INTRODUCTION TO SOLVATION MODELS FOR THEORETICAL CHEMISTRY · SOLVATION MODELS EXPLICIT MODELS...
Transcript of INTRODUCTION TO SOLVATION MODELS FOR THEORETICAL CHEMISTRY · SOLVATION MODELS EXPLICIT MODELS...
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INTRODUCTION TO SOLVATION
MODELS FOR THEORETICAL
CHEMISTRY
WALDEMAR KULIGe-mail: [email protected]
SPRING SCHOOL IN COMPUTATIONAL CHEMISTRY 2016
HELSINKI, FINLAND
MARCH 11th 2016
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Solvation is an interaction of a solute with the
solvent, which leads to stabilization of the
solute species in the solution.
IUPAC, Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”) (1997)
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Solvation is an interaction of a solute with the
solvent, which leads to stabilization of the
solute species in the solution.
IUPAC, Compendium of Chemical Terminology, 2nd ed. (the “Gold Book”) (1997)
Solvation – the process of surrounding solute
particles (ions) by solvent
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Solvent is a substance that dissolves a solute,
resulting in solution
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Solvent is a substance that dissolves a solute,
resulting in solution
Usually a liquid, but can also be a solid (e.g.
alloys) or a gas (e.g. air)
source: www.carcolors.co.nzsource: cikguwong.blogspot.com
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Solvent is a substance that dissolves a solute,
resulting in solution
SOLVENTS
POLAR
ε > 15
NON-POLAR
ε < 15
ε – dielectric constant
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Solvent is a substance that dissolves a solute,
resulting in solution
SOLVENTS
POLARWater
Acetone
Methanol
…
NON-POLARToluene
Cyclohexane
Chloroform
…
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Solvent is a substance that dissolves a solute,
resulting in solution
SOLVENTS
POLAR NON-POLAR
PROTIC APROTIC
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Solvent is a substance that dissolves a solute,
resulting in solution
SOLVENTS
POLAR NON-POLAR
PROTIC APROTIC
Protic solvent is a solvent that
contains labile proton (usually has
a hydroxyl, carboxyl or amine
group).
Aprotic solvents cannot donate
protons.
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Solvent is a substance that dissolves a solute,
resulting in solution
SOLVENTS
POLAR NON-POLAR
PROTICWater
Formic acid
…
APROTICAcetone
Tetrahydrofuran
…
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SOLVATION MODELS
EXPLICIT MODELS
consider molecular details
of each solvent molecule
IMPLICIT MODELS
treat solvent as a continuous
medium
source: www.k-state.edu
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SOLVATION MODELS
EXPLICIT MODELS
consider molecular details
of each solvent molecule
IMPLICIT MODELS
treat solvent as a continuous
medium
HYBRID MODELS
Treat first (and second)
solvation sphere explicitly
while the rest of the solvent is
treated in implicit way
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SOLVATION MODELS
EXPLICIT MODELS
consider molecular details
of each solvent molecule
IMPLICIT MODELS
treat solvent as a continuous
medium
HYBRID MODELS
Each model can be further subdivided based on
the used level of theory:
QM (quantum mechanical) or MM (classical)
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EXPLICIT MODELS
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EXPLICIT MODELS
� Include individual solvent molecules
� Calculate free energy of solvation by simulating
solute-solvent interactions
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EXPLICIT MODELS
� Include individual solvent molecules
� Calculate free energy of solvation by simulating
solute-solvent interactions
QM
by solving the Schrödinger equation
HF
DFT
MP2
CI
CC
…
MM
by defining an empirical interaction
potential (force field)
3-site models (SPC, TIP3P)
4-site models (TIP4P, BF)
5-site models (BNS, ST2, TIP5P)
…
solute-solvent interactions
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EXPLICIT MODELS (MM)
SPC TIP3P
r(OH), Å 1.0 0.9572
HOH, deg 109.47 104.52
A × 10−3, kcal Å12/mol
629.4 582.0
B, kcal Å6/mol 625.5 595.0
q(O) −0.82 −0.834
q(H) +0.41 +0.417
O
H H
q(O)
q(H)
parameters of the model
source: http://www1.lsbu.ac.uk/water/water_models.htmlgreat webpage about
water models!
