Q-Chem Workshop Tasks

Transcription

1 Marek Freindorf Q-Chem Workshop Tasks Washington DC August 2009

2 Basic Calculations Carbon Dioxide, Example 1A 1. Calculate an optimal geometry of carbon dioxide using the B3LYP/6-31+G* level of theory 2. For the optimal geometry, calculate molecular vibrations using the same level of theory 3. For the optimal geometry, calculate atomic charges and atomic populations, using the NBO analysis and applying the same level of theory 4. For the optimal geometry, calculate NMR shielding tensors using the same level of theory 5. Repeat the same calculations using the BLYP/6-31+G* level of theory, and compare the results with B3LYP Page 1

3 Basic Calculations CH4-F Reaction, Example 1B 1. Calculate an optimal geometry of the CH4-F anion using the B3LYP/6-31+G* level of theory, for the constrained distance between F and C atoms 2. Repeat the same calculations for different values of the C-F constrained distance 3. Repeat the same calculations for different values of the C-H constrained distance 4. Report in a graph the potential energy surface of the CH4-F reaction 5. Repeat the same calculations using the BLYP/6-31+G* level of theory, and compare the results with B3LYP Page 2

4 Basic Calculations Ammonia, Example 1C 1. Calculate an optimal geometry of ammonia using the B3LYP/6-31+G* level of theory 2. For the optimal geometry, calculate molecular vibrations using the same level of theory 3. For the optimal geometry, calculate atomic charges and atomic populations, using the NBO analysis and applying the same level of theory 4. For the optimal geometry, calculate NMR shielding tensors using the same level of theory 5. Repeat the same calculations using the BLYP/6-31+G* level of theory, and compare the results with B3LYP Page 3

5 Basic Calculations CH3F-Cl Reaction, Example 1D 1. Calculate an optimal geometry of the CH3F-Cl anion using the B3LYP/6-31+G* level of theory, for the constrained distance between Cl and C atoms 2. Repeat the same calculations for different values of the C-Cl constrained distance 3. Repeat the same calculations for different values of the C-F constrained distance 4. Report in a graph the potential energy surface of the CH3F-Cl reaction 5. Repeat the same calculations using the BLYP/6-31+G* level of theory, and compare the results with B3LYP Page 4

6 Intermolecular Interactions CH3OH-HF, Example 2A 1. Calculate an optimal geometry of the CH3OH-HF complex where the HF molecule is a hydrogen bond donor, using the B3LYP/6-31G* level of theory 2. Calculate optimal geometries of each monomer using the same level of theory 3. Repeat the calculations according to points 1 and 2 using the 6-31+G* and G** basis sets 4. Repeat the calculations according to points 1, 2 and 3 using the BLYP level of theory 5. Repeat the calculations according to points 1, 2, 3 and 4 applying the DFT_D (Empirical_Grimme) method 6. Report final hydrogen bond energies, hydrogen bond distances and hydrogen bond angles Page 1

7 Intermolecular Interactions CH2O-H2O, Example 2B 1. Calculate an optimal geometry of the CH2O-H2O complex, using the B3LYP/6-31+G* level of theory 2. Constrain the interatomic distance between oxygen from keton and hydrogen from water, and recalculate the optimal geometry 3. Repeat the calculations according to point 2, for different values of the constrained distance 4. Repeat the calculations according to points 1, 2 and 3 using the SM8 solvation model 5. Report in a form of a graph the potential energy surfaces of the interaction between water and keton with and without the solvation correction Page 2

8 Intermolecular Interactions CH3OH-HCl, Example 2C 1. Calculate an optimal geometry of the CH3OH-HCl complex where the HCl molecule is a hydrogen bond donor, using the B3LYP/6-31G* level of theory 2. Calculate optimal geometries of each monomer using the same level of theory 3. Repeat the calculations according to points 1 and 2 using the 6-31+G* and G** basis sets 4. Repeat the calculations according to points 1, 2 and 3 using the BLYP level of theory 5. Repeat the calculations according to points 1, 2, 3 and 4 applying the DFT_D (Empirical_Grimme) method 6. Report final hydrogen bond energies, hydrogen bond distances and hydrogen bond angles Page 3

9 Intermolecular Interactions CH2O-CH3OH, Example 2D 1. Calculate an optimal geometry of the CH2O-CH3OH complex, using the B3LYP/6-31+G* level of theory 2. Constrain the interatomic distance between oxygen from keton and hydrogen from alcohol, and recalculate the optimal geometry 3. Repeat the calculations according to point 2, for different values of the constrained distance 4. Repeat the calculations according to points 1, 2 and 3 using the SM8 solvation model 5. Report in a form of a graph the potential energy surfaces of the interaction between alcohol and keton with and without the solvation correction Page 4

