Crystal field effects on the topological properties of the electron density in molecular crystals: The case of urea

Abstract

The Quantum Theory of Atoms in Molecules, due to Bader, is applied to periodic systems. Results for molecular and crystalline urea are presented. Changes in both bond critical points and atomic properties due to changes of chemical environment are described. A rationale for the different lengths of the in-plane and out-of-plane hydrogen bonds and for the lengthening of the CO bond in bulk urea is provided in terms of the properties of the Laplacian of the oxygen atom electron density distribution. An evaluation of molecular and atomic volume changes indicates that the decrease of molecular volume upon change of phase from gas to solid originates primarily from a contraction of the atomic basins directly involved in hydrogen bonds. Other atoms show a small expansion. The considerable decrease of oxygen and hydrogen atomic volumes is related to the mutual penetration of their van der Waals envelopes following hydrogen bond formation. The results confirm that urea is more polar in the solid phase.

Electron density analysis of large (molecular and periodic) systems: A parallel implementation

“…The present implementation takes advantage of the several significant improvements recently made in Crystal in terms of increased parallel and massive-parallel scalability, reduced use of memory per node and increased exploitation of symmetry at all steps of the calculation, which recently allowed the program to be run in parallel mode over 32'000 CPUs and to study systems containing up to about 14'000 atoms and 200'000 basis functions. [17][18][19] Specific features of the current implementation are: i) possibility of studying systems of any dimensionality within the same formal and numerical framework (from 0D molecules, to 1D polymers, nanotubes, helices and nano-rods, to 2D slabs and 3D crystals); ii) efficient use of several DFT functionals, belonging to four rungs of the well-known "Jacob's ladder" 20 (local density approximation, LDA, generalized gradient approximation, GGA, global or range-separated hybrids and meta-GGA); iii) full exploitation of any residual symmetry; iv) parallelization of all algorithms related to the evaluation of ρ(r), its gradient and Laplacian, of the X-ray structure factors, of Bader's topological analysis (as generalized to periodic systems by C. Gatti's Topond package, 21,22 which has recently been merged into the Crystal program), of directional Compton profiles, of the electrostatic potential and its derivatives, of the electronic band structure and density-of-states. The Crystal program adopts an atom-centered basis set of Gaussian-type functions (GTF); all density matrix-based algorithms have been parallelized on the number of orbital shell-shell pairs, which guarantees a good load balance among processors and thus a satisfactory speedup for most systems.…”

Spin density in YTiO3 : I. Joint refinement of polarized neutron diffraction and magnetic x-ray diffraction data leading to insights into orbital ordering

“…One unpaired electron per Ti atom was attributed as initial guess. The theoretical spin populations obtained by Bader analysis performed by the TOPOND package [34] are presented in Table III. The theoretical 3d-orbital populations reported in Table III were estimated by applying the previously defined orbital model refinement to the calculated magnetic structure factors.The calculated spin density in the Figure 5 for comparison with the results of the model refinement on experimental data ( figure 4(a)).…”

Evidence of Polaron Excitations in Low Temperature Raman Spectra of Oxalic Acid Dihydrate

“…Extra large grid was used. Basis sets for carbon, hydrogen and oxygen of the 6-31G** type were transferred from the study of urea by Gatti et al 28 . This basis set has been found adequate for calculations on molecular crystals by Barone 29 .…”