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Related Concept Videos

NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

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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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¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

1.1K
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...
1.1K
Chemical Shift: Internal References and Solvent Effects01:17

Chemical Shift: Internal References and Solvent Effects

739
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...
739
Proton (¹H) NMR: Chemical Shift01:07

Proton (¹H) NMR: Chemical Shift

1.9K
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...
1.9K
¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

2.5K
Protons in identical electronic environments within a molecule are chemically equivalent and have the same chemical shift. The replacement test is a useful tool to identify chemical equivalence and predict NMR spectra. A substituent replaces each of the protons being examined and the resulting molecules are compared. If the same molecule is obtained, the protons are equivalent or homotopic. Replacement of any hydrogens in ethane by chlorine yields chloroethane because all six protons are...
2.5K
NMR Spectroscopy Of Amines01:19

NMR Spectroscopy Of Amines

9.3K
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...
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein

Adilakshmi Dwarasala1, Mehdi Rahimi1, John L Markley1,2

  • 1Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA.

Membranes
|September 22, 2022
PubMed
Summary
This summary is machine-generated.

Solid-state NMR (ssNMR) spectra analysis is challenging. We developed ssPINE, an automated algorithm for protein backbone and side-chain assignments from complex ssNMR data, improving biomolecular structure determination.

Keywords:
MAS-NMRassignmentautomationmembrane proteinssolid-state NMRssPINE

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Chemistry

Background:

  • Solid-state NMR (ssNMR) offers advantages over solution NMR for large biomolecules but presents interpretation challenges due to dipolar interactions.
  • Technological advancements in ssNMR, including stable isotope labeling and advanced pulse sequences, enable studies of complex systems like membrane proteins.
  • A gap exists in computational tools for analyzing complex ssNMR data, hindering efficient structure determination.

Purpose of the Study:

  • To develop an automated computational tool for analyzing complex solid-state NMR spectra.
  • To address the tedious process of signal recognition, correlation, categorization, and assignment in multidimensional ssNMR data.
  • To facilitate structure-function studies of challenging protein systems, including membrane proteins.

Main Methods:

  • Development of an automated algorithm named 'ssPINE' for ssNMR spectral analysis.
  • ssPINE accepts protein sequences and peak lists from various ssNMR experiments as input.
  • The software provides automated backbone and side-chain assignments.

Main Results:

  • An alpha version of the ssPINE software has been developed.
  • ssPINE successfully automates the recognition, correlation, categorization, and assignment of signals in complex ssNMR spectra.
  • The software is made freely available via a web submission form.

Conclusions:

  • The ssPINE algorithm significantly streamlines the analysis of complex ssNMR data.
  • Automated assignments by ssPINE facilitate more efficient structure determination of biomolecules, especially membrane proteins.
  • The availability of ssPINE through a web form democratizes access to advanced ssNMR data analysis tools.