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Related Concept Videos

Stereoisomerism02:52

Stereoisomerism

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Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula.
Transition metal complexes often exist as geometric isomers, in which the same atoms are connected through the same types of bonds but with differences in their orientation in space. Coordination complexes with two different ligands in the cis and trans positions from a ligand of interest form isomers. For example, the octahedral [Co(NH3)4Cl2]+ ion has two isomers (Figure 1) In the cis...
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Metal-Ligand Bonds02:51

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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.
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Crystal Field Theory - Octahedral Complexes02:58

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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...
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Ligand Binding Sites02:40

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Ligand Binding Sites02:40

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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...
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Complexometric Titration: Ligands00:43

Complexometric Titration: Ligands

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Different monodentate and polydentate ligands are used as complexing agents in complexometric titration reactions. The formation of complexes by mono- and bidentate ligands involves two or more intermediate steps, limiting their use as complexing agents. In comparison, polydentate ligands can form complexes with metal ions in a single-step process, facilitating sharper end points. This means polydentate ligands, such as amino carboxylic acid derivatives, are most commonly employed in...
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Related Experiment Video

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Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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AceDRG: a stereochemical description generator for ligands.

Fei Long1, Robert A Nicholls1, Paul Emsley1

  • 1Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England.

Acta Crystallographica. Section D, Structural Biology
|February 9, 2017
PubMed
Summary

AceDRG derives stereochemical information for small molecules using atom typing from the Crystallography Open Database. This program generates ideal bond lengths, angles, and conformations for ligands, aiding structural refinement and model building.

Keywords:
AceDRGCrystallography Open DatabaseRDKitligand chemistryrefinement

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Area of Science:

  • Computational chemistry and structural biology.

Background:

  • Accurate stereochemical information is crucial for small molecule structure determination and refinement.
  • Existing methods may lack comprehensive data for diverse chemical environments.

Purpose of the Study:

  • To develop AceDRG, a program for deriving stereochemical information of small molecules.
  • To create a standardized, machine-readable database of chemical and topological environments.
  • To facilitate ligand incorporation in structural biology workflows.

Main Methods:

  • Utilizes local chemical and topological environment-based atom typing.
  • Derives and organizes bond lengths and angles from the Crystallography Open Database (COD).
  • Employs RDKit for chemistry perception and file format interpretation (SMILES, mmCIF, SDF, MOL, MOL2).

Main Results:

  • Classified all atoms, bonds, and angles from the COD based on generated atom types.
  • Generated machine-readable tables of stereochemical data freely available from CCP4.
  • AceDRG successfully derives ideal bond lengths, angles, plane groups, aromaticity, and chirality.

Conclusions:

  • AceDRG provides essential stereochemical information for ligands, enhancing structural refinement.
  • The generated data and coordinate sets are compatible with major refinement and model-building software (REFMAC5, Coot, PHENIX, BUSTER).
  • AceDRG streamlines the process of incorporating small molecules into crystallographic models.