Electron density is not spherical: the many applications of the transferable aspherical atom model

Exploiting the full potential of cryo-EM maps

“…In X-ray crystallography, the concept of computing the structure factors from ab initio derived molecular electron densities was implemented in the HAR [10] and references cited therein). Libraries of atomic fragment electron densities were also created [ 36 , 37 ], including biologically relevant atom types. The atomic electron densities are expressed using multipolar expansion up to hexadecapolar level.…”

Molecular Dynamics Investigations of Thermomechanical Characteristics of Solid and Hollow Spherical Platinum Nanoparticles during Additive Manufacturing

“…LAMMPS with EAM/FS potential (12) can describe the force of interactions (13) between Pt atoms, and the positions and trajectories of each Pt atom of solid and hollow spherical Pt nanoparticles at each time step during AM, where the electron density is obtained from the wave function, and then the atoms that must be calculated for each atomic energy are embedded in the local electron density energy. (14) The fitting method has been proposed by Daw et al (15) The common neighbor analysis (16) can simulate both solid and hollow spherical Pt nanoparticles in AM and visualize each lattice structure at each time step. The gyration radius (Rg) is used to calculate the mean square displacement (MSD) (17) between atoms and the center of mass of both solid and hollow spherical Pt nanoparticles in AM.…”

Influence of N-protonation on electronic properties of acridine derivatives by quantum crystallography

“…Aspherical atom renement considers the non-spherical nature of the electron density distribution around atoms providing more accurate structural parameters, displacement parameters, and hydrogen-bond lengths compared to traditional renement methods. 32,33 Aspherical atom renement can be performed using various quantum crystallographic methods, including Hirshfeld atom renement (HAR). 34,35 HAR uses aspherical atomic scattering factors obtained from the quantummechanical calculation of electron density (usually using DFT methods) to rene X-ray crystal structures 36,37 and is the most advanced method of rening X-ray crystal structures, providing structural parameters for hydrogen atoms including both the H-atom positions and their anisotropic displacement parameters.…”