Models

Element

class Element(**kwargs)[source]

Chemical element.

For full list of available data with references see Data and data acess for documentation on accessing data.

Parameters:
  • abundance_crust (float) – Abundance in the earth’s crust in mg/kg

  • abundance_sea (float) – Abundance in the seas in mg/L

  • annotation (str) – Annotations regarding the data

  • atomic_number (int) – Atomic number

  • atomic_radius (float) – Atomic radius in pm

  • atomic_radius_rahm (float) – Atomic radius by Rahm et al. in pm

  • atomic_volume (float) – Atomic volume in cm3/mol

  • atomic_weight (float) – Relative atomic weight as the ratio of the average mass of atoms of the element to 1/12 of the mass of an atom of 12C

  • block (str) – Block in periodic table, s, p, d, f

  • boiling_point (float) – Boiling temperature in K

  • c6 (float) – C_6 dispersion coefficient in a.u. from X. Chu & A. Dalgarno, J. Chem. Phys., 121(9), 4083-4088 (2004) doi:10.1063/1.1779576, and the value for Hydrogen was taken from K. T. Tang, J. M. Norbeck and P. R. Certain, J. Chem. Phys. 64, 3063 (1976), doi:10.1063/1.432569

  • c6_gb (float) – C_6 dispersion coefficient in a.u. from Gould, T., & Bučko, T. (2016). JCTC, 12(8), 3603-3613. http://doi.org/10.1021/acs.jctc.6b00361

  • cas (str) – Chemical Abstracts Service identifier

  • covalent_radius_bragg (float) – Covalent radius in pm from

  • covalent_radius_cordero (float) – Covalent radius in pm from Cordero, B., Gómez, V., Platero-Prats, A. E., Revés, M., Echeverría, J., Cremades, E., … Alvarez, S. (2008). Covalent radii revisited. Dalton Transactions, (21), 2832. doi:10.1039/b801115j

  • covalent_radius_pyykko (float) – Single bond covalent radius in pm Pyykkö, P., & Atsumi, M. (2009). Molecular Single-Bond Covalent Radii for Elements 1-118. Chemistry - A European Journal, 15(1), 186-197. doi:10.1002/chem.200800987

  • covalent_radius_pyykko_double (float) – Double bond covalent radius in pm from P. Pyykkö et al.

  • covalent_radius_pyykko_triple (float) – Triple bond covalent radius in pm from P. Pyykkö et al.

  • cpk_color (str) – CPK color of the atom in HEX, see http://jmol.sourceforge.net/jscolors/#color_U

  • density (float) – Density at 295K in g/cm3

  • description (str) – Short description of the element

  • dipole_polarizability (float) – Dipole polarizability in atomic units

  • dipole_polarizability_unc (float) – Uncertainty of the dipole polarizability

  • discoverers (str) – The discoverers of the element

  • discovery_location (str) – The location where the element was discovered

  • discovery_year (int) – The year the element was discovered

  • electron_affinity (float) – Electron affinity in eV

  • electrophilicity (float) – Parr’s electrophilicity index

  • econf (str) – Ground state electron configuration

  • evaporation_heat (float) – Evaporation heat in kJ/mol

  • fusion_heat (float) – Fusion heat in kJ/mol

  • gas_basicity (float) – Gas basicity

  • geochemical_class (str) – Geochemical classification of the elements

  • glawe_number (int) – Glawe number (scale)

  • goldschmidt_class (str) – Goldschmidt classification of the elements

  • group_id (int) – Group number

  • heat_of_formation (float) – Heat of formation in kJ/mol

  • inchi (str) – International Chemical Identifier

  • is_monoisotopic (bool) – A flag marking if the element is monoisotopic

  • jmol_color (str) – Color of the atom as used in Jmol, in HEX, see http://jmol.sourceforge.net/jscolors/#color_U

  • lattice_constant (float) – Lattice constant in ang

  • lattice_structure (str) – Lattice structure code

  • mass (float) – Relative atomic mass. Ratio of the average mass of atoms of the element to 1/12 of the mass of an atom of 12C

  • mendeleev_number (int) – Mendeleev number

  • melting_point (float) – Melting temperature in K

  • metallic_radius (float) – Single-bond metallic radius or metallic radius, have been calculated by Pauling using interatomic distances and an equation relating such distances with bond number

  • metallic_radius_c12 (float) – Metallic radius obtained by Pauling with an assumed number of nearest neighbors equal to 12

