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@article{1383185, author = {Gresh, Nohad and NaseemandKhan, Sehr and Lagardere, Louis and Piquemal, JeanandPhilip and Šponerová, Judit and Šponer, Jiří}, article_location = {WASHINGTON}, article_number = {16}, doi = {http://dx.doi.org/10.1021/acs.jpcb.7b01836}, 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}, language = {eng}, issn = {1520-6106}, journal = {Journal of Physical Chemistry B}, title = {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}, url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b01836}, volume = {121}, year = {2017} }
TY - JOUR ID - 1383185 AU - Gresh, Nohad - Naseem-Khan, Sehr - Lagardere, Louis - Piquemal, Jean-Philip - Šponerová, Judit - Šponer, Jiří PY - 2017 TI - 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 JF - Journal of Physical Chemistry B VL - 121 IS - 16 SP - 3997-4014 EP - 3997-4014 PB - AMER CHEMICAL SOC SN - 15206106 KW - INTERMOLECULAR INTERACTION ENERGIES KW - QUANTUM-CHEMICAL COMPUTATIONS KW - CLASSICAL DRUDE OSCILLATOR KW - KIT PROMOTER QUADRUPLEX KW - FORCE-FIELD KW - TELOMERIC DNA KW - DISTRIBUTED MULTIPOLES KW - PERTURBATION-THEORY KW - CRYSTAL-STRUCTURE KW - HARTREE-FOCK UR - http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b01836 L2 - http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b01836 N2 - 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. ER -
GRESH, Nohad, Sehr NASEEM-KHAN, Louis LAGARDERE, Jean-Philip PIQUEMAL, Judit ŠPONEROVÁ a Jiří ŠPONER. 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. \textit{Journal of Physical Chemistry B}. WASHINGTON: AMER CHEMICAL SOC, 2017, roč.~121, č.~16, s.~3997-4014. ISSN~1520-6106. Dostupné z: https://dx.doi.org/10.1021/acs.jpcb.7b01836.
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