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OPEN A database of synthetic inelastic

Data Descriptor neutron scattering spectra from
molecules and crystals
Yongqiang Cheng , Matthew B. Stone & Anibal J. Ramirez-Cuesta

Inelastic neutron scattering (INS) is a powerful tool to study the vibrational dynamics in a material.
The analysis and interpretation of the INS spectra, however, are often nontrivial. Unlike diffraction,
for which one can quickly calculate the scattering pattern from the structure, the calculation of INS
spectra from the structure involves multiple steps requiring significant experience and computational
resources. To overcome this barrier, a database of INS spectra consisting of commonly seen materials
will be a valuable reference, and it will also lay the foundation of advanced data-driven analysis
and interpretation of INS spectra. Here we report such a database compiled for over 20,000 organic
molecules and over 10,000 inorganic crystals. The INS spectra are obtained from a streamlined
workflow, and the synthetic INS spectra are also verified by available experimental data. The database
is expected to greatly facilitate INS data analysis, and it can also enable the utilization of advanced
analytics such as data mining and machine learning.

Notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725
with the U.S. Department of Energy. The United States Government retains and the publisher, by
accepting the article for publication, acknowledges that the United States Government retains a non-
exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this
manuscript, or allow others to do so, for United States Government purposes. The Department of
Energy will provide public access to these results of federally sponsored research in accordance with
the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).

Background & Summary

Neutrons, like X-rays, can be used to measure the atomic-level structure and dynamics in a material1,2.
Compared to X-ray scattering, neutron scattering has some unique advantages, making it a very useful com-
plementary tool to provide a complete picture of where atoms are and what they do3. Thermal neutrons used
in most neutron scattering experiments have energy and momentum comparable to phonons, the vibrational
quanta in materials, so that the vibrational dynamics can be measured with high accuracy and resolution using
inelastic neutron scattering (INS). Thanks to the high neutron scattering cross-sections of light elements, neu-
trons are very sensitive to H, C, O, etc., which are sometimes difficult to see with X-rays especially when in the
presence of heavier elements. Unlike Raman or Infrared spectroscopy, INS does not suffer from selection rules,
meaning that all phonons can in principle contribute to the total scattering intensity, making it an ideal tech-
nique to measure phonon dispersion and phonon density of states (PDOS). Neutrons are also highly penetrat-
ing, so that the measured data reflect the statistical results of the bulk sample. It also means more complex and
intrusive sample environment can be tolerated. Neutrons also have a magnetic moment allowing them to couple
to magnetic moments in materials. This makes them especially useful for studying magnetic structures and
magnetic excitations. In actual INS experiments, the magnetic excitations will very often overlap significantly in
momentum and energy transfer with the phonon spectrum. Neutron scattering has been used to study materials
with fundamental and practical interest in a large variety of areas covering condensed matter physics, chemistry,
biology, geology, and engineering4–6.

Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, USA. ✉ e-mail:
[email protected]

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Structure database Vibraonal analysis INS simulaon

QM8 (20,000+ molecules) Gaussian

OCLIMAX
Phonondb (10,000+ crystals) Phonopy

Fig. 1 Workflow used to produce the INS spectra database. The QM8 database was used for organic molecules,
and the Phonondb was used for inorganic crystals. The vibrational analysis was performed using Gaussian 09
and Phonopy codes, and the resulting INS simulation was produced using OCLIMAX software.

Fig. 2 Distribution of number of molecules as a function of molecular size (number of atoms, including
hydrogen) in the QM8 database.

When a neutron beam interacts with a material, the neutrons can be scattered elastically or inelastically1.
One is able to determine long range ordered structures using diffraction measurements which integrate over all
energy transfers, both elastic and inelastic scattering, similar to X-ray diffraction. The data analysis is essentially
a refinement process involving calculating the diffraction pattern from a candidate structural model, compar-
ing with experiment, adjusting/optimizing the structural model, and repeating until numerical convergence
criteria are achieved. This procedure works because the diffraction pattern due to the long-range order can be
analytically and quickly calculated from the structure. In the analysis of INS, however, a similar protocol would
be extremely difficult to implement, because there is in general no easy way to obtain the INS spectrum directly
from the structure. A typical procedure involves structural optimization and then calculation of vibrational
modes, often from density functional theory (DFT) or other first-principles methods5. The entire process can
take hours or days depending on the complexity of the structure, thus making an iterative process computation-
ally restrictive. Such calculations also require special expertise and significant computing resources (hardware
and software). Simulations of INS spectra from the vibrational modes are also more complicated than calculat-
ing the diffraction and only recently become more accessible to general users with the development of additional
software tools such as the OCLIMAX program7,8.
The lack of a venue to quickly “predict” the INS spectra from a structure model, even by a crude approxima-
tion, has been a major hurdle in the analysis and interpretation of INS spectra. Users need this capability when
they are writing a proposal, planning for an experiment, making decisions during the experiment, or performing
analysis after the experiment. Even individuals interested in magnetic scattering can make use of this capability
in order to assist in distinguishing magnetic from vibrational scattering channels. To this end, having a database
containing the INS spectra of commonly seen materials will be extremely useful. However, due to the extremely
limited resources for neutron scattering, an experimental database is expensive and time-consuming to com-
pile. The currently available ISIS database9 and DCS database10 contain 837 and 11 spectra, respectively. In this
work, we have created a large-scale synthetic database containing simulated INS spectra for 20,000+ organic
molecules and 10,000+ inorganic crystals. It is made publicly available for use and download for research and
development purposes. The database can be used as a reference to search for the target or similar samples of
interest, or as training datasets for more advanced analysis using data mining or machine learning.

