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相关概念视频

Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

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Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
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Inductively Coupled Plasma-Mass Spectrometry (ICP-MS): Interferences01:20

Inductively Coupled Plasma-Mass Spectrometry (ICP-MS): Interferences

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Inductively coupled plasma–mass spectrometry (ICP–MS) is a highly selective and sensitive technique for accurate elemental analysis. Though the analysis of ICP–MS mass spectra is comparatively straightforward, it is affected by spectroscopic and non-spectroscopic interferences. Spectroscopic interferences arise when the plasma contains ionic species with an m/z value the same as the analyte ion. Spectroscopic interference can be categorized as isobaric, polyatomic ions, and...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
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在S66数据集中的非对应相互作用的参考方法之间存在系统的差异.

Benjamin X Shi1, Flaviano Della Pia1, Yasmine S Al-Hamdani2,3,4

  • 1Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

The Journal of chemical physics
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概括
此摘要是机器生成的。

量子扩散蒙特卡洛 (DMC) 和合集群理论[CCSD(T]显示了较大的系统在非共价相互作用中的差异. 在静电相互作用中,DMC结合更强,在分散中更弱,与相互作用比率相关.

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科学领域:

  • 计算化学是一种计算化学.
  • 量子力学就是量子力学.
  • 电子结构理论 电子结构理论

背景情况:

  • 准确的模拟非共价相互作用对于各种化学应用至关重要.
  • 量子扩散蒙特卡洛 (DMC) 和合集群理论与单一,双重和扰动三重激发 [CCSD(T]是非共价相互作用的既定方法.
  • 在较大的系统中,DMC和CCSD之间观察到超过7.5kcal/mol的差异,其起源和规模尚不清楚.

研究的目的:

  • 系统地研究DMC和CCSD之间的差异,用于中型复合体中的非共价相互作用.
  • 确定影响这些差异幅度和方向的因素.
  • 为未来的方法开发提供基准系统.

主要方法:

  • 使用先进的量子扩散蒙特卡洛 (DMC) 计算S66数据集的相互作用能量.
  • 作为比较的参考方法,雇佣的CCSD (T) 作为比较的参考方法.
  • 进行了能量分解分析,以将差异与静电和分散贡献相关联.

主要成果:

  • 对于以静电为主导的系统,DMC预测的结合比CCSD更强.
  • 对于分散主导的系统,DMC预测的结合比CCSD (T) 弱.
  • 差异的大小与静电与分散相互作用的比率相关.

结论:

  • 确定了特定的系统,乙酸二元体 (ID 20) 和 uracil-cyclopentane 二元体 (ID 42),表现出明显的差异.
  • 这些发现凸显了电子结构方法进一步发展的必要性.
  • 识别的模型系统为验证和改进DMC和CCSD提供了具有成本效益的基准.