  • molar_heat_capacity (flaot) – Molar heat capacity in J/mol K

  • molcas_gv_color (str) – Color of an atom in HEX from MOLCAS GV http://www.molcas.org/GV/

  • name (str) – Name in English

  • name_origin (str) – Origin of the name

  • nist_webbook_url (str) – URL for the NIST Chemistry WebBook

  • period (int) – Period in periodic table

  • pettifor_number (int) – Pettifor scale

  • proton_affinity (float) – Proton affinity

  • series (int) – Index to chemical series

  • sources (str) – Sources of the element

  • specific_heat_capacity (float) – Specific heat in J/g K @ 20 C

  • symbol (str) – Chemical symbol

  • thermal_conductivity (float) – Thermal conductivity in @/m K @25 C

  • uses (str) – Uses of the element

  • vdw_radius (float) – Van der Waals radius in pm from W. M. Haynes, Handbook of Chemistry and Physics 95th Edition, CRC Press, New York, 2014, ISBN-10: 1482208679, ISBN-13: 978-1482208672.

  • vdw_radius_bondi (float) – Van der Waals radius according to Bondi in pm

  • vdw_radius_truhlar (float) – Van der Waals radius according to Truhlar in pm

  • vdw_radius_rt (float) – Van der Waals radius according to Rowland and Taylor in pm

  • vdw_radius_batsanov (float) – Van der Waals radius according to Batsanov in pm

  • vdw_radius_dreiding (float) – Van der Waals radius from the DREIDING force field in pm

  • vdw_radius_uff (float) – Van der Waals radius from the UFF in pm

  • vdw_radius_mm3 (float) – Van der Waals radius from MM3 in pm

  • oxistates (list) – Oxidation states

  • ionenergies (dict) – Ionization energies in eV parsed from http://physics.nist.gov/cgi-bin/ASD/ie.pl on April 13, 2015

property boiling_point: float | Dict[str, float]

Boiling point

covalent_radius

Return the default covalent radius which is covalent_radius_pyykko

electronegativity(scale: str = 'pauling', **kwargs) float[source]

Calculate the electronegativity using one of the methods

Parameters:
  • scale – Name of the electronegativity scale, one of

  • kwargs – keyword arguments that are passed to compute a specific electronegativity

electronegativity_allen() float[source]

Allen’s electronegativity

electronegativity_allred_rochow(radius='covalent_radius_pyykko') float[source]

Allred-Rochow’s electronegativity

electronegativity_cottrell_sutton(radius='covalent_radius_pyykko') float[source]

Cottrell-Sutton’s electronegativity

electronegativity_ghosh() float[source]

Ghosh’s electronegativity

electronegativity_gordy(radius='covalent_radius_pyykko') float[source]

Gordy’s electronegativity

electronegativity_li_xue(charge: int = 1, radius: str = 'crystal_radius') Dict[Tuple[str, str], float][source]

Calculate the electronegativity of an atom according to the definition of Li and Xue

Parameters:
  • charge – charge of the ion

  • radius – type of radius to be used in the calculation, either crystal_radius as recommended in the paper or ionic_radius

Returns:

dictionary with electronegativities as values and

coordination string as keys or tuple of coordination and spin if the ion is LS or HS

Return type:

out (dict)

electronegativity_martynov_batsanov() float[source]

Calculates the electronegativity value according to Martynov and Batsanov as the average of the ionization energies of the valence electrons

\[\chi_{MB} = \sqrt{\frac{1}{n_{v}}\sum^{n_{v}}_{k=1} I_{k}}\]

where:

  • \(n_{v}\) is the number of valence electrons

  • \(I_{k}\) is the \(k\) th ionization potential.

electronegativity_mulliken(charge: int = 0) float[source]

Return the absolute electronegativity (Mulliken scale).

Parameters:

charge – charge of the ion

The value of electonegativity is calculated as:

\[\]

chi = frac{I + A}{2}

where:

  • \(I\) is the ionization energy,

  • \(A\) is the electron affinity

electronegativity_nagle() float[source]

Nagle’s electronegativity

electronegativity_pauling() float[source]

Pauling’s electronegativity

electronegativity_sanderson(radius='covalent_radius_pyykko') float[source]

Sanderson electronegativity

Parameters:

radius – radius to use in the calculation

electronegativity_scales(name: str = None) Callable | List[str][source]

Available electronegativity scales

electrons

Return the number of electrons.

electrophilicity() float | None[source]

Calculate electrophilicity index

\[\omega = \frac{\mu}{2\eta}\]
hardness(charge: int = 0) float | None[source]

Return the absolute hardness, calculated as

Parameters:

charge – Charge of the cation for which the hardness will be calculated. Defaultf to 0.

\[\eta = \frac{IE - EA}{2}\]

where:

  • \(IE\) is the ionization energy,

  • \(EA\) is the electron affinity

inchi

International Chemical Identifier.