Methods
The INS spectra for organic molecules and inorganic crystals are produced following the workflow shown in
Fig. 1. Specifically, for organic molecules, the molecules in QM8 database11–13 were used (molecules containing
8 or fewer non-hydrogen atoms). The distribution of molecular size in this database can be found in Fig. 2.
With the starting molecular structure, potential energy minimization (optimization) and vibrational analysis
were performed using Gaussian 0914, with the following accuracy and key parameters: B3LYP/6-311++G(d,p)
OPT = (Tight) Int = (Grid = Ultrafine) CPHF = (Grid = Fine). There are 21,786 molecules in the QM8 data-
base, but 93 failed to reach convergence in the Gaussian calculation. The results for 21,693 molecules are then
converted to INS spectra for VISION/TOSCA using OCLIMAX. VISION15 and TOSCA16 are two indirect
geometry neutron spectrometers at the Spallation Neutron Source and ISIS, respectively. They are optimized
to measure hydrogen containing materials with a focus on applications in chemistry. The calculated spectra for

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Fig. 3 Distribution of number of crystal structures as a function of unit cell volume in the inorganic crystal
(phonondb) database. The bin size is 5 Å3. Note that there are a small number of unit cells with volume larger
than 3000 Å3 not shown in this figure.

Fig. 4 Histogram of the occurrence of each element in the inorganic crystal database (phonondb). Note that the
y-axis is in logarithmic scale.

these instruments can be produced using the default parameters in OCLIMAX software, with an energy unit
of cm−1 (commonly used in chemical spectroscopy). Also produced from OCLIMAX is an xyz file containing
the normal modes, as well as the calculated INS intensity for each individual mode. This allows one to quickly
determine the underlying physical origin of features in the calculated spectrum.
For inorganic crystals, we chose the phonondb@kyoto-u created by Togo17–19 as our starting point because
unlike some other PDOS databases, this one includes force constants for each crystal calculated from DFT
(VASP20). This allows us to run customized phonon calculations using Phonopy21 to obtain the needed eigen-
values and eigenvectors within the full Brillouin zone for INS simulations. Some statistical information on the
10,032 crystals in this database is shown in Figs. 3,4 and Supplementary Table 1. Note that due to the incomplete
neutron scattering cross-section information of Xe22, nine Xe-containing compounds were not calculated for INS.
The 2D S(Q,E) spectra for the 10,023 inorganic crystals were calculated in the energy range of 0–150 meV (bin
size 0.5 meV, 1 meV = 8.066 cm−1), Q range of 0–15 Å−1 (bin size 0.05 Å−1), using an energy resolution of 1.5 meV.
The calculations were performed on a computer cluster with 1600 CPU cores. It took about a day of computing
time in total, meaning that it would not be an issue to regenerate this database for a different instrument, sample
environment, E/Q range, or temperature range. In addition to the 2D S(Q,E), VISION/TOSCA spectra, PDOS
and elemental-specific partial PDOS, as well as the corresponding neutron-weighted PDOS, are also calculated.
Data Records
All data files are available at Zenodo23. Data files for each structure model are included in a subfolder. For the
QM8 molecular database, there are five files in each subfolder: an INFO-* file containing the SMILES24 string
as well as the IUPAC name (if available) for the particular molecule, a *.com file containing the input for the
Gaussian simulation (which also contains the atomic coordinates), a *vis_inc_0K.csv file containing the sim-
ulated INS spectra, a *.xyz file containing the displacement of each vibrational modes (can be visualized with

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Fig. 5 Examples of simulated INS spectra for organic molecules. The legend shows the SMILES24 representation
of each molecule. The x-axis is frequency in units of wavenumber (cm−1) and the y-axis is the calculated
normalized scattering intensity. Intensity is normalized such that the strongest peak has a unitary value.
The spectra shown here are the total spectra including all contributions from fundamental excitations,
combinations, overtones, and phonon wings.

