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相关概念视频

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.1K
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.
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Torsional Pendulum01:09

Torsional Pendulum

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A torsional pendulum involves the oscillation of a rigid body in which the restoring force is provided by the torsion in the string from which the rigid body is suspended. Ideally, the string should be massless; practically, its mass is much smaller than the rigid body's mass and is neglected.
As long as the rigid body's angular displacement is small, its oscillation can be modeled as a linear angular oscillation. The amplitude of the oscillation is an angle. The role of mass is played...
5.4K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

808
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...
808
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

12.2K
Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
12.2K
IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration01:16

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

1.2K
A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
According to Hooke's law, the vibrational frequency is directly proportional to...
1.2K
Bending and Torsional Moments01:20

Bending and Torsional Moments

3.6K
Bending and torsional moments are two fundamental concepts in structural engineering. They play an important role in understanding the behavior of materials and structures under different loading conditions.
The reaction developed in a structural element when subjected to an external force causes the element to bend. When a structural element bends upwards, it creates compressive normal forces on the top and tensile normal forces on the bottom, resulting in a couple that determines the bending...
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Magnetic Tweezers for the Measurement of Twist and Torque
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了解和量化分子灵活性:扭转角度 Bin 字符串.

Jessica Braun1, Paul Katzberger1, Gregory A Landrum1

  • 1Department of Chemistry and Applied Biosciences, ETH Zurich Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland.

Journal of chemical information and modeling
|October 10, 2024
PubMed
概括
此摘要是机器生成的。

我们引入扭矩角 bin 字符串 (TABS) 来量化分子灵活性. 这种新方法比RMSD更有效地估计了 conformational 整体大小,并对分子 conformational 空间进行分离.

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相关实验视频

Last Updated: Jun 10, 2025

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科学领域:

  • 计算化学是一种计算化学.
  • 分子建模分子建模
  • 结构生物学是结构生物学.

背景情况:

  • 分子灵活性对于理解分子性质和形状组合至关重要.
  • 在计算化学中,量化分子灵活性和表示构造空间是具有挑战性的.
  • 像RMSD这样的现有方法在离散构造空间方面存在局限性.

研究的目的:

  • 为了引入扭矩角 bin 字符串 (TABS) 作为一种新的离散向量表示,适用于 conformers.
  • 提出nTABS作为一种估计分子构造组合大小的方法.
  • 为了证明TABS对RMSD的优势,以分辨构造空间和评估组合完整性.

主要方法:

  • 开发TABS,一个基于二面角的离散向量表示.
  • 使用RDKit的ETKDGv3符合器生成器来生成符合器.
  • 从小分子晶体学数据中集成的扭转偏好.
  • 与基于RMSD的分类相比,TABS对合规组合的分类.

主要成果:

  • nTABS为小分子的构造空间大小提供了上限估计.
  • TABS有效地分离了构造空间,克服了RMSD的局限性,如分子大小依赖和值选择.
  • TABS允许快速检查结构空间覆盖面.

结论:

  • TABS提供了一种强大而有意义的方法来分离分子构造空间.
  • 这种方法增强了在计算化学中对形态集合的分析.
  • TABS提供了一种有价值的工具,用于评估生成的符合器件组的完整性.