r(OH)
HOH
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EXPLICIT MODELS – MM
about 46! distinct water
models
B.Guillot, J. Mol. Liq. 101 (2002) 219-260
Model Type σ Å 6 ε kJ mol-1 6 l1
Å l2
Å q1
(e) q2
(e) θ° φ°
SSD [511] -8 3.016 15.319 - - - - 109.47 109.4
SPC [94] a 3.166 0.650 1.0000 - +0.410 -0.8200 109.47 -
SPC/E [3] a 3.166 0.650 1.0000 - +0.4238 -0.8476 109.47 -
SPC/HW (D2O) [220] a 3.166 0.650 1.0000 - +0.4350 -0.8700 109.47 -
SPC/Fw 2 [994] a 3.166 0.650 1.0120 - +0.410 -0.8200 113.24 -
TIP3P [180] a 3.15061 0.6364 0.9572 - +0.4170 -0.8340 104.52 -
TIP3P/Fw2 [994] a 3.1506 0.6368 0.9600 - +0.4170 -0.8340 104.5 -
iAMOEBA2 [2031] a 3.6453 0.8235 0.9584 - +0.29701 -0.59402 106.48 -
QCT[1251] a15 3.140 0.753 0.9614 - +0.6064 -1.2128104.06
7-
PPC 1, 2 [3] b 3.23400 0.6000 0.9430 0.06 +0.5170 -1.0340 106.00 127.0
TIP4P [180] c 3.15365 0.6480 0.9572 0.15 +0.5200 -1.0400 104.52 52.26
TIP4P-Ew [649] c 3.16435 0.680946 0.9572 0.125 +0.52422 -1.04844 104.52 52.26
TIP4P-FQ [197] c 3.15365 0.6480 0.9572 0.15 +0.631 -1.261 104.52 52.26
TIP4P/Ice [838] c 3.1668 0.8822 0.9572 0.1577 +0.5897 -1.1794 104.52 52.26
TIP4P/2005 [984] c 3.1589 0.7749 0.9572 0.1546 +0.5564 -1.1128 104.52 52.26
TIP4P/2005f [1765] c 3.1644 0.7749 0.9419 0.1546 +0.5564 -1.1128 107.4 53.7
source: http://www1.lsbu.ac.uk/water/water_models.html
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Water model has to be compatible
with the model describing the rest of
the system!
Always read the original paper
describing how given force field has
been derived
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EXPLICIT MODELS – MD “real life” example
chignolin
Water density
P. Florova, et al. JCTC 6 (2010) 3569
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EXPLICIT MODELS – MD “real life” example
P. Florova, et al. JCTC 6 (2010) 3569
EK-peptide
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IMPLICIT MODELS
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IMPLICIT MODELS
� Solvent is an uniform, polarizable medium with fixed
dielectric constant while the solute is placed inside
the cavity in the medium
� Free energy of solvation is given by
∆Gsolv = ∆Gcav + ∆Gdisp + ∆Gelec (+ ∆Ghb)
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IMPLICIT MODELS
� Free energy of solvation is given by
∆Gsolv = ∆Gcav + ∆Gdisp + ∆Gelec (+ ∆Ghb)
Free energy required to form the solute cavity
(due to the entropic penalty of reorganization of the solvent
molecules around the solute and the work done in creating
the cavity)
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IMPLICIT MODELS
� Free energy of solvation is given by
∆Gsolv = ∆Gcav + ∆Gdisp + ∆Gelec (+ ∆Ghb)
Van der Waals interaction
between solute and solvent.
Free energy required to form the solute cavity
(due to the entropic penalty of reorganization of the solvent
molecules around the solute and the work done in creating
the cavity)
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IMPLICIT MODELS
� Free energy of solvation is given by
∆Gsolv = ∆Gcav + ∆Gdisp + ∆Gelec (+ ∆Ghb)
electrostaticcomponent
(polarization between solute and solvent
induces charge redistribution)
Van der Waals interaction
between solute and solvent.
