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 Concept Videos

Valence Bond Theory02:42

Valence Bond Theory

8.5K
Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
8.5K
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

26.2K
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
26.2K
Crystal Field Theory - Tetrahedral and Square Planar Complexes02:46

Crystal Field Theory - Tetrahedral and Square Planar Complexes

41.7K
Tetrahedral Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
41.7K
Colors and Magnetism03:02

Colors and Magnetism

11.6K
Color in Coordination Complexes
When atoms or molecules absorb light at the proper frequency, their electrons are excited to higher-energy orbitals. For many main group atoms and molecules, the absorbed photons are in the ultraviolet range of the electromagnetic spectrum, which cannot be detected by the human eye. For coordination compounds, the energy difference between the d orbitals often allows photons in the visible range to be absorbed and emitted, which is seen as colors by the human...
11.6K
Continuous Charge Distributions01:17

Continuous Charge Distributions

6.8K
Imagine a bucket of water. It contains many molecules, of the order of 1026 molecules. Thus, although it contains discrete elements (molecules) at the microscopic level, macroscopically, it can be considered continuous. Small volume elements of water, infinitesimal compared to the bulk of the bucket's volume, still contain many molecules. Under this framework, quantized matter is approximated as continuous for practical purposes.
The electric charge can also be subjected to an analogical...
6.8K
Complexation Equilibria: The Chelate Effect01:19

Complexation Equilibria: The Chelate Effect

470
In complexation reactions, metal atoms or cations interact with ligands to form donor-acceptor adducts called metal complexes. Ligands that bind through one donor site are monodentate, ligands with two donor sites are bidentate, and those with more than two donor sites are polydentate ligands. For example, ethylene diamine is a bidentate ligand that binds through two nitrogen donor atoms, forming a five-membered ring. EDTA is a polydentate ligand that binds through four oxygen and two nitrogen...
470

You might also read

Related Articles

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

Sort by
Same author

Beyond Single Structures: The Role of Structural Ensembles in Discrete-Continuum Modeling of Highly Charged Metal Ions.

Journal of chemical theory and computation·2026
Same author

Electron Pushing: Variants That Alter the Catalytic Distribution of Electrons in Dihydroorotate Dehydrogenase 1B from <i>Lactococcus lactis</i>.

Biochemistry·2025
Same author

Deciphering Atomic Polarizability: The Absolute Radii and Orbital Contributions Visited.

The journal of physical chemistry. A·2025
Same author

Accuracy of Discrete-Continuum Solvation Model for Cations: A Benchmark Study.

The journal of physical chemistry. B·2024
Same author

Development of Accurate Force Fields for Mg<sup>2+</sup> and Triphosphate Interactions in ATP·Mg<sup>2+</sup> and GTP·Mg<sup>2+</sup> Complexes.

Journal of chemical theory and computation·2024
Same author

Exploring Ion Polarizabilities and Their Correlation with van der Waals Radii: A Theoretical Investigation.

Journal of chemical theory and computation·2024

Related Experiment Video

Updated: Jun 10, 2025

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

5.6K

Parameterization of a Fluctuating Charge Model for Complexes Containing 3d Transition Metals.

Luke Landry1, Pengfei Li1

  • 1Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60660, United States.

The Journal of Physical Chemistry. B
|October 12, 2024
PubMed
Summary

This study introduces a faster fluctuating charge (FQ) model for accurately calculating partial atomic charges in metalloproteins containing 3d transition metals. This method accelerates simulations of crucial biological systems, improving our understanding of metalloprotein function.

More Related Videos

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
08:04

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

8.4K
Finite Element Modelling of a Cellular Electric Microenvironment
08:23

Finite Element Modelling of a Cellular Electric Microenvironment

Published on: May 18, 2021

3.4K

Related Experiment Videos

Last Updated: Jun 10, 2025

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

5.6K
Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids
08:04

Excitonic Hamiltonians for Calculating Optical Absorption Spectra and Optoelectronic Properties of Molecular Aggregates and Solids

Published on: May 27, 2020

8.4K
Finite Element Modelling of a Cellular Electric Microenvironment
08:23

Finite Element Modelling of a Cellular Electric Microenvironment

Published on: May 18, 2021

3.4K

Area of Science:

  • Computational Chemistry
  • Biophysics
  • Structural Biology

Background:

  • Metalloproteins are vital in biological processes, and molecular dynamics (MD) simulations are key to studying them.
  • Accurate partial charges, crucial for classical force fields in MD, are typically derived from time-consuming quantum mechanical (QM) calculations.
  • Fluctuating charge (FQ) models offer a faster alternative for deriving partial charges, enabling large-scale screening.

Purpose of the Study:

  • To extend a previously developed FQ model for zinc to include other essential 3d transition metals (Cr, Mn, Fe, Co, Ni) relevant to life sciences.
  • To accurately reproduce partial charges for 3d metal complexes with biologically relevant ligands.
  • To validate the FQ model's performance in MD simulations of complex metalloprotein active sites.

Main Methods:

  • Parametrization of a fluctuating charge (FQ) model using CM5 charges as the target for 3d transition metal complexes.
  • Application of the developed FQ model to derive atomic charges for metalloproteins.
  • Performance evaluation through molecular dynamics (MD) simulations of metalloprotein active sites, including those with iron-sulfur clusters and dimanganese sites.

Main Results:

  • The extended FQ model accurately reproduces partial charges for 3d transition metal complexes with biologically relevant ligands.
  • MD simulations using FQ-derived charges demonstrated excellent performance in modeling metalloprotein sites with multiple metal ions.
  • The FQ model's performance in simulations was comparable to that of RESP charges, a standard method.

Conclusions:

  • The developed FQ model provides an efficient and accurate method for deriving partial atomic charges for metalloproteins containing 3d transition metals.
  • This approach significantly accelerates the parametrization process, facilitating more extensive simulations of metalloprotein systems.
  • The study enhances the capability of computational tools for investigating the structure and function of metalloproteins in biological research.