.. _gbsa: -------------------- 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. .. contents:: 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 .. code:: bash > xtb coord --alpb water As an example the energy printout of a singlepoint calculation of a H₂O molecule in implicit water is given. .. code:: bash ::::::::::::::::::::::::::::::::::::::::::::::::::::: :: SUMMARY :: ::::::::::::::::::::::::::::::::::::::::::::::::::::: :: total energy -5.080125650447 Eh :: :: total w/o Gsasa/hb -5.072630011432 Eh :: :: gradient norm 0.000116027126 Eh/a0 :: :: HOMO-LUMO gap 14.677994988515 eV :: ::.................................................:: :: SCC energy -5.114015528669 Eh :: :: -> isotropic ES 0.042942180411 Eh :: :: -> anisotropic ES -0.000536031457 Eh :: :: -> anisotropic XC -0.000425709023 Eh :: :: -> dispersion -0.000131265012 Eh :: :: -> Gsolv -0.011732627293 Eh :: :: -> Gelec -0.004236988278 Eh :: :: -> Gsasa 0.000208166036 Eh :: :: -> Ghb -0.009561248178 Eh :: :: -> Gshift 0.001857443127 Eh :: :: repulsion energy 0.033889878222 Eh :: :: add. restraining 0.000000000000 Eh :: :: total charge 0.000000000000 e :: ::::::::::::::::::::::::::::::::::::::::::::::::::::: 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 .. code:: bash > 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 x DMSO x x x x x Ethanol x x x Ether x x x x x Ethylacetate x x x Furane x x x Hexadecane x x x Hexane x x x x Methanol x x x 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 .. code-block:: text $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 .. code-block:: text $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 ================ For solvation free energies, the state of the inital gas and final liquid solution can be changed with a solution state correction. This is explained in detail in the following table and in [A Universal pH Scale for All Solvents: Background, Theory, and Justification (IUPAC Technical Report)](https://doi.org/10.1515/pac-2019-0504), section 2.2. By default no solution state correction is applied (gsolv, default), which is comparable with most other solvation models (SMD, COSMO-RS, ...). For normal production runs, the option ``bar1mol`` should be used. For explicit comparisons with ``reference`` state corrected COSMO-RS, the ``reference`` option should be used (includes solvent-specific correction for infinite dilution). Solution state correction is available for the ALPB and GBSA solvation models. ================== ==================================================================== Name Definition ================== ==================================================================== gsolv (default) 1 L of ideal gas and 1 L of liquid solution bar1mol 1 bar of ideal gas and 1 mol/L liquid solution reference 1 bar of ideal gas and 1 mol/L liquid solution at infinite dilution ================== ==================================================================== The reference state can be set via .. code:: bash 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 .. code-block:: none $write gbsa=true The printout for a branched octane isomer using ALPB(Water) looks like .. code-block:: none * generalized Born model for continuum solvation # Z Born rad/Å 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.