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

Newman Projections

Newman Projections

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...

Molecular Shapes

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...

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.

Fischer Projections

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines.

Molecular Geometry and Dipole Moments

Molecular Geometry and Dipole Moments

The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:

Lewis Structures of Molecular Compounds and Polyatomic Ions

Lewis Structures of Molecular Compounds and Polyatomic Ions

To draw Lewis structures for complicated molecules and molecular ions, it is helpful to follow a step-by-step procedure as outlined:

You might also read

Related Articles

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

Sort by

Same author

Coarse-Grained Simulations Reveal Salt- and Length-Dependent Condensation of G4C2 RNA Repeats.

The journal of physical chemistry letters·2026

Same author

Lipid Composition Determines Hybrid Nanoparticle Selectivity: Beyond Membrane Mimicry in Cancer Targeting.

Nano letters·2026

Same author

Ultrasound-responsive liposomes: A mechanistic framework to decode the effects of acoustic parameters.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

The Role of Water Volume Fraction on Water Adsorption in Anion Exchange Membranes.

Macromolecules·2026

Same author

Coarse-Grained Martini 3 Model of Chondroitin Sulfate A.

Journal of chemical theory and computation·2026

Same author

Martini 3 Building Blocks for Lipid Nanoparticle Design.

Journal of chemical theory and computation·2025

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

Same journal

Derisking Affinity Optimization for Macrocycles and Cyclic Peptides: High-Precision Free Energy Simulations across Five Diverse Targets.

Journal of chemical information and modeling·2026

Same journal

An End-User Audit of Reproducibility, Data Leakage, and Overfitting of the Top-Ranked ADMET Prediction Models in TDC Leaderboards.

Journal of chemical information and modeling·2026

Same journal

PFASGroups: An Open-Source Framework for Automated Identification, Structural Classification, and Prioritization of Per- and Polyfluoroalkyl Substances.

Journal of chemical information and modeling·2026

Same journal

DeepKbhb: Context-Aware Prediction of Human Lysine β-Hydroxybutyrylation Sites.

Journal of chemical information and modeling·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 20, 2025

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex

Published on: July 27, 2022

CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions.

Fabian Grünewald^1,2, Leif Seute¹, Riccardo Alessandri³

¹Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

Journal of Chemical Information and Modeling

|March 24, 2025

Summary

This summary is machine-generated.

We introduce CGsmiles, a new notation for coarse-grained (CG) models, enabling efficient chemical space exploration and multiresolution molecular representation. This format addresses limitations in current methods, facilitating high-throughput screening and machine learning applications.

More Related Videos

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

Related Experiment Videos

Last Updated: May 20, 2025

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex

Line Shape Analysis of Dynamic NMR Spectra for Characterizing Coordination Sphere Rearrangements at a Chiral Rhenium Polyhydride Complex

Published on: July 27, 2022

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

Area of Science:

Computational Chemistry
Cheminformatics
Materials Science

Background:

Coarse-grained (CG) models simplify molecular representations for faster simulations, crucial for high-throughput (HT) screening and exploring vast chemical spaces.
Existing CG models lack standardized data formats for describing atom grouping (mapping), hindering scalability and data sharing.
The Martini force field exemplifies CG models but requires robust notation for its growing molecular library.

Purpose of the Study:

To introduce CGsmiles, a novel line notation for representing coarse-grained molecules and their hierarchical relationships.
To address the lack of standardized mapping and indexing capabilities in current coarse-grained modeling.
To demonstrate the utility of CGsmiles in facilitating multiresolution analysis and machine learning applications.

Main Methods:

Developed CGsmiles, a line notation inspired by SMILES and BigSMILES, encoding molecular graphs and particle properties.
Incorporated a framework for seamless conversion between coarse-grained and fine-grained resolutions within a single string.
Analyzed a benchmark set of 407 molecules from the Martini force field using the CGsmiles syntax.

Main Results:

CGsmiles successfully encodes molecular graphs and particle properties, independent of resolution.
The notation enables representation of multiple resolutions and hierarchical relationships in a single string.
Demonstrated CGsmiles' utility by constructing machine learning models for partition coefficient prediction using multiresolution data.

Conclusions:

CGsmiles provides a versatile and rigorous solution for describing coarse-grained models and their mappings.
The notation overcomes significant barriers in coarse-grained modeling, enabling true high-throughput capabilities.
CGsmiles is applicable to polymers and other complex systems, enhancing molecular simulation and data analysis.