Spin System

At the heart of any mrsimulator calculation is the definition of a SpinSystem object describing the sites and couplings within a spin system. Each Simulator object holds a list of SpinSystem objects which will be used to calculate frequency contributions.

Site

A site object holds single-site NMR interaction parameters, which include the nuclear shielding and quadrupolar interaction parameters. Consider the example below of a Site object for a deuterium nucleus created in Python.

# Import objects for the Site
from mrsimulator import Site
from mrsimulator.spin_system.tensors import SymmetricTensor

# Create the site object
H2_site = Site(
    isotope="2H",
    isotropic_chemical_shift=4.1,  # in ppm
    shielding_symmetric=SymmetricTensor(
        zeta=12.12,  # in ppm
        eta=0.82,
        alpha=5.45,  # in radians
        beta=4.82,  # in radians
        gamma=0.5,  # in radians
    ),
    quadrupolar=SymmetricTensor(
        Cq=1.47e6,  # in Hz
        eta=0.27,
        alpha=0.212,  # in radians
        beta=1.231,  # in radians
        gamma=3.1415,  # in radians
    ),
)

The isotope key holds the spin isotope, here given a value of 2H. The isotropic_chemical_shift is the isotropic chemical shift of the site isotope, \(^2\text{H}\), here given as 4.1 ppm. We have additionally defined an optional shielding_symmetric key, whose value is a second-rank traceless symmetric nuclear shielding tensor represented by a SymmetricTensor object.

Note

We parameterize a SymmetricTensor using the Haeberlen convention with parameters zeta and eta, defined as the shielding anisotropy and asymmetry, respectively. The Euler angle orientations, alpha, beta, and gamma are the relative orientation of the nuclear shielding tensor from a common reference frame.

Since deuterium is a quadrupolar nucleus, \(I>1/2\), there also can be a quadrupolar coupling interaction between the nuclear quadrupole moment and the surrounding electric field gradient (EFG) tensor, defined in the optional quadrupolar key. An EFG tensor is a second-rank traceless symmetric tensor, and we describe its components with Cq and eta, i.e., the quadrupolar coupling constant and asymmetry parameter, respectively. Additionally, we use the Euler angle orientations, alpha, beta, and gamma, which are the relative orientation of the EFG tensor from a common reference frame.

See Table 2 and Table 4 for further information on the Site and SymmetricTensor objects and their attributes, respectively.

Also, all objects in mrsimulator have the attribute property_units which provides the units for all class properties.

print(Site().property_units)
# {'isotropic_chemical_shift': 'ppm'}

print(SymmetricTensor().property_units)
# {'zeta': 'ppm', 'Cq': 'Hz', 'D': 'Hz', 'alpha': 'rad', 'beta': 'rad', 'gamma': 'rad'}

Coupling

A coupling object holds two site NMR interaction parameters, which can include the J-coupling and the dipolar coupling interaction parameters. Consider the example below of a Coupling object between two sites

# Import the Coupling object
from mrsimulator import Coupling

coupling = Coupling(
    site_index=[0, 1],
    isotropic_j=15,  # in Hz
    j_symmetric=SymmetricTensor(
        zeta=12.12,  # in Hz
        eta=0.82,
        alpha=2.45,  # in radians
        beta=1.75,  # in radians
        gamma=0.15,  # in radians
    ),
    dipolar=SymmetricTensor(
        D=1.7e3,  # in Hz
        alpha=0.12,  # in radians
        beta=0.231,  # in radians
        gamma=1.1415,  # in radians
    ),
)

The site_index key holds a list of two integers corresponding to the index of the two coupled sites within the spin system. The ordering of the integers is irrelevant.

The value of the isotropic_j is the isotropic J-coupling, here given as 15 Hz. We have additionally defined an optional j_symmetric key, whose value holds a SymmetricTensor object representing the traceless 2nd-rank symmetric J-coupling tensor.

Additionally, the dipolar coupling interaction between the coupled nuclei is defined with an optional dipolar key. A dipolar tensor is a second-rank traceless symmetric tensor, and we describe the dipolar coupling constant with the parameter D. The Euler angle orientations, alpha, beta, and gamma are the relative orientation of the dipolar tensor from a common reference frame.

