Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

2.3K
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...
2.3K
¹H NMR: Pople Notation01:09

¹H NMR: Pople Notation

1.7K
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).
A proton...
1.7K
Electronic Structure of Atoms02:28

Electronic Structure of Atoms

20.9K

An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum...
20.9K
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule01:10

Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule

1.1K
In the AX proton spin system, proton A can sense the two spin states of a coupled proton X, resulting in a doublet NMR signal with two peaks of equal (1:1) intensity. When proton A is coupled to two equivalent protons (AX2 spin system), the spin states of each X can be aligned with or against the external field, creating three possible scenarios. This results in a 1:2:1  triplet signal, where the central peak corresponds to the chemical shift of A and is twice as large or intense as the...
1.1K
The Aufbau Principle and Hund's Rule03:02

The Aufbau Principle and Hund's Rule

45.7K
To determine the electron configuration for any particular atom, we can build the structures in the order of atomic numbers. Beginning with hydrogen, and continuing across the periods of the periodic table, we add one proton at a time to the nucleus and one electron to the proper subshell until we have described the electron configurations of all the elements. This procedure is called the aufbau principle, from the German word aufbau (“to build up”). Each added electron occupies the...
45.7K
Newman Projections02:06

Newman Projections

16.3K
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
16.3K

You might also read

Related Articles

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

Sort by
Same author

Construction of an Interpretable Regression Model for Yield Prediction and Mechanistic Insight Enabled by Automated Reaction Path Exploration.

Journal of the American Chemical Society·2026
Same author

Reprogramming RiPP scaffolds through skeletal editing unlocks chemical space.

Chemical science·2026
Same author

Size of Biomolecular Condensates Dictates Fate in Liquid-Solid Phase Transitions through Amorphous-Amyloid Competition.

Journal of the American Chemical Society·2026
Same author

Fe-electrocatalytic deoxygenative Giese reaction.

Nature communications·2025
Same author

Automated Evaluation Method for Aggregation-Induced Circularly Polarized Luminescence of Platinum(II) Complexes With 1,1'-Bi-2-naphthol Derivatives as Ligands.

Chirality·2025
Same author

Beyond the Nucleus: Cytoplasmic Dominance in Follicular Thyroid Carcinoma Detection Using Single-Cell Raman Imaging across Multiple Devices.

Analytical chemistry·2025
Same journal

Advancing Biochemical Molecule Registration, Representation and Search for New Drug Modalities.

Journal of chemical information and modeling·2026
Same journal

A Unified Molecular Graph and Protein Language Model Framework for Predicting Human Drug-Hormone Receptor Interactions with Structure-Aware Validation.

Journal of chemical information and modeling·2026
Same journal

Intricate Role of Cholesterol in Membrane Fusion.

Journal of chemical information and modeling·2026
Same journal

tmGNN-XAI: An Explainable Graph Neural Network Tool for Predicting Electronic Properties of Transition Metal Complexes from SMILES.

Journal of chemical information and modeling·2026
Same journal

QSAR in the Browser: An Interactive Cheminformatics Web Application.

Journal of chemical information and modeling·2026
Same journal

FoldDoF: Utilizing the Primary Degrees of Freedom of Protein Backbone for Geometric Modeling and Generation.

Journal of chemical information and modeling·2026
See all related articles

Related Experiment Video

Updated: May 29, 2025

Picometer-Precision Atomic Position Tracking through Electron Microscopy
15:04

Picometer-Precision Atomic Position Tracking through Electron Microscopy

Published on: July 3, 2021

6.7K

Enumeration Approach to Atom-to-Atom Mapping Accelerated by Ising Computing.

Mohammad Ali1,2, Yuta Mizuno1,3,4, Seiji Akiyama4,5

  • 1Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo 060-8628, Hokkaido, Japan.

Journal of Chemical Information and Modeling
|February 2, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces a novel rule-free algorithm for atom-to-atom mapping (AAM) in chemical reactions. By utilizing Ising computing, it efficiently finds all optimal atom correspondences, overcoming limitations of traditional methods.

More Related Videos

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.1K
Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

15.3K

Related Experiment Videos

Last Updated: May 29, 2025

Picometer-Precision Atomic Position Tracking through Electron Microscopy
15:04

Picometer-Precision Atomic Position Tracking through Electron Microscopy

Published on: July 3, 2021

6.7K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.1K
Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

15.3K

Area of Science:

  • Chemoinformatics
  • Computational Chemistry
  • Chemical Informatics

Background:

  • Atom-to-atom mapping (AAM) is crucial for understanding chemical transformations.
  • Current automatic AAM tools struggle with complex reactions due to combinatorial challenges and reliance on reaction rules.
  • Accurate AAM is vital for various chemoinformatics applications.

Purpose of the Study:

  • To develop a rule-free AAM algorithm that accurately identifies atom correspondences.
  • To address the computational challenges of AAM for complex chemical reactions.
  • To improve the efficiency and accuracy of automatic AAM.

Main Methods:

  • Proposed a rule-free AAM algorithm enumerating all atom-to-atom correspondences.
  • Employed Ising computing to optimize the minimization of bond cleavages and formations.
  • Evaluated the algorithm's performance against conventional combinatorial optimization and heuristic-based AAM methods.

Main Results:

  • The Ising computing framework significantly reduced computation times for AAM.
  • The proposed algorithm successfully identified correct AAM solutions for all benchmark problems.
  • Conventional heuristic-based AAM algorithms failed on several problems, highlighting the limitations of rule-based approaches.

Conclusions:

  • Rule-free AAM using Ising computing is a feasible and efficient approach for complex chemical reactions.
  • Enumerating all optimal correspondences that minimize bond changes is critical for accurate AAM.
  • This method offers a significant advancement over existing AAM tools in chemoinformatics.