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

J 2017

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

GRESH, Nohad; Sehr NASEEM-KHAN; Louis LAGARDERE; Jean-Philip PIQUEMAL; Judit ŠPONEROVÁ et al.

Základní údaje

Originální název

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

Autoři

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

Vydání

Journal of Physical Chemistry B, WASHINGTON, AMER CHEMICAL SOC, 2017, 1520-6106

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.146

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/17:00096979

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

INTERMOLECULAR INTERACTION ENERGIES; QUANTUM-CHEMICAL COMPUTATIONS; CLASSICAL DRUDE OSCILLATOR; KIT PROMOTER QUADRUPLEX; FORCE-FIELD; TELOMERIC DNA; DISTRIBUTED MULTIPOLES; PERTURBATION-THEORY; CRYSTAL-STRUCTURE; HARTREE-FOCK

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 16. 6. 2017 14:07, Mgr. Eva Špillingová

Anotace

V originále

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.

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

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. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2017, roč. 121, č. 16, s. 3997-4014. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.7b01836.

@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 = {https://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://doi.org/10.1021/acs.jpcb.7b01836.

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