Density functional theory study of interaction, bonding and affinity of group IIb transition metal cations with nucleic acid bases

Bagchi, Sabyasachi; Mandal, Debasish; Ghosh, Debarati; Das, Abhijit K.

doi:10.1016/j.chemphys.2012.03.003

Cited by 10 publications

(8 citation statements)

References 78 publications

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“…The complexation (structure, energetics) of cytosine or cytosine-containing base pairs with metal ions has been extensively investigated [42][43][44][45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60] contrarily to the behavior upon collision of metal/cytosine complexes, which is poorly described in the literature. [61][62][63] It has also attracted much less attention than metal/uracil complexes.…”

Section: Low-energy Cid Spectra Of the [Pb(cytosine)àh] + Ionmentioning

confidence: 99%

Gas‐Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple‐Photon Dissociation Spectroscopy Study

et al. 2014

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Gas-phase interactions between Pb(2+) ions and cytosine (C) were studied by combining tandem mass spectrometry, infrared multiple photon dissociation spectroscopy, and density functional theory (DFT) calculations. Both singly and doubly charged complexes were generated by electrospray. The [Pb(C)-H](+) complex was extensively studied, and this study shows that two structures, involving the interaction of the metal with the deprotonated canonical keto-amino tautomer of cytosine, are generated in the gas phase; the prominent structure is the bidentate form involving both the N1 and O2 electronegative centers. The DFT study also points out a significant charge transfer from the nucleobase to the low-lying p orbitals of the metal and a strong polarization of the base upon complexation. The various potential energy surfaces explored to account for the fragmentation observed are consistent with the high abundance of the [PbNH2](+) fragment ion.

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Section: Low-energy Cid Spectra Of the [Pb(cytosine)àh] + Ionmentioning

confidence: 99%

Gas‐Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple‐Photon Dissociation Spectroscopy Study

et al. 2014

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“…Interactions with active centers of guanine located in major groove of DNA (N7 and O at C6 atom) have been discussed for years [26][27][28][29][30][31]. More specific interactions with other centers of guanine were also described [32][33][34]. However, despite the extensive literature on this topic, insufficient attention to effects of intermolecular interactions with different active centers of guanine tautomers on their electronic structure has been paid.…”

Section: Introductionmentioning

confidence: 99%

Aromaticity of H-bonded and metal complexes of guanine tautomers

2015

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) on structural and p-electron delocalization changes in four most stable guanine tautomers and their structural subunits has been studied in the gas phase using the B3LYP/6-311??G(2d,2p) computational level. In both cases, i.e., H-bonding and metal complexation, the strongest interactions are found in bifurcated complexes of the keto guanine tautomers. Interactions in which the functional groups participate (NH 2 or C=O) regularly lead to the greatest geometric and aromaticity changes. As a consequence, aromaticity of substituted six-membered rings is decisive for aromaticity of whole ring system in guanine tautomers. Aromaticity of guanine tautomers and their structural subunits changes in the same way (increase or decrease) depending on particular type of interactions. Graphical Abstract

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“…The ZnN7 distance is 1.978 Å, close to the value (2.00 Å) computed at the DFT level. 53,54 The distance between the O11 atom and the Zn(II) ion is 3.530 Å, and the C5N7Zn angle is 132.2°. In comparison to the QM/MM guanosine monophosphate (GMP) optimized geometry in water, 57 which is also planar, the main differences in bond distances (Table 2) are related to the C2N3 and C6O11 bonds, elongated by 0.04 and 0.06 Å, respectively.…”

Section: Identification Of the Most Favorable Zn(ii) Bindingmentioning

confidence: 99%

Water Solvated Zn(II)–Guanine Complex: Structural Aspects and Luminescence Properties

Vasconcelos Sanches de Araújo,

Borin

2023

J. Phys. Chem. A

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Understanding the role of metal ions in living organisms and their interactions with biological compounds is fundamental for our health and for developing technological devices for bioinorganic applications. In this work, structural aspects and photophysical mechanisms involved in the luminescence of the Zn(II)−guanine complex in water were studied by using computational quantum chemical methods, providing molecular-level explanations for reported experimental findings. Structural aspects were investigated with def2-SVP basis sets, Density Functional Theory, Resolution of Identity Algebraic Diagrammatic Construction in Second-Order (RI-ADC(2)), Polarizable Continuum Model (PCM), and Conductor-like Screening Model (COSMO) methods. Spectroscopic properties and photophysical deactivation mechanisms were explored with the atomic natural orbital basis sets including relativistic and semicore correlation (ANO-RCC-VDZP) basis sets, Multistate Complete-Active-Space Second-Order Perturbation Theory (MS-CASPT2), and Polarizable Continuum Model (PCM) methods. Our results indicate that Zn(II) ions bind preferentially to the N7 position, and three water molecules in its coordination sphere are sufficient for describing the photophysical properties. The complexation with Zn(II) ions and solvation effects favor fluorescence because the minimum energy region of the S 1 (L a ) ( 1 ππ*) ((L a ) min ) potential energy hypersurface is stabilized, the (L a /GS) crossing region is destabilized, and a high energetic barrier along the pathway from the (L a ) min and (L a /GS) regions hampers fast nonradiative return of the electronic population to the ground state, as observed for isolated 9H-guanine.

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Density functional theory study of interaction, bonding and affinity of group IIb transition metal cations with nucleic acid bases

Cited by 10 publications

References 78 publications

Gas‐Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple‐Photon Dissociation Spectroscopy Study

Gas‐Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple‐Photon Dissociation Spectroscopy Study

Aromaticity of H-bonded and metal complexes of guanine tautomers

Water Solvated Zn(II)–Guanine Complex: Structural Aspects and Luminescence Properties

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