Real-World Predictions from Ab Initio Molecular Dynamics Simulations - Multiscale Molecular Methods in Applied Chemistry - page 141

was the most stable, in aqueous solution the zwitterionic state was more stable as
has been observed for alanine [ 164 ].
Salts, ions, and ionic liquids in water are widely studied in AIMD. Several
anions [ 165 - 172 ], cations [ 153 , 165 , 173 - 182 ], and ion pairs [ 164 , 183 , 184 ], as
well as ionic liquids ion pairs [ 185 ] in water were studied using AIMD. In all cases
structural as well as dynamical properties of the ion's hydration shell were exam-
ined. In some cases the influence of the solvated ions on the water molecules were
studied within the Wannier approach. In general, little effect of the halogen ions on
the dipole moments of the water molecules in the first hydration shell was observed,
while further water molecules remain unaffected. In contrast to this, it was observed
that cations increase the dipole moments of the first hydration shell water by
approximately 0.2-0.5 D. The second hydration shell and the bulk phase water
molecules were mostly unaffected with regard to the dipole moment by the cations
as well [ 91 ].

4.3 Chemical Reactions

4.3.1 Metal-Free Organic Reactions

In the following, AIMD studies of the S N 2 reaction shall be briefly reviewed. Other
metal-free organic reactions like the Diels-Alder and the Wittig reaction have been
discussed elsewhere [ 91 ].
Between 1999 and 2004, several S N 2 reactions of the type

X ! Y

þ þ ð ¼

CH 3 ;

; ...Þ

RY RX R CH 2 Cl

were investigated from AIMD simulations in vacuum as well as in solution
[ 186 - 192 ]. Raugei et al. found that the dipole moment changed drastically along
the applied reaction coordinate in a gas phase S N 2 reaction investigation [ 186 ]. In a
subsequent study, Raugei et al. added one and two water molecules to the reactants,
and they observed important hydrogen bonds between the substrate as well as the
ion X and the water molecules [ 187 ].
The complete substitution reaction in water was calculated by Pagliai et al. in
2003 [ 189 ]. The authors investigated hydrogen bonds from Wannier functions and
the electron localization function (ELF) during the reaction. They found the charge
at the transition states to be delocalized and, as a result, weakened and shorter lived
hydrogens bonds. Similar results were obtained in other investigations [ 188 , 190 ].
In 2003 and 2004, Ammal et al. [ 191 ] and Yang et al. [ 192 ] showed how
temperature and dynamical effects can alter the chemical reactions even more
than classical concepts in organic chemistry predict.