Geometry of uracil

Table 1. Geometries of uracil U and thiouracil nucleobases. Bond lengths are in A, bond angles in degrees.

F. 17.3 Graphical representation of the geometry of Uracil with the four explicit water molecules of the first solvation shell, embedded in the PCM cavity (see Refs. [164, 165])... 

Figure 5 (a) Pathway from a displacement along the g direction of the conical intersection Si -Sq. Following the gradient of the So surface leads to the So minimum. The energies of the So, Si, and S2 states relative to the minimum of So are plotted as a function of a dihedral angle. Reproduced with permission from Refs. 56. (b) Geometries of uracil at the minima of So, Si and at the conical intersections S2-S1 and Si-So. 

When the monosodium salts of uracil and similar pyrimidines react with diphenyl phosphorochloridate, phosphorylation takes place on oxygen unless other suitable nucleophilic centres are present and free.69 The reaction between the sodium salt of a 1,3-dicarbonyl compound and diethyl phosphorochloridothionate yields the Z-vinylphosphorothionate if the tetrabutylammonium salt is employed, the product has E geometry. This phenomenon has been interpreted in terms of the shape of the... 

Figure 10-2. Singly occupied molecular orbitals of uracil obtained with the ROKS method for vertical excitation (a) and at 5] optimized geometry (b). H atoms are shown in white, C atoms in light grey, O atoms in dark grey, and N atoms in black...

Figure 3. (a) Internal coordinates of the Cq+ -Uracil system, (b) Geometry of the Uracil molecule. 

The geometries of the ground state as well as of the singly and doubly ionized Uracil molecules have been optimized by means of DFT calculations using the B3-LYP functional. The vertical and adiabatic first and second ionization potentials presented in Table 2 compare favourably to previous calculations [25, 26] and to experimental data [27,28],... 

Figure 5.3 Optimized geometries of the pyrimidine nucleobases thymine (a), cytosine (b), and uracil (c). The molecules lie in the xy-piane with the y-axis point upward and the x-axis to the right.

Pi-pi complex between a model for a polar component of a herbicide (uracil) and a model for a salt binding site (guanidinium bicarbonate) is shown in Figure 2. The geometry was computed from initio calculations (36). It should be noted that in the lowest energy geometry shown in Figure 2, the dipole moment of uracil is antiparallel to the dipole moment of the salt. 

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