Calculation of absolute molecular entropies and heat capacities made simple

Abstract

We propose a fully-automated composite scheme for the accurate and numerically stable calculation of molecular entropies by efficiently combining density-functional theory (DFT), semi-empirical methods (SQM), and force-field (FF) approximations. The...

A Novel Azaphilone Muyophilone A From the Endophytic Fungus Muyocopron laterale 0307-2

“…Conformational searches for compound 3 were first performed using the MMFF94S force field ( Halgren, 1999 ) and the resulted conformers within 0–10 kcal/mol ( Supplementary Table S1 ) were optimized through density functional theory (DFT). The benchmark performed suggests the dispersion-corrected functional B3LYP-D3BJ owns a high accuracy, and the method is proposed for biochemically relevant systems ( Pracht and Grimme, 2021 ; Katsyuba et al, 2019 ). Those conformers within 0–10 kcal/mol were optimized through the B3LYP-D3BJ/6-31G(d) level, and the optimized structures with relative energies ranging from 0 to 4 kcal/mol were further re-optimized at the B3LYP-D3BJ/6-311G (2d,p) level ( Rassolov et al, 1998 ).…”

Effects of Temperature on Enantiomerization Energy and Distribution of Isomers in the Chiral Cu13 Cluster

“…[ 43 , 85 , 86 ] or any standard text relating to thermodynamics [ 87 , 88 ]. The total partition function Q is the product of the q trasn , q rot , q vib , and q elec [ 86 , 89 ] computed under the rigid rotor, harmonic oscillator, Born–Oppenheimer, ideal gas, and particle-in-a-box approximations [ 43 , 47 ]. The thermal populations P(T) at absolute temperature T or the so-called probability of a particular isomer is computed with Equation (1): where , is the Boltzmann constant, T is the temperature, and ∆G k is the Gibbs free energy of the kth isomer.…”

Unravelling the structures of sodiated β-cyclodextrin and its fragments

“…Additional, targeted manual adjustment and supplementation of the structural pool analysed were performed to reduce the chance that chemically relevant species had been neglected. Subsequent simulations utilizing the CREST package, [58][59][60] which systemically places a sodium ion at each lone pair of the molecule, with subsequent molecular dynamics using a semiempirical engine followed by B3LYP/6-31G(d) and B3LYP/6-31+G(d,p) calculations broadened the pool of low (and high) energy candidate structures but failed to generate new global minima. All minima were tested by vibrational analysis (all real frequencies).…”