molecular modeling: geometry optimization c372 introduction to cheminformatics ii kelsey forsythe
TRANSCRIPT
Molecular Modeling:Molecular Modeling:Geometry OptimizationGeometry Optimization
C372C372
Introduction to Introduction to Cheminformatics IICheminformatics II
Kelsey ForsytheKelsey Forsythe
Geometry OptimizationGeometry Optimization
Le Chatliers’ PrincipleLe Chatliers’ PrincipleThe optimum geometry is the The optimum geometry is the
geometry which minimizes the strain geometry which minimizes the strain on a given system. Any perturbation on a given system. Any perturbation from this geometry will induce the from this geometry will induce the
system to change so as to reduce this system to change so as to reduce this perturbation unless prevented by perturbation unless prevented by
external forcesexternal forcesMathematical Surface Reflects This Principle!!
Why Extrema?Why Extrema? Equilibrium structure/conformer MOST Equilibrium structure/conformer MOST
likely observed? likely observed? Once geometrically optimum structure found Once geometrically optimum structure found
can calculate energy, frequencies etc. to can calculate energy, frequencies etc. to compare with experimentcompare with experiment
Use in other simulations (e.g. dynamics Use in other simulations (e.g. dynamics calculation)calculation)
Used in reaction rate calculations (e.g. Used in reaction rate calculations (e.g. saddlesaddlereaction timereaction time ))
Characteristics of transition stateCharacteristics of transition state PES interpolation (Collins et al)PES interpolation (Collins et al)
NomenclatureNomenclature
PES equivalent to Born-PES equivalent to Born-Oppenheimer surfaceOppenheimer surface
Point on surface corresponds to Point on surface corresponds to position of nuclei position of nuclei
Minimum and MaximumMinimum and Maximum LocalLocal Global Global Saddle point (min and max)Saddle point (min and max)
CyclohexaneCyclohexane
Local maxima
Global minimum
Global maxima
Local minima
Ex. PESEx. PES
Saddle point
Local minimumGlobal minimum
Recall glycine?Recall glycine?
Global
Local
MethodsMethods
Steepest DescentSteepest Descent Conjugate GradientConjugate Gradient Fletcher Powell Fletcher Powell SimplexSimplex Geometric Direct Geometric Direct
Inversion of Inversion of Iterative SubspaceIterative Subspace
Newton-RaphsonNewton-Raphson
Minimize w.r. each Minimize w.r. each
individualindividual coordinate coordinate No gradients requiredNo gradients required No gradients requiredNo gradients required
Methods (1-d)Methods (1-d)
No Functional FormNo Functional Form Bracketing Bracketing Parabolic Interpolation (Brent’s method) Parabolic Interpolation (Brent’s method)
Methods (1-d)(w/ gradients)Methods (1-d)(w/ gradients)
Steepest DescentSteepest Descent
Methods (n-d)(w/o Methods (n-d)(w/o gradients)gradients)
Line SearchLine Search SimplexSimplex Fletcher-PowellFletcher-Powell
Methods (n-d)(w/ gradients)Methods (n-d)(w/ gradients)
Conjugate Gradient (space Conjugate Gradient (space N) N) Fletcher-Reeves Fletcher-Reeves Polak-RibierePolak-Ribiere
Quasi-Newton/Variable Metric (space Quasi-Newton/Variable Metric (space NN22)) Davidon-Fletcher-PowellDavidon-Fletcher-Powell Broyden-Fletcher-Goldfarb-ShannoBroyden-Fletcher-Goldfarb-Shanno
Multidimensional MethodsMultidimensional Methods
Stochastic TunnelingStochastic Tunneling
Monte CarloMonte Carlo
Simulated AnnealingSimulated Annealing
Genetic AlgorithmGenetic Algorithm
Surface Surface smoothing: smoothing: proteinsproteins
Multi-dimensionalMulti-dimensional
Global (uphill Global (uphill jumps allowed)jumps allowed)
BottleneckBottleneck Typically many function evaluations are required Typically many function evaluations are required
in order to estimate derivatives and in order to estimate derivatives and interpolate/extrapolate along PESinterpolate/extrapolate along PES
Want simple analytic form for energy !Want simple analytic form for energy !
q1
q2
q3
.
.qn
E(q1,q2..)Molecular mechanics
Semi-Empirical
Ab Initio
Analytic?
