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Preparation of Alkynes: Alkylation Reaction02:27

Preparation of Alkynes: Alkylation Reaction

Introduction
Alkylation of terminal alkynes with primary alkyl halides in the presence of a strong base like sodium amide is one of the common methods for the synthesis of longer carbon-chain alkynes. For example, treatment of 1-propyne with sodium amide followed by reaction with ethyl bromide yields 2-pentyne.
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Nucleophilic acyl substitution is an important class of substitution reactions involving a nucleophile and an acyl compound, such as carboxylic acids and their derivatives. In these reactions, the leaving group attached to the acyl group is substituted by a nucleophile. The general mechanism proceeds via two steps.
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One of the common methods to prepare nitriles is the dehydration of amides. This method requires strong dehydrating agents like phosphorous pentoxide or boiling acetic anhydride for converting amides to nitriles. Another reagent namely, thionyl chloride also accomplishes the dehydration of amides, where amide acts as a nucleophile. The first step of the mechanism involves the nucleophilic attack by the amide on the thionyl chloride to form an intermediate. In the next step, the electron pairs...
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Reactions of α-Halocarbonyl Compounds: Nucleophilic Substitution

Nucleophilic substitution in α-halocarbonyl compounds can be achieved via an SN2 pathway. The reaction in α-haloketones is generally carried out with less basic nucleophiles. The use of strong basic nucleophiles leads to the generation of α-haloenolate ions, which often participate in other side reactions.
Methods of Sterilization II: Chemical Methods01:30

Methods of Sterilization II: Chemical Methods

In healthcare, the chemical method of sterilization uses chemical sterilants to treat surgical instruments and medical supplies to help prevent the transmission of infectious pathogens to patients. Due to heat sensitivity, most medical supplies and equipment should not be exposed to high temperatures. These parts include rubber, plastic, glass, and other similar elements.
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Related Experiment Video

Updated: Jul 15, 2026

Chemoselective Modification of Viral Surfaces via Bioorthogonal Click Chemistry
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Chemoselective Modification of Viral Surfaces via Bioorthogonal Click Chemistry

Published on: August 19, 2012

Hydration of mononucleotides.

Dengfeng Liu1, Thomas Wyttenbach, Michael T Bowers

  • 1Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.

Journal of the American Chemical Society
|November 23, 2006
PubMed
Summary

This study investigated how water molecules hydrate (bind to) the four deoxyribonucleotides (dAMP, dCMP, dGMP, dTMP) in both charged states. Hydration enthalpies were similar for anionic nucleotides, with water primarily binding to the phosphate group.

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Published on: July 26, 2018

Area of Science:

  • Biophysical Chemistry
  • Computational Chemistry
  • Molecular Hydration

Background:

  • Understanding nucleotide hydration is crucial for DNA stability and function.
  • Water's role in stabilizing charged biomolecules like nucleotides is complex.
  • Previous studies have explored nucleotide-water interactions, but detailed hydration energetics remain an active research area.

Purpose of the Study:

  • To experimentally and theoretically investigate the sequential hydration of protonated and deprotonated deoxyribonucleotides (dAMP, dCMP, dGMP, dTMP).
  • To determine the thermodynamic parameters (enthalpies of hydration) for the addition of water molecules.
  • To elucidate the binding sites of water molecules and their influence on nucleotide structure and stability.

Main Methods:

  • Experimental: Equilibrium measurements using electrospray mass spectrometry with a drift cell in positive and negative ion modes.
  • Theoretical: Molecular modeling and density functional theory (DFT) calculations.
  • Analysis of hydration enthalpies (ΔH°n) for the first four water molecules (n=1-4).

Main Results:

  • For deprotonated nucleotides, hydration enthalpies were similar across all four types, with the first water molecule binding to the phosphate group.
  • Protonated nucleotides showed varied hydration enthalpies, with dAMP exhibiting distinct behavior due to self-solvation of its charge-carrying group.
  • Water molecules were observed to cluster around the phosphate group or hydrate different functional groups, including deoxyribose and nucleobases.

Conclusions:

  • Individual water molecules play a significant role in stabilizing deoxyribonucleotides through specific binding interactions.
  • The binding sites and energetics of hydration differ between protonated and deprotonated nucleotide forms, particularly for dAMP.
  • These hydration insights inform the understanding of competition between nucleotide hydration and Watson-Crick base pairing in biological systems.