TY - JOUR
T1 - Theoretical studies on the intermolecular interactions of potentially primordial base-pair analogues
AU - Šponer, Judit E.
AU - Vázquez-Mayagoitia, Álvaro
AU - Sumpter, Bobby G.
AU - Leszczynski, Jerzy
AU - Šponer, Jiří
AU - Otyepka, Michal
AU - Banáš, Pavel
AU - Fuentes-Cabrera, Miguel
PY - 2010/3/8
Y1 - 2010/3/8
N2 - Recent experimental studies on the Watson-Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two N-H⋯O hydrogen bonds separated by one N-H⋯N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitais and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.
AB - Recent experimental studies on the Watson-Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two N-H⋯O hydrogen bonds separated by one N-H⋯N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitais and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.
KW - Ab initio calculations
KW - Base pairing
KW - Molecular dynamics
KW - Origin of life
KW - Prebiotic chemistry
UR - http://www.scopus.com/inward/record.url?scp=77649219347&partnerID=8YFLogxK
U2 - 10.1002/chem.200902068
DO - 10.1002/chem.200902068
M3 - Article
C2 - 20119984
AN - SCOPUS:77649219347
SN - 0947-6539
VL - 16
SP - 3057
EP - 3065
JO - Chemistry - A European Journal
JF - Chemistry - A European Journal
IS - 10
ER -