Free energy required to form the solute cavity
(due to the entropic penalty of reorganization of the solvent
molecules around the solute and the work done in creating
the cavity)
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IMPLICIT MODELS
� Free energy of solvation is given by
∆Gsolv = ∆Gcav + ∆Gdisp + ∆Gelec (+ ∆Ghb)
electrostaticcomponent
(polarization between solute and solvent
induces charge redistribution)
Van der Waals interaction
between solute and solvent.
Free energy required to form the solute cavity
(due to the entropic penalty of reorganization of the solvent
molecules around the solute and the work done in creating
the cavity)
hydrogen bonding term
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IMPLICIT MODELS
-+
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-+ Solute shape cavity of
vacuum is introduced into
the solvent
-+
IMPLICIT MODELS
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-+ Solute shape cavity of
vacuum is introduced into
the solvent
-+ -+Solute charge density is
placed in solute the cavity
+ -
IMPLICIT MODELS
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-+ Solute shape cavity of
vacuum is introduced into
the solvent
-+ -+Solute charge density is
placed in solute the cavity
+ -
-+
+ -
Solvent molecules reorient
and polarize in response to
the solute charge density
IMPLICIT MODELS
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-+ Solute shape cavity of
vacuum is introduced into
the solvent
-+ -+Solute charge density is
placed in solute the cavity
+ -
-+Solute polarizes in
response to solvent
polarization
+ -
Solvent molecules reorient
and polarize in response to
the solute charge density
-+
+ -
IMPLICIT MODELS
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IMPLICIT MODELS
Models differ in the following aspects:
1) Size and shape of the solute cavity
-+
+ -
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IMPLICIT MODELS
Models differ in the following aspects:
1) Size and shape of the solute cavity
2) Level of solute description
-+
+ -
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IMPLICIT MODELS
Models differ in the following aspects:
1) Size and shape of the solute cavity
2) Level of solute description
3) Dielectric medium description
-+
+ -
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IMPLICIT MODELS
Models differ in the following aspects:
1) Size and shape of the solute cavity
2) Level of solute description
3) Dielectric medium description
4) The cavity calculation method
-+
+ -
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IMPLICIT MODELS
Models differ in the following aspects:
1) Size and shape of the solute cavity
2) Level of solute description
3) Dielectric medium description
4) The cavity calculation method
5) Representation of charge distribution
-+
+ -
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IMPLICIT MODELS 1) Size and shape of the solute cavity
spherical ellipsoidal van der Waals
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IMPLICIT MODELS 1) Size and shape of the solute cavity
source: ieeexplore.ieee.org
atoms
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IMPLICIT MODELS 1) Size and shape of the solute cavity
source: ieeexplore.ieee.org
atoms
van der Waals
surface
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IMPLICIT MODELS 1) Size and shape of the solute cavity
source: ieeexplore.ieee.org
atoms
van der Waals
surface
probe
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IMPLICIT MODELS 1) Size and shape of the solute cavity
source: ieeexplore.ieee.org
atoms
van der Waals
surface
solvent excluded
surface (SES)(Connolly surface,
molecular surface)
probe
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IMPLICIT MODELS 1) Size and shape of the solute cavity
source: ieeexplore.ieee.org
atoms
van der Waals
surface
solvent accessible surface (SAS)(Lee-Richards molecular surface)
probe
solvent excluded
surface (SES)(Connolly surface,
molecular surface)
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IMPLICIT MODELS 2) Level of solute description
Level of description
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IMPLICIT MODELS 2) Level of solute description
Level of description
classical molecular
mechanics
semi-empirical
quantum
mechanics
DFT
post-HF
MP2, CI, CC, …
ACCURACY
