In drug optimisation calculations, the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accur...

The study proposes an improved feature extraction method that is called Wavelet Cepstral Coefficients (WCC). In traditional cepstral analysis, the cepstrums are calculated with the use of the Discrete Fourier Transform (DFT). Owing to the fact that the DFT calculation assumes signal stationary between frames which in practice is not quite true, the WCC replaces the DFT block in the traditional ...

Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size...

In drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accur...

The possible conformations in the most stable structure of cyclophosphamide were investigated at the DFT-B3LYP and MP2/6-311G** levels of calculation. The axial structure is calculated to be lower in energy than the equatorial form of cyclophosphamide by 5 (MP2) to 6 (DFT) kcal mol−1 because of a very weak anomeric effect and weak conjugation. Further it is the same structure as the one found i...

The GW-technology corrects the Kohn-Sham (KS) single particle energies and single particle states for artifacts of the exchange-correlation (XC) functional of the underlying density functional theory (DFT) calculation. We present the formalism and implementation of GW adapted for standard quantum chemistry packages. Our implementation is tested using a typical set of molecules. We find that alr...

We present the TRIQS/DFTTools package, an application based on the TRIQS library that connects this toolbox to realistic materials calculations based on density functional theory (DFT). In particular, TRIQS/DFTTools together with TRIQS allows an efficient implementation of DFT plus dynamical mean-field theory (DMFT) calculations. It supplies tools and methods to construct Wannier functions and ...

A first-principles embedding theory that combines the salient features of density functional theory ~DFT! and traditional quantum chemical methods is presented. The method involves constructing a DFT-based embedding potential and then using it as a one-electron operator within a very accurate ab initio calculation. We demonstrate how DFT calculations can be systematically improved via this proc...

The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shift and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock (HF) level. The addition of d polarization function...