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Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.1K
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...
1.1K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.4K
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.
1.4K
Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule01:10

Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule

2.2K
In the AX proton spin system, proton A can sense the two spin states of a coupled proton X, resulting in a doublet NMR signal with two peaks of equal (1:1) intensity. When proton A is coupled to two equivalent protons (AX2 spin system), the spin states of each X can be aligned with or against the external field, creating three possible scenarios. This results in a 1:2:1  triplet signal, where the central peak corresponds to the chemical shift of A and is twice as large or intense as the...
2.2K
Chirality at Nitrogen, Phosphorus, and Sulfur02:30

Chirality at Nitrogen, Phosphorus, and Sulfur

6.6K
Chirality is most prevalent in carbon-based tetrahedral compounds, but this important facet of molecular symmetry extends to sp3-hybridized nitrogen, phosphorus and sulfur centers, including trivalent molecules with lone pairs. Here, the lone pair behaves as a functional group in addition to the other three substituents to form an analogous tetrahedral center that can be chiral.
A consequence of chirality is the need for enantiomeric resolution. While this is theoretically possible for all...
6.6K
Structure of Amines01:19

Structure of Amines

3.0K
The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are...
3.0K
¹H NMR: Pople Notation01:09

¹H NMR: Pople Notation

2.3K
The Pople nomenclature system classifies spin systems based on the difference between their chemical shifts. Coupled spins are denoted by capital letters with subscripts indicating the number of equivalent nuclei. When the coupled nuclei have well-separated chemical shifts, they are assigned letters that are far apart in the alphabet, such as A and X. When the difference in chemical shifts is small, coupled nuclei are named using adjacent letters of the alphabet (AB, MN, or XY).
A proton...
2.3K

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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

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Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase.

Lili Cao1, Ulf Ryde1

  • 1Department of Theoretical Chemistry, Lund University, PO Box 124, 221 00 Lund, Sweden.

Acta Crystallographica. Section D, Structural Biology
|November 2, 2020
PubMed
Summary
This summary is machine-generated.

Quantum refinement (QM) improves protein structures by replacing empirical restraints with QM calculations. The ComQumX-2QM method handles multiple conformations, enhancing electron density maps and providing accurate structural insights for enzymes like nitrogenase.

Keywords:
P-clustercrystallographic refinementmultiple conformationsnitrogenasequantum refinement

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Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biochemistry

Background:

  • X-ray crystallography is crucial for determining protein structures at atomic resolution.
  • Standard refinement relies on empirical restraints, which can be inaccurate for nonstandard regions like metal sites.
  • Quantum refinement (QM) offers a way to improve accuracy by incorporating QM calculations for specific regions.

Purpose of the Study:

  • To extend the QM refinement approach to handle multiple conformations within a protein structure.
  • To apply this enhanced method (ComQumX-2QM) to analyze complex metal clusters in enzymes.
  • To improve the accuracy of crystallographic structures, particularly for regions with conformational heterogeneity.

Main Methods:

  • Developed ComQumX-2QM, an extension of QM refinement allowing separate QM calculations for each conformation.
  • Applied ComQumX-2QM to analyze the P-cluster in two crystal structures of the enzyme nitrogenase.
  • Utilized QM strain energies to assess the quality of the refined structures.

Main Results:

  • ComQumX-2QM successfully refined structures with multiple conformations, leading to improved electron-density maps and Z-scores.
  • Analysis of nitrogenase revealed a mixture of oxidation states (PN and P2+) in a 1.0 Å resolution structure, with previously undetected atomic differences.
  • The 2.1 Å resolution structure was re-interpreted as a 50/50 mixture of P1+ and P2+ states, correcting significant inaccuracies in Fe-Fe and Fe-S distances.

Conclusions:

  • The ComQumX-2QM approach effectively refines protein crystal structures containing multiple conformations.
  • This method provides more accurate structural data for complex systems, such as the P-cluster in nitrogenase.
  • QM strain energy serves as a reliable metric for evaluating the quality of QM-refined structures.