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IMPLICIT MODELS 3) Dielectric medium description
- In most cases, homogenous static medium with fixed
dielectric constant
ε
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IMPLICIT MODELS 3) Dielectric medium description
- In most cases, homogenous static medium with fixed
dielectric constant
- Rarely, distance (from the solute) dependence may be
allowed
ε
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IMPLICIT MODELS 3) Dielectric medium description
- In most cases, homogenous static medium with fixed
dielectric constant
- Rarely, distance (from the solute) dependence may be
allowed
- Exceptionally, the rate of the process dependence may
be introduced (the response of the solvent is different
for “fast” processes)
ε
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IMPLICIT MODELS 4) The cavity calculation method
5) Representation of charge distribution
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IMPLICIT MODELS
Polarizable Continuum Model (PCM)
• Cavity
– Overlapping van der Waals spheres (PCM and CPCM)
– Solvent accessible surface
– Isodensity surface (IPCM, SCIPCM)
• Electrostatic potential from solute and polarization of solvent
must obey Poisson equation
• Electrostatic interactions calculated numerically
• Different formulations: DPCM, IPCM, SCIPCM, IEFPCM, …
Gaussian09: SCFR=PCM
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IMPLICIT MODELS
Conductor-like Screening Model (COSMO)
• Cavity
– Based on solvent accessible surface (SAS)
• Electrostatic interactions are treated in more approximated
manner
‒ Solvent treated as conductor not dielectric (ε = ∞)
• Good approximation in very polar solvents
Gaussian09: SCFR=CPCM
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Accuracy of Continuum Models
PCM > COSMO
IMPLICIT MODELS
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Accuracy of Continuum Models
PCM > COSMO
IMPLICIT MODELS
not always!experimental confirmation needed!
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HYBRID MODELS
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HYBRID MODELS
source: www.essexgroup.soton.ac.uk
QM/MM approach
source: http://www.nobelprize.org
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HYBRID MODELS
E = EQM + EMM + EQM/MM
Energy of the
QM subsystem
Energy of the
MM subsystem
Interaction energy
QM
MM
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HYBRID MODELS
E = EQM + EMM + EQM/MM
Energy of the
QM subsystem
Energy of the
MM subsystem
Interaction energy
Difficult part:
how do QM and MM interact?
QM
MM
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HYBRID MODELS
CURRENT APPROACHES:
• Karplus & co-workers:
QM: DFT, HF, AM1 MM: CHARMM QM/MM: link atoms
• Friesner & co-workers:
QM: DFT, HF MM: OPLS-AA QM/MM: hybrid orbitals
• Gao & co-workers:
QM: AM1 MM: CHARMM QM/MM: hybrid orbitals*
• Yang & co-workers:
QM: DFT MM: CHARMM QM/MM: link atoms*
* specific parametrization
QM
MM
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HYBRID MODELS
QM
MM
USE CAREFULLY!
TEST THOROUGHLY!
source: journals.sfu.ca
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SUMMARY
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EXPLICIT vs. IMPLICIT MODELS
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 equilibration
•Often solvent and solute are not
polarizable.
•Small size of the system -> large
fluctuations
•Artificial boundary between the
solute and solvent
• “Bad” model for treating short range
effects (dispersion and cavity)
source: www.k-state.edu, events.prace-ri.eu/event/210/material/22/0.pdf
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EXAMPLES
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IMPLICIT vs. EXPLICIT MODELS
Bull. Korean Chem. Soc. 33 (2012) 828
exp. NMR structure
Generalized Born model TIP3P model
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IMPLICIT vs. EXPLICIT MODELS
Spaeth et al. JCP 134 (2011) 164902
PS-PEG nanoparticles self-assembly
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Thank you very much for your kind attention
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N15 nuclear shielding of diazines in solution
IMPLICIT vs. EXPLICIT MODELS
source: http://www.esqc.org/2013/static/lectures/2_Mennucci.pdf
Part of a solvent effect is missing Solvent effect is correct
IMPLICIT SOLVENT MIXED SOLVENT
D. Mennucci, JACS 124 (2002) 1506