The Ethidium-UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State
| Autor: | Pawel Dziekonski, Tomasz Janowski, Peter Pulay, Robert W. Góra, W. Andrzej Sokalski, Karol M. Langner |
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| Rok vydání: | 2015 |
| Předmět: |
chemistry.chemical_classification
Electronic correlation Intercalation (chemistry) Intermolecular force Solvation Polarizable continuum model Computer Science Applications Delocalized electron chemistry Fragmentation (mass spectrometry) Computational chemistry Chemical physics Physical and Theoretical Chemistry Counterion |
| Zdroj: | Journal of chemical theory and computation. 7(8) |
| ISSN: | 1549-9618 |
| Popis: | We report a systematic analysis of the intermolecular interactions of cationic ethidium intercalated into a UA/AU step of RNA for a single conformation based on crystallographic coordinates. Interaction energies at the MP2/6-31G** level were partitioned into electrostatic, exchange, delocalization, and correlation components. Various pairwise interaction models built from chemically intuitive fragments reproduce within a few percent values obtained when treating the intercalation site as a whole. Gas phase results are very sensitive to the charge state of the two phosphate groups, with the electrostatic term nearly tripling when the counterions are removed. But this is largely compensated by solvation, an effect represented here within the polarizable continuum model. In a few cases, more diffuse and larger basis sets as well as QCISD(T) corrections were applied in an effort to estimate plausible ethidium-nucleobase electron correlation effects. |
| Databáze: | OpenAIRE |
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