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相关概念视频

Entropy and Solvation02:05

Entropy and Solvation

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The process of surrounding a solute with solvent is called solvation. It involves evenly distributing the solute within the solvent. The rule of thumb for determining a solvent for a given compound is that like dissolves like. A good solvent has molecular characteristics similar to those of the compound to be dissolved. For example, polar solutions dissolve polar solutes, and apolar solvents dissolve apolar solutes. A polar solvent is a solvent that has a high dielectric constant (ϵ...
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Adiabatic Processes for an Ideal Gas01:18

Adiabatic Processes for an Ideal Gas

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When an ideal gas is compressed adiabatically, that is, without adding heat, work is done on it, and its temperature increases. In an adiabatic expansion, the gas does work, and its temperature drops. Adiabatic compressions actually occur in the cylinders of a car, where the compressions of the gas-air mixture take place so quickly that there is no time for the mixture to exchange heat with its environment. Nevertheless, because work is done on the mixture during the compression, its...
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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

1.2K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
1.2K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
924
Constant Volume Calorimetry02:41

Constant Volume Calorimetry

27.9K
Calorimeters are useful to determine the heat released or absorbed by a chemical reaction. Coffee cup calorimeters are designed to operate at constant (atmospheric) pressure and are convenient to measure heat flow (or enthalpy change) accompanying processes that occur in solution at constant pressure. A different type of calorimeter that operates at constant volume, colloquially known as a bomb calorimeter, is used to measure the energy produced by reactions that yield large amounts of heat and...
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Gibbs Free Energy and Thermodynamic Favorability02:23

Gibbs Free Energy and Thermodynamic Favorability

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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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溶体温和的亚底离子自由能量动力学,用于增强符合规范空间采样.

Shitanshu Bajpai1, Charlles R A Abreu2, Nisanth N Nair1

  • 1Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016 Kanpur, India.

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概括
此摘要是机器生成的。

我们开发了Solute Tempered d-AFED (STed-AFED),这是一个结合d-AFED/TAMD和REST2的新增采样方法. 这种方法通过将集体基于变量的采样与全球和整合,显著改善了大型生物分子系统的构造性采样.

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科学领域:

  • 计算化学是一种计算化学.
  • 分子动力学模拟的模拟.
  • 生物物理学的生物物理.

背景情况:

  • 改进的采样方法通过改进构造性采样来加速分子动力学 (MD) 模拟.
  • 基于集体变量 (CV) 的方法和通用集体技术,如温度加速分子动力学 (TAMD) /驱动的亚亚巴特自由能量动力学 (d-AFED) 和具有溶液温度的复制品交换 (REST2) 对于研究复杂系统至关重要.
  • 大型生物分子系统通常需要结合策略,因为存在显著的热障碍.

研究的目的:

  • 引入和验证一种新的增强采样方法,即溶性温化d-AFED (STed-AFED).
  • 为了将d-AFED/TAMD和REST2的强度结合起来,以获得更优质的形状采样.
  • 为了证明该方法在小和蛋白质上的有效性.

主要方法:

  • 通过在OpenMM-UFEDMM接口中集成d-AFED/TAMD和REST2来实现STed-AFED.
  • 应用STed-AFED方法来探索chignolin,Trp-cage和villin.的形状景观.
  • 利用在高温下进行温度调节的扩展变量和缩放的溶解物-溶剂相互作用来进行增强的探索.

主要成果:

  • STed-AFED方法有效地结合了基于CV的增强采样和全球和.
  • 对于小和蛋白质来说,已经证明了改进的 conformational 采样效率.
  • 成功地绘制出以前对标准方法具有挑战性的复杂形状景观.

结论:

  • STed-AFED代表了分子动力学增强采样技术的重大进步.
  • 综合方法克服了单个方法的局限性,特别是对于大型和复杂的生物分子系统.
  • 这种方法为计算生物物理学中的详细构造分析提供了强大的工具.