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相关概念视频

Calculating Standard Free Energy Changes02:49

Calculating Standard Free Energy Changes

22.2K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
22.2K
Gibbs Free Energy02:39

Gibbs Free Energy

34.4K
One of the challenges of using the second law of thermodynamics to determine if a process is spontaneous is that it requires measurements of the entropy change for the system and the entropy change for the surroundings. An alternative approach involving a new thermodynamic property defined in terms of system properties only was introduced in the late nineteenth century by American mathematician Josiah Willard Gibbs. This new property is called the Gibbs free energy (G) (or simply the free...
34.4K
Free Energy Changes for Nonstandard States03:25

Free Energy Changes for Nonstandard States

11.7K
The free energy change for a process taking place with reactants and products present under nonstandard conditions (pressures other than 1 bar; concentrations other than 1 M) is related to the standard free energy change according to this equation:
 
where R is the gas constant (8.314 J/K·mol), T is the absolute temperature in kelvin, and Q is the reaction quotient. This equation may be used to predict the spontaneity of a process under any given set of conditions.
Reaction Quotient...
11.7K
Free Energy01:21

Free Energy

48.7K
Free energy—abbreviated as G for the scientist Gibbs who discovered it—is a measurement of useful energy that can be extracted from a reaction to do work. It is the energy in a chemical reaction that is available after entropy is accounted for. Reactions that take in energy are considered endergonic and reactions that release energy are exergonic. Plants carry out endergonic reactions by taking in sunlight and carbon dioxide to produce glucose and oxygen. Animals, in turn, break...
48.7K
Path Between Thermodynamics States01:21

Path Between Thermodynamics States

3.4K
Consider the two thermodynamic processes involving an ideal gas that are represented by paths AC and ABC in Figure 1:
3.4K
Bond Dissociation Energy and Activation Energy02:13

Bond Dissociation Energy and Activation Energy

9.5K
Bond energy is the energy required to break a bond homolytically. These values are usually expressed in units of kcal/mol or kJ/mol and are referred to as bond dissociation energies when given for specific bonds or average bond energies when indicated for a given type of bond over many compounds. Firstly, the bond dissociation energy for a single bond is weaker than that of a double bond, which in turn is weaker than that of a triple bond. Secondly, hydrogen forms relatively strong bonds with...
9.5K

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Updated: Sep 17, 2025

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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基于沿着字符串路径的路径集体变量进行绑定自由能量计算.

Alessia Ghidini1, Andrea Cavalli1, Benoît Roux2

  • 1Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.

The journal of physical chemistry. B
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概括

这项研究引入了一种新的几何路线,使用字符串方法和路径集体变量 (PCV) 来计算药物受体结合的自由能量. 这种计算方法准确地确定了分子结合亲和力,这对于药物发现至关重要.

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科学领域:

  • 计算化学和生物物理学
  • 分子动力学模拟的模拟.
  • 药物的发现和设计.

背景情况:

  • 准确计算结合的自由能量对于药物发现至关重要.
  • 分子动力学 (MD) 模拟是研究分子相互作用的强大工具.
  • 现有的具有约束力的自由能量计算方法存在局限性.

研究的目的:

  • 开发和验证一种新的"几何路线"来计算具有约束力的自由能量.
  • 严格地将连接体-受体分离过程映射到一个定义的路径上.
  • 将新方法与已知的炼金术方法进行比较.

主要方法:

  • 使用弦方法构建一个曲线分离路径.
  • 使用路径集体变量 (PCV) 来定义纵向和直角顺序参数.
  • 沿着定义的路径计算平均力潜力.
  • 将该方法应用于糖原合成酶激酶-3β (GSK-3β) 抑制剂.

主要成果:

  • 成功地将整个联体受体解离过程映射到一个曲线路径上.
  • 在这个路径上使用PCV计算结合的自由能量的能力.
  • 获得了与GSK-3β抑制剂标准化学双解方法相似的结果.

结论:

  • 拟议的几何路线提供了一种严格而有效的方法,用于具有约束力的自由能量计算.
  • 这种方法在分子动力学模拟中为炼化方法提供了有价值的替代方案.
  • 该研究验证了PCV和弦方法在复杂分子结合研究中的实用性.