8.35E-28 8.77567E+14 20568787140 2.03098E-18 1.05374E-188.35E-28 8.77567E+14 20568787140 1.77569E-18 9.66155E-198.35E-28 8.77567E+14 20568787140 1.54682E-18 8.82365E-198.35E-28 8.77567E+14 20568787140 1.34201E-18 8.02375E-198.35E-28 8.77567E+14 20568787140 1.15913E-18 7.26185E-198.35E-28 8.77567E+14 20568787140 9.96207E-19 6.53795E-198.35E-28 8.77567E+14 20568787140 8.51451E-19 5.85205E-198.35E-28 8.77567E+14 20568787140 7.23209E-19 5.20415E-198.35E-28 8.77567E+14 20568787140 6.09973E-19 4.59425E-198.35E-28 8.77567E+14 20568787140 5.10362E-19 4.02235E-198.35E-28 8.77567E+14 20568787140 4.2311E-19 3.48845E-198.35E-28 8.77567E+14 20568787140 3.47061E-19 2.99255E-198.35E-28 8.77567E+14 20568787140 2.81155E-19 2.53465E-198.35E-28 8.77567E+14 20568787140 2.24426E-19 2.11475E-198.35E-28 8.77567E+14 20568787140 1.75987E-19 1.73285E-198.35E-28 8.77567E+14 20568787140 1.35031E-19 1.38895E-198.35E-28 8.77567E+14 20568787140 1.0082E-19 1.08305E-198.35E-28 8.77567E+14 20568787140 7.26787E-20 8.15147E-208.35E-28 8.77567E+14 20568787140 4.99924E-20 5.85247E-208.35E-28 8.77567E+14 20568787140 3.22001E-20 3.93347E-208.35E-28 8.77567E+14 20568787140 1.87901E-20 2.39447E-208.35E-28 8.77567E+14 20568787140 9.29638E-21 1.23547E-208.35E-28 8.77567E+14 20568787140 3.29443E-21 4.56475E-21
Empirical Potential for Hydrogen Molecule
0
2E-19
4E-19
6E-19
8E-19
1E-18
1.2E-18
1.4E-18
0 0.5 1 1.5 2 2.5 3 3.5 4
What is the optimum point?What is the optimum point?
?
?
?
0)(=
rdrdV
vv
At extremum
Local vs. Global?Local vs. Global?Conformational Analysis (Equilibrium Conformer)
Equilibrium Geometry
A conformational analysis is global geometry optimization which yields multiple structurally stable conformational geometries (i.e. equilibrium geometries)
An equilibrium geometry may be a local geometry optimization which finds the closest minimum for a given structure (conformer)
or an equilibrium conformer
• BOTH are geometry optimizations (i.e. finding wherethe potential gradient is zero)•Elocal greater than or equal to Eglobal
Geometry OptimizationGeometry Optimization
Basic Scheme Basic Scheme Find first derivative (gradient) of Find first derivative (gradient) of
potential energypotential energy Set equal to zeroSet equal to zero Find value of coordinate(s) which Find value of coordinate(s) which
satisfy equationsatisfy equation
Modeling Potential energy Modeling Potential energy (1-d)(1-d)
€
U(r) U(req ) −dU
dr r= req
(r − req ) +1
2
d2U
dr2
r= req
(r − req )2
€
−1
3
d3U
drr= req
(r − req )3 ....+1
n!
