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Related Concept Videos

NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

3.5K
The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
For instance, the proton...
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NMR Spectroscopy Of Amines01:19

NMR Spectroscopy Of Amines

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In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is...
11.4K
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

1.6K
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
1.6K
Proton (¹H) NMR: Chemical Shift01:07

Proton (¹H) NMR: Chemical Shift

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Organic molecules primarily contain carbon and hydrogen atoms. While all the hydrogen isotopes are NMR-active, protium or hydrogen-1 is the most abundant. It has a significant energy separation between its nuclear spin states due to its large gyromagnetic ratio. As per Boltzmann's distribution, an increase in the energy separation implies a greater excess population of nuclei available for excitation, resulting in a strong NMR absorption signal.
Absorption signals of all the protium nuclei...
3.7K
Carbon-13 (¹³C) NMR: Overview01:10

Carbon-13 (¹³C) NMR: Overview

7.8K
Carbon-13 is a naturally occurring NMR-active isotope of carbon with a low natural abundance of 1.1%. In contrast, carbon-12 is the most abundant isotope of carbon with zero nuclear spin. Therefore, it is NMR inactive. The gyromagnetic ratio of carbon-13 is smaller than that of protons. As a result, carbon-13 resonance is about 6000 times weaker than proton resonance. For a given magnetic field strength, the resonance frequency of carbon-13 is about one-fourth of the resonance frequency for...
7.8K
Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

1.5K
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...
1.5K

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Evaluating amber force fields using computed NMR chemical shifts.

David R Koes1, John K Vries1

  • 1Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260.

Proteins
|July 9, 2017
PubMed
Summary
This summary is machine-generated.

This study evaluates AMBER force fields using NMR chemical shifts from molecular dynamics simulations. Newer force fields, particularly ff14ipq and ff15ipq, demonstrate improved accuracy in predicting protein structures.

Keywords:
chemical shiftmolecular dynamicsmolecular mechanicspeptide bondsquantum mechanicsα-helixβ-sheet

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Area of Science:

  • Computational chemistry
  • Biomolecular simulations
  • Protein structure analysis

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding protein dynamics.
  • Accurate force fields are essential for reliable MD simulations.
  • NMR chemical shifts provide sensitive probes of local atomic environments.

Purpose of the Study:

  • To evaluate the performance of various AMBER force fields (ff94-ff15ipq) using NMR chemical shifts.
  • To identify which force fields best reproduce experimental chemical shift data for proteins.
  • To understand how force field imperfections affect computed chemical shifts.

Main Methods:

  • Computed NMR chemical shifts (¹H, ¹⁵N, ¹³Cα) from MD simulations using a template matching approach.
  • Generated a library of conformers with chemical shifts from ab initio quantum calculations.
  • Compared computed shifts with experimental values for eight model proteins, analyzing RMS errors, secondary structure, and residue-specific performance.

Main Results:

  • The implicitly polarized charge method force fields (ff14ipq, ff15ipq) outperformed older AMBER force fields.
  • Peptide proton chemical shifts were most effective in distinguishing force field performance.
  • Force field accuracy varied significantly with residue position and local nonbonded interactions.

Conclusions:

  • The developed approach effectively identifies force field deficiencies through NMR chemical shift analysis.
  • Newer AMBER force fields, especially those using implicitly polarized charges, offer improved accuracy for protein simulations.
  • Understanding residue-specific performance is key to selecting appropriate force fields for molecular modeling.