mrsimulator:docs v0.8.0.dev0
  • Table Of Contents
      • Simulation Gallery
        • 1D NMR simulation (small molecules/crystalline solids)
        • 1D NMR simulation (macromolecules/amorphous solids)
        • 2D NMR simulation (Crystalline solids)
        • 2D NMR simulation (Disordered/Amorphous solids)
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Table of Contents

Introduction

  • Installation
  • Getting Started
  • Isotopomers Example
  • Least-Squares Fitting Example

User Documentation

  • Spin System
  • Spin System Distributions
  • Methods Library
  • Method
  • Simulator
  • Signal Processor
  • mrsimulator I/O

Galleries

  • Simulation Gallery
    • 1D NMR simulation (small molecules/crystalline solids)
    • 1D NMR simulation (macromolecules/amorphous solids)
    • 2D NMR simulation (Crystalline solids)
    • 2D NMR simulation (Disordered/Amorphous solids)
  • Fitting (Least Squares) Gallery
  • Signal Processing Gallery

Theory

  • Transition Frequency Components
  • Models

API and references

  • Simulation API
  • Signal-Processor API
  • Models API
  • Fitting Utility API

Project details

  • Changelog
  • Authors and Credits
  • License
  • Acknowledgment

Simulation Gallery¶

In this section, we use the mrsimulator tools to create spin systems and simulate spectrum with practical/experimental applications. These examples illustrate

  • building spin systems (uncoupled and weakly-coupled),

  • building NMR methods,

  • simulating spectrum, and

  • processing spectrum (e.g. adding line-broadening).

For applications related to least-squares fitting, see the Fitting (Least Squares) Gallery.

1D NMR simulation (small molecules/crystalline solids)¶

The following examples are the NMR spectrum simulation of small molecules and crystalline solids for the following methods:

  • Bloch decay method (BlochDecaySpectrum),

  • Central transition selective Bloch decay method (BlochDecayCTSpectrum).

  • Generic one-dimensional method (Method1D).

Wollastonite, ²⁹Si (I=1/2)

Wollastonite, ²⁹Si (I=1/2)

Wollastonite, ²⁹Si (I=1/2)
Potassium Sulfate, ³³S (I=3/2)

Potassium Sulfate, ³³S (I=3/2)

Potassium Sulfate, ³³S (I=3/2)
Coesite, ¹⁷O (I=5/2)

Coesite, ¹⁷O (I=5/2)

Coesite, ¹⁷O (I=5/2)
Non-coincidental Quad and CSA, ¹⁷O (I=5/2)

Non-coincidental Quad and CSA, ¹⁷O (I=5/2)

Non-coincidental Quad and CSA, ¹⁷O (I=5/2)
Arbitrary spin transition (single-quantum)

Arbitrary spin transition (single-quantum)

Arbitrary spin transition (single-quantum)
Arbitrary spin transition (multi-quantum)

Arbitrary spin transition (multi-quantum)

Arbitrary spin transition (multi-quantum)
Coupled spin-1/2 (Static dipolar spectrum)

Coupled spin-1/2 (Static dipolar spectrum)

Coupled spin-1/2 (Static dipolar spectrum)
Coupled spin-1/2 (CSA + heteronuclear dipolar + J-couplings)

Coupled spin-1/2 (CSA + heteronuclear dipolar + J-couplings)

Coupled spin-1/2 (CSA + heteronuclear dipolar + J-couplings)
Writing Custom methods (HahnEcho)

Writing Custom methods (HahnEcho)

Writing Custom methods (HahnEcho)

1D NMR simulation (macromolecules/amorphous solids)¶

The following examples are the NMR spectrum simulation of macromolecules and amorphous materials for the following methods:

  • Bloch decay method (BlochDecaySpectrum),

  • Central transition selective Bloch decay method (BlochDecayCTSpectrum).

For NMR simulation of amorphous solids, we also show examples of simulating spectrum using user-defined model or using commonly accepted models such as Czjzek or extended Czjzek distribution.