dnU
drn
r= req
(r − req )n€
=
€
≈
Modeling Potential energy Modeling Potential energy (>1-d)(>1-d)
€
U(v r a + δ
v r ) = U(ra ) −
dU
dr r= ra
δri
i
∑ +1
2δri
d2U
dridrj r= req
δrj + .....i, ji≤ j
∑
≈ c -v b δ
v r +
1
2δ
v r T A
≈δ
v r
Hessian
Find Equilibrium Geometry Find Equilibrium Geometry for the Morse Oscillatorfor the Morse Oscillator
)()(0
)()(0
)()(0
2)(0
00
00
00
0
)1(2
) )1(2
))(0( )1(2
)1(
RRaRRa
RRaRRa
RRaRRa
RRaHH
eeaD
aeeD
eaeDdRdV
eDV
−−−−
−−−−
−−−−
−−
−=
−=
−−×−=
−=
Find Equilibrium Geometry Find Equilibrium Geometry for the Morse Oscillatorfor the Morse Oscillator
BottlenecksBottlenecks
No Functional FormNo Functional Form More than one variableMore than one variable Coupling between variablesCoupling between variables
Geometry OptimizationGeometry Optimization(No Functional Form) (No Functional Form)
Bracketing (w/parabolic fitting)Bracketing (w/parabolic fitting) Find energy (EFind energy (E11) for given value of coordinate x) for given value of coordinate xii
Change coordinate (xChange coordinate (xi+1i+1=x=xii--x) to give Ex) to give E22
Change coordinate (xChange coordinate (xi+2i+2=x=xii + +x) to give Ex) to give E33
If (EIf (E22>E>E11 and E and E33>E>E11) then x) then xi+1i+1> x> xminmin >x >xi+2i+2
Fit to parabola and find parabolic minimumFit to parabola and find parabolic minimum Use value of coordinate at minimum as starting Use value of coordinate at minimum as starting
point for next iterationpoint for next iteration Repeat to satisfaction (Minimum Energy error Repeat to satisfaction (Minimum Energy error
tolerance)tolerance)
8.35E-28 8.77567E+14 20568787140 2.03098E-18 1.05374E-188.35E-28 8.77567E+14 20568787140 1.77569E-18 9.66155E-198.35E-28 8.77567E+14 20568787140 1.54682E-18 8.82365E-198.35E-28 8.77567E+14 20568787140 1.34201E-18 8.02375E-198.35E-28 8.77567E+14 20568787140 1.15913E-18 7.26185E-198.35E-28 8.77567E+14 20568787140 9.96207E-19 6.53795E-198.35E-28 8.77567E+14 20568787140 8.51451E-19 5.85205E-198.35E-28 8.77567E+14 20568787140 7.23209E-19 5.20415E-198.35E-28 8.77567E+14 20568787140 6.09973E-19 4.59425E-198.35E-28 8.77567E+14 20568787140 5.10362E-19 4.02235E-198.35E-28 8.77567E+14 20568787140 4.2311E-19 3.48845E-198.35E-28 8.77567E+14 20568787140 3.47061E-19 2.99255E-198.35E-28 8.77567E+14 20568787140 2.81155E-19 2.53465E-198.35E-28 8.77567E+14 20568787140 2.24426E-19 2.11475E-198.35E-28 8.77567E+14 20568787140 1.75987E-19 1.73285E-198.35E-28 8.77567E+14 20568787140 1.35031E-19 1.38895E-198.35E-28 8.77567E+14 20568787140 1.0082E-19 1.08305E-198.35E-28 8.77567E+14 20568787140 7.26787E-20 8.15147E-208.35E-28 8.77567E+14 20568787140 4.99924E-20 5.85247E-208.35E-28 8.77567E+14 20568787140 3.22001E-20 3.93347E-208.35E-28 8.77567E+14 20568787140 1.87901E-20 2.39447E-208.35E-28 8.77567E+14 20568787140 9.29638E-21 1.23547E-208.35E-28 8.77567E+14 20568787140 3.29443E-21 4.56475E-21
Empirical Potential for Hydrogen Molecule
0
2E-19
4E-19
6E-19
8E-19
1E-18
1.2E-18
1.4E-18
0 0.5 1 1.5 2 2.5 3 3.5 4
What is the optimum point?What is the optimum point?
HO-trivial case
1
42
3 34
Line SearchLine Search
For given point V(rFor given point V(raa) choose u vector) choose u vector u chosen in direction opposite to gradient u chosen in direction opposite to gradient
(I.e. steepest descent)(I.e. steepest descent) ApproachesApproaches
Constant Constant Steepest descentSteepest descent
Minimize V(xMinimize V(xii++ u)u)
Want Want s.t. vectors f and u perpendiculars.t. vectors f and u perpendicular
Repeat to minimumRepeat to minimum
€
vu = −
dV
dv x i
uxx ii
vvv +=+
€
dV (v x i+1)
dλ=
dV
dv x i+1
⎛
⎝ ⎜
⎞
⎠ ⎟
f1 2 3
Td
v x i+1
dλu
{= 0
Line Search(1-d)Line Search(1-d)
Steepest Descent (Gradient Descent Steepest Descent (Gradient Descent Method)Method)
ix
ii
dx
dfu
uxx
=
+==
+
.022)( 23 +−= xxxf
Conjugate MethodsConjugate Methods
No “Spoiling”No “Spoiling” Reduces #iterationsReduces #iterations Numerical GradientNumerical Gradient
Powell Method (Powell Method (speedspeednn22)) Analytic GradientAnalytic Gradient
Conjugate Gradient (speed Conjugate Gradient (speed n)n)