Backend Properties
The basic structure for a molecule entry in the D3TaLES database is described in the
Data Structure section. As noted there, the backend database centers around individual
raw data entries. Therefore, a data entry may be in one of the following data collections: computation,
experimentation, ml, nlp, and backend_synthesis.
Computation
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
_id |
A unique identifier for the data hashed from identifying properties | string |
mol_id |
A unique identifier for the molecule | string |
submission_info |
Information about who submitted the data and how | object |
calculation_type |
Type of calculation file opt_cation, neutral_cation, etc. | string |
runtime |
The job runtime in core hours | number |
data |
Data extracted from raw file | object |
Molecular DFT
The structural and electronic information derived from molecular DFT calculations on a molecule entry in database.
Read more about conditions here.
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
conditions |
Parameters used for calculations | object |
charge |
Electronic charge on the molecule | number |
spin_multiplicity |
Spin multiplicity of the molecule | integer |
is_groundState |
Whether the calculation charge is the ground state charge | boolean |
number_of_electrons |
Number of electrons in the molecule | integer |
omega |
Omega value derived from omega tuning process | number |
geometry |
Description of a molecule geometry | object |
scf_dipole_moment |
The X, Y, and Z dipole components of electric dipole moment. Units: Debye | object |
scf_total_energy |
Total energy calculated using the self-consistent field method. Units: eV | object |
homo |
Highest occupied molecular orbital. Units: eV | object |
homo_1 |
Second highest occupied molecular orbital (HOMO-1). Units: eV | object |
lumo |
Lowest unoccupied molecular orbital. Units: eV | object |
lumo_1 |
Second lowest unoccupied molecular orbital (LUMO+1). Units: eV | object |
gibbs_correction |
Gibbs entropy correction. Units: eV | object |
radical_buried_vol |
Buried volume at the maximum fractional spin. Units: A^3 | object |
radical_spin |
The fractional spin positioned on the radial. Units: % as decimal | object |
radical_stability_score |
Score for radical stability from Chem. Sci., 2021, 12, 13158–13166 | object |
frequency_dict |
A list for each freq calculation and for each mode of a dict with {“frequency”: freq in cm-1, “symmetry”: symmetry tag “r_mass”: Reduce mass, “f_constant”: force constant, “IR_intensity”: IR Intensity, “mode”: normal mode}. The normal mode is a 1D vector of dx, dy dz of each atom. | array |
excitations |
TD-DFT excited states such as single, triplet, adiabatic, etc. Returns a list of tuple for each transition such as [(energy (eV), lambda (nm), oscillatory strength), … ] | object |
singlet_plotting |
Dictionary for plotting singlet spectra | object |
Periodic DFT
The structural and electronic information derived from periodic DFT calculations on a system using molecule instance(s) in the database.
Read more about conditions here.
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
conditions |
Parameters used for calculations | object |
task_name |
Description of the system studied and the type of calculation performed. | string |
adsorbate |
Atom or molecule adsorbing to the surface. | object |
bulk |
The bulk material used to generate the slab. | object |
slab |
The surface on which the molecule adsorbs. | object |
slab_adsorbate |
The slab + adsorbate system. | object |
cleavage_energy |
The energy required to cleave the surface along a specific plane. Units: eV | number |
nearest_surface_neighbors |
The atoms closest to a specific atom in the slab. | object |
adsorption_site |
The site over which the adsorbate is positioned. | object |
adsorption_energy |
The change in energy associated with adsorption. Energy(slab + adsorbate) - energy (slab) - energy (adsorbate). Units: eV | number |
electronic_descriptors |
Properties related to electronic band structure calculations. | object |
charge_analysis |
Changes in bader and DDEC6 charges as a result of adsorption. | object |
Molecular Dynamics (under development)
The structural and electronic information derived from molecular dynamics (MD) calculations on a system using molecule instance(s) in the database.
Read more about conditions here.
