Solvation Models
• Many reactions take place in solution
• Short-range effects
• Typically concentrated in the first solvation sphere
• Examples: H-bonds, preferential orientation near an ion
• Long-range effects
• Polarization (charge screening)
Solvent Effects
solvent
• Explicit Solvent vs. Implicit Solvent
Explicit: placing real molecules
Implicit: treating the solvent as a continuous medium (Reaction Field
Method)
Some are hybrids of the above two:
– Treat first solvation sphere explicitly while treating
surrounding solvent by a continuum model
– These usually treat inner solvation shell quantum
mechanically, outer solvation shell classically
Solvation Methods in Molecular Simulations
explicit
solvent
implicit
solvent
Two Kinds of Solvation Models
Models Explicit solvent models Continuum solvation
models
Features All solvent molecules are
explicitly represented.
Respresent solvent as a
continuous medium.
Advantages Detail information is
provided. Generally more
accurate.
Simple, inexpensive to
calculate
Disadvantages Expensive for
computation
Ignore specific short-range
effects. Less accurate.
Continuum (Reaction Field)
Models
• Consider solvent as a uniform polarizable medium of fixed
dielectric constant  having a solute molecule M placed in a
suitably shaped cavity.
• Solute induces polarization at the interface of cavity.
• This polarization acts back on the solute changing its
wavefunction.
• Various solvation models use different schemes for
evaluation of solvation effects.
• Problems arise when electrostatics do not dominate solventsolute
interactions
Models Differ in 5 Aspects
1. Size and shape of the solute cavity
2. Method of calculating the cavity creation and
the dispersion contributions
3. How the charge distribution of solute M is
represented
4. Whether the solute M is described classically or
quantum mechanically
5. How the dielectric medium is described.
(these 5 aspects will be considered in turn on the following slides)
Solute Cavity Size and Shape
Spherical Ellipsoidal van de Waals
(Born) (Onsager)
(Kirkwood)
N C
O
H
H
CH3
N C
O
H
H
CH3
N C
O
H
H
C
H
H
H
r
r
The Cavity
•Simple models
Sphere Ellipsoid
•Molecular
shaped models
Van der Waals surface
Determined by QM wave function
and/or electron density
Solvent accessible surface
Not
accessible
to solvent
Visualizing cavity
1. Geomview software (in the modules).
2. Works only with Gaussian 03
3. SCRF=(read) in the route section of the job
4.“geomview” in the SCRF specification
5. Visualize the “tesserae.off” file
The walls of cavity determine the interaction interface (Solvent
Excluded Surface, SES)
Size of the solvent molecule determines the Solvent Accessible
Surface (SAS
Conductor like screening model
Why Implicit Solvent?
Method Explicit Solvent
(all-atom description)
Implicit Solvent
(Continuum description)
Pros
•Full details on the molecular
structures
•Realistic physical picture of the
system
•No explicit solvent atoms
•Treatment of solute at highest
level possible (QM)
Cons
•Many atoms--> expensive
•Long runs required to equilibrate
solvent to solute
•Often solvent and solute are not
polarizable.
•Large fluctuations due to use of
small system size
•Need to define an artificial
boundary between the solute and
solvent
•No “good” model for treating
short range effects (dispersion
and cavity)
Explicit QM Water Models
• Sometimes as few as 3 explicit water molecules
can be used to model a reaction adequately:
CHOO
H
H
+ C Cl HCl+
CO
H
O
H
H
C Cl
O H
H
O
H
H
O
H
H
O
H
H
H
Cl
Could use HF, DFT, MP2, CISD(T) or other theory.
Explicit Hybrid Solvation Model
Red = highest
level of theory
(MP2, CISDT)
Blue = intermed.
level of theory
(HF, AM1, PM3)
Black = lowest
level of theory
(MM2, MMFF),
or Continuum
O
H
H
O H
H
O
H
H
ClCH
O
H
H
O
H
H O
H
H
O
H
HO
H
H
O
H
H
OH
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
H
O
H
Practical task
1. Model the Cl − + CH 3 Br → CH 3 Cl + Br −
2. Find the energy barrier for the reaction
3. Select any solvent from Gaussian library (be not concerned
about solubility of species or chemical relevance)
4. Assume Sn1 and Sn2 reaction pathways
5. Use “SCRF=(solvent=XY)” in the route section of the
calculation
Procedure
1. Use B3LYP 6-31+g(d,p) method
2. Usage of difuse functions when dealing with anions is
crucial!
3. Use ultrafine integration grid
4. Use Frequency calculations to be sure where on PES you
are
5. For the scan use the distance between C and Cl as RC
6. Negative value of step defines two atoms approaching
Turbomole
1. Prepare job using define module (see presentation 6 for
help)
2. Setup COSMO using cosmoprep module
3. Set epsilon to 78.4 and rsolv to 1.93
4. Leave all other values at their default
5. Define radii of atoms using “r all o” for optimized values
6. Optimize all geometries