Investigation of hydrogen bonding in small nucleobases using DFT, AIM, NCI and NBO technique

Mazumdar, Pradyumna; Kashyap, Angarag; Choudhury, Diganta

doi:10.1016/j.comptc.2023.114188

Cited by 10 publications

(6 citation statements)

References 43 publications

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“…Finally, for GT2 there are hydrogen bonds:

CH\cdots \mathbf{O}

and

NH\cdots \mathbf{N}

. The findings reported by Choudhury et al [66] support this information.…”

Section: Resultsmentioning

confidence: 59%

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Evaluation of the electronic density at critical points of hydrogen bonds: PM7 a good alternative to ab‐initio methods

Soriano‐Agueda

2024

Int J of Quantum Chemistry

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Hydrogen bonds are of vital importance in the formation and functioning of organic molecules; their characterization with theoretical tools is a task of interest to the scientific community. Commonly, the electron density at the bond critical point is used to characterize bonds. Generally this task is carried out with ab‐initio methods. In this study, the PM7 semi‐empirical approach is used to evaluate the quality of the electron density at the hydrogen bond critical points (HBCPs). The research takes into account dimers, nucleobases and alpha‐helices bonded by hydrogen bonds: , , , , , and . The results are compared with second‐order Møller–Plesset and density functional theory. The findings demonstrate that PM7 is a reliable alternative for explaining the electron density trends at the HBCPs.

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“…Finally, for GT2 there are hydrogen bonds:

CH\cdots \mathbf{O}

and

NH\cdots \mathbf{N}

. The findings reported by Choudhury et al [66] support this information.…”

Section: Resultsmentioning

confidence: 59%

“… Note : In the case of KS‐DFT, the methodology used by Choudhury et al [66] is:

\omega

B97XD/6‐311++G(2d,2p). All values in a.u. …”

Section: Resultsmentioning

confidence: 99%

Evaluation of the electronic density at critical points of hydrogen bonds: PM7 a good alternative to ab‐initio methods

Soriano‐Agueda

2024

Int J of Quantum Chemistry

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“…It is well known that DFT is a useful method to investigate the intermolecular hydrogen bonding and can recognize the action sites clearly [51,52]. Therefore, DFT calculations were performed on the AA-cytosine system in the liquid phase.…”

Section: Molecular Geometrymentioning

confidence: 99%

“…QTAIM was also proved to be an effective method to study the nature of intermolecular hydrogen bonding [51,52]. In this system, QTAIM analyses were conducted on the twelve AA-cytosine complexes.…”

Section: Qtaim Analysesmentioning

confidence: 99%

“…), sign (λ 2 )ρ and δ(g) (a.u.) at BCPs and binding energies (E HB , kcal/mol) of hydrogen bonding in AA-cytosine complexes analysis was shown to be e cient for studying intermolecular and intramolecular hydrogen bonding, for which the second-order perturbation stabilization energies E 2 was associated with the existence of hydrogen bonding[51,57, 58]. To further reveal the property of the hydrogen bonding, NBO were performed and the orbitals of the electron donor and acceptor in twelve AA-cytosine complexes and their E 2 values (kcal/mol) were listed in Table2.…”

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confidence: 99%

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Experimental and Theoretical Study on the Hydrogen Bonding between Ascorbic Acid and Cytosine

Li,

Yang,

Wang

et al. 2023

Preprint

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The intermolecular interactions of DNA/RNA with drugs exhibit important applications in human health and drug design. We investigated the interaction between ascorbic acid (AA), a commonly used drug in clinic, and cytosine, an important base of nucleic acids in DNA/RNA, in aqueous solution by cyclic voltammetry (CV), 1H nuclear magnetic resonance (1H NMR), density functional theory (DFT), quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) and independent gradient model based on Hirshfeld partition (IGMH). The CV and 1H NMR results revealed that the hydroxyl groups on enediol of AA interacted with cytosine, making the electro-oxidation of AA difficult to occur and the downfield shift of H atoms (CH) on cytosine ring. Quantum chemistry calculations further proved the existence of O-H···N, O-H···O, C-H···N, C-H···O and N-H···O hydrogen bonding in the mixed system. It was found that the H atoms (H9 and H11) on enediol of AA, the N atom (N31) and carbonyl oxygen atom (O32) on the cytosine ring were the main action sites, for which H11 and N31 are more prone to be interacted with than H9 and O32.

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Investigating Hydrogen Bonding Interactions in Aniline‐Acetone Binary Mixture through Molecular Dynamics Simulations

Ajmal Rahman,

Abdulkareem,

Swathi

et al. 2024

ChemistrySelect

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Binary liquid systems serve as valuable prototypes for comprehending biologically and chemically relevant properties of hydrogen bonds, revealing both noteworthy patterns and anomalies in their behaviour. Aniline, acetone and their binary mixtures with other liquids are used in various industrial processes, drug design, and as cleaning agents. This study is a molecular dynamics exploration of aniline and acetone binary mixture, over a concentration range of 9 : 1–1 : 9 for each component. The investigation includes employing techniques such as radial distribution function (RDF), coordination number calculation, hydrogen bond statistics, and graph theoretical analysis (GTA) through the NetworkX module in python, cluster analysis, Voronoi entropy calculation, interaction energy calculation and FTIR spectroscopy for all concentrations studied. The results uncover a compelling trend: a decrease in the number of hydrogen bonds as the concentration of acetone increases. Additionally, increased acetone concentration correlates positively with the breakdown of larger and more complex hydrogen‐bonded structures, indicating the formation of small hydrogen‐bond structures.

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Investigation of hydrogen bonding in small nucleobases using DFT, AIM, NCI and NBO technique

Cited by 10 publications

References 43 publications

Evaluation of the electronic density at critical points of hydrogen bonds: PM7 a good alternative to ab‐initio methods

Evaluation of the electronic density at critical points of hydrogen bonds: PM7 a good alternative to ab‐initio methods

Experimental and Theoretical Study on the Hydrogen Bonding between Ascorbic Acid and Cytosine

Investigating Hydrogen Bonding Interactions in Aniline‐Acetone Binary Mixture through Molecular Dynamics Simulations

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