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

Hydrogen bonds in molecular mechanics force fields.

Jan Hermans1

  • 1Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599.

Advances in Protein Chemistry
|April 4, 2006
PubMed
Summary

Molecular mechanics force fields face challenges in accurately describing polar interactions. Current methods struggle with simple point charges, especially for hydrogen bonds, prompting research into improved models.

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

The amino acid dipeptide: small but still influential after 50 years.

Proceedings of the National Academy of Sciences of the United States of America·2011
Same author

Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state.

The journal of physical chemistry. A·2007
Same author

Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data.

Acta biochimica Polonica·2006
Same author

Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR.

Journal of biomolecular NMR·2005
Same author

Protein imperfections: separating intrinsic from extrinsic variation of torsion angles.

Acta crystallographica. Section D, Biological crystallography·2004
Same author

Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling.

Methods in enzymology·2003

Area of Science:

  • Computational chemistry
  • Molecular modeling

Background:

  • Molecular mechanics force fields are essential for simulating molecular behavior.
  • Current force fields often use simple point charge models.
  • These models inadequately represent interactions involving polar molecules and hydrogen bonds.

Purpose of the Study:

  • To review the formulation and parametrization of molecular mechanics force fields.
  • To highlight technical and inherent problems in current models.
  • To discuss advancements in describing polar interactions.

Main Methods:

  • Review of existing literature on force field development.
  • Analysis of the limitations of simple point charge models.
  • Examination of current strategies for improving polar interaction descriptions.

Related Experiment Videos

Main Results:

  • Simple point charge models are insufficient for accurate polar interaction energies and forces.
  • Inadequacies are particularly evident in interactions between polar molecules and within macromolecules (e.g., hydrogen bonds).
  • Ongoing research focuses on enhancing the representation of polar forces.

Conclusions:

  • Improvements in force field parametrization are crucial for accurate molecular simulations.
  • Addressing the limitations of polar interaction descriptions is a key area of research.
  • Developing more sophisticated models is necessary for capturing complex molecular interactions.