See: https://en.wikipedia.org/wiki/International_Chemical_Identifier

init_on_load() None[source]

Initialize the ElectronicConfiguration class as attribute of self

mass

Return the atomic_weight if defined or mass number otherwise.

mass_str() str[source]

String representation of atomic weight

property melting_point: float | Dict[str, float]

Melting point

property nist_webbook_url: str

URL for the NIST Chemistry WebBook

nvalence(method: str = None) int[source]

Return the number of valence electrons

oxidation_states(category: str = 'main') List[int][source]

Utility method for accessing oxidation states.

Parameters:

category (str) – Category of oxidation state, Either - main - for main, most common, oxidataion states - extended - for less common oxidation states - all - all oxidation states

oxides() List[str][source]

Return a list of possible oxides based on the oxidation number

protons

Return the number of protons.

softness(charge: int = 0) float | None[source]

Return the absolute softness.

Parameters:

charge – Charge of the cation for which the hardness will be calculated

\[S = \frac{1}{2\eta}\]

where :

  • \(\eta\) is the absolute hardness

specific_heat

Alias for specific_heat_capacity for backwards compatibility

zeff(n: int = None, o: str = None, method: str = 'slater', alle: bool = False) float | None[source]

Return the effective nuclear charge for (n, s)

Parameters:
  • method

    Method to calculate the screening constant, the choices are

    • slater, for Slater’s method as in Slater, J. C. (1930).

      Atomic Shielding Constants. Physical Review, 36(1), 57–64. doi:10.1103/PhysRev.36.57

    • clementi for values of screening constants from Clementi, E.,

      & Raimondi, D. L. (1963). Atomic Screening Constants from SCF Functions. The Journal of Chemical Physics, 38(11), 2686. doi:10.1063/1.1733573 and Clementi, E. (1967). Atomic Screening Constants from SCF Functions. II. Atoms with 37 to 86 Electrons. The Journal of Chemical Physics, 47(4), 1300. doi:10.1063/1.1712084

  • n – Principal quantum number

  • o – Orbital label, (s, p, d, …)

  • alle – Use all the valence electrons, i.e. calculate screening for an extra electron when method=’slater’, if method=’clementi’ this option is ignored

Ion

class Ion(label, q=1)[source]

Class representating atomic ions

ionic_potential(radius_most_reliable: bool = True) float[source]

Calculate the ionic potential

Parameters:

radius_most_reliable – flag to use the most reliable ionic radius, default is True

unicode_ion_symbol() str[source]

Return a unicode string symbol of the ion

IonicRadius

class IonicRadius(**kwargs)[source]

Effective ionic radii and crystal radii in pm retrieved from [1].

Parameters:
  • atomic_number (int) – Atomic number

  • charge (int) – Charge of the ion

  • econf (str) – Electronic configuration of the ion

  • coordination (str) – Type of coordination

  • spin (str) – Spin state: HS - high spin, LS - low spin

  • crystal_radius (float) – Crystal radius in pm

  • ionic_radius (float) – Ionic radius in pm

  • origin (str) – Source of the data

  • most_reliable (bool) – Most reliable value (see reference)

IonizationEnergy

class IonizationEnergy(**kwargs)[source]

Ionization energy of an element

Parameters:

Isotope

class Isotope(**kwargs)[source]
Parameters:
  • abundance (float) – Abundance of the isotope

  • abundance_uncertainty (float) – Abundance uncertainty

  • atomic_number (int) – Atomic number

  • discovery_year (int) – Year the isotope was discovered

  • g_factor (float) – Dimensionless magnetic moment

  • g_factor_uncertainty (float) – Uncertainty for the g_factor

  • half_life (float) – Half life time

  • half_life_uncertainty (float) – Uncertainty for the half_life

  • half_life_unit (str) – Unit for the half life time

  • is_radioactive (bool) – A flag marking wheather the isotope is radioactive

  • mass (float) – Mass of the isotope

  • mass_number (int) – Mass number of the isotope

  • mass_uncertainty (float) – Uncertainty of the mass value

  • parity (str) – Parity, if present, it can be either + or -

  • quadrupole_moment (float) – Quadrupole moment

  • quadrupole_moment_uncertainty (float) – Uncertainty for the quadrupole_moment

  • spin (str) – Nuclear spin

is_stable

Flag to indicate whether the isotope is stable

ScreeningConstant

class ScreeningConstant(**kwargs)[source]

