QM/MM with polarizable force fields

This (technical) example shows how to make an input for the QM/MM methods DRF and QM/FQ in which both polarizable force fields are used.

You can study chemistry in solution, as contrasted to the gas phase, with the implementation of implicit solvation models (continuum solvation) like COSMO and SM12, or explicit solvation models like molecular dynamics or multi-level methods. Many multi-level methods exist that can treat solvation effects, like QM/MM with mechanical or electrostatic embedding, QM/MM with polarizable force-fields like DRF and QM/FQ, or frozen density embedding (FDE). Using implicit solvation models is relatively straightforward. For explicit solvation models using multi-level methods, like DRF and QM/FQ you will need to define regions.

The geometry for such QM/MM calculations could be taken from snapshots of a molecular dynamics calculation.

DRF

To demonstrate how to set up a DIM/QM DRF (Discrete Solvent Reaction Field) calculation using AMSinput, we will use water in water as an example. DRF is a QM/MM method in which the MM atoms interact with the QM region via induced dipoles and static charges. DRF facilitates calculating the optical properties of molecules. One should use the ‘Single Point’ Task.

Download the following xyz file: file water_in_water.xyz
Open AMSinput: File → Import Coordinates… and select ‘water_in_water.xyz’
Select Task Single Point
Select XC functional Model:SAOP
Select Basis set TZ2P and Core None
Select Numerical Quality Good
Use the panel bar Properties → Excitations (UV/Vis), CD command
For the ‘Type of excitations’ option, Select ‘SingletOnly’
Select the middle water molecule
(for example with Model → Coordinates and select the first 3 atoms)
Use the panel bar Model → Regions command
click the AddButton button next to Regions, and rename Region_1 to Solute
Select all other atoms of the complex (by Select → Invert Selection)
click the AddButton button again, and rename Region_2 to Solvent
Use the panel bar Model → DIM/QM command
For the ‘Method’ option, Select ‘DRF’
Click the check button ‘QM part’ for the ‘Solute’ region
Click the check button ‘DIM part’ for the ‘Solvent’ region

In the next step atomic charges for the DRF region are computed using MDC-Q charges (LDA functional, DZP basis set). The atomic polarizabilities are taken from a inner database including fitted parameters for the H, C, N, O, F, S, Cl, Br, and I atoms, and non-optimized parameters for most other atoms.

For the ‘Select charges’ option, Select ‘MDC-Q’
Save as ‘Water_DRF’
File → Run
/scm-uploads/doc.2021/Tutorials/_images/drfinput.png

QM/FQ

To demonstrate how to set up a QM/FQ (Quantum Mechanics/Fluctuating Charges) calculation using AMSinput, we will use 2-methyloxirane in water as an example. QM/FQ is a QM/MM method in which the MM atoms interact with the QM region via induced charges. The FQ charges are determined self-consistently along with the ground-state QM density. QM/FQ also facilitates calculating the optical properties of molecules. Since the charges depend on the QM density, explicit terms also appear within response equations that are solved to simulate spectroscopic and excited-state properties of the QM system.

One should use the ‘Single Point’ Task.

Download the following xyz file: file methyloxirane_in_water.xyz
Open AMSinput: File → Import Coordinates… and select ‘methyloxirane_in_water.xyz’
Select Task Single Point
Select XC functional GGA:PBE
Select Basis set TZP and Core None
Select Numerical Quality Good
Use the panel bar Properties → Excitations (UV/Vis), CD command
For the ‘Type of excitations’ option, Select ‘SingletOnly’
Select the 2-methyloxirane molecule
Use the panel bar Model → Regions command
click the AddButton button next to Regions, and rename Region_1 to Solute
Select all other atoms of the complex (by Select → Invert Selection)
click the AddButton button again, and rename Region_2 to Solvent
Click on the right arrow at the end of the ‘Solvent’ line
Use the ‘Hidden’ command from the menu that appears
/scm-uploads/doc.2021/Tutorials/_images/hiddenregion.png

Hidden here means that the molecules in the ‘Solvent’ region are hidden. The ‘Solvent’ region is still visible because it is colored.

The GUI has parameters for QM/FQ in case water is the solvent in the FQ region.

Use the panel bar Model → QM/FQ command
Check the Enable checkbutton
Click the check button ‘QM part’ for the ‘Solute’ region
Click the check button ‘FQ part’ for the ‘Solvent’ region
Save as ‘methyloxirane_QMFQ’
File → Run
/scm-uploads/doc.2021/Tutorials/_images/qmfqinput.png