在SAMPL9日志P挑战中,拓-水分区系数的扩展组合预测
Steven R Goold1, Robert M Raddi1, Vincent A Voelz1
1Department of Chemistry, Temple University, Philadelphia, PA, USA. voelz@temple.edu.
Physical chemistry chemical physics : PCCP
|March 5, 2025
概括
这项研究使用了分子模拟来准确预测水和之间的分割系数 (log P) 对药物样分子的对数. 扩展组合方法取得了良好的准确性,这表明它对于预测不同溶剂中疏水性的有用性.
科学领域:
- 计算化学计算化学
- 物理化学 物理化学
- 药物发现 药物发现 药物发现
背景情况:
- 分割系数 (log P) 的对数量化分子疏水性,对于预测药物的生物可用性和膜透性至关重要.
- 虽然水-八醇日志P预测是准确的,但预测对其他溶剂如二烯的日志P是不那么确定的.
- 需要计算方法来准确预测各种溶剂系统的log P.
研究的目的:
- 评估基于分子模拟的绝对自由能量方法,用于预测水-托卢日志P.
- 为了评估扩展组合 (EE) 方法的准确性,在一个盲测试中对蛋白质和体 (SAMPL) 建模的统计评估进行LOG P挑战.
- 为了研究OpenFF 2.0.0力场对水-托卢日志P的预测能力.
主要方法:
- 使用扩展组合 (EE) 方法与王兰道平面直方图采样进行自由能量估计.
- 采用了一个模拟工作流,其中包括OpenFF 2.0.0力场和优化的炼金术中间时间表.
- 在盲目测试环境中将该方法应用于16种具有酸性质的类似药物化合物.
主要成果:
- EE工作流实现了2.26 kcal mol−1 (1.65 log P单位) 的 RMSD,以及自由能量转移预测的R2为0.80.
- 模拟方法证明了对测试化合物的合理准确的log P预测能力.
- 对异常值的分析表明,通过精细的力场参数,可以提高精度.
结论:
- 扩展组合的自由能量计算提供了一个可行且相当准确的方法来预测水-托卢日志P.
- 该研究强调了分子模拟的潜力,用于描述各种非极性溶剂中的小分子疏水性.
- 进一步开发力场参数可以提高这种计算方法的预测准确性.
相关概念视频
Extraction: Partition and Distribution Coefficients
1.7K
The distribution law or Nernst's distribution law is the law that governs the distribution of a solute between two immiscible solvents. This law, also known as the partition law, states that if a solute is added to the mixture of two immiscible solvents at a constant temperature, the solute is distributed between the two solvents in such a way that the ratio of solute concentrations in the solvents remains constant at equilibrium.
For extracting a solute from an aqueous phase into an...
For extracting a solute from an aqueous phase into an...
1.7K
Vapor Pressure Lowering
25.9K
The equilibrium vapor pressure of a liquid is the pressure exerted by its gaseous phase when vaporization and condensation are occurring at equal rates:
Dissolving a nonvolatile substance in volatile liquid results in a lowering of the liquid’s vapor pressure. This phenomenon can be explained by considering the effect of added solute molecules on the liquid's vaporization and condensation processes. To vaporize, solvent molecules must be present at the surface of the solution....
Dissolving a nonvolatile substance in volatile liquid results in a lowering of the liquid’s vapor pressure. This phenomenon can be explained by considering the effect of added solute molecules on the liquid's vaporization and condensation processes. To vaporize, solvent molecules must be present at the surface of the solution....
25.9K
Ideal Solutions
19.0K
According to Raoult’s law, the partial vapor pressure of a solvent in a solution is equal or identical to the vapor pressure of the pure solvent multiplied by its mole fraction in the solution. However, Raoult's Law is only valid for ideal solutions. For a solution to be ideal, the solvent-solute interaction must be just as strong as a solvent-solvent or solute-solute interaction. This suggests that both the solute and the solvent would use the same amount of energy to escape to the...
19.0K
Distillation: Vapor–Liquid Equilibria
2.6K
Distillation is a separation technique that takes advantage of the boiling point properties of disparate elements in a mixture. To perform distillation, we begin by heating a miscible mixture of two liquids with a significant difference in boiling points (at least 20°C). As the solution heats up and reaches the bubble point of the more volatile component, some molecules of the more volatile component transition into the gas phase and travel upward into the condenser, which is a glass tube...
2.6K
UV–Vis Spectrum
1.0K
When light passes through a substance, a portion of the light is absorbed while the remaining light is reflected or transmitted. If the molecule absorbs light between the wavelengths of 180–400 nm range, the UV spectrum is obtained, and if it absorbs light in the 400–780 nm wavelength range, the visible spectrum is obtained.
The UV–Vis spectrum of a molecule is the plot of its absorbance versus wavelength. The plot is drawn by taking molar...
The UV–Vis spectrum of a molecule is the plot of its absorbance versus wavelength. The plot is drawn by taking molar...
1.0K
Real Gases: Effects of Intermolecular Forces and Molecular Volume Deriving Van der Waals Equation
34.3K
Thus far, the ideal gas law, PV = nRT, has been applied to a variety of different types of problems, ranging from reaction stoichiometry and empirical and molecular formula problems to determining the density and molar mass of a gas. However, the behavior of a gas is often non-ideal, meaning that the observed relationships between its pressure, volume, and temperature are not accurately described by the gas laws.
34.3K