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
conditions |
Parameters used for calculations | object |
viscosity |
Viscosity. Units: | object |
diffusivity |
Diffusivity. Units: | object |
Experimentation
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
_id |
A unique identifier for the data | string |
mol_id |
A unique identifier for the molecule | string |
submission_info |
Information about who/when submitted the data | object |
experiment_type |
Type of experiment run | string |
data |
Data extracted from raw file | object |
Cyclic Voltammetry
CV data extracted from a datafile produced during a CV experiment on a molecule entry in database.
Read more about conditions here.
Read more about instrument properteis here.
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
file_name |
Name of file uploaded | string |
header |
CV file header | string |
note |
CV file description | string |
date_recorded |
Date and time CV data was collected | string |
conditions |
CV conditions | object |
data_points_per_scan |
Number of data points per scan | number |
initial_p_n |
string |
|
segment |
Number of forward or backward segments | integer |
sample_interval |
Sample potential interval (V) | object |
peak_potential |
Highest potential reached | object |
quiet_time |
Quiet time in seconds | object |
sensitivity |
Sensitivity in (A/V) | object |
scan_data |
List of scans | array |
middle_sweep |
Middle sweep list | array |
forward |
Data points from forward scan | array |
reverse |
Data points from reverse scan | array |
reversibility |
List of reversibility categorizations for peaks | array |
e_half |
List of E 1/2 for peaks | array |
peak_splittings |
List of peak splittings for peaks | array |
plot_data |
Data points from reverse scan | array |
Infrared Spectroscopy (IR)
IR data extracted from a datafile produced during a IR experiment on a molecule entry in database.
Read more about conditions here.
Read more about instrument properteis here.
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
file_name |
Name of file uploaded | string |
header |
IR file header | string |
note |
IR file description | string |
data_recorded |
Date and time IR data was collected | string |
conditions |
IR conditions | object |
wavelength_range |
range of wavelength in nm | object |
window |
Window used in IR | object |
optical_velocity |
The speed of the moving mirror. Units: cm/s | object |
aperture |
Type of apeture used in IR | object |
gain |
Description of the instrument's gain (sensitivity) | string |
scan_data |
Data points gather from IR scan | array |
UV-Vis Spectroscopy (UV-Vis)
UV-Vis data extracted from a datafile produced during a UV-Vis experiment on a molecule entry in database.
Read more about conditions here.
Read more about instrument properteis here.
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
file_name |
Name of file uploaded | string |
header |
UV Vis file header | string |
note |
UV Vis file description | string |
data_recorded |
Date and time UV Vis data was collected | string |
conditions |
UV Vis conditions | object |
integration_time |
The time allowed for the detector to collect photons | number |
wavelength_range |
Range of wavelength. Unit: nm | object |
absorbance_data |
Data points gather from UV-Vis scan | array |
Natural Language Processing (NLP)
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
_id |
Article's digital object identifier (DOI) | string |
date_accessed |
DOI | string |
abstract |
Article abstract | string |
authors |
List of author names | array |
publish_date |
Date the article was published | string |
publisher |
Name of the article's publisher | string |
downloaded_ip |
IP address that downloaded the article | string |
journal |
Name of the journal that published the article | string |
title |
Article title | string |
main_text |
Main text for the article | object |
pdf_location |
Path to PDF storage location at Iowa State University | string |
SI |
Supplementary information | object |
relevant |
Whether or not the article is relevant to D3TaLES | boolean |
last_updated |
Date this NLP data was last updated | string |
extracted_molecules |
List of molecules with associated properties extracted from the paper | array |
Machine Learning (ML)
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
_id |
A unique identifier for the data hashed from identifying properties | string |
mol_id |
A unique identifier for the molecule | string |
submission_info |
Information about who/when submitted the data | object |
Synthesis
To Visualize the Schema for these properties, click here
Property |
Description | Data Type |
|---|---|---|
_id |
A unique identifier for the data hashed from identifying properties | string |
mol_id |
A unique identifier for the molecule | string |
submission_info |
Information about who/when submitted the data | object |