Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters.

Jinfeng Liu1, Lian-Wen Qi1, John Z H Zhang2,3,4

  • 1State Key Laboratory of Natural Medicines, Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University , Nanjing, 210009, China.

Journal of Chemical Theory and Computation
|April 6, 2017
PubMed
Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Predicting Nirmatrelvir Resistance in SARS-CoV-2 M<sup>pro</sup> Mutants with an Integrated Computational Framework.

The journal of physical chemistry. B·2026
Same author

FragScan: A Quantitative Fragment Scanning Strategy for Rational Drug Discovery.

Journal of chemical information and modeling·2026
Same author

SAKE-PP: A Spatial-Attention Equivariant Network for Accurate Ranking of Protein-Protein Interaction Models.

JACS Au·2026
Same author

Recent Advances in Computer-Aided Drug Design and Drug Discovery.

Molecules (Basel, Switzerland)·2026
Same author

Semiconductor Superlattice with Remarkable Raman Enhancement for Ultrafast Culture-Free Sensing of Multiple Pathogens.

Journal of the American Chemical Society·2026
Same author

Real-time visualization of collagen assembly uncovers metastable properties in hierarchical organization.

Nature communications·2026

The electrostatically embedded generalized molecular fractionation (EE-GMF) method accurately calculates energies for large ion-water clusters. This approach significantly reduces computational cost while maintaining high accuracy for quantum mechanical (QM) interactions.

Area of Science:

  • Computational chemistry
  • Physical chemistry
  • Quantum mechanics

Background:

  • Calculating quantum mechanical (QM) energies for ion-water clusters is computationally demanding.
  • Fragmentation methods are common for smaller systems but less explored for large ion-water clusters due to significant many-body QM interactions and charge-transfer effects.

Purpose of the Study:

  • To apply and validate the electrostatically embedded generalized molecular fractionation (EE-GMF) method for accurate QM energy calculations of large ion-water clusters.
  • To assess the impact of fragment size and interaction thresholds on computational accuracy and cost.

Main Methods:

  • Utilized the EE-GMF method for full QM calculations on large ion-water clusters (up to 15 Na+, 15 Cl-, 119 water molecules).
  • Systematically validated the method using varying fragment sizes and distance thresholds (6 Å) for two-body and three-body QM interactions.

Related Experiment Videos

  • Performed calculations at various ab initio levels: HF, B3LYP, M06-2X, and MP2.

    • Main Results:

    • EE-GMF provides accurate ground-state energies for large ion-water clusters with significantly reduced computational cost.
    • Deviations from full system calculations were within a few kcal/mol.
    • Energy calculations converged with distance thresholds > 6 Å for both two-body and three-body QM interactions, highlighting the importance of three-body interactions.

    Conclusions:

    • The EE-GMF method is a computationally efficient and accurate approach for large ion-water clusters.
    • Three-body interactions are crucial for accurate energy calculations in these systems.
    • EE-GMF can reliably reproduce relative energy profiles of ion-water clusters.