Protein GB1, ¹³C and ¹⁵N (I=1/2)

Protein GB1, ¹³C and ¹⁵N (I=1/2)

Protein GB1, ¹³C and ¹⁵N (I=1/2)
Amorphous material, ²⁹Si (I=1/2)

Amorphous material, ²⁹Si (I=1/2)

Amorphous material, ²⁹Si (I=1/2)
Amorphous material, ²⁷Al (I=5/2)

Amorphous material, ²⁷Al (I=5/2)

Amorphous material, ²⁷Al (I=5/2)
Czjzek distribution (Shielding and Quadrupolar)

Czjzek distribution (Shielding and Quadrupolar)

Czjzek distribution (Shielding and Quadrupolar)
Extended Czjzek distribution (Shielding and Quadrupolar)

Extended Czjzek distribution (Shielding and Quadrupolar)

Extended Czjzek distribution (Shielding and Quadrupolar)

2D NMR simulation (Crystalline solids)¶

The following examples are the NMR spectrum simulation for crystalline solids. The examples include the illustrations for the following methods:

  • Triple-quantum variable-angle spinning (i.e., 3Q-MAS) using the specialized ThreeQ_VAS() method.

  • Satellite-transition variable-angle spinning (i.e., ST-MAS) using the specialized ST1_VAS() method.

  • Switched Angle Spinning (SAS) using the generic Method() object.

  • MAS-detected Dynamic Angle Spinning (DAS) using the generic Method() object.

  • Correlation of Anisotropies Separated Through Echo Refocusing (COASTER) using the generic Method() object.

  • Phase Adjusted Spinning Sidebands (PASS and QPASS) and Magic-Angle Turning (MAT and QMAT) using the specialized SSB2D() method.

RbNO₃, ⁸⁷Rb (I=3/2) 3QMAS

RbNO₃, ⁸⁷Rb (I=3/2) 3QMAS

RbNO₃, ⁸⁷Rb (I=3/2) 3QMAS
Albite, ²⁷Al (I=5/2) 3QMAS

Albite, ²⁷Al (I=5/2) 3QMAS

Albite, ²⁷Al (I=5/2) 3QMAS
RbNO₃, ⁸⁷Rb (I=3/2) STMAS

RbNO₃, ⁸⁷Rb (I=3/2) STMAS

RbNO₃, ⁸⁷Rb (I=3/2) STMAS
Rb₂SO₄, ⁸⁷Rb (I=3/2) SAS

Rb₂SO₄, ⁸⁷Rb (I=3/2) SAS

Rb₂SO₄, ⁸⁷Rb (I=3/2) SAS
Rb₂CrO₄, ⁸⁷Rb (I=3/2) SAS

Rb₂CrO₄, ⁸⁷Rb (I=3/2) SAS

Rb₂CrO₄, ⁸⁷Rb (I=3/2) SAS
Coesite, ¹⁷O (I=5/2) 3QMAS

Coesite, ¹⁷O (I=5/2) 3QMAS

Coesite, ¹⁷O (I=5/2) 3QMAS
Coesite, ¹⁷O (I=5/2) DAS

Coesite, ¹⁷O (I=5/2) DAS

Coesite, ¹⁷O (I=5/2) DAS
Rb₂CrO₄, ⁸⁷Rb (I=3/2) COASTER

Rb₂CrO₄, ⁸⁷Rb (I=3/2) COASTER

Rb₂CrO₄, ⁸⁷Rb (I=3/2) COASTER
Itraconazole, ¹³C (I=1/2) PASS

Itraconazole, ¹³C (I=1/2) PASS

Itraconazole, ¹³C (I=1/2) PASS
Rb₂SO₄, ⁸⁷Rb (I=3/2) QMAT

Rb₂SO₄, ⁸⁷Rb (I=3/2) QMAT

Rb₂SO₄, ⁸⁷Rb (I=3/2) QMAT
Wollastonite, ²⁹Si (I=1/2), MAF

Wollastonite, ²⁹Si (I=1/2), MAF

Wollastonite, ²⁹Si (I=1/2), MAF
MCl₂.2D₂O, ²H (I=1) Shifting-d echo

MCl₂.2D₂O, ²H (I=1) Shifting-d echo

MCl₂.2D₂O, ²H (I=1) Shifting-d echo

2D NMR simulation (Disordered/Amorphous solids)¶

The following examples are the NMR spectrum simulation for amorphous solids. The examples include the illustrations for the following methods:

  • Triple-quantum variable-angle spinning (ThreeQ_VAS())

Simulating site disorder (crystalline)

Simulating site disorder (crystalline)

Simulating site disorder (crystalline)
Czjzek distribution, ²⁷Al (I=5/2) 3QMAS

Czjzek distribution, ²⁷Al (I=5/2) 3QMAS

Czjzek distribution, ²⁷Al (I=5/2) 3QMAS

Download all examples in Python source code: examples_python.zip

Download all examples in Jupyter notebooks: examples_jupyter.zip

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