Computational protocol: Lactones from the Sponge-Derived Fungus Talaromyces rugulosus

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Protocol publication

[…] Geometry optimizations (B3LYP/6-31G(d) in vacuo, B97D/TZVP [,] and CAM-B3LYP/TZVP [] with PCM solvent model for MeCN), and TDDFT calculations were performed with Gaussian 09 using various functionals (B3LYP, BH&HLYP, CAM-B3LYP and PBE0) and the TZVP basis set []. ECD spectra were generated as the sum of Gaussians with 2400 and 3000 cm−1 half-height width (corresponding to c.a. 14 and 17 nm at 240 nm), using dipole-velocity computed rotational strengths []. Mixed torsional/low mode conformational searches were carried out by means of the Macromodel 10.8.011 software (New York, NY, USA) using Merck Molecular Force Field (MMFF) with implicit solvent model for CHCl3 applying a 21 kJ/mol energy window []. Boltzmann distributions were estimated from the B3LYP, B97D and CAM-B3LYP energies. In the case of the B3LYP/6-31G(d) in vacuo level, ZPVE corrections were applied. The MOLEKEL software package (New York, NY, USA) was used for visualization of the results []. […]

Pipeline specifications

Software tools MacroModel, Molekel
Application Drug design
Organisms Oryza sativa, Mus musculus
Diseases Lymphoma, Drug-Related Side Effects and Adverse Reactions
Chemicals Lactones