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New variants of SARS-CoV-2 are being reported worldwide. The World Health Organization has reported Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) as the variants of concern. There are speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19 occurs through the interaction of the spike protein's receptor-binding domain (RBD) with the peptidase domain of the human ACE-2 (hACE-2) receptor. This study aims to get a molecular-level understanding of the mechanism behind the increased infection rate in the alpha variant. We have computationally studied the spike protein interaction in both the wild-type and B.1.1.7 variant with the hACE-2 receptor using molecular dynamics and MM-GBSA based binding free energy calculations. The binding free energy difference shows that the mutant variant of the spike protein has increased binding affinity for the hACE-2 receptor (

Correction for ‘Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7’ by N. Arul Murugan et al., Phys. Chem. Chem. Phys., 2022, 24, 20371–20380, https://doi.org/10.1039/D2CP00469K.

In order to explore the possibilities of simulating metallochromism by modern molecular modeling, we apply a sequential hybrid quantum-classical approach to a prototype metallochromic system-the Al(3+) ion and pyrimidinedione (PY) dye complex. The complex shows several structural features with relevance for the metallochromism: the PY dye exhibits conformers with dynamical transitions between twisted structures, which are inhibited by the addition of the metal ion leading to planarization and a conformational arrest: the Al(3+) ion behaves like a structure-modifier for both intra and intermolecular degrees of freedom and with respect to the intermolecular solvation shell structure. The sequential approach that we have employed uses DFT/MM molecular dynamics for structure modeling and TDDFT/PCM for property modeling. The computed metallochromic shift between PY and the Al(PY)(3+) complex in DMSO solvent is obtained in excellent agreement with experiment. The results infer optimism for future use of such modeling techniques to design metallochromic indicators.

Solvation shell structure of a 7-piperidino-5,9-methanobenzo[8] annulene (PMA) in water has been investigated in ambient conditions using both molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) calculations. From the MD calculations, we find that this molecule exists in three major conformational states out of which two are in twist-boat forms and one in chair form. Due to the limited time scale accessible in CPMD simulations, we have studied all the three conformational states separately using CPMD. The molecular geometry, electronic charge distribution and solvation structure for all three forms are investigated. The stability order of the chair and twist-boat conformations in water solvent has been reversed when compared to the gaseous phase results and in the case of polar aprotic solvents (J. Org. Chem., 1999, 61, 5979). From the radial distribution function, we find that the solvent density around the chair form is significantly lower, which has to be directly related to the smaller solvent accessible area for this conformation and this is in complete agreement with earlier reports. Among the findings are that the solvation shell structure around the nitrogen atom in the chair form of PMA is considerably different from the open conformational forms or the twist-boat forms. The dipole moment for the closed form is found to be significantly larger when compared to the twist-boat forms.