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Related Concept Videos

Coordination Number and Geometry02:57

Coordination Number and Geometry

For transition metal complexes, the coordination number determines the geometry around the central metal ion. Table 1 compares coordination numbers to molecular geometry. The most common structures of the complexes in coordination compounds are octahedral, tetrahedral, and square planar.
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
Valence Bond Theory02:42

Valence Bond Theory

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...
Colors and Magnetism03:02

Colors and Magnetism

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 eye.
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

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...
Coordination Compounds and Nomenclature02:54

Coordination Compounds and Nomenclature

In most main group element compounds, the valence electrons of the isolated atoms combine to form chemical bonds that satisfy the octet rule. For instance, the four valence electrons of carbon overlap with electrons from four hydrogen atoms to form CH4. The one valence electron leaves sodium and adds to the seven valence electrons of chlorine to form the ionic formula unit NaCl (Figure 1a). Transition metals do not normally bond in this fashion. They primarily form coordinate covalent bonds, a...

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Related Experiment Video

Updated: May 22, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

FindGeo: a tool for determining metal coordination geometry.

Claudia Andreini1, Gabriele Cavallaro, Serena Lorenzini

  • 1Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. andreini@cerm.unifi.it

Bioinformatics (Oxford, England)
|May 5, 2012
PubMed
Summary

FindGeo is a new tool that determines the coordination geometry of metals in biological structures. It accurately identifies metal-coordinating atoms and their geometric arrangements, improving data reliability.

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Last Updated: May 22, 2026

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Metals are crucial for protein and nucleic acid structure and function.
  • Accurate determination of metal coordination geometry is essential for understanding biological roles.
  • Current methods for retrieving this information from literature are often incomplete or inaccurate.

Purpose of the Study:

  • To develop a tool for rapid and accurate determination of metal coordination geometry in biological macromolecules.
  • To provide a reliable method for analyzing metal-ligand interactions in structural data.

Main Methods:

  • Developed FindGeo, a computational tool for geometry determination.
  • Utilizes superposition of metal-coordinating atoms against a library of ideal geometries.
  • Ranks geometries using Root Mean Square Deviation (RMSD) for best fit assignment.

Main Results:

  • FindGeo accurately determines the coordination geometry of selected or all metals within a structure.
  • Provides a standardized and reliable method for assessing metal coordination environments.
  • Overcomes limitations of literature-based information retrieval.

Conclusions:

  • FindGeo offers a valuable solution for researchers studying metalloproteins and nucleic acids.
  • Enhances the accuracy and accessibility of critical structural information regarding metal coordination.
  • Facilitates a deeper understanding of metal-specific roles in biological systems.