Computational prediction for designing novel ketonic derivatives as potential inhibitors for breast cancer: A trade-off between drug likeness and inhibition potency

Unlike simple molecular screening, a combined hybrid computational methodology has been applied which includes quantum chemical methods, molecular docking, and molecular dynamics simulations to design some novel ketonic derivatives. The current study contains the derivatives of an experimental ligand which are designed as a trade-off between drug likeness and inhibition strength. We investigate the interaction of various newly designed ketonic compounds with the breast cancer receptor known as the Estrogen Receptor Alpha (ERα). The molecular structures of all newly designed ligands were studied quantum chemically in terms of their fully optimized structures, 3-D molecular orbital distributions, global chemical descriptors, molecular electrostatic potentials and energies of frontier molecular orbitals (FMOs). All ligands under study show good binding affinities with the ERα protein. The ligands CMR2 and CMR4 exhibit improved molecular docking interactions. The intermolecular interactions indicate that CMR4 demonstrates better hydrophobic and hydrogen bonding interactions with protein (ERα). Furthermore, molecular dynamics simulations were conducted on ligands and reference drugs interacting with the ERα protein over a time span of 120 nanoseconds. The molecular dynamics results are interpreted in terms of ligand-protein stability and flexible behaviour based on their respective values of RMSD, RMSF, H-bonds, the radius of gyration, and SASA graphs. To analyse ligand-protein interactions throughout the entire 120 ns trajectory, a more advanced MM/PBSA method is utilized, where six selected ligands (CMR1, CMR2, CMR3, CMR4, CMR5 and CMR9) illustrate promising results for inhibition of the ERα receptor as assessed through MM/BBSA analysis. The CMR9 has the highest MM/BBSA binding free energy (-14.46 kcal/mol). The ADMET analysis reveals that CMR4 has maximum intestinal absorption (6.68) and clearance rate (0.1). All the compounds are non-toxic and safe to use. These findings indicate the potential of involving different computational techniques to design the ligand structures and to study the ligand-protein interactions for better understanding and achieving more potent synthetic inhibitors for breast cancer.

Computational insight into the crystal structures of cubane and azacubanes

CONTEXT

Using quantum chemistry and atom-atom potential methods, the molecular and crystal structures of cubane 1 and all types of unsubstituted azacubanes 2-22 were calculated. Alternative possible polymorphs of cubane 1 have been proposed. The thermochemical properties of azacubanes in the gas and solid phases were assessed. Thermodynamic aspects of stability are considered, and a significant decrease in stability is revealed upon transition from cubane 1 to octaazacubane 22. It has been shown that the density and energetic properties of azacubanes depend nonlinearly on the number of nitrogen atoms in the structure and the density of octaazacubane 22 at room temperature is 1.546 g cm-3, which is significantly lower than the previously given estimate.

METHODS

In this work, DFT calculations were conducted through the software Gaussian 09 using B3LYP functional with basis set aug-cc-PVDZ and the Grimme dispersion correction D2. For crystal structure optimization, the atom-atom potential methods with PMC (packing of molecules in crystal) program were used. Charges for molecular electrostatic potential were fitted by FitMEP, and enthalpies of formation in gas phase were assessed by G3B3.

Many-body analysis and spectroscopic characterization of diazene oligomers: A theoretical study

The present study reports the many-body analysis and spectroscopic characterization of linear and cyclic diazene oligomers in gas and water solvent states. The oligomers of diazene from monomer to pentamer have been considered for the study. The spectroscopic studies such as geometrical parameters, infrared spectra, electronic absorption spectra, and natural transition orbitals (NTOs) were reported. Many-body analysis techniques have been implemented to study the interactions among the diazene oligomers. These calculations have been performed using exchange and correlation functional (B3LYP) and 6-311++G (d,p) basis set. The geometrical parameters and infrared modes of monomer diazene in the gas state are well-matched with the available experimental determinations at this level of theory. A significant change in vibrational modes of linear and cyclic diazene oligomers has been observed in the gas phase-to-water solvent state. The time-dependent density functional theory (TD-DFT) has been used to calculate the electronic absorption spectra of diazene oligomers. The Wavelength of electronic transitions, oscillator strength, and HOMO to LUMO gap has been reported. Many-body analysis shows that two-, three-, four-, and five-body energies have a remarkable contribution to the binding energy in addition to relaxation energies. All these calculations have been performed using Gaussian 16 program package.

