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Related Concept Videos

Stereoisomerism02:52

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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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Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
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The Pople nomenclature system classifies spin systems based on the difference between their chemical shifts. Coupled spins are denoted by capital letters with subscripts indicating the number of equivalent nuclei. When the coupled nuclei have well-separated chemical shifts, they are assigned letters that are far apart in the alphabet, such as A and X. When the difference in chemical shifts is small, coupled nuclei are named using adjacent letters of the alphabet (AB, MN, or XY).
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Isotopes01:12

Isotopes

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Elements have a set number of protons that determines their atomic number (Z). For example, all atoms with eight protons are oxygen; however, the number of neutrons can vary for atoms of the same element. The sum of the number of protons and the number of neutrons is the mass number (A). Atoms with the same atomic number but different mass numbers are called isotopes. Elements can have multiple isotopes, for example, carbon-12, carbon-13, and carbon-14.
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Radioactivity and Nuclear Equations03:18

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Nuclear chemistry is the study of reactions that involve changes in nuclear structure. The nucleus of an atom is composed of protons and, except for hydrogen, neutrons. The number of protons in the nucleus is called the atomic number (Z) of the element, and the sum of the number of protons and the number of neutrons is the mass number (A). Atoms with the same atomic number but different mass numbers are isotopes of the same element.
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Thermal Sigmatropic Reactions: Overview01:16

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Sigmatropic rearrangements are a class of pericyclic reactions in which a σ bond migrates from one part of a π system to another. These are intramolecular rearrangements where the total number of σ and π bonds remain unchanged.
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Design and Operation of a Continuous 13C and 15N Labeling Chamber for Uniform or Differential, Metabolic and Structural, Plant Isotope Labeling
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Combining Graph Transformations and Semigroups for Isotopic Labeling Design.

Jakob L Andersen1, Daniel Merkle1,2, Peter S Rasmussen1

  • 1Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|November 22, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces a novel mathematical approach using transformation semigroups to trace atoms in biochemical reaction networks for isotope labeling design. This method aids in distinguishing pathway activities, exemplified by glycolysis.

Keywords:
algorithmic cheminformaticschemical reaction networkscomputational biologydouble pushoutgraph transformations

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Area of Science:

  • Biochemistry and Systems Biology
  • Computational Chemistry
  • Graph Theory and Abstract Algebra

Background:

  • Chemical reaction networks are fundamental to understanding biochemical systems.
  • Tracing individual atoms and designing effective isotope labeling strategies remain challenging.
  • Existing methods may lack the mathematical rigor for detailed pathway analysis.

Purpose of the Study:

  • To develop a mathematically rigorous approach for isotope labeling design in biochemical systems.
  • To enable automatic tracing of individual atoms within complex chemical reaction networks.
  • To create a method for distinguishing alternative pathway activities using informative atom labeling.

Main Methods:

  • Representing chemical reaction networks as directed hypergraphs.
  • Converting these networks into transformation semigroups, where molecular symmetries are permutations and reactions are semigroup transformations.
  • Developing an algorithm for automatic inference of informative atom labeling.

Main Results:

  • The double pushout approach provides an abstraction level for tracing atoms in reaction networks.
  • Transformation semigroups effectively model molecular symmetries and chemical reactions.
  • The proposed labeling inference approach successfully distinguishes between alternative pathways.

Conclusions:

  • The developed mathematical framework offers a rigorous method for isotope labeling design.
  • This approach enhances the analysis of biochemical pathways by enabling precise atom tracing.
  • Application to glycolysis demonstrates the method's utility in understanding complex metabolic processes.