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Related Concept Videos

Chemical Formulas02:52

Chemical Formulas

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A chemical formula presents information about the proportions of atoms constituting a particular chemical compound or molecule, mainly using symbols of elements and numbers. At times other symbols, such as dashes, parentheses, brackets, commas, plus, and minus signs, are also used. A chemical formula can be one of three types – molecular, empirical, and structural.
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Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

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The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
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Chemical Equations03:10

Chemical Equations

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Chemical equations represent the identities and relative quantities of substances involved in a chemical reaction. The substances undergoing reaction are called reactants, and their formulas are placed on the left side of the equation. The substances generated by the reaction are called products, and their formulas are placed on the right side of the equation. Plus signs (+) separate individual reactant and product formulas, and an arrow (→) separates the reactant and product (left and right)...
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Chemical Reactions01:19

Chemical Reactions

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A chemical reaction is a process by which the bonds in the atoms of substances are rearranged to generate new substances. Matter cannot be created or destroyed in a chemical reaction—the same type and number of atoms that make up the reactants are still present in the products. Merely, the rearrangement of chemical bonds produces new compounds.
Chemical Reactions Rearrange Atoms into New Substances
A chemical reaction takes starting materials—the reactants—and changes them...
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Structural Isomerism02:34

Structural Isomerism

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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.
Linkage isomers occur when the coordination compound contains a ligand that can bind to the transition metal center through two different atoms. For example, the CN− ligand can bind through the carbon atom or through the nitrogen atom. Similarly, SCN− can...
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Standard Entropy Change for a Reaction03:00

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Entropy is a state function, so the standard entropy change for a chemical reaction (ΔS°rxn) can be calculated from the difference in standard entropy between the products and the reactants.
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PubChem chemical structure standardization.

Volker D Hähnke1,2, Sunghwan Kim1, Evan E Bolton3

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD, 20894, USA.

Journal of Cheminformatics
|August 12, 2018
PubMed
Summary
This summary is machine-generated.

PubChem standardization effectively processes chemical structures, with a low rejection rate of 0.36%. While 44% of structures are modified, PubChem ensures data quality and accessibility for chemical information.

Keywords:
AromaticityInChIKekulizationPubChemStandardizationTautomerism

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Area of Science:

  • Chemical Informatics
  • Computational Chemistry
  • Bioinformatics

Background:

  • PubChem serves as a critical chemical information repository, encompassing Substance, Compound, and BioAssay databases.
  • Chemical structures submitted to the Substance database undergo automated standardization to create unique entries in the Compound database.

Purpose of the Study:

  • To detail PubChem's structure standardization methodologies.
  • To analyze the success rates, rejection causes, and modifications during standardization.
  • To compare PubChem standardization with IUPAC International Chemical Identifier (InChI) software normalization.

Main Methods:

  • Analysis of PubChem's structure standardization process.
  • Evaluation of structure rejection rates and reasons (e.g., invalid atom valences).
  • Comparison of standardized structures with those derived from InChI conversion.

Main Results:

  • A low rejection rate of 0.36% was observed, primarily due to uncorrectable invalid atom valences.
  • Forty-four percent of standardized structures undergo modifications, reducing the unique structure count.
  • Standardization is efficient, but edge cases dominate processing time; 60% of PubChem structures differ from InChI results, often due to tautomer preferences.

Conclusions:

  • PubChem standardization effectively manages chemical diversity and eliminates invalid structures.
  • Future developments aim to enhance tautomer and stereocenter handling.
  • The standardization service is publicly available via web and programmatic interfaces.