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Measuring Reaction Rates03:09

Measuring Reaction Rates

Polarimetry finds application in chemical kinetics to measure the concentration and reaction kinetics of optically active substances during a chemical reaction. Optically active substances have the capability of rotating the plane of polarization of linearly polarized light passing through them—a feature called optical rotation. Optical activity is attributed to the molecular structure of substances. Normal monochromatic light is unpolarized and possesses oscillations of the electrical field in...
Multi-Step Reactions02:31

Multi-Step Reactions

Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
Chemical Reactions02:26

Chemical Reactions

A balanced chemical equation provides the information of chemical formulas of the reactants and products involved in the chemical change. A reaction’s stoichiometry helps predict how much of the reactant is needed to produce the desired amount of product, or in some cases, how much product will be formed from a specific amount of the reactant.
The relative amounts of reactants and products represented in a balanced chemical equation are often referred to as stoichiometric amounts. However, in...
Chemical Reactions01:19

Chemical Reactions

A chemical reaction is a process by which the bonds in the atoms of substances are rearranged to generate new substances. Matter cannot be created or destroyed in a chemical reaction—the same type and number of atoms that make up the reactants are still present in the products. Merely, the rearrangement of chemical bonds produces new compounds.
Chemical Reactions Rearrange Atoms into New Substances
A chemical reaction takes starting materials—the reactants—and changes them into different...
Coupled Reactions01:17

Coupled Reactions

Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions. 
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions. Cells...

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Updated: Jun 10, 2026

Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling
08:24

Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling

Published on: November 11, 2008

An open-source java platform for automated reaction mapping.

John D Crabtree1, Dinesh P Mehta, Tina M Kouri

  • 1Department of Computer Information Systems, University of North Alabama, Florence, Alabama 35632, USA. jcrabtree@una.edu

Journal of Chemical Information and Modeling
|August 19, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces open-source software for reaction mapping in cheminformatics and bioinformatics. The library enables versatile reaction viewing, mapping, and classification for researchers.

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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

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Last Updated: Jun 10, 2026

Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling
08:24

Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling

Published on: November 11, 2008

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Area of Science:

  • Computational chemistry and biology
  • Software engineering for scientific research

Background:

  • Reaction mapping is crucial for cheminformatics and bioinformatics.
  • Existing tools may lack modularity and flexibility.
  • Need for adaptable software in scientific research.

Purpose of the Study:

  • To present modular, open-source software applications for reaction mapping.
  • To describe the architecture of a core reaction mapping library.
  • To showcase two distinct applications built on this library.

Main Methods:

  • Development of a modular, open-source reaction mapping library.
  • Implementation of a generic reaction viewer and mapper.
  • Creation of a rule-based reaction classification application.

Main Results:

  • Successful development of a core reaction mapping library.
  • Demonstration of a functional reaction viewer and mapper.
  • Implementation of a user-modifiable reaction classification tool.

Conclusions:

  • The presented software offers a flexible and extensible platform for reaction analysis.
  • The modular design facilitates integration and further development in cheminformatics and bioinformatics.
  • End-user customization of reaction classification rules is achieved.