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phbuilder:在GROMACS中有效地设置恒定pH分子动力学模拟的工具

Anton Jansen1, Noora Aho2, Gerrit Groenhof2

  • 1Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.

Journal of chemical information and modeling
|January 12, 2024
PubMed
概括

phbuilder简化了在GROMACS.中设置恒定pH分子动力学 (MD) 模拟. 这个新工具自动化了输入文件的准备,使先进的pH依赖性研究更容易获得.

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相关概念视频

pH01:24

pH

The potential of hydrogen (pH) is a measure of the acidity or basicity of a water-based solution determined by the concentration of hydronium ions (H3O+). In one liter of pure water at neutral pH, there are 1×10−7 moles of hydronium ions. However, the extensive range of hydronium ion concentrations present in water-based solutions makes measuring pH in moles cumbersome. Therefore, a pH scale was developed to convert moles of hydronium ions into the negative logarithm of the hydronium ion...
Strong Acid and Base Solutions03:22

Strong Acid and Base Solutions

A strong acid is a compound that dissociates completely in an aqueous solution and produces a concentration of hydronium ions equal to the initial concentration of acid. For example, 0.20 M hydrobromic acid will dissociate completely in water and produces 0.20 M of hydronium ions and 0.20 M of bromide ions.
Weak Base Solutions03:21

Weak Base Solutions

Some compounds produce hydroxide ions when dissolved by chemically reacting with water molecules. In all cases, these compounds react only partially and so are classified as weak bases. These types of compounds are also abundant in nature and important commodities in various technologies. For example, global production of the weak base ammonia is typically well over 100 metric tons annually, being widely used as an agricultural fertilizer, a raw material for chemical synthesis of other...
Calculating pH Changes in a Buffer Solution02:45

Calculating pH Changes in a Buffer Solution

A buffer can prevent a sudden drop or increase in the pH of a solution after the addition of a strong acid or base up to its buffering capacity; however, such addition of a strong acid or base does result in the slight pH change of the solution. The small pH change can be calculated by determining the resulting change in the concentration of buffer components, i.e., a weak acid and its conjugate base or vice versa. The concentrations obtained using these stoichiometric calculations can be used...
pH01:24

pH

The potential of hydrogen (pH) is a measure of the acidity or basicity of a water-based solution determined by the concentration of hydronium ions (H3O+). In one liter of pure water at neutral pH, there are 1×10−7 moles of hydronium ions. However, the extensive range of hydronium ion concentrations present in water-based solutions makes measuring pH in moles cumbersome. Therefore, a pH scale was developed to convert moles of hydronium ions into the negative logarithm of the hydronium ion...
Acid–Base Equilibria: Activity-Based Definition of pH01:10

Acid–Base Equilibria: Activity-Based Definition of pH

For an ideal solution, the pH is defined as the negative logarithm of the hydrogen ion concentration. For a non-ideal solution, an accurate measurement of the pH must consider the negative logarithm of the hydrogen ion activity rather than concentration. In such a solution, the pH can be more accurately defined as the negative logarithm of a product of the hydrogen ion concentration and its activity coefficient.
In solutions of very low ionic strength—for example, pure water—the activity...