Scribd
Upload
66 views2 pages

Procedure For Marvin Sketch

MarvinSketch, developed by ChemAxon, is a comprehensive chemical structure editor that allows users to create, edit, and analyze small molecules in various formats. The software supports advanced features such as bond optimization in 2D and 3D, reaction editing, and property predictions, making it essential for chemists in research and industry. Its user-friendly interface and compatibility with multiple file formats enhance its utility in drug discovery and cheminformatics.

Uploaded by

debbanerjee1514
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
66 views2 pages

Procedure For Marvin Sketch

MarvinSketch, developed by ChemAxon, is a comprehensive chemical structure editor that allows users to create, edit, and analyze small molecules in various formats. The software supports advanced features such as bond optimization in 2D and 3D, reaction editing, and property predictions, making it essential for chemists in research and industry. Its user-friendly interface and compatibility with multiple file formats enhance its utility in drug discovery and cheminformatics.

Uploaded by

debbanerjee1514
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
You are on page 1/ 2

Small Molecule sketching using Marvin sketch and bond optimization in

2D & 3D format (SDF, MOL2 file formats)


Aim: To create a new blank small molecules using Marvin sketch
Introduction: MarvinSketch, developed by ChemAxon, is a powerful and intuitive
chemical structure editor designed for creating, editing, and analyzing chemical structures
and reactions. Known for its precision and flexibility, MarvinSketch supports a wide
range of chemical representations, including stereochemistry, isotopes, polymers, and
Markush structures. It also offers tools for drawing and balancing reactions, predicting
molecular properties such as pKa, logP, and tautomers, and generating IUPAC-compliant
names.
The software integrates seamlessly with other ChemAxon tools like MarvinView and
JChem, enabling advanced visualization, data analysis, and database integration.
Available as both a desktop application and a web-based tool, MarvinSketch provides
cross-platform support for Windows, macOS, and Linux. Its ability to handle complex
chemical calculations and its compatibility with various file formats, including SMILES
and InChI, make it an essential tool for chemists in research, education, and industry.
Trusted for its chemical intelligence and user-friendly interface, MarvinSketch simplifies
workflows in fields such as drug discovery, material science, and cheminformatics,
making it a versatile solution for professionals worldwide.
Query: small molecule (aspirin)
URL:https://marvinjs-demo.chemaxon.com
Toolbar Overview:
 Element Selector: Choose atoms like Carbon (C), Oxygen (O), Nitrogen (N), etc.
 Bond Tools: Add single, double, triple, or aromatic bonds.
 Templates: Quickly insert common structures (e.g., benzene, cyclohexane).
 Eraser Tool: Remove atoms, bonds, or substructures.
 Zoom & Pan: Adjust the view of the molecule for detailed editing
PROCEDURE:
 Visit ChemAxon's Marvin JS page: https://marvinjs-demo.chemaxon.com
1. Sketch a Molecule:
 Click on an atom (default is Carbon) to place it on the canvas.
 Drag from the atom to add bonds and connect other atoms.
 Use the templates for rings or functional groups (e.g., amines, alcohols).
 Right-click on an atom to assign isotopes, charges, or lone pairs.
 Select an existing bond and change its type (single, double, etc.).
 Add stereochemistry (e.g., wedges for chirality).
 Right-click on an atom to set valency, formal charge, or isotopic mass.
 Use the templates (bottom toolbar) for quick addition of common groups.
 Place groups directly onto atoms (e.g., a hydroxyl group) using element bar on right
side.
2. Optimize Bonds in 2D (Clean Structure)
Draw the Molecule:Use the Marvin JS editor to sketch your molecule.
Use the Clean 2D Tool:

 Locate the Clean 2D button.


 Click the button after completing your sketch.
 The molecule will undergo optimization:
Bonds will be adjusted to standard lengths.
Angles will be corrected for clarity.
3. Optimize bonds in 3D
Use the clean 3D tool:

o Locate the clean 3D button.


o Click the tool after completion of 2D optimization.
o The 3D geometry will be adjusted to stable torsion angles.
o Use the 3D rotate tool to rotate and visualize the structure from different
angles.
4. Save or Export Molecules
Export File:

o Click onSave/Export.
o Format >Choose a file format:
 MDL MOLfile for .mol file
 MDL SDfile for .sdffile
 Can also obtain the SMILES format for easy handling.
The obtain MOL or SDF file contain all the 3D data of the chemical structure of compound
and can be used for docking and simulation studies.
Results and discussion:
The use of MarvinSketch, powered by ChemAxon, demonstrated its effectiveness as a
versatile chemical structure editor for a wide range of applications. The tool accurately
created complex molecular structures, including stereochemical configurations, and isotopes,
showcasing its robust chemical intelligence. Reaction editing and balancing were efficiently
performed, with the software providing precise atom mapping and mechanism visualization.

You might also like

pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy