mrsimulator:docs v0.7.0rc2
  • 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
  • Ethanol Example

User Documentation

  • Spin System
  • Spin System Distributions
  • Methods Library
  • Method (For advanced users)
  • Query Objects
  • Simulator
  • Signal Processing
  • 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

  • How does mrsimulator work?
  • Models

API and references

  • Simulation API
  • Signal-processing API
  • Models API
  • Fitting Utility API
  • C-API References

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)

Figure 84 Wollastonite, ²⁹Si (I=1/2)¶

Potassium Sulfate, ³³S (I=3/2)

Figure 85 Potassium Sulfate, ³³S (I=3/2)¶

Coesite, ¹⁷O (I=5/2)

Figure 86 Coesite, ¹⁷O (I=5/2)¶

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

Figure 87 Non-coincidental Quad and CSA, ¹⁷O (I=5/2)¶

Arbitrary spin transition (single-quantum)

Figure 88 Arbitrary spin transition (single-quantum)¶

Arbitrary spin transition (multi-quantum)

Figure 89 Arbitrary spin transition (multi-quantum)¶

Coupled spin-1/2 (Static dipolar spectrum)

Figure 90 Coupled spin-1/2 (Static dipolar spectrum)¶

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

Figure 91 Coupled spin-1/2 (CSA + heteronuclear dipolar + J-couplings)¶

Writing Custom methods (HahnEcho)

Figure 92 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)

Figure 93 Protein GB1, ¹³C and ¹⁵N (I=1/2)¶

Amorphous material, ²⁹Si (I=1/2)

Figure 94 Amorphous material, ²⁹Si (I=1/2)¶

Amorphous material, ²⁷Al (I=5/2)

Figure 95 Amorphous material, ²⁷Al (I=5/2)¶

Czjzek distribution (Shielding and Quadrupolar)

Figure 96 Czjzek distribution (Shielding and Quadrupolar)¶

Extended Czjzek distribution (Shielding and Quadrupolar)

Figure 97 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

Figure 98 RbNO₃, ⁸⁷Rb (I=3/2) 3QMAS¶

Albite, ²⁷Al (I=5/2) 3QMAS

Figure 99 Albite, ²⁷Al (I=5/2) 3QMAS¶

RbNO₃, ⁸⁷Rb (I=3/2) STMAS

Figure 100 RbNO₃, ⁸⁷Rb (I=3/2) STMAS¶

Rb₂SO₄, ⁸⁷Rb (I=3/2) SAS

Figure 101 Rb₂SO₄, ⁸⁷Rb (I=3/2) SAS¶

Rb₂CrO₄, ⁸⁷Rb (I=3/2) SAS

Figure 102 Rb₂CrO₄, ⁸⁷Rb (I=3/2) SAS¶

Coesite, ¹⁷O (I=5/2) 3QMAS

Figure 103 Coesite, ¹⁷O (I=5/2) 3QMAS¶

Coesite, ¹⁷O (I=5/2) DAS

Figure 104 Coesite, ¹⁷O (I=5/2) DAS¶

Rb₂CrO₄, ⁸⁷Rb (I=3/2) COASTER

Figure 105 Rb₂CrO₄, ⁸⁷Rb (I=3/2) COASTER¶

Itraconazole, ¹³C (I=1/2) PASS

Figure 106 Itraconazole, ¹³C (I=1/2) PASS¶

Rb₂SO₄, ⁸⁷Rb (I=3/2) QMAT

Figure 107 Rb₂SO₄, ⁸⁷Rb (I=3/2) QMAT¶

Wollastonite, ²⁹Si (I=1/2), MAF

Figure 108 Wollastonite, ²⁹Si (I=1/2), MAF¶

MCl₂.2D₂O, ²H (I=1) Shifting-d echo

Figure 109 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)

Figure 110 Simulating site disorder (crystalline)¶

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

Figure 111 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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