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Crystal Field Theory - Octahedral Complexes

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...

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Ligand Binding Sites

Ligand Binding Sites

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Determination of Crystal Structures

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...

Crystal Field Theory - Tetrahedral and Square Planar Complexes

Crystal Field Theory - Tetrahedral and Square Planar Complexes

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...

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Related Experiment Video

Updated: Apr 27, 2026

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Automated identification of crystallographic ligands using sparse-density representations.

C G Carolan¹, V S Lamzin¹

¹European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.

Acta Crystallographica. Section D, Biological Crystallography

|July 10, 2014

Summary

A new computational method automatically identifies ligands in protein structures using density maps. This technique efficiently matches molecular features, aiding drug discovery and structure determination.

Keywords:

drug design ligands macromolecular X-ray crystallography shape descriptors

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Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

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Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Area of Science:

Structural Biology
Computational Chemistry
Drug Discovery

Background:

Macromolecular crystallography is crucial for determining 3D protein structures.
Identifying bound ligands within electron density maps is challenging.
Accurate ligand identification is vital for understanding biological function and drug design.

Purpose of the Study:

To develop and validate a novel computational procedure for automatic ligand identification in macromolecular crystallography.
To assess the method's efficiency and accuracy using experimental data.

Main Methods:

Sparse parameterization of electron density clusters.
Matching pseudo-atomic grids to conformationally variant ligands.
Utilizing mathematical descriptors for molecular shape, size, and topology.

Main Results:

The procedure rapidly identified the correct ligand from a candidate database.
Successful identification was achieved on experimental data from the Protein Data Bank.
The method demonstrated high accuracy in ligand localization within electron density maps.

Conclusions:

The developed method offers an efficient and automated solution for ligand identification.
It is suitable for fragment-based drug screening and macromolecular structure completion.
This advancement can accelerate drug discovery and structural biology research.