# Intramolecular Versus Intermolecular Bonding in Drug Gemcitabine and Nucleobases: A Computational Study

https://mdr.nims.go.jp/datasets/34ac21b5-f0ff-4f34-bca1-54f5febdbc74

## File

- [molecules30(2025)2732.pdf](https://mdr.nims.go.jp/filesets/a325e22b-b9b6-4427-950e-a84d854e8550/download) ([Detail](https://mdr.nims.go.jp/filesets/a325e22b-b9b6-4427-950e-a84d854e8550.md))

## Id

34ac21b5-f0ff-4f34-bca1-54f5febdbc74

## Local identifier



## Visibility

open_to_public

## State

published

## Created at

2025-11-26T02:53:55.106080Z

## Updated at

2025-11-26T23:30:18.733302Z

## Published at

2025-11-26T23:24:02.703820Z

## Doi



## First published url

https://doi.org/10.3390/molecules30132732

## Date published

2025-06-25

## Recorded date published



## Resource type

journal_article

## Manuscript type

vor

## Collection



## Title

- title: 'Intramolecular Versus Intermolecular Bonding in Drug Gemcitabine and Nucleobases:
    A Computational Study'
  title_type: original
  lang: en

## Description

- description: "The adsorption of the drug gemcitabine on nucleobases was investigated
    using a dispersioncorrected density functional theory (DFT) study. The planar
    structure of complexes is more stable than those with stacked and buckle-angled
    configurations. The complexes were found to possess at least two intermolecular
    hydrogen bonds. The binding energy and interaction energy are both negative, with
    the highest values observed for the gemcitabine–guanine and the lowest in the
    gemcitabine–thymine complex. The complex formation was found to be an enthalpy-driven
    process. Pyrimidine nucleobases have a lower enthalpy of formation than purine
    nucleobases. The computed HOMA and NICS values on the gemcitabine–nucleobase complexes
    show a substantial increase compared to the pristine nucleobases. \r\nAn MESP
    analysis of the complexes shows a directional interaction and electron density
    shift between the gemcitabine and the nucleobases. A QTAIM analysis indicates
    that the intermolecular hydrogen bonds have a partial covalent character. The
    computed bond energy demonstrates that intermolecular NH···N bonds are more potent
    than other bonds. An energy decomposition analysis using the DLPNO−CCSD(T) method
    indicates that the complexes exhibit a substantial electrostatic attraction, and
    dispersion contributes the least towards the system stability. The intermolecular
    bonds are stronger than the intramolecular bonds in the drug–nucleobase complexes.
    The strength of intramolecular bonds is determined by the deformation of the gemcitabine
    ring during the complex formation. \r\n"
  description_type: abstract
  lang: und

## Creator

- name: Natarajan Sathiyamoorthy Venkataramanan
  role: author
- name: Ambigapathy Suvitha
  role: author
- name: Ryoji Sahara
  role: author
  orcid: https://orcid.org/0000-0003-0788-2985
  organization: National Institute for Materials Science

## Contact agent



## Publisher

organization: MDPI AG

## Managing organization



## Keyword

- subject: drug
  schema: not_defined
- subject: nucleobases
  schema: not_defined
- subject: non-covalent interactions
  schema: not_defined
- subject: DFT calculations
  schema: not_defined
- subject: energy decomposition analysis
  schema: not_defined

## Rights

- identifier: https://creativecommons.org/licenses/by/4.0/

## Other identifier(s)



## Data origin

- data_origin_type: other

## Embargo



## Journal

- title: Molecules
  issn: '14203049'
  volume: '30'
  issue: '13'
  article_number: '2732'

## Conference



## Related item



## Funding



## Instrument



## Instrument operator



## Instrument managing organization



## Measurement method



## Specimen



## Chemical composition



## Structure for specimen



## Structural feature for specimen



## Specific property for specimen



## Process for specimen treatment



## Computational method



## Energy level/transition state



## Software



## Custom property



## Fileset

- id: a325e22b-b9b6-4427-950e-a84d854e8550
  filename: molecules30(2025)2732.pdf
  content_type: application/pdf
  size: 1947781
  md5: a57fe09e4147a2d6cb85ae5eecd60ad0

## Thumbnail

fileset_id: a325e22b-b9b6-4427-950e-a84d854e8550
filename: molecules30(2025)2732.pdf