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www.nextnano.com/documentation/tools/nextnano3/reference/input_file/keywords/buffer-solutions.html

 

Buffer solutions: To control pH values in electrolytes.

It is possible to overwrite the database entries of $buffer-solutions by this keyword and its specifiers in the input file. You can also define a completely new buffer which is not contained in the database. If you overwrite a buffer that is contained in the database, it is necessary that you include all specifiers, including the ones that you do not want to overwrite. The program then uses all the values given in the input file and ignores all database entries.

 

!------------------------------------------------------!
$buffer-solutions                          optional    !
 buffer-name             character         required    !
 number-of-ions          integer           required    !
 ion-valency             double_array      required    !
 ion-name-1              character         required    !
 ion-name-2              character         required    !
 ion-name-3              character         optional    !
(only necessary for some buffers, e.g. PBS)
 ion-name-4              character         optional    !
(only necessary for some buffers, e.g. PBS)
 pKa                     double_array      required    !
pKa at 25░ C ( = 298.15 K)
 dpKa_dT                 double_array      required    !
d pKa / d T
 z_acid                  double_array      required    !
charge on the conjugate acid species
$end_buffer-solutions                      optional    !
!------------------------------------------------------!

 

Syntax

 

Example 1: MOPS

!------------------------------------------------!
$buffer-solutions                                !
                                                 !
 buffer-name    = MOPS                           !
MOPS  (C7H15NO4S)  +  NaOH
 number-of-ions = 2                              !
 ion-valency    = -1d0  +1d0                     !
(C7H14NO4S)-   Na+
 ion-name-1     = Mops^-                         !  C7H15NO4S <==> (C7H14NO4S)- + H+
 ion-name-2     = Na^+                           !
 pKa            = 7.31d0                         !
pKa at 25░ C ( = 298.15 K)
                                                 ! (Note: This pKa is thermodynamic value. The working pKa' is 7.20.)
 dpKa_dT        = -0.011d0                       !
d pKa   / d T
 z_acid         = 0d0                            !
charge on the conjugate acid species (0 = C7H15NO4S)
                                                 !
$end_buffer-solutions                            !
!------------------------------------------------!

 

Example 2: PBS (phosphate buffer)

The phosphate buffer is special (and thus more complicated) because it consists of three pKa values (and it thus has four different ions).

!------------------------------------------------!
$buffer-solutions                                !
                                                 !
 buffer-name    = PBS                            !
PBS (phosphate buffer)
 number-of-ions = 4                              !
 ion-valency    = -1d0  -2d0  -3d0  1d0          !
(H2PO4)-     (HPO4)2-     (PO4)3-     Na+
 ion-name-1     = H2PO4^-                        ! NaH2PO4 <==> (H2PO4)- +   Na+
 ion-name-2     = HPO4^2-                        !
Na2HPO4 <==> (HPO4)2- + 2 Na+
 ion-name-3     = PO4^3-                         !
 ion-name-4     = Na^+                           !
 pKa            = 2.15d0     7.21d0    12.33d0   !
pKa,1    pKa,2    pKa,3    at 25░ C ( = 298.15 K)
 dpKa_dT        = 0.0044d0  -0.0028d0  -0.026d0  !
d pKa   / d T
 z_acid         = 0d0       -1d0       -2d0      !
charge on the conjugate acid species (0 = H3PO4, -1 = (H2PO4)- , -2 = (HPO4)2-)
                                                 !
$end_buffer-solutions                            !
!------------------------------------------------!

 

For the explanations of the specifiers, please have a look at the database section of the keyword $buffer-solutions.