Implicit Solvation

In this chapter, all neccessary information will be given in order to use the implicit solvent model ALPB in xTB calculations. Parameterized solvents and available grids are given as well.

General command-line control

Note

The ALPB solvation model is implemented in version 6.3.3 or newer, use --gbsa in older versions instead.

The analytical linearized Poisson-Boltzmann (ALPB) model is envoked with the flag --alpb [Solvent]. As an example the single point calculation employing the ALPB model for solvation in water would be started by

> xtb coord --alpb water

As an example the energy printout of a singlepoint calculation of a H₂O molecule in implicit water is given.

:::::::::::::::::::::::::::::::::::::::::::::::::::::
::                     SUMMARY                     ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy               -5.080052453799 Eh   ::
:: total w/o Gsasa/hb         -5.072629830168 Eh   ::
:: gradient norm               0.004391355361 Eh/α ::
:: HOMO-LUMO gap              14.784541887474 eV   ::
::.................................................::
:: SCC energy                 -5.113963912352 Eh   ::
:: -> isotropic ES             0.042951967946 Eh   ::
:: -> anisotropic ES          -0.000414697277 Eh   ::
:: -> anisotropic XC          -0.000390138125 Eh   ::
:: -> dispersion              -0.000131341861 Eh   ::
:: -> Gsolv                   -0.011759733450 Eh   ::
::    -> Gborn                -0.004337109820 Eh   ::
::    -> Gsasa                 0.000220003644 Eh   ::
::    -> Ghb                  -0.009500070401 Eh   ::
::    -> Gshift                0.001857443127 Eh   ::
:: repulsion energy            0.033911458523 Eh   ::
:: add. restraining            0.000000000000 Eh   ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::

The solvation free energy is printed as Gsolv and is also added to all total energy printouts.

Optimizing a geometry with the ALPB model can be done with the following input

> xtb coord --opt --alpb water

The order of the flags can be altered and the input is not case sensitive. Like in a optimization without ALPB the optimized coordinates are written to a new file (xtbopt.coord). In General the ALPB can be used in combination with all available run types implemented in the xtb.

Parameterized Solvents

The ALPB model is parameterized for the Hamiltonian of GFN1-xTB, GFN2-xTB, and the GFN-FF, but not for GFN0-xTB. For the GFN1-xTB and GFN2-xTB Hamltonians also a generalized Born (GB) model with surface area (SA) contributions, dubbed GBSA is available. Here is a list of the available solvents.

solvents GFN1(ALPB) GFN1(GBSA) GFN2(ALPB) GFN2(GBSA) GFN-FF
Acetone x x x x x
Acetonitrile x x x x x
Aniline x   x   x
Benzaldehyde x   x   x
Benzene x x x x x
CH₂Cl₂ x x x x x
CHCl₃ x x x x x
CS₂ x x x x x
Dioxane x   x   x
DMF x   x   x
DMSO x x x x x
Ether x x x x x
Ethylacetate x   x   x
Furane x   x   x
Hexandecane x   x   x
Hexane x   x x x
Methanol   x   x  
Nitromethane x   x   x
Octanol x   x   x
Octanol (wet) x   x   x
Phenol x   x   x
Toluene x x x x x
THF x x x x x
Water (H₂O) x x x x x

To get the legacy GBSA model setup a detailed input with

$gbsa
   kernel=still

and invoke the program with the --gbsa flag instead of the --alpb flag.

Available Grids

Different Lebedev grids for the calculation of the SASA term are implemented in xtb. The grids are independent of the used GFNn method and are set in the detailed input as

$gbsa
   gbsagrid=tight

The default grid level is normal. The available grid levels are given in the table below with the corresponding number of gridpoints.

Gridlevel Gridpoints
normal 230
tight 974
verytight 2030
extreme 5810

Larger grids increase the computation time and reduce numerical noise in the energy. They may help to converge geometry optimizations with ALPB for large molecules which would otherwise not converge due to numerical noise.

Reference States

The default reference state option is bar1M which should not be changed for normal production runs. In order to compare the solvation free energy with solvation free energies from COSMO-RS the reference state can be set to reference which corresponds to the same reference option as in COSMO-RS. This could be done with

> xtb coord --opt --alpb water reference

Extended Functionality

Solvent Accessable Surface Area

Note

feature implemented in version 6.2

To get more insights and diagnostics for a ALPB calculation the Born radii and the solvent accessable surface area can be printed by toggling the property-printout with

$write
   gbsa=true

The printout for a branched octane isomer using ALPB(Water) looks like

* generalized Born model for continuum solvation

  #   Z   Born rad/Š   SASA/Ų    H-bond
  1   6 C      3.761     0.000     0.000
  2   6 C      3.761     0.000     0.000
  3   6 C      2.741     1.820    -0.000
  4   6 C      2.741     1.839    -0.000
  5   6 C      2.741     1.817    -0.000
  6   6 C      2.741     1.820    -0.000
  7   6 C      2.741     1.839    -0.000
  8   6 C      2.741     1.817    -0.000
  9   1 H      2.136    11.404    -0.015
 10   1 H      2.130    12.571    -0.017
 11   1 H      2.098    14.966    -0.020
 12   1 H      2.130    12.563    -0.017
 13   1 H      2.098    14.979    -0.020
 14   1 H      2.136    11.403    -0.015
 15   1 H      2.136    11.412    -0.015
 16   1 H      2.130    12.524    -0.017
 17   1 H      2.098    14.948    -0.020
 18   1 H      2.136    11.404    -0.015
 19   1 H      2.130    12.571    -0.017
 20   1 H      2.098    14.966    -0.020
 21   1 H      2.130    12.563    -0.017
 22   1 H      2.098    14.979    -0.020
 23   1 H      2.136    11.403    -0.015
 24   1 H      2.136    11.412    -0.015
 25   1 H      2.130    12.524    -0.017
 26   1 H      2.098    14.948    -0.020

total SASA / Ų :      244.491

The quartary carbon atoms are shown with no solvent accessable surface area, which means they are completely buried in the molecule leading to large Born radii.