals the importance of dispersion interaction in the TTF-related stacking systems. The dispersion interaction density plot vividly shows the magnitude and distribution of the dispersion interaction, providing a revealing insight into the stacking interactions in crystal structures. The results show that the GFN2-xTB and DLPNO-CCSD(T) methods could achieve accuracy at an affordable computational cost, which would be valuable in understanding the nature of parallel stacking in supramolecular systems.