Using Density Functional Theory To Study Neutral and Ionized Stacked Thymine Dimers

Nakarada, Đura; Etinski, Mihajlo; Petković, Milena

doi:10.1021/acs.jpca.6b06493

Cited by 7 publications

(6 citation statements)

References 64 publications

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“…The dimerization of substituted trans -1,2-bis( n -pyridyl)ethylene dihydrochloride and trans - n -stilbazole hydrochlorides has earlier been observed within the CB8 cavity experimentally by Ramamurthy et al and yielded a syn dimer. , Theoretically Gejji et al studied the dimerization within the cavitand and noticed the anti -head-to-head conformer is more stabilized inside the cavity . Furthermore, the interaction energy between the CB7 and nucleobases is much higher than the reported nucleobase dimer formation energies. − From the above results and the present work, it is clear that the CB n cavity has the ability to include two guest molecules of appropriate size; however, when guest molecules are aligned in parallel configuration, they can yield a syn head–head dimer.…”

Section: Resultsmentioning

confidence: 92%

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches

Venkataramanan

Suvitha

2017

J. Phys. Chem. B

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The encapsulation of nucleobases inside CB7 has gained prominence due to its use as anticancer and antiviral drugs. With this respect, the nonconvalent interactions existing in the nucleobases encapsulated inside the CB7 cavity have been analyzed employing the dispersion corrected density functional theory. The CBn cavity has the ability to encapsulate two guest nucleobases molecules when they are aligned in parallel configuration. The computed association energy using the two- and three-body correction method computed at B3LYP-D3 level is close to the experimental estimate. The use of dispersion corrected DFs is essential to identify the correct binding energies. The solvation energy plays a vital role in the estimation of association energy. QTAIM analysis shows that the Laplacian of the charge density (∇ρ) is negative and the presence of covalent interaction between the guest and host molecule. The NCI-RDG isosurface shows the presence of noncovalent intermolecular interactions such as van der Waals and hydrogen bonding. The existence of "splattering" of charges in guanine@CB7 molecule is responsible for its higher stability. From the AIM, NCI-RDG, and EDA results, we conclude that noncovalent and electrostatic interaction with partial covalent character exists in the intermolecular bonding between the host and the guest nucleobases. The ramification of such intermolecular bonds is reflected in the H NMR andNMR spectra.

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Section: Resultsmentioning

confidence: 92%

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches

Venkataramanan

Suvitha

2017

J. Phys. Chem. B

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“…Despite significant previous efforts on understanding the effects of methylation on base pairing, a systematic analysis on the effect of posttranscriptional methylation on stacking interactions in RNA nucleobases is not available in literature. Nevertheless, studies have analyzed the effects of base modifications on the properties of DNA in context of providing structural insights into epigenetic modifications, [17–19] or to further understand the intermolecular interactions in specific methylated, [18,20,21] canonical [16,17,19–23] and noncanonical nucleobases [24] . In addition, studies have analyzed the methylation effects on stacking of nucleobases with the aromatic rings of specific amino acids [22] .…”

Section: Introductionmentioning

confidence: 99%

Influence of the Number, Nature and Position of Methyl Posttranscriptional Modifications on Nucleobase Stacking in RNA

et al. 2021

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DFT calculations are employed to quantify the influence of the presence, number, nature, and position of posttranscriptional methylation on stacking strength of RNA bases. We carry out detailed potential energy scans of the variation in stacking energies with characteristic geometrical parameters in three categories of forty stacked dimers – canonical base homodimers (N||N), methylated base homodimers (mN||mN) and heterodimers of canonical bases and methylated counterparts (N||mN). Our analysis reveals that neutral methylation invariably enhances the stacking of bases. Further, N||mN stacking is stronger than mN||mN stacking and charged N||mN exhibit strongest stacking among all dimers. This indicates that methylations greatly enhance stacking when dispersed in RNA sequences containing identical bases. Comparison of stacks involving singly‐ and doubly‐methylated purines reveal that incremental methylation enhances the stacking in neutral dimers. Although methylation at the carbon position of neutral pyrimidine dimers greatly enhances the stacking, methylation on the 5‐membered ring imparts better stacking compared to methylation on the 6‐membered ring in adenine dimers. However, methylation at the ring nitrogen (N1) provides better stacking than the amino group (N2) in guanine dimers. Our results thus highlight subtle structural effects of methylation on RNA base stacking and will enhance our understanding of the physicochemical principles of RNA structure and dynamics.

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“…In solvents with low hydrogen-bonding capacity, as well as in gas phase, the association proceeds via formation of planar hydrogen-bonded dimers. Stacked and T-shaped structures were shown to be less stable. − The association might also proceed beyond the dimer stage, but the number of monomers in the aggregates depends on the nature of nucleobases. , The infrared spectra of hydrogen-bonded aggregates are usually measured in the region from 2800 to 3600 cm –1 in which N–H and H–N–H symmetric and asymmetric stretching vibrations are active. Their spectral red-shifts caused by hydrogen bonding depend on the bonding strength .…”

Section: Introductionmentioning

confidence: 99%

New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics

Milovanovic

Kojić

Petković

et al. 2018

J. Chem. Theory Comput.

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Nucleobases spontaneously aggregate in water by forming stacked dimers and multimers. It is assumed that the main contributions to the aggregation stem from hydrophobic and base-base dispersion interactions. By studying the uracil monomer and dimer in bulk water with the first principle molecular dynamics, we discuss dimer structure and provide evidence that stacking increases the uracil-water hydrogen bonding strength and alters the hydration structure of uracil. These changes have a significant influence on the intensity and shift of the carbonyl stretching band as revealed by simulated infrared absorption spectra of the monomer and dimer and available experimental spectra. The contributions of dipole-dipole, dispersion, and water mediated forces to the stacking are discussed. The reported findings are valuable for understanding the microscopic mechanism of heteroaromatic association in water which is relevant to a large range of chemical and biological systems.

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Using Density Functional Theory To Study Neutral and Ionized Stacked Thymine Dimers

Cited by 7 publications

References 64 publications

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches

Influence of the Number, Nature and Position of Methyl Posttranscriptional Modifications on Nucleobase Stacking in RNA

New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics

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