See Table 3 and Table 4 for further information on the Site and SymmetricTensor objects and their attributes, respectively.

SpinSystem

The SpinSystem object is a collection of sites and couplings. Below are examples of different spin systems along with discussion on each attribute.

Single Site Spin System

Here we create a relatively unexciting single site proton spin system

# Import the SpinSystem object
from mrsimulator import SpinSystem

H1_site = Site(isotope="1H")

single_site_sys = SpinSystem(
    name="1H spin system",
    description="A single site proton spin system",
    sites=[H1_site],
    abundance=80,  # percentage
)

We find four keywords at the root level of our SpinSystem object definition: name, description, sites, and abundance. The value of the name key is the optional name of the spin system. Likewise, the value of the description key is an optional string describing the spin system.

The value of the sites key is a list of Site objects. Here, this list is simply the single object, H1_site. The value of the abundance key is the abundance of the spin system, here given a value of 80%. If the abundance key is omitted, the abundance defaults to 100%.

See Table 1 for further description of the SpinSystem class and its attributes.

Multi Site Spin System

To create a spin system with more than one site, we simply add more site objects to the sites list. Here we create a \(^{13}\text{C}\) site and add it along with the previous proton site to a new spin system.

# Create the new Site object
C13_site = Site(
    isotope="13C",
    isotropic_chemical_shift=-53.2,  # in ppm
    shielding_symmetric=SymmetricTensor(
        zeta=90.5,  # in ppm
        eta=0.64,
    ),
)

# Create a new SpinSystem object with both Sites
multi_site_sys = SpinSystem(
    name="Multi site spin system",
    description="A spin system with multiple sites",
    sites=[H1_site, C13_site],
    abundance=0.148,  # percentage
)

Again we see the optional name and description attributes. The sites attribute is now a list of two Site objects, the previous \(^1\text{H}\) site and the new \(^{13}\text{C}\) site. We have also set the abundance of this spin system to 0.148%. By leveraging the abundance attribute, multiple spin systems with varying abundances can be simulated together. See our Isotopomers Example where isotopomers of varying abundance are simulated in tandem.

Coupled Spin System

To create couplings between sites, we simply need to add a list of Coupling objects to a spin system. Below we create a \(^{2}\text{H}\) and \(^{13}\text{C}\) site as well as a coupling between them.

# Create site objects
H2_site = Site(
    isotope="2H",
    isotropic_chemical_shift=4.1,  # in ppm
    shielding_symmetric=SymmetricTensor(
        zeta=12.12,  # in ppm
        eta=0.82,
        alpha=5.45,  # in radians
        beta=4.82,  # in radians
        gamma=0.5,  # in radians
    ),
    quadrupolar=SymmetricTensor(
        Cq=1.47e6,  # in Hz
        eta=0.27,
        alpha=0.212,  # in radians
        beta=1.231,  # in radians
        gamma=3.1415,  # in radians
    ),
)
C13_site = Site(
    isotope="13C",
    isotropic_chemical_shift=-53.2,  # in ppm
    shielding_symmetric=SymmetricTensor(
        zeta=90.5,  # in ppm
        eta=0.64,
    ),
)

# Create coupling object
H2_C13_coupling = Coupling(
    site_index=[0, 1],
    isotropic_j=15,  # in Hz
    j_symmetric=SymmetricTensor(
        zeta=12.12,  # in Hz
        eta=0.82,
        alpha=2.45,  # in radians
        beta=1.75,  # in radians
        gamma=0.15,  # in radians
    ),
    dipolar=SymmetricTensor(
        D=1.7e3,  # in Hz
        alpha=0.12,  # in radians
        beta=0.231,  # in radians
        gamma=1.1415,  # in radians
    ),
)

We now have the site objects and the coupling object to make a coupled spin system. We now construct such a spin system.

coupled_spin_system = SpinSystem(sites=[H2_site, C13_site], couplings=[H2_C13_coupling])

In contrast to the previous examples, we have omitted the optional name, description, and abundance keywords. The name and description for coupled_spin_system will both be None and the abundance will be 100%.

