Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in π-stacking and hydrogen-bonding behavior

Guerra, Célia Fonseca; Wijst, Tushar van der; Poater, Jordi; Swart, Marcel; Bickelhaupt, F. Matthias

doi:10.1007/s00214-009-0634-9

Cited by 123 publications

(86 citation statements)

References 68 publications

(97 reference statements)

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“…We used DFT/BLYP-D3/TZP because it has been proven many times in the past that they provide satisfactory results for non-covalent interactions [57][58][59]. The empirical Grimme correction (D3) [60] was used as implemented in the ADF program.…”

Section: Methodsmentioning

confidence: 99%

Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH3)2BH3 and KN(CH3)2BH3

2016

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Abstract:In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH 3 ) 2 BH 3 and KN(CH 3 ) 2 BH 3 was performed by means of the charge and energy decomposition method (ETS-NOCV) as well as the Interacting Quantum Atoms (IQA) approach. It was determined that both crystals are stabilized by electrostatically dominated intra-and intermolecular M¨¨¨H-B interactions (M = Li, K). For LiN(CH 3 ) 2 BH 3 the intramolecular charge transfer appeared (B-HÑLi) to be more pronounced compared with the corresponding intermolecular contribution. We clarified for the first time, based on the ETS-NOCV and IQA methods, that homopolar BH¨¨¨HB interactions in LiN(CH 3 ) 2 BH 3 can be considered as destabilizing (due to the dominance of repulsion caused by negatively charged borane units), despite the fact that some charge delocalization within BH¨¨¨HB contacts is enforced (which explains H¨¨¨H bond critical points found from the QTAIM method). Interestingly, quite similar (to BH¨¨¨HB) intermolecular homopolar dihydrogen bonds CH¨¨¨HC appared to significantly stabilize both crystals-the ETS-NOCV scheme allowed us to conclude that CH¨¨¨HC interactions are dispersion dominated, however, the electrostatic and σ/σ*(C-H) charge transfer contributions are also important. These interactions appeared to be more pronounced in KN(CH 3 ) 2 BH 3 compared with LiN(CH 3 ) 2 BH 3 .

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Section: Methodsmentioning

confidence: 99%

Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH3)2BH3 and KN(CH3)2BH3

2016

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“…The PBE functional has been shown to offer a good compromise between speed and accuracy in describing biological compounds 16 , and is frequently used in this context [17][18][19][20][21] . The LDA functional provides a less realistic description of the system's dynamics but usefully demonstrates the behaviour of the single-step perturbation where the MM and QM phase-spaces differ more markedly.…”

Section: Introductionmentioning

confidence: 99%

Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation

2014

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The use of the Zwanzig equation in the calculation of single-step perturbations to provide first principles (ab initio) Quantum Mechanics (QM) correction terms to Molecular Mechanics (MM) free energy cycles is well established. A rigorous test of the ability to converge such calculations would be very useful in this context. In this work, we perform a direct assessment of the convergence of the MM to QM perturbation, by attempting the reverse QM to MM perturbation. This required the generation of extensive QM molecular dynamics trajectories, using Density Functional Theory (DFT), within the representative biological system of a DNA Adenosine-Thymidine dimer.Over 100 ps of dynamics with the PBE functional and 6.25 ps with the LDA functional were generated. We demonstrate that calculations with total potential energies are very poorly convergent due to a lack of overlap of phase space distributions between ensembles. Whilst not theoretically rigorous, the use of interaction energies provides far superior convergence, despite the presence of non-classical charge transfer effects within the DFT trajectories. The source of poor phase space overlap for total energies is diagnosed, the approximate quantification of overlaps suggesting that even for the comparatively simple system considered here convergence of total energy calculations within a reasonable simulation time is unfeasible.

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“…To partially overtake these limitations, Grimme proposed a dispersion corrected DFT scheme (DFT-D), where an empirical C 6 R -6 term is added to usual DFT equations [78]. With this correction, DFT methods can be successfully applied to study intermolecular interactions in biological systems [79][80][81][82]. Additionally, novel meta-hybrid functionals developed by Zhao and Truhlar, and more precisely the M06-2X variation, have also been shown to adequately model non-covalent interactions [83][84][85].…”

Section: Methodsmentioning

confidence: 99%

“…2 kcal/mol larger than the predicted by M06-2X and xB97X-D. As Bickelhaupt and coworkers discussed, B3LYP often fails to reproduce the reaction barrier [77] so that this outcome is unsurprising. Additionally, these authors demonstrated that B3LYP is not adequate for mimicking biological systems involving p-stacking interactions [82]. Interestingly, B3LYP seems to overestimate the reactions barrier for the Mg-induced PT, an unexpected error sign.…”

Section: The High-layer Methodsmentioning

confidence: 99%

Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study

2012

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We investigate the descriptions of several density functional theory functionals in modeling the interactions between DNA and magnesium, the divalent cation with the largest intracellular concentration. Precisely, the metal-induced proton transfer (PT) in the guanine-cytosine base pairs is analyzed within an hybrid two-layers QM/QM approach (ONIOM) by combining several functionals: BP86, B3LYP, B97-D, xB97x-D and M06-2X, as well as the MP2 approach. The aqueous environment is simulated through, on the one hand, explicit solvent molecules present in the first hydration shell and, on the other hand, the well-known polarizable continuum model for the effects of solvation beyond this first shell. Calculations with all methods indicate that the Mg 2? cation coordination to DNA promotes a single PT reaction from the guanine to the cytosine base, characterized by a low back-reaction barrier. M06-2X and xB97x-D functionals provide consistent results for the simulation of PT reactions. These methods can be combined with B97-D functional in ONIOM partition for the description of the stacking effects.

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Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in π-stacking and hydrogen-bonding behavior

Cited by 123 publications

References 68 publications

Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH3)2BH3 and KN(CH3)2BH3

Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH3)2BH3 and KN(CH3)2BH3

Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation

Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study

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