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@article{1185380, author = {Gkionis, Konstantinos and Kruse, Holger and Platts, James and Mládek, Arnošt and Koča, Jaroslav and Šponer, Jiří}, article_location = {Washington DC}, article_number = {3}, doi = {http://dx.doi.org/10.1021/ct4009969}, keywords = {MOLECULAR-DYNAMICS SIMULATIONS; GAUSSIAN-BASIS SETS; TETRAMOLECULAR G-QUADRUPLEXES; HUMAN TELOMERIC QUADRUPLEX; AIM TOPOLOGICAL ANALYSIS; FORCE-FIELD; STRUCTURAL DYNAMICS; NUCLEIC-ACIDS; ELECTRONIC DENSITY; DIELECTRIC MEDIUM}, language = {eng}, issn = {1549-9618}, journal = {Journal of Chemical Theory and Computation}, title = {Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations}, url = {http://pubs.acs.org/doi/pdf/10.1021/ct4009969}, volume = {10}, year = {2014} }
TY - JOUR ID - 1185380 AU - Gkionis, Konstantinos - Kruse, Holger - Platts, James - Mládek, Arnošt - Koča, Jaroslav - Šponer, Jiří PY - 2014 TI - Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations JF - Journal of Chemical Theory and Computation VL - 10 IS - 3 SP - 1326-1340 EP - 1326-1340 PB - American Chemical Society SN - 15499618 KW - MOLECULAR-DYNAMICS SIMULATIONS KW - GAUSSIAN-BASIS SETS KW - TETRAMOLECULAR G-QUADRUPLEXES KW - HUMAN TELOMERIC QUADRUPLEX KW - AIM TOPOLOGICAL ANALYSIS KW - FORCE-FIELD KW - STRUCTURAL DYNAMICS KW - NUCLEIC-ACIDS KW - ELECTRONIC DENSITY KW - DIELECTRIC MEDIUM UR - http://pubs.acs.org/doi/pdf/10.1021/ct4009969 L2 - http://pubs.acs.org/doi/pdf/10.1021/ct4009969 N2 - Molecular mechanical (MM) force fields are commonly employed for biomolecular simulations. Despite their success, the nonpolarizable nature of contemporary additive force fields limits their performance, especially in long simulations and when strong polarization effects are present. Guanine quadruplex D(R)NA molecules have been successfully studied by MM simulations in the past. However, the G-stems are stabilized by a chain of monovalent cations that create sizable polarization effects. Indeed, simulation studies revealed several problems that have been tentatively attributed to the lack of polarization. Here, we provide a detailed comparison between quantum chemical (QM) DFT-D3 and MM potential energy surfaces of ion binding to G-stems and assess differences that may affect MM simulations. We suggest that MM describes binding of a single ion to the G-stem rather well. However, polarization effects become very significant when a second ion is present. We suggest that the MM approximation substantially limits accuracy of description of energy and dynamics of multiple ions inside the G-stems and binding of ions at the stem loop junctions. The difference between QM and MM descriptions is also explored using symmetry-adapted perturbation theory and quantum theory of atoms in molecules analyses, which reveal a delicate balance of electrostatic and induction effects. ER -
GKIONIS, Konstantinos, Holger KRUSE, James PLATTS, Arnošt MLÁDEK, Jaroslav KOČA and Jiří ŠPONER. Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2014, vol.~10, No~3, p.~1326-1340. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct4009969.
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