Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

Protons in identical electronic environments within a molecule are chemically equivalent and have the same chemical shift. The replacement test is a useful tool to identify chemical equivalence and predict NMR spectra. A substituent replaces each of the protons being examined and the resulting molecules are compared. If the same molecule is obtained, the protons are equivalent or homotopic. Replacement of any hydrogens in ethane by chlorine yields chloroethane because all six protons are...

Stereoisomerism

Stereoisomerism

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...

Structural Isomerism

Structural Isomerism

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Determination of bonding radii from small-molecule crystal structures.

Journal of cheminformatics·2026

Same author

Off-target detection of CRISPR-Cas9 nuclease <i>in vitro</i> with CROFT-Seq.

Synthetic biology (Oxford, England)·2026

Same author

Insights into respiratory microbiome composition and systemic inflammatory biomarkers of bronchiectasis patients.

Microbiology spectrum·2024

Same author

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

Digital discovery·2024

Same author

Aortic disease and cardiomyopathy in patients with a novel DNMT3A gene variant causing Tatton-Brown-Rahman syndrome.

Clinical epigenetics·2024

Same author

Human nasal microbiota shifts in healthy and chronic respiratory disease conditions.

BMC microbiology·2024

Same journal

Computational design of low-volatility lubricants for space using interpretable machine learning.

Journal of cheminformatics·2026

Same journal

OpenStats: how to combine statistics and research data management (RDM) to leverage efficient scientific data analysis by guided statistics.

Journal of cheminformatics·2026

Same journal

Unified heterogeneity-aware benchmark of drug synergy prediction: a cross-study analysis of traditional machine learning and graph deep learning models.

Journal of cheminformatics·2026

Same journal

Count your bits: fingerprint benchmarking to assess broad chemical space representation.

Journal of cheminformatics·2026

Same journal

Sampling out-of-distribution chemical spaces via Bayesian flow.

Journal of cheminformatics·2026

Same journal

Hold on tight: the kinetic profiling of opioid receptor ligands using the CORAL-MD.

Journal of cheminformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Aug 9, 2025

$Microcrystallography of Protein Crystals and In Cellulo Diffraction$

Microcrystallography of Protein Crystals and In Cellulo Diffraction

Published on: July 21, 2017

Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions.

Andrius Merkys¹, Antanas Vaitkus², Algirdas Grybauskas²

¹Sector of Crystallography and Chemical Informatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania. andrius.merkys@gmc.vu.lt.

Journal of Cheminformatics

|February 23, 2023

Summary

This summary is machine-generated.

This study introduces a novel method for cross-checking chemical descriptions using molecular graph isomorphism. It identifies inconsistencies and suggests minimal simplifications for coherent chemical representations, aiding database curation.

Keywords:

Crystallography Open Database Graph isomorphism Molecular graphs SMILES

More Related Videos

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Related Experiment Videos

Last Updated: Aug 9, 2025

$Microcrystallography of Protein Crystals and In Cellulo Diffraction$

Microcrystallography of Protein Crystals and In Cellulo Diffraction

Published on: July 21, 2017

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Area of Science:

Chemistry
Computational Chemistry
Crystallography

Background:

Chemical reports often contain multiple, potentially supplementary, machine-readable descriptions.
Ensuring coherence and completeness of chemical representations is crucial for data integrity.

Purpose of the Study:

To present a method for cross-checking multiple machine-readable chemical descriptions.
To identify coherently described entries and those requiring curation in databases.

Main Methods:

Utilizing a canonical representation and isomorphism of molecular graphs.
Developing an algorithm to derive minimal simplifications for matching descriptions.
Applying the algorithm to cross-check chemical descriptions from the Crystallography Open Database.

Main Results:

The method successfully cross-checks chemical descriptions.
Identified both coherently described entries and those needing further curation.
Demonstrated the utility of molecular graph isomorphism for data validation.

Conclusions:

The proposed algorithm provides a robust approach for verifying chemical data consistency.
Facilitates automated curation of chemical databases.
Enhances the reliability of machine-readable chemical information.