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Interactive Molecular Model Assembly with 3D Printing
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实验晶体几何学和气相计算对扭矩偏好进行系统比较
Dakota L Folmsbee1,2, David R Koes3, Geoffrey R Hutchison1,4
1Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States.
Journal of chemical information and modeling
|November 24, 2023
概括
像GFN2-xTB这样的计算方法可以准确地预测分子扭矩偏好,为符合性采样提供了对实验数据的可靠替代方案. 这使得新的方法能够独立于结晶的限制.
科学领域:
- 计算化学计算化学
- 分子建模分子建模
- 药物发现 药物发现 药物发现
背景情况:
- 合规采样方法通常依赖于对扭曲偏好的实验晶体学数据.
- 这种依赖限制了样本采集到稳定,可访问和可结晶的分子.
- 由于缺乏全面的实验数据,现有的方法面临局限性.
研究的目的:
- 评估半实证方法用于推导扭转角分布的适用性.
- 为了比较来自实验晶体学和气相计算对应器的扭曲偏好.
- 开发独立于实验限制的新的符合性采样策略.
主要方法:
- 使用GFN2-xTB方法对300多万种化合物进行详尽的扭矩采样.
- 实验晶体学对应器与气相计算对应器的比较.
- 开发基于高斯的适合和采样分布,用于扭矩采样.
主要成果:
- GFN2-xTB准确地捕捉了扭矩偏好,显示了与实验气相几何形状的最小偏差.
- 扭转偏好的差异主要是由于有限的实验晶体学数据.
- GFN2方法提供了可靠的扭矩偏好,适合计算采样.
结论:
- 半经验方法,如GFN2-xTB提供准确可靠的扭矩偏好,适合合器采样.
- 本研究提出量子扭矩衍生的距离几何学 (QTDG) 作为ETKDG的替代方案.
- 这些发现使得能够开发出新的符合性采样方法,不受实验数据的约束.
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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...
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Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3 hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
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Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
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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...
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