Gas-phase geometry optimization

Moreover, as seen from Table 2, gas-phase geometry optimization for 3 provided a C2 symmetry, whereas bond lengths and/or bond angles that are equivalent in C2 symmetry slightly differ in the experimental crystal structure that shows no symmetry (Cj). The same applies to the PCM calculations. These small differences are most probably due to the influence of crystal packing effects and impact of the surrounding cations on molecular structure of 3. 

The question of methanol protonation was revisited by Shah et al. (237, 238), who used first-principles calculations to study the adsorption of methanol in chabazite and sodalite. The computational demands of this technique are such that only the most symmetrical zeolite lattices are accessible at present, but this limitation is sure to change in the future. Pseudopotentials were used to model the core electrons, verified by reproduction of the lattice parameter of a-quartz and the gas-phase geometry of methanol. In chabazite, methanol was found to be adsorbed in the 8-ring channel of the structure. The optimized structure corresponds to the ion-paired complex, previously designated as a saddle point on the basis of cluster calculations. No stable minimum was found corresponding to the neutral complex. Shah et al. (237) concluded that any barrier to protonation is more than compensated for by the electrostatic potential within the 8-ring. 

All MST-PCM calculations were performed at the HF/6-31 G(d) level. As usual in MST calculations the gas phase geometry of the molecules was fully optimized and subsequently used for calculations in solution. Calculations were performed using a locally modified version of Monstergauss [27],... 

In the second family of approaches, explicit solvent molecules are placed around the gas phase stationary point structures. In some cases, the gas phase geometries are held constant and only the geometries and/or positions of the surrounding solvent molecules are optimized, and in other cases, the structure of the whole system (often called a supermolecule 32) is optimized. The supermolecule approach generally only involves explicit solvent molecules from the first (and occasionally second) solvation shell of the solute. 

Figure 1 Optimized gas-phase geometries [B3LYP/6-311 - -G(d,p)] of the parent compiexes Fe(CO)3- " -siioie and [Fe(CO)3-Tj -eiioivi]". ...

Since a vast majority of NMR experiments are performed in solution, incorporation of solvent within the computation is a reasonable expectation. One might anticipate inclusion of solvent using a continuum method as described in Section 1.4.2. In a consistent manner, the molecular geometry should be optimized with the solvent field, and the chemical shifts computed with this geometry and with the solvent field. As will be demonstrated below, optimization in the solvent field turns out to oftentimes be unnecessary and the gas-phase geometry will suffice. 

Solvation energies were computed at the double-c level using a self-consistent reaction field approach based on numerical solutions of the Poisson-Boltzmann equation 58-60). These were computed at the optimized gas-phase geometry utilizing an appropriate dielectric constant for comparison to the experimental conditions (e = 37.5 for acetonitrile e = 20.7 for acetone). The standard set of optimized radii in Jaguar were employed Mo (1.526 A), W (1.534 A), H (1.150 A), C (1.900 A), O (1.600 A). Vibrational analyses using analytical frequencies were computed at the double-q level, ensuring all stationary points to be minima. 

Ground-state geometries of 7AI(H20) =i 5 complexes in the gas phase were optimized with the second-order M0l-ler-Plesset Perturbation Theory (MP2) with the resolution-of-the-identity (RI) approximation for the electron repulsion integrals [48, 49]. The split valence polarized (SVP)... 

However, describing larger molecules with more degrees of freedom employing these symmetry functions is very difficult, and the complexity of the equations increases rapidly. This is the reason why for a NN PES for ethanol at Au(lll), which is the only NN PES so far constructed for a molecule containing more than two atoms at a surface, the internal molecular structure has been frozen to the optimized gas-phase geometry. ... 

Solvent effects (i.e. THF, s = 7.4257) were introduced by a discrete-continuum model two THF molecules were explicitly included in the calculations as potential ligands (see above), and the effect of the bulk solvent was considered with a continuum method, the PCM approach [39], by means of single point calculations at all optimized gas phase geometries. In this method, the radii of the spheres employed to create the cavity for the solute were defined with the UFF model,. which is the default in Gaussian09. 

Solvent effects (i.e. dichloromethane, s = 8.930) were introduced through single point calculations at optimized gas-phase geometries for all the minima and transition states by means of a continuum method, the PCM approach [62] implemented in GaussianOS. Moreover, the default cavity model (i.e. UA 0) was modified by adding... 

Solvent elfects (i.e. toluene, e = 2.3741) have been introduced by means of a continuum model, the SMD [60] solvation model implemented in Gaussian09, performing single point calculations at all the optimized gas phase geometries. 

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