• Issue

    Journal of Computational Chemistry: Volume 42, Issue 28

    1991-2048
    October 30, 2021

ISSUE INFORMATION

Free Access

Issue Information

  • Pages: 1991-1995
  • First Published: 08 September 2021

FULL PAPERS

Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes

  • Pages: 1996-2003
  • First Published: 16 August 2021
Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes

Temperature accelerated sliced sampling (TASS) is a powerful method for the exploration and computation of high-dimensional free energy landscapes (HDFEL). Here we introduce a new method for the reconstruction of HDFEL for TASS. With this method, weighted histogram analysis method can be completely avoided and TASS can be performed with less number of windows without compromising on the accuracy. The proposed method significantly improves the efficiency of the TASS approach.

MCML: Combining physical constraints with experimental data for a multi-purpose meta-generalized gradient approximation

  • Pages: 2004-2013
  • First Published: 18 August 2021
MCML: Combining physical constraints with experimental data for a multi-purpose meta-generalized gradient approximation

MCML is an empirical exchange-correlation density functional which obeys physical constraints and was trained against experimental data. This combined physical modeling and data scientific approach leads to simultaneous improvements of predictions for crystal structural properties and bulk, surface, and gas phase reaction energetics. The spread of the shown ensemble of perturbations to the MCML exchange enhancement accounts for potential uncertainties in the empirical functional form, enabling the estimation of errors of computed materials predictions.

Hydration of selenolate moiety: Ab initio investigation of properties of O–H⋯Se(–) hydrogen bonds in CH3Se(–)⋯(H2O)n clusters

  • Pages: 2014-2023
  • First Published: 20 August 2021
Hydration of selenolate moiety: Ab initio investigation of properties of O–H⋯Se(–) hydrogen bonds in CH3Se(–)⋯(H2O)n clusters

Weak O–H···Se(–) hydrogen bonds perturb the electronic shell of selenolate R–Se(–) fragment in of active center of selenium-containing glutathione peroxidase (GPx) enzymes significantly. It was shown that taking into account of the influence of a neighboring to the selenium atom functional groups of a protein or a solvent molecules is extremely important for agreement of computational data with experimental ones.