Nuclear screening constants from Clementi, E., & Raimondi, D. L. (1963). Atomic Screening Constants from SCF Functions. The Journal of Chemical Physics, 38(11), 2686. doi:10.1063/1.1733573 and Clementi, E. (1967). Atomic Screening Constants from SCF Functions. II. Atoms with 37 to 86 Electrons. The Journal of Chemical Physics, 47(4), 1300. doi:10.1063/1.1712084

Args::

atomic_number (int): Atomic number n (int): Principal quantum number s (str): Subshell label, (s, p, d, …) screening (float): Screening constant

Series

class Series(**kwargs)[source]

Name of the series in the periodic table.

Parameters:
  • name (str) – Name of the series

  • color (str) – The HEX representation of a color of the series, the colors were obtained from ColorBrewer the qualitative 10-class paired colormap

Group

class Group(**kwargs)[source]

Name of the group in the periodic table.

Parameters:
  • group_id (int) – group number

  • symbol – (str): group symbol

  • name (str) – group name

OxidationState

class OxidationState(**kwargs)[source]

Oxidation states of an element

Parameters:
  • atomic_number (int) – Atomic number

  • oxidation_state (int) – Oxidation state

  • category (str) – Either main or extended flag to indicate the type of oxidation state.

PropertyMetadata

class PropertyMetadata(**kwargs)[source]

Metadata for properties of elements and isotopes.

Parameters:
  • annotations (str) – Additional information about the property.

  • attribute_name (str) – Name of the attribute of the ORM class.

  • category (str) – Category of the property.

  • citation_keys (str) – Comma separated list of citation keys. See references.bib for full bibliography.

  • class_name (str) – Name of the ORM class.

  • column_name (str) – Name of the column in the database.

  • description (str) – Description of the property.

  • table_name (str) – Name of the table in the database.

  • unit (str) – Unit of the property.

  • value_origin (ValueOrigin) – Origin of the value, either stored or computed.

ElectronicConfiguration

class ElectronicConfiguration(conf: str | Dict = None, atomre: str = None, shellre: str = None)[source]

Electronic configuration handler

property atomre: Pattern

Regular expression for atomic symbols

property conf: OrderedDict

Return the configuration

electrons_per_shell() Dict[str, int][source]

Return number of electrons per shell as dict

get_largest_core() Tuple[source]

Find the largest noble gas core possible for the current configuration and return the symbol of the corresponding noble gas element.

get_valence()[source]

Find the valence configuration i.e. remove the largest noble gas core from the current configuration and return the result.

ionize(n: int = 1)[source]

Remove n electrons from and return a new ElectronicConfiguration object

last_subshell(wrt: str = 'order')[source]

Return the valence shell

max_l(n: int) int[source]

Return the largest value of azimutal quantum number for a given value of principal quantum number

Parameters:

n – int Principal quantum number

Returns:

int

Azimutal quantum number

Return type:

l

max_n() int[source]

Return the largest value of principal quantum number for the atom

ne() int[source]

Number of electrons

nvalence(block: str, period: int, method: str = None) int[source]

Return the number of valence electrons

parse(string: str) None[source]

Parse a string with electronic configuration into an OrderedDict representation

shell2int() List[Tuple[int]][source]

configuration as list of tuples (n, l, e)

property shellre: Pattern

Regular expression for the shell

slater_screening(n: int, o: str, alle: bool = False)[source]

Calculate the screening constant using the approach introduced by Slater in Slater, J. C. (1930). Atomic Shielding Constants. Physical Review, 36(1), 57-64. doi:10.1103/PhysRev.36.57

Parameters:
  • n – int Principal quantum number

  • o – str orbtial label, (s, p, d, …)

  • alle – bool Use all the valence electrons, i.e. calculate screening for an extra electron

sort(inplace: bool = True)[source]

Sort the occupations OD

spin_occupations()[source]

For each subshell calculate the number of alpha, beta electrons, electron pairs and unpaired electrons

spin_only_magnetic_moment() float[source]

Return the magnetic moment insluding only spin of the electrons and not the angular momentum

to_str() str[source]

Return a string with the configuration

unpaired_electrons() int[source]

Number of unpaired electrons