Publication details

Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li+, Na+, K+, and Rb+ Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential

Authors

GRESH Nohad NASEEM-KHAN Sehr LAGARDERE Louis PIQUEMAL Jean-Philip ŠPONEROVÁ Judit ŠPONER Jiří

Year of publication 2017
Type Article in Periodical
Magazine / Source Journal of Physical Chemistry B
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b01836
Doi http://dx.doi.org/10.1021/acs.jpcb.7b01836
Field Physical chemistry and theoretical chemistry
Keywords INTERMOLECULAR INTERACTION ENERGIES; QUANTUM-CHEMICAL COMPUTATIONS; CLASSICAL DRUDE OSCILLATOR; KIT PROMOTER QUADRUPLEX; FORCE-FIELD; TELOMERIC DNA; DISTRIBUTED MULTIPOLES; PERTURBATION-THEORY; CRYSTAL-STRUCTURE; HARTREE-FOCK
Description Stacking of guanine quartets (GQs) can trigger the formation of DNA or RNA quadruple helices, which play numerous biochemical roles. The GQs are stabilized by alkali cations, mainly K+ and Na+, which can reside in, or channel through, the central axis of the GQ stems. Further, ion conduction through GQ wires can be leveraged for nanochemistry applications. G-quadruplex systems have been extensively studied by classical molecular dynamics (MD) simulations using pair-additive force fields or by quantum-chemical (QC) calculations. However, the non-polarizable force fields are very approximate, while QC calculations lack the necessary sampling. Thus, ultimate description of GQ systems would require long-enough simulations using advanced polarizable molecular mechanics (MM). However, to perform such calculations, it is first mandatory to evaluate the methods accuracy using benchmark QC. We report such an evaluation for SIBFA polarizable MM, bearing on the channeling (movement) of an alkali cation (Li+, Na+, K+, or Rb+) along the axis of two stacked G quartets interacting with either one or two ions. The QC energy profiles display markedly different features depending upon the cation but can be retrieved in the majority of cases by the SIBFA profiles. An appropriate balance of first-order (electrostatic and short-range repulsion) and second-order (polarization, charge-transfer, and dispersion) contributions within Delta E is mandatory. With two cations in the channel, the relative weights of the second-order contributions increase steadily upon increasing the ion size. In the G8 complexes with two K+ or two Rb+ cations, the sum of polarization and charge-transfer exceeds the first order terms for all ion positions.
Related projects: