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Related Concept Videos

Alkali Metals03:06

Alkali Metals

19.9K
Group 1 elements are soft and shiny metallic solids. They are malleable, ductile, and good conductors of heat and electricity. The melting points of the alkali metals are unusually low for metals and decrease going down the group, while the density increases going down the group with the exception of potassium (Table 1).
Table 1: Properties of the alkali metals
19.9K
Preparation of Alkynes: Alkylation Reaction02:27

Preparation of Alkynes: Alkylation Reaction

10.7K
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.
10.7K
Basicity of Aliphatic Amines01:21

Basicity of Aliphatic Amines

6.2K
Amines can behave as Brønsted–Lowry bases by accepting a proton from the acid to form corresponding conjugate acids. Due to a lone pair of nonbonding electrons, aliphatic amines can also act as Lewis bases by forming a covalent bond with an electrophile.
To measure the basicity of amines, two conventions are generally used. The first defines Kb as the basicity constant for the deprotonation reaction of water by the amine, as presented in Figure 1. Conventionally, lower Kb indicates...
6.2K
Reduction of Alkynes to trans-Alkenes: Sodium in Liquid Ammonia02:10

Reduction of Alkynes to trans-Alkenes: Sodium in Liquid Ammonia

9.6K
Alkynes can be reduced to trans-alkenes using sodium or lithium in liquid ammonia. The reaction, known as dissolving metal reduction, proceeds with an anti addition of hydrogen across the carbon–carbon triple bond to form the trans product. Since ammonia exists as a gas (bp = −33°C) at room temperature, the reaction is carried out at low temperatures using a mixture of dry ice (sublimes at −78°C) and acetone. 
When dissolved in liquid ammonia, an alkali metal,...
9.6K
Preparation of Alkynes: Dehydrohalogenation02:34

Preparation of Alkynes: Dehydrohalogenation

16.4K
Introduction
Alkynes can be prepared by dehydrohalogenation of vicinal or geminal dihalides in the presence of a strong base like sodium amide in liquid ammonia. The reaction proceeds with the loss of two equivalents of hydrogen halide (HX) via two successive E2 elimination reactions.
16.4K
Nomenclature of Alkynes02:39

Nomenclature of Alkynes

19.1K
Alkynes are unsaturated hydrocarbons characterized by the presence of carbon-carbon triple bonds and have a general formula CnH2n-2. The nomenclature of alkynes follows a set of rules similar to alkanes and alkenes; however, alkynes bear the suffix "-yne" instead of "-ane" or "-ene." There are two approaches to naming alkynes:
19.1K

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Updated: Sep 11, 2025

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
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alchemlyb: the simple alchemistry library.

Zhiyi Wu1, David L Dotson2,3, Irfan Alibay4

  • 1Exscientia plc, Schroedinger Building, Oxford, United Kingdom.

Journal of Open Source Software
|August 18, 2025
PubMed
Summary
This summary is machine-generated.

alchemlyb is an open-source Python package simplifying alchemical free energy calculations for drug discovery. It offers tools for data analysis, preprocessing, and quality assessment, making complex methods accessible to more researchers.

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Area of Science:

  • Computational Chemistry
  • Computational Biology
  • Drug Discovery

Background:

  • Alchemical free energy calculations are crucial in computational chemistry and biology, particularly for drug discovery.
  • Analyzing these calculations involves complex workflows from data extraction to final estimations.

Purpose of the Study:

  • To introduce alchemlyb, an open-source Python package designed for the analysis of alchemical free energy calculations.
  • To provide a user-friendly tool that simplifies complex free energy analysis workflows.

Main Methods:

  • alchemlyb offers composable building blocks for data extraction from various molecular simulation packages.
  • Includes preprocessing steps like time series decorrelation and utilizes diverse estimators for free energy derivation.
  • Provides quality analysis tools for convergence checking and visualization.

Main Results:

  • The package integrates these building blocks into high-level, end-to-end workflows.
  • These workflows streamline the analysis pipeline from initial data input to final results.
  • Enhances accessibility for researchers across diverse scientific backgrounds.

Conclusions:

  • alchemlyb effectively democratizes the use of alchemical free energy calculations.
  • It empowers researchers beyond computational chemistry specialists to perform these analyses.
  • Facilitates more efficient drug discovery and molecular modeling research.