Substituted adenine quartets: interplay between substituent effect, hydrogen bonding, and aromaticity

Szatyłowicz, Halina; Marek, Paulina H.; Stasyuk, Olga A.; Krygowski, Tadeusz M.; Solà, Miquel

doi:10.1039/d0ra04585c

Cited by 6 publications

(7 citation statements)

References 52 publications

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“…Comparison of HOMA5 and HOMA6 values for the substituted adenine monomers (with NO 2 , Cl, F, H, Me, NH 2 ) with their values for adenine tetramers (A 4 ) clearly shows that π-electron system of the five-membered rings is almost not affected during the tetramer formation, in contrast to π-electron system of the six-membered rings. 103 Among different types of adenine quartet, aromaticity of both adenine rings in A 4 -N3 tetramer (Scheme 8) is more sensitive to electronic nature of the substituents than in other tetramers. In general, to increase aromaticity of the five-membered rings the electron-accepting substituents should be introduced at the C2 or C8 positions, or the electron-donating substituent at the N9 position.…”

Section: Quartetsmentioning

confidence: 99%

Aromaticity of nucleic acid bases

Szatyłowicz

Stasyuk

Solà

et al. 2020

WIREs Comput Mol Sci

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3D shape and the resulting physicochemical properties of double‐helical DNA/RNA structures are determined not only by individual nucleobases, but also by their additive intermolecular interactions. Energetic contribution from aromatic π–π stacking to the stabilization of DNA/RNA is not small and sometimes even comparable to that from H‐bonding. The basis of the stacking interactions lies in the π‐electron structure of individual nucleobases, which can be described by various aromaticity indices. Heteroatoms and exocyclic functional groups make the electronic structure of nucleobases different from aromatic hydrocarbons. Consequently, the cyclic π‐electron delocalization is not the only factor responsible for the relative stability of their tautomers. This review puts the spotlight on interplay between aromaticity of purine and pyrimidine nucleobases and their tautomeric preferences, as well as on the effects of different noncovalent interactions (hydrogen bonding, metal ion coordination, and π–π stacking) on π‐electron delocalization of five‐ and six‐membered rings in individual nucleobases and their complexes. This article is categorized under: Structure and Mechanism > Molecular Structures Electronic Structure Theory > Density Functional Theory

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Section: Quartetsmentioning

confidence: 99%

Aromaticity of nucleic acid bases

Szatyłowicz

Stasyuk

Solà

et al. 2020

WIREs Comput Mol Sci

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“…[29] Recently, Rodgers et al, [30] have also shown that 5-methylation on protonated cytidine dimers increases its hydrogen bonding energy. Besides, Szatylowicz et al [31] have analyzed the effects of substituents like NO 2 , Cl, F, H, CH 3 , and NH 2 in three remote positions of adenine and its three cyclic tetramers. In one of their complexes with a nitro group, they have also shown that the presence of side weak interactions can increase the stability of the quartet.…”

Section: Introductionmentioning

confidence: 99%

“…Recently, Rodgers et al., [30] have also shown that 5‐methylation on protonated cytidine dimers increases its hydrogen bonding energy. Besides, Szatylowicz et al [31] . have analyzed the effects of substituents like NO 2 , Cl, F, H, CH 3 , and NH 2 in three remote positions of adenine and its three cyclic tetramers.…”

Section: Introductionmentioning

confidence: 99%

Impact of Covalent Modifications on the Hydrogen Bond Strengths in Diaminotriazine Supramolecules

et al. 2022

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Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In this work, we have computationally investigated how substituents can be exploited to improve the binding strength of M supramolecules. Two types of covalent modifications were studied: the substitution of an H atom within an amine group −NHR, and the replacement of the whole −NH2 group (R=H, F, CH3 and COCH3). Through our dispersion‐corrected density functional theory computations, we explain which covalent modification will show the best self‐assembling capabilities, and why the binding energy is enhanced. Our charge density and molecular orbital analyses indicate that the best substituents are those that generate a charge accumulation on the endocyclic N atom, providing an improvement of the electrostatic attraction. At the same time the substituent assists the main N−H⋅⋅⋅N hydrogen bonds by interacting with the amino group of the other monomer. We also show how the selected group notably boosts the strength of hexameric rosettes. This research, therefore, provides molecular tools for the rational design of emerging materials based on uneven hydrogen‐bonded arrangements.

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“…The aromaticity of cyclic structures is a key parameter for their reactivity. , Aromatic rings show diamagnetism and increase the stability of the structures. In contrast, antiaromatic rings show paramagnetism and less stability.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Conformational, Structural, Magnetic, and Electronic Properties Related to Antioxidant Activity: Revisiting Flavan, Anthocyanidin, Flavanone, Flavonol, Isoflavone, Flavone, and Flavan-3-ol

2021

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Understanding the antioxidant activity of flavonoids is important to investigate their biological activities as well as to design novel molecules with low toxicity and high activity. Aromaticity is a chemical property found in cyclic structures that plays an important role in their stability and reactivity, and its investigation can help us to understand the antioxidant activity of some heterocyclic compounds. In the present study, we applied the density functional theory (DFT) to investigate the properties of seven flavonoid structures with well-reported antioxidant activity: flavan, anthocyanidin, flavanone, flavonol, isoflavone, flavone, and flavan-3-ol. Conformational, structural, magnetic, and electronic analyses were performed using nuclear magnetic resonance, ionization potentials, electron affinity, bond dissociation energy, proton affinity, frontier molecular orbitals (highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO)), and aromaticity through nucleus-independent chemical shifts to analyze these seven flavonoid structures. We revised the influence of hydroxyl groups on the properties of flavonoids and also investigated the influence of the aromaticity of these seven flavonoids on the antioxidant activity.

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Substituted adenine quartets: interplay between substituent effect, hydrogen bonding, and aromaticity

Abstract: Substituent effects on hydrogen bonds in adenine quartets and aromaticity of adenine rings depend on the quartet type. A4-N3 and A4-N7 quartets are more responsive to the electronic nature of substituents than A4-N1.

Cited by 6 publications

References 52 publications

Aromaticity of nucleic acid bases

Aromaticity of nucleic acid bases

Impact of Covalent Modifications on the Hydrogen Bond Strengths in Diaminotriazine Supramolecules

Analysis of Conformational, Structural, Magnetic, and Electronic Properties Related to Antioxidant Activity: Revisiting Flavan, Anthocyanidin, Flavanone, Flavonol, Isoflavone, Flavone, and Flavan-3-ol

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