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Halogens

Halogens

Group 17 elements, known as halogens, are nonmetals. At room temperature, fluorine and chlorine are gases, bromine is a liquid, and iodine a solid. Astatine is a highly unstable radioactive element, so currently, most of its properties are unknown due to its short half-life. Tennessine is a synthetic element also predicted to be in this group.

Halogenation of Alkenes

Halogenation of Alkenes

Halogenation is the addition of chlorine or bromine across the double bond in an alkene to yield a vicinal dihalide. The reaction occurs in the presence of inert and non-nucleophilic solvents, such as methylene chloride, chloroform, or carbon tetrachloride.
Consider the bromination of cyclopentene. Molecular bromine is polarized in the proximity of the π electrons of cyclopentene. An electrophilic bromine atom adds across the double bond, forming a cyclic bromonium ion intermediate.

Diazonium Group Substitution with Halogens and Cyanide: Sandmeyer and Schiemann Reactions

Diazonium Group Substitution with Halogens and Cyanide: Sandmeyer and Schiemann Reactions

Arenediazonium substitution reactions occur when the diazonium group is substituted by various functional groups such as halides, hydroxyl, nitrile, etc. For instance, arenediazonium salts react with copper(I) salts of chloride, bromide, or cyanide to form corresponding aryl chlorides, bromides, and nitriles. These reactions are named Sandmeyer reactions. Although the mechanism of this reaction is complicated, as illustrated in Figure 1, they are believed to progress via an aryl copper...

Radical Halogenation: Thermodynamics

Radical Halogenation: Thermodynamics

The thermodynamic favorability of a reaction is determined by the change in Gibbs free energy (ΔG). ΔG has two components- enthalpy (ΔH) and entropy (ΔS). The entropy component is negligible for alkane halogenation because the number of reactants and product molecules are equal. In this case, the ΔG is governed only by the enthalpy component. The most crucial factor that determines ΔH is the strength of the bonds. ΔH can be determined by comparing the energy...

Radical Halogenation: Stereochemistry

Radical Halogenation: Stereochemistry

Stereochemistry is the study of the different spatial arrangements of atoms in a given molecule. The stereochemistry of radical halogenations can be understood from three different situations:
Halogenation to form a new chiral center:

Reactions at the Benzylic Position: Halogenation

Reactions at the Benzylic Position: Halogenation

Benzylic halogenation takes place under conditions that favor radical reactions such as heat, light, or a free radical initiator like peroxide.

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Updated: Feb 13, 2026

DNA Electrophoresis Using Thiazole Orange Instead of Ethidium Bromide or Alternative Dyes

DNA Electrophoresis Using Thiazole Orange Instead of Ethidium Bromide or Alternative Dyes

Published on: March 31, 2019

Halogen-containing thiazole orange analogues - new fluorogenic DNA stains.

Aleksey A Vasilev¹, Meglena I Kandinska², Stanimir S Stoyanov²

¹Department of Pharmaceutical and Applied Organic Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier Blvd., 1164 Sofia, Bulgaria.

Beilstein Journal of Organic Chemistry

|March 23, 2018

Summary

New cyanine dyes, analogous to thiazole orange (TO), were synthesized. These dyes exhibit enhanced fluorescence upon binding to double-stranded DNA (dsDNA), showing potential for molecular probe development.

Keywords:

DFT calculations cyanine dyes green synthesis nucleic acids thiazole orange

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DNA Electrophoresis Using Thiazole Orange Instead of Ethidium Bromide or Alternative Dyes

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Published on: March 31, 2019

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Area of Science:

Organic Chemistry
Biophysical Chemistry
Molecular Spectroscopy

Background:

Thiazole orange (TO) is a commercial fluorescent dye used for detecting double-stranded DNA (dsDNA).
Development of novel TO analogues can lead to improved or alternative DNA-binding probes.
Cyanine dyes offer tunable photophysical properties based on their structural modifications.

Purpose of the Study:

To synthesize novel asymmetric monomeric monomethine cyanine dyes as analogues of thiazole orange (TO).
To investigate the photophysical properties and dsDNA binding interactions of these new cyanine dyes.
To explore the influence of substituent groups on the chromophores' behavior.

Main Methods:

Synthesis of novel cyanine dyes using an efficient and environmentally benign procedure.
Characterization of synthesized dyes using UV-vis absorption and fluorescence spectroscopy.
Computational analysis including Density Functional Theory (DFT) and Time-Dependent DFT (TD-DFT) calculations.

Main Results:

Successful synthesis of novel asymmetric monomethine cyanine dyes (5a-d) in good to excellent yields.
Absorption maxima observed between 509-519 nm with high molar absorptivities (63000-91480 L·mol⁻¹·cm⁻¹).
Dyes exhibited low intrinsic fluorescence but showed strong fluorescence enhancement upon binding to dsDNA.

Conclusions:

The synthesized cyanine dyes are effective dsDNA binders with significant fluorescence turn-on response.
Substituent effects on the chromophore influence the spectroscopic properties and DNA interaction.
These novel dyes show promise as fluorescent probes for dsDNA detection.