Effect of new DFT methods on spectroscopy and NLO analysis of 2-Bromo-5-nitrothiozole and nitrosodimethylamine

The present study reports the effect of new DFT methods introduced in Gaussian 16 viz B2PLYP, B2PLYPD, DSDPBEP86, and MPW2LPLYP on spectroscopy and nonlinear optical (NLO) properties. The 2-Bromo-5-nitrothiozole and nitrosodimethylamine are considered for the study. In addition to new methods, old DFT, MP2, and HF methods are also considered. The spectroscopic study of geometrical parameters, vibrational, electronic absorption spectra, and HOMO-LUMO gap with their molecular orbitals have been reported. The geometrical parameters such as optimized energy, dipole moment, bond length, and angles have been reported. The diffuse and polarized basis set 6-311 +  + G(d,p) has been used for the study. The first- and second-order hyperpolarizabilities have also been reported for both molecules at all methods. This study shows that these two molecules are responsive to nonlinear optical (NLO), which reflects its enhanced applicability in the development of photonic devices. The finite field approach has been applied for calculating first (β) and second hyperpolarizabilities (ϒ) respectively. The HOMO-LUMO energy gap of nitrosodimethylamine is found to be greater than that of 2-Bromo-5-nitrothiozole. Gaussian16 program package has been used for all these calculations.

Spectroscopy and second hyperpolarizability of odd spin states of acetonitrile: Theoretical study

The present study reports the spectroscopic characterization and second hyperpolarizability of odd spin states of acetonitrile in gas phase and water solvent. The odd spin states of acetonitrile are singlet, triplet and quintet spin state of acetonitrile have been considered for the study. The spectroscopic characterization viz. energy, geometrical parameters, infrared and electronic absorption spectra, molecular orbitals (MOs) their energies and natural transitions orbitals (NTOs) in gas phase and water solvent state reported at B3LYP/aug-cc-pVDZ level of theory. The second hyperpolarizability values are obtained using various methods and basis sets for comparison. It has been observed that the second hyperpolarizability values for the odd spin states of acetonitrile are more positive than the first hyperpolarizability. It is clearly seen that the effect of spin on spectroscopic parameters except on energy. The singlet gas phase acetonitrile calculations are well matching with the available experimental determinations. The TDDFT approach has been used to study electronic absorption spectra of all spin states of acetonitrile in gas phase and in water solvent. The IEFPCM model implemented in studying acetonitrile in water solvent at B3LYP/aug-cc-pVDZ level of theory. It is observed that HOMO to LUMO gap is larger for singlet than the triplet and quintet spin state and it decrease with an increase in strength of an applied field. All these calculations performed using Gaussian 16 program package.

Theoretical Study of Possible Reaction Mechanisms for the Formation of Carbodiimide in the Interstellar Medium (ISM) and Polarizabilities of Carbodiimide

The Structure of carbodiimide has been studied by using quantum chemical methods. Carbodiimide (HNCNH) has been detected towards Sagittarius B2 (N) in interstellar medium (ISM). Two reaction mechanisms have been proposed to study the formation of interstellar Carbodiimide. The first reaction mechanism is based on molecule-radical and the second one is a radical-radical mechanism, through previously detected interstellar molecules or radicals. Quantum chemical calculations have been performed by using density functional theory (DFT) and Moller-Plesset second order perturbation (MP2) theory, in gas phase as well as in polarizable continuum model (PCM). The proposed reaction paths are exothermic and barrierless which indicates the possibility of carbodiimide formation in ISM. Several basis sets have been used to verify the validity and accuracy of the results. The isotropic and anisotropic polarizabilities of carbodiimide have been calculated from relevant tensor components for both reaction mechanisms with the help of data obtained by DFT/B3LYP and MP2 methods using aug-cc-pVTZ basis sets in gaseous phase as well as in PCM.