Tutorial  #3:  Exploring  Poten4al  Energy  Surface  

with  Q-­‐Chem  

PES:  Concepts  and  defini4ons  

Sta4onary  points:  Minima  and  saddle  points  Op4miza4on  and  transi4on-­‐state  search  

Chemical  Reac4on  

Reactant � Product �

Transition State�

Reac4on  Barrier  

Reac4on  Energy  

4  

Basic  job  types  

Op4miza4on:  OPT  (note  on  symmetry)    Op4miza4on  with  constraints    PES  scans      FREQ:  harmonic  frequencies  and  normal  modes    Transi4on  state  search  and  rxn  coordinate  

5  

Op4miza4on  with  constrains  $molecule 0 1 C .141915 .332682 .000000 O .141915 -1.088318 .000000 H 1.186989 .656186 .000000 H -.348433 .742676 .887862 H -.348433 .742676 -.887862 H -.773953 -1.385902 .000000 $end $rem JOBTYPE opt ......... $end $opt CONSTRAINT stre 1 2 1.8 bend 2 1 4 110.0 bend 2 1 5 110.0E ENDCONSTRAINT $end

Exercise  3-­‐1:    Op4mize  formaldehyde    geometry  at  a  stretched    CO  bond  (2.0  A)    

Constraints  can  be  set  in  IQmol:      -­‐  select  2  or  3  or  4  atoms;  -­‐  Build-­‐>Set  Constraint.  

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PES  scans  

$molecule 0 1 .... $end $rem JOBTYPE PES_SCAN ......... $end $scan tors 1 2 3 4 -180 180 15 $end

Exercise  3-­‐2:    Perform  PES  scan  along  CCCC  torsion  in  butane  with  Hartree-­‐Fock/STO-­‐3G.    IQmol  does  not  support  scans  yet,  edit  input  manually.    Hint:  To  figure  out  how  to  set  scan,  use  Display-­‐Index  to  get  atom  numbering;  also  use  select  tool  to  figure  out  ini4al  values  

7  

Transi4on-­‐state  search  

Reactant � Product �

Transition State�

Reac4on  Barrier  

Reac4on  Energy  

JOBTYPE  TS  

Success depends on! the quality of the guess structure!!! !!

Transi4on  state  op4miza4on  

•  Exercise 3-3: read geometry, setup 3 consequent jobs, add manually “geom_opt_hessian read”

•  Geometry: tutorial/ts.dialanine.xyz •  See tutorial/ts.dialanine.in

Job1:  JOBTYPE    =  FREQ  

Job2:  JOBTYPE  =  TS  

GEOM_OPT_HESSIAN  =  READ  Job  3:  

JOBTYPE    =  FREQ  

Linear  interpola4on  

Freezing  string  method  

•  Behn,  Zimmerman,  Sharada,  Bell,  Head-­‐Gordon  –  J.  Chem.  Phys.  135,  224108  (2011)  –  J.  Chem.  Theory  Comput.  7,  4019  (2011)  –  J.  Chem.  Theory  Comput.  8,  5166  (2012)  –  J.  Chem.  Phys.  140,  164115  (2014)  

• Webinar  by  Mar4n  Head-­‐Gordon:  –  hjps://www.youtube.com/watch?v=JBBblxGEXxo  

Freezing  string  method  

FSM  sample  input  $molecule 0 1 Si 0.71979 -0.08082 -0.76577 H 0.73262 -1.27801 0.22990 H 1.10451 0.93673 0.34825 H -1.32980 0.23894 -0.28240 H -1.22713 0.18317 0.47002 **** Si 0.00019 0.00027 -0.00040 H 0.65128 -1.35033 -0.06530 H 1.05811 1.06282 0.06417 H -0.84585 0.20738 -1.22253 H -0.86374 0.07986 1.22406 end $rem jobtype fsm fsm_ngrad 3 fsm_nnode 20 exchange b3lyp basis 6-31g scf_max_cycles 250 symmetry flase sym_ignore true $end

Reactant:  SiH2  +  H2  

Product:  SiH4  

FSM  calcula4on  not  yet  fully  supported  by  IQmol  

FSM  sample  input  (con4nued)  

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@@@ $rem jobtype ts scf_guess read geom_opt_print 4 geom_opt_dmax 100 geom_opt_hessian read geom_opt_max_cycles 1500 exchange B3LYP basis 6-31G max_scf_cycles 250 symmetry false sym_ignore true $end $molecule read $end

TS  search  from  the  highest-­‐energy  point  along  the  freezing  sr4ng      

Exercise  3-­‐4:    TS  search  with  FSM  tutorial/fsm_silane.in  

Automated  TS  search:  FSM    

14  

-­‐291.86  

-­‐291.84  

-­‐291.82  

-­‐291.8  

-­‐291.78  

-­‐291.76  

-­‐291.74  

0   5   10   15   20   25  

Energy  (H

a)  

Node  

SiH2  +  H2  -­‐>  SiH4  

TS  guess  

Reactant  

Product  

Input  to  P-­‐RFO  along  with    approximate  hessian,  which    then  op4mizes  TS  

Intrinsic  reac4on  path  

•  Go  downhill  from  the  transi4on  state  to  see  which  two  minima  it  connects  to  

•  JOBTYPE  =  RPATH  

•  Exercise  3-­‐5:    Perform  RPATH  calcula4on  with    –  tutorial/rpath.hcn.in