Protonation

crest is also a useful tool for protonating and deprotonating structures. Both can also be combined to tautomerize structures. In the following, we will try this for the dipeptide consisting of alanine and glycine (Ala-Gly).

20

C     2.081440     0.615100    -0.508430
C     2.742230     1.824030    -1.200820
N     4.117790     1.799870    -1.190410
C     4.943570     2.827040    -1.822060
C     6.440080     2.569360    -1.637600
O     7.351600     3.252270    -2.069090
N     0.610100     0.695090    -0.538780
O     2.095560     2.724940    -1.739670
O     6.705220     1.463410    -0.897460
H     0.303080     1.426060     0.103770
H     0.338420     1.050680    -1.460480
C     2.488753    -0.593400    -1.198448
H     2.416500     0.557400     0.532050
H     4.614100     1.081980    -0.670550
H     4.699850     3.794460    -1.373720
H     4.722890     2.844690    -2.894180
H     7.687400     1.448620    -0.860340
H     2.029201    -1.457008    -0.719999
H     2.170233    -0.542411    -2.238576
H     3.572730    -0.688405    -1.154998

Protonation

Protonation screening can be requested with:

crest struc.xyz --protonate

This uses GFN2-xTB by default. All protomers found by crest are stored in protonated.xyz.

Compute the protomers for Ala-Gly and determine the energetic ordering. Does the lowest protomer align with chemical intuition?

Deprotonation

Similar to protonation, the deprotonation screening for Ala-Gly can be invoked with:

crest struc.xyz --deprotonate

All found structures are stored in deprotonated.xyz.

Compute the protomers for Ala-Gly and determine the energetic ordering.

Combining Protonation and Deprotonation

crest can combine the protonation and deprotonation screenings to find tautomers.

crest struc.xyz --tautomerize

The found tautomers will be stored at tautomers.xyz. Compute and check all the tautomers. Can you find the zwitterion? If not, why?