A list of Coupling objects passed to the couplings keywords. The site_index attribute of H2_C13_coupling correspond to the index of H2_site and C13_site in the sites list. If we were to add more sites, site_index might need to be updated to reflect the index H2_site` and C13_site in the sites list. Again, our Isotopomers Example has good usage cases for multiple couplings in a spin system.


Table 1 The attributes of a SpinSystem object.

Attributes

Type

Description

name

String

An optional attribute with a name for the spin system. Naming is a good practice as it improves the readability, especially when multiple spin systems are present. The default value is an empty string.

label

String

An optional attribute giving a label to the spin system. Like name, it has no effect on a simulation and is purely for readability.

description

String

An optional attribute describing the spin system. The default value is an empty string.

sites

List

An optional list of Site objects. The default value is an empty list.

couplings

List

An optional list of coupling objects. The default value is an empty list.

abundance

String

An optional quantity representing the abundance of the spin system. The abundance is given as percentage, for example, 25.4 for 25.4%. This value is useful when multiple spin systems are present. The default value is 100.

Table 2 The attributes of a Site object.

Attribute name

Type

Description

name, label, and description

String

All three are optional attributes giving context to a Site object. The default value for all three is an empty string.

isotope

String

A required isotope string given as the atomic number followed by the isotope symbol, for example, 13C, 29Si, 27Al, and so on.

isotropic_chemical_shift

ScalarQuantity

An optional physical quantity describing the isotropic chemical shift of the site. The value is given in ppm, for example, 10 for 10 ppm. The default value is 0.

shielding_symmetric

SymmetricTensor

An optional object describing the second-rank traceless symmetric nuclear shielding tensor following the Haeberlen convention. The default is None. See the description for the SymmetricTensor object.

quadrupolar

SymmetricTensor

An optional object describing the second-rank traceless electric quadrupole tensor. The default is None. See the description for the SymmetricTensor object.

Table 3 The attributes of a Coupling object.

Attribute name

Type

Description

site_index

List of two integers

A required list with integers corresponding to the site index of the coupled sites, for example, [0, 1], [2, 1]. The order of the integers is irrelevant.

isotropic_j

ScalarQuantity

An optional physical quantity describing the isotropic J-coupling in Hz. The default value is 0.

j_symmetric

SymmetricTensor

An optional object describing the second-rank traceless symmetric J-coupling tensor following the Haeberlen convention. The default is None. See the description for the SymmetricTensor object.

dipolar

SymmetricTensor

An optional object describing the second-rank traceless dipolar tensor. The default is None. See the description for the SymmetricTensor object.

Table 4 The attributes of a SymmetricTensor object.

Attribute name

Type

Description

zeta

or

Cq

or

D

ScalarQuantity

A required quantity.

Nuclear shielding: The shielding anisotropy, zeta, calculated using the Haeberlen convention. The value is a physical quantity given in ppm, for example, 10

Electric quadrupole: The quadrupole coupling constant, Cq. The value is a physical quantity given in units of Hz, for example, 3.1e6 for 3.1 MHz.

J-coupling: The J-coupling anisotropy, zeta, calculated using the Haeberlen convention. The value is a physical quantity given in Hz, for example, 10 for 10 Hz.

Dipolar-coupling: The dipolar-coupling constant, D. The value is a physical quantity given in Hz, for example, 9e6 for 9 kHz.

eta

Float

A required asymmetry parameter calculated using the Haeberlen convention, for example, 0.75. The parameter is set to zero for the dipolar tensor.

alpha

ScalarQuantity

An optional Euler angle, \(\alpha\). For example, 2.1 for 2.1 radians. The default value is 0.

beta

ScalarQuantity

An optional Euler angle, \(\beta\). For example, 1.5708 for 90 degrees. The default value is 0.

gamma

ScalarQuantity

An optional Euler angle, \(\gamma\). For example, 0.5 for 0.5 radians. The default value is 0.