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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...
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The free energy change associated with dissolving a solute in a liter of solvent is called the free energy of a solution, ΔGsolution. The overall ΔGsolution is expressed as the balance of ΔGinteraction against the always-favorable free-energy of mixing, ΔGmixing. Solution formation is favorable if  ΔGsolution is less than zero, whereas it is unfavorable if ΔGsolution is greater than zero. In short, for a solution to form and complete dissolution to take place,...
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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...
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The spontaneity of a process depends upon the temperature of the system. Phase transitions, for example, will proceed spontaneously in one direction or the other depending upon the temperature of the substance in question. Likewise, some chemical reactions can also exhibit temperature-dependent spontaneities. To illustrate this concept, the equation relating free energy change to the enthalpy and entropy changes for the process is considered:
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Energy diagrams are important to understand the dynamics of a system. The topology of an energy diagram helps illustrate the equilibrium points of the system.
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没有平衡的自由能量模拟:最大限度地减少分散.

Eleonora Serra1,2, Alessia Ghidini3, Sergio Decherchi4

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此摘要是机器生成的。

使用不平衡模拟来估计蛋白质 - 配体结合的自由能量是具有挑战性的,因为不可逆转的工作. 优化水模型和路径集体变量大大提高了自由能量估计器的趋同.

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科学领域:

  • 计算化学计算化学
  • 生物物理学的生物物理.
  • 分子动力学分子动力学

背景情况:

  • 建立了平衡自由能量估计方法.
  • 没有平衡的模拟提供并行,但面临着趋同的挑战.
  • 蛋白质 - 配体结合的自由能量估计在药物发现中至关重要.

研究的目的:

  • 通过不平衡模拟来研究蛋白质 - 配体结合自由能量估计的挑战.
  • 分析模拟参数对估计器趋同的影响.
  • 提供提高模拟效率的策略.

主要方法:

  • 没有平衡的分子动力学模拟.
  • 物理路径采样用于蛋白质 - 配体结合.
  • 分析自由能量估计器 (例如,克鲁克斯方程).
  • 水模型和路径集体变量的系统变化.

主要成果:

  • 在模拟过程中产生的不可逆转的工作阻碍了估计器的趋同.
  • 水模型对自由能源估计器的收率产生了关键影响.
  • 路径集体变量的参数化显著影响了趋同.
  • 在模拟中确定了影响散射的关键因素.

结论:

  • 不平衡模拟需要仔细选择参数,以进行可靠的自由能量计算.
  • 优化的水模型和集体变量提高了融合速度.
  • 实际的策略可以最大限度地减少消散并提高计算效率.