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Related Concept Videos

Structure and Nomenclature of Thiols and Sulfides02:17

Structure and Nomenclature of Thiols and Sulfides

Thiols and sulfides are sulfur analogs of alcohols and ethers, respectively, where the sulfur atom takes the place of the oxygen atom. Thus, thiols are generally represented as RSH, where R is an alkyl substituent and —SH is the functional group. On the other hand, in sulfides, the central sulfur atom is bonded to two hydrocarbon groups on either side. Depending upon the type of group, sulfides can be either symmetrical or asymmetrical. Both thiols and sulfides display a bent geometry, similar...
Acid Strength and Molecular Structure03:05

Acid Strength and Molecular Structure

Binary Acids and Bases
In the absence of any leveling effect, the acid strength of binary compounds of hydrogen with nonmetals (A) increases as the H-A bond strength decreases down a group in the periodic table. For group 17, the order of increasing acidity is HF < HCl < HBr < HI. Likewise, for group 16, the order of increasing acid strength is H2O < H2S < H2Se < H2Te. Across a row in the periodic table, the acid strength of binary hydrogen compounds increases with increasing...
Structures of Carboxylic Acid Derivatives01:28

Structures of Carboxylic Acid Derivatives

Structure of Carboxylic Acid Derivatives
Carboxylic acid derivatives contain an acyl group attached to a heteroatom such as chlorine, oxygen, or nitrogen. The carbonyl carbon and oxygen are both sp2-hybridized with an unhybridized p orbital.
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Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Molecular Structure and Acidity02:34

Molecular Structure and Acidity

An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...

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Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
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Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Chemical substructure search in SQL.

Adel Golovin1, Kim Henrick

  • 1EMBL-EBI Hinston Hall Genome Campus, Cambridge, UK.

Journal of Chemical Information and Modeling
|December 17, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a fast chemical substructure search method using SQL queries and graph symmetry analysis. The technique, based on breadth-first search algorithms, achieves linear time performance for complex molecular interactions.

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Area of Science:

  • Computational chemistry
  • Bioinformatics
  • Database management

Background:

  • Chemical substructure searching is crucial for drug discovery and molecular analysis.
  • Existing methods for large-scale chemical databases can be computationally intensive.
  • Intermolecular interactions present complex graph structures that challenge traditional search algorithms.

Purpose of the Study:

  • To develop a novel, efficient technique for fast chemical substructure searching within relational databases.
  • To adapt this technique for analyzing complex networks of intermolecular interactions.
  • To demonstrate that subgraph isomorphism can be treated as a polynomial time problem.

Main Methods:

  • Implementation of breadth-first search (BFS) algorithms within Relational Database Management Systems (RDBMS).
  • Utilizing standard SQL queries for substructure matching.
  • Incorporating query graph symmetry analysis to derive additional search constraints.

Main Results:

  • Achieved fast chemical substructure search performance using standard SQL.
  • Extended the technique to handle nonplanar graphs in intermolecular interaction networks.
  • Demonstrated linear time performance for these complex graph searches, with methods to reduce the linear coefficient.

Conclusions:

  • The developed technique offers an efficient solution for chemical substructure searching and molecular interaction analysis.
  • The findings suggest subgraph isomorphism is a polynomial time problem, with implications for algorithm complexity theory.
  • Accessible online applications showcase the practical utility of this novel search method.