Q-Chem Workshop. Doubletree Hotel 2085 S. Harbor Boulevard Anaheim, CA March 26, Schedule

Transcription

1 Q-Chem Workshop Doubletree Hotel 2085 S. Harbor Boulevard Anaheim, CA March 26, :30 Schedule Welcome remarks, Prof. Peter Gill, Australian National Univ and President of Q-Chem 8:45-9:15 Prof. Peter Gill: New ways of thinking about old problems 9:15-9:45 Prof. Anna Krylov, University of Southern California: "Unleashing Q-Chem'sarsenal of correlated and excited-state methods to understand Green Fluorescent Protein photocycle" 9:45-10:15 Prof. Paul Ha-Yeon Cheong, Oregon State University: "Elucidation of the Mechanisms and Stereomechanics in Proline Sulfonamide Organocatalysis" 10:15-10:30 Coffee Break 10:30 11:00 Avogadro and QUI, Dr. Zhengting Gan 11:00-12:00 Tutorial I. DFT optimization, vibration analysis, TS search, Dr. Yihan Shao 12:00 1:00 Lunch 1:00 1:30 Prof. Martin Head-Gordon, University of California at Berkeley: "Electronic structure of molecules with strongly correlated electrons: New methods and example applications" 1:30 2:00 Prof. John Herbert, Ohio State University: "New developments in 'polarizable continuum' implicit solvent models for QM, MM, and QM/MM applications" 2:00 2:30 Dr. Jing Kong, CEO and Chief Scientist of Q-Chem: "Unlimited possibilities: Overview of Q-Chem 4.0 Features 2:30 2:45 Coffee Break 2:45 3:30 Tutorial II, MP2, CC, and excited states, Dr. Yihan Shao 3:30 4:15 Tutorial III, Intermolecular interactions, solvation effect, and QM/MM, Dr. Yihan Shao 2 4:15 4:30 Free discussion and concluding remarks, Dr. Jing Kong 1

2 History Q-Chem was founded in the early 1990s Q-Chem 2.1, 2000 Kong et al, J. Comput. Chem. 2000, 21, 1532 Q-Chem 3.0, 2006 Shao et al, Phys. Chem. Chem. Phys. 2006, 8, 3172 Q-Chem 4.0, this month 3 Features From over 100+ developers High efficiency on desktops, multicores, GPUs SCF (Hartree-Fock, DFT), MP2, CC Ground-state and excited States Single molecule and molecular complexes Gas-phase or condensed phase (solvent or biological environment) A complete list of our features can be found at 4 2

3 Outline Part 0, Software installation Part 1, Hartree-Fockand DFT Part 2, MP2, Coupled-cluster and Excited States Part 3, Intermolecular interaction and QM/MM 5 Software setup In this workshop, we will use three programs Q-Chem QUI, Q-Chem user interface Avogadro, molecular builder Please go to to download these programs 6 3

4 QUI Geometry can be inserted by hand or by Paste XYZ from Avogadro Calculation setup Preview of Q-Chem input file 7 QUI preferences 8 4

5 Builder Manipulate Select Avogadro Measurement Navigate (Left: rotate; Middle: zoom; Right: translate) 9 Part 1 Hartree-Fock and DFT Single point energy, geometry optimization Vibrational spectroscopy, NMR Transition state search, internal reaction path 10 5

6 Build an ethanol molecule 11 Hartree-Fock//6-31G* calculation 12 6

7 SCF energy Final SCF energy 13 Mulliken charges 14 7

8 Natural orbital analysis 15 Natural orbital analysis 16 8

9 MO and density plots Make cube files that can be read by Avogardo HOMO and LUMO Nx, xmin, xmax Ny, ymin, ymax Nz, zmin, zmax Coordinates in Angstroms Ground-state density Number of MO, density, Transition density, Attachment/density plots 17 MO and density plots Run Q-Chem with qchem save input output scr $QCSCRATCH/scr/plots contains mo.13.cube, mo.14.cube and dens.0.cube 18 9

10 Geometry optimization 19 Vibrational analysis 20 10

11 NMR calculation 21 NMR shielding 22 11

12 Transition state search Make that there is one imaginary frequency Follow reaction path down to reactant and product 23 Reaction path 24 12

13 Exercises Exercise 1.1 Optimize the geometry of ethanol (C 2 H 5 OH) and its protonatedspecies (C 2 H 5 OH 2+ ) with B3LYP/6-31+G*. Compute Mullikencharges and natural atomic charges to see how the extra proton affects the charge distribution. Exercise 1.2 Optimize the geometry of formaldehyde (H 2 CO) run a frequency calculation at the optimized geometry use Avogadro to visualize its vibrational modes. 25 Part 2 MP2 methods Coupled-cluster methods Excited State Methods 26 13

14 MP2 27 MP

15 RIMP2 29 RIMP2 Compare this to MP2 energy:

16 Dual-basis RIMP2 31 Dual-basis RIMP2 Method SCF Energy Correlation Energy Total Energy SCF Time MP RIMP db-rimp Total Time 32 16

17 CCSD 33 CCSD 34 17

18 TDDFT 35 TDDFT calculation 36 18

19 Molecular Orbitals 37 Molecular Orbitals 38 19

20 Exercises Exercise 2.1 Optimize the geometry of cis-butadiene and transbutadiene with ωb97x-d (exchange = omegab97x- D)//6-31G* Compute the energy difference for the two optimized structures with B3LYP, B3LYP-D (add empirical_dispersion= true ) and ωb97x-d MP2//cc-pVTZ, RIMP2//cc-pVTZ, db-rimp2//cc-pvtz 39 Exercise 2.2 Exercises Optimize the CIS//6-31+G* geometry for the first excited state of formaldehyde (H 2 CO) cis_state_derivative = 1 Compare it to the ground-state geometry 40 20

21 Part 3 Intermoleculear Interaction Solvation QM/MM 41 Formamide dimer Benchmark Energy and Geometry DataBase

22 BSSE calculation 43 Energy Decomposition Analysis 44 22

23 EDA 45 BSSE results CCSD(T)//CBS: kcal/mol = kJ/mol B3LYP B3LYP-D 46 23

24 SM8 47 SM8 results 48 24

25 QM/MM 49 Exercises Exercise 3.1 Pick a molecular complex from the S22 dataset ( compute its binding energy with DFT and RIMP2 Exercise 3.2 Optimize the geometry of the complex above with SM8 solvation model Compare the optimized solvated geometry to the original gas-phase geometry 50 25