10 QM/MM Method CH2FNH2 - Protein, Example 3A 1. Load from the workshop website the PDB files for Q-Chem and extraxt the pcaf-qm-1.pdb and "pcaf-chrmm.txt" files. Open the pcaf-qm-1.pdb file using Avogadro 2. Using QUI, paste the coordinates into the input file, and open the "pcaf-chrmm.txt" file with external charges 3. Calculate an optimal geometry of the CH2FNH2 molecule using the B3LYP/6-31+G* level of theory inside the protein 4. For the optimal geometry, calculate molecular vibrations of the molecule inside the protein 5. Repeat the calculations according to point 3 and 4 in the gas phase 6. Report in a table atomic charges, a dipole moment and frequencies of molecular vibrations in the gas phase and in Page 1

11 QM/MM Method CH3OH - Protein, Example 3B 1. Load from the workshop website the PDB files for Q-Chem and extraxt the pcaf-qm-2.pdb and "pcaf-chrmm.txt" files. Open the pcaf-qm-2.pdb file using Avogadro 2. Using QUI, paste the coordinates into the input file, and open the "pcaf-chrmm.txt" file with external charges 3. Calculate an optimal geometry of the CH3OH molecule using the B3LYP/6-31+G* level of theory inside the protein 4. For the optimal geometry, calculate molecular vibrations of the molecule inside the protein 5. Repeat the calculations according to point 3 and 4 in the gas phase 6. Report in a table atomic charges, a dipole moment and frequencies of molecular vibrations in the gas phase and in Page 2

12 QM/MM Method CH3COH - Protein, Example 3C 1. Load from the workshop website the PDB files for Q-Chem and extraxt the pcaf-qm-3.pdb and "pcaf-chrmm.txt" files. Open the pcaf-qm-3.pdb file using Avogadro 2. Using QUI, paste the coordinates into the input file, and open the "pcaf-chrmm.txt" file with external charges 3. Calculate an optimal geometry of the CH3COH molecule using the B3LYP/6-31+G* level of theory inside the protein 4. For the optimal geometry, calculate molecular vibrations of the molecule inside the protein 5. Repeat the calculations according to point 3 and 4 in the gas phase 6. Report in a table atomic charges, a dipole moment and frequencies of molecular vibrations in the gas phase and in Page 3

13 QM/MM Method CH3SH - Protein, Example 3D 1. Load from the workshop website the PDB files for Q-Chem and extraxt the pcaf-qm-4.pdb and "pcaf-chrmm.txt" files. Open the pcaf-qm-4.pdb file using Avogadro 2. Using QUI, paste the coordinates into the input file, and open the "pcaf-chrmm.txt" file with external charges 3. Calculate an optimal geometry of the CH3SH molecule using the B3LYP/6-31+G* level of theory inside the protein 4. For the optimal geometry, calculate molecular vibrations of the molecule inside the protein 5. Repeat the calculations according to point 3 and 4 in the gas phase 6. Report in a table atomic charges, a dipole moment and frequencies of molecular vibrations in the gas phase and in Page 4

14 CHARMM/Q-Chem H2O - Protein, Example 4A 1. Load from the workshop website the PDB files for CHARMM/Q-Chem and extract the pcaf-min-1.pdb file 2. Upload the pcaf-min-1.pdb file to the charmming.org webserver 3. Calculate minimization, heating and equilibration of the protein with the water molecule 4. Analyze the root mean square (RMS) deviation 5. Repeat the calculations according to point 3 and 4 with fixed positions of non-hydrogen atoms 6. Compare RMS results from the simulations with and without fixed non-hydrogen atoms Page 1

15 CHARMM/Q-Chem H2O - Protein, Example 4B 1. Load from the workshop website the PDB files for CHARMM/Q-Chem and extract the pcaf-min-1.pdb file 2. Upload the pcaf-min-1.pdb file to the charmming.org webserver 3. Calculate QM/MM minimization of the protein with the water molecule 4. Analyze the root mean square (RMS) deviation 5. Repeat the calculations according to point 3 and 4 with fixed positions of non-hydrogen atoms 6. Compare RMS results from the simulations with and without fixed non-hydrogen atoms Page 2

16 CHARMM/Q-Chem H2O - Protein, Example 4C 1. Load from the workshop website the PDB files for CHARMM/Q-Chem and extract the pcaf-min-2.pdb file 2. Upload the pcaf-min-2.pdb file to the charmming.org webserver 3. Calculate minimization, heating and equilibration of the protein with two water molecules 4. Analyze the root mean square (RMS) deviation 5. Repeat the calculations according to point 3 and 4 with fixed positions of non-hydrogen atoms 6. Compare RMS results from the simulations with and without fixed non-hydrogen atoms Page 3

17 CHARMM/Q-Chem H2O - Protein, Example 4D 1. Load from the workshop website the PDB files for CHARMM/Q-Chem and extract the pcaf-min-2.pdb file 2. Upload the pcaf-min-2.pdb file to the charmming.org webserver 3. Calculate QM/MM minimization of the protein with two water molecules 4. Analyze the root mean square (RMS) deviation 5. Repeat the calculations according to point 3 and 4 with fixed positions of non-hydrogen atoms 6. Compare RMS results from the simulations with and without fixed non-hydrogen atoms Page 4