Contains codes, plots and data used in our study of intramolecular ion pair interactions.
The benchmark set comprises 26 small molecules made of a cationic terminal and an anionic terminal connected by a linker. We select three groups for each unit.
C1: ammonium (-NH3+), C2: formamidinium ( [-C(NH2)=NH2]+ ), C3: guanidinium ( [-C(NH2)(NH2)=NH2]+ )
A1: hydroxy ([-O]-), A2: carboxylate ( [-C(=O)O]- ), A3: sulphate ( [-S(=O)(=O)O]- )
L1: -(CH2)3-, L2: -(CH2)6-, L3: -(CH2)9-
Overall we can have 27 ion-pair molecules {C1,C2,C3} x {L1,L2,L3} x {A1,A2,A3}. Out of these, C2-L1-A1 is left out because it could not be converged in the ion-pair geometry. The rest comprise the benchmark26 set. For these, structures were relaxed with N-H restraints to converge to ion-pair systems. These calculations were performed with the Orca code at the wB97X-D3/def2TZVP level. The input/output files are here https://github.com/moldis-group/SI_IntraIonPair/tree/main/DFT_IO_files_opt_benchmark26.
Intramolecular interaction energies for the 26 benchmark systems are extracted from PSI4 (ver. 1.1) output files with notebooks/collect_ISAPT.ipynb and collected in csv_files/benchmark26_ISAPT_Psi4_1.1.csv
ISAPT results with PSI4 (ver. 1.4) are collected in csv_files/benchmark26_ISAPT_Psi4_1.4.csv
Across PSI4 versions, the results do not vary.
Comparison of results from various levels of theory in vacuum phase is done with notebooks/collect_vacuum_phase_benchmark26.ipynb
For all four peptides, the ion-pair interaction energies are calculated with notebooks/Case_study_large_peptide.ipynb
Understanding the role of intramolecular ion-pair interactions in conformational stability using an ab initio thermodynamic cycle
Sabyasachi Chakraborty, Kalyaneswar Mandal, and Raghunathan Ramakrishnan
https://doi.org/10.1021/acs.jpcb.2c06803
Journal of Physical Chemistry B 127 (2023) 648-660.