This computational study focuses on the mechanism of the consecutive decomposition of FOX‐7 and compares the results with recent experimental study [J. Phys. Chem. A 2023, 127, 7707] under 202 nm photolysis (592 kJ/mol). The mechanisms of forming these compounds, including cyanamide variants (HNCNH and NH2CN), hydroxylamine (NH2OH), nitrosamine (NH2NO), diaminoacetylene (H2NCCNH2), cyanogen (NCCN)

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The biomolecules interact with their partners in an aqueous media; thus, their solvation energy is an important thermodynamics quantity. In previous works (J. Chem. Theory Comput. 14(2): 1020–1032), we demonstrated that the Poisson–Boltzmann (PB) approach reproduces solvation energy calculated via thermodynamic integration (TI) protocol if the structures of proteins are kept rigid. However, proteins

Prediction of protein fitness from computational modeling is an area of active research in rational protein design. Here, we investigated whether protein fluctuations computed from molecular dynamics simulations can be used to predict the expression levels of SARS‐CoV‐2 receptor binding domain (RBD) mutants determined in the deep mutational scanning experiment of Starr et al. [Science (New York, N

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We demonstrate that combining a shifted clustering algorithm with a fast‐marching‐based algorithm can generate accurate approximations of the minimum energy path (MEP) given a free energy landscape (FEL). Using this approximation as the initial guess for the MEP, followed by further refinement with the string method (referred to as the fast marching tree (FMT)‐string combined approach), significantly

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