Testing a Variety of Electronic-Structure-Based Methods for the Relative Energies of 5-Formyluracil Crystals

Abstract

The lattice energies of the experimental and several hypothetical crystal structures of the RNA base uracil derivative 5-formyluracil are calculated with a range of methods, based either on the electronic structure of the molecule or the lattice. The explicit modeling of the polarization within the crystal in the model intermolecular potential and the inclusion of an empirical dispersion correction to the periodic density functional energy (DFT-D2) were the only methods able to calculate the energy balance between different conformations, hydrogen bonding, and π-π stacking possibilities sufficiently accurately to give the observed structure as the most stable. Even these two methods underestimated the density of the room temperature structure, showing the need for improvement in the modeling of organic crystal structures.

Four Polymorphs of Methyl Paraben: Structural Relationships and Relative Energy Differences

“…18 Periodic electronic structure calculations were carried out with the CASTEP plane wave code 19 using the Perdew–Burke–Ernzerhof (PBE) generalized gradient approximation (GGA) exchange-correlation density functional 20 and ultrasoft pseudopotentials 21 with the addition of either the Grimme (G06) 22 or Tkatchenko and Scheffler (TS) 23 semiempirical dispersion corrections. The results reported here were obtained using a plane wave cutoff energy of 780 eV and a Monkhorst-Pack 24 Brillouin zone sampling grid of spacing 2π × 0.07 Å –1 ; the required force tolerance for a successful geometry optimization in each run was 0.05 eV Å –1 .…”

Are the Crystal Structures of Enantiopure and Racemic Mandelic Acids Determined by Kinetics or Thermodynamics?

“…47 Full details and the crystal energy landscape at this stage are in SI Figure 8. To approximate the effect of the crystalline environment on the charge distribution and conformational energies 48 we estimated the effect of polarization through a polarizable continuum model (PCM) 49 using the MP2 wavefunction with a dielectric constant of ε=3. This is the crystal energy landscape in Figure 3.…”

Site Selectivity of Halogen Oxygen Bonding in 5- and 6-Haloderivatives of Uracil

“…In a continuation of a long-term interest in crystal engineering of DNA/RNA bases [12][13][14][15][16][17][18][19][20][21] and in systems exhibiting halogen bonding via alternative donors [8,11], this work focuses on the XBs exhibited by pyrimidine nucleobases carrying at the C6 position a halogen atom and at the C2 and the C4 positions two nucleophilic oxygen atoms. This investigation was then extended to the two new polymorphs obtained for 5-chloro and 5-bromouracil and their (1:1) cocrystal (Scheme 1).…”