Fig. 6 Assignment of toluene vibrational modes to the INS peaks, using the mode.csv file and xyz file provided
in the database.

Jmol25), and a *modes.csv file containing the calculated INS intensity for each normal mode. Some examples
of the simulated INS spectra are shown in Fig. 5. When the simulated INS spectrum and the intensity of each
mode are plotted together, as shown in Fig. 6, it becomes clear that which mode is responsible for the INS peak
observed in the total spectrum. The corresponding normal modes can then be visualized using the xyz file.
For the inorganic crystal database, each subfolder also contains five files: a structure.cif file for the crystal
structure, a vis_inc_0K.csv file containing the simulated VISION/TOSCA spectra, a powder_2Dmesh_coh_0K.
csv file containing the simulated powder S(Q,E), a vis_nwdos.csv file containing the neutron weighted PDOS, a
vis_dos.csv file containing the true PDOS, and a gamma_modes.xyz file containing the displacements of gamma
point phonons for visualization. Note that the INS spectra and PDOS are calculated on phonons sampled in the
full Brillouin zone; the gamma point phonon files are provided for visualization only and not used for INS or
PDOS calculations. Examples of the simulated 2D S(Q,E) are shown in Fig. 7.
Technical Validation
Although the procedure shown in Fig. 1 to produce the simulated INS spectra hasn’t been previously used on
large scale dataset in a high-throughput fashion, it has a proven record to be generally reliable and accurate, as
reported in literature (e.g., publications that used OCLIMAX7 for INS simulations). Here we provide further
validation by directly comparing spectra from the database with experimental data. For molecular systems, the

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Fig. 7 Examples of simulated 2D INS spectra, or S(Q,E), for inorganic crystals. The x-axis is momentum
transfer in units of Å−1 and the y-axis is energy transfer in units of meV. This view of the calculated spectrum is
similar to what would be measured by direct geometry neutron chopper spectrometers29.

Fig. 8 Comparison of the simulated and experimental INS spectra for toluene. The simulated partial spectra
are also shown, corresponding to contributions from each level of excitations. For example, [0- > 1] means
fundamental excitations. [0- > 2] means two-phonon excitations. W[0- > 1] refers to the phonon wing from
fundamental excitations, etc. The experimental spectrum is offset vertically for clarity of the figure.

comparison is made for toluene (C7H8), as shown in Fig. 8. The simulated total spectrum agrees very well with
the experimental spectrum collected at VISION. All major peaks can be unambiguously assigned. Furthermore,
the simulated partial spectra clearly tell us which peaks are from fundamental excitations, which peaks are
from combinations and overtones, and which part of the intensity comes mainly from phonon wings (inter-
molecular modes in the solid state). It should be noted that in an INS experiment, one measures a solid sample,
not a single molecule. In the INS simulations for molecules, the intermolecular interactions are approximately
accounted for by the wing calculation5. This simplification seems to work well for relatively large molecules with

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Fig. 9 Comparison of experimental (left) and simulated (right) S(Q,E) for silicon powder. The experimental
spectrum was collected at SEQUOIA with an incident energy of 60 meV. The simulated spectrum is taken from
the database which was obtained with the generic parameters not specifically optimized for the experimental
conditions and resolution (which may explain some of the discrepancies). The experimental spectrum also
contains contribution from the aluminium sample holder, which has relatively high intensity at around 20 meV
and 4 Å−1.

weak intermolecular interactions (such as toluene in Fig. 8), but tends to fail for very small molecules (those
containing only a few atoms) with strong intermolecular interactions (such as water ice, ammonia, or methane).
Fortunately, experimental data for these very “simple” molecular systems are usually available9.
Figure 9 illustrates a comparison of 2D S(Q,E) for silicon powder. While the simulation was done with
generic parameters as described above and defined in the params file, and not specifically for the instrument
setup at SEQUOIA26 used to collect the experimental data, the agreement is still satisfactory. Note that there is a
small contribution from the aluminium sample container in the experimental spectra, as described in the figure
caption.

Usage Notes
Two tables listing all entries in the database are provided, which can help users to quickly find/locate the files
they need. A Python script to plot data is also provided. The INS data files are all in ASCII format and can be
imported in text editors and other software packages for post-processing. They can also be loaded in Mantid27
and DAVE28, which are often used to analyse and visualize INS data.

Code availability
Gaussian 0914, Phonopy21, and OCLIMAX7 are used to generate the datasets. Gaussian 09 is commercial software
that requires the users to purchase a license. Phonopy and OCLIMAX are freely available to the public. All
parameters used in the calculations are provided in the database as input files.

Received: 31 October 2022; Accepted: 22 December 2022;

Published: xx xx xxxx

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Acknowledgements
A portion of this research used resources at the Spallation Neutron Source, a DOE Office of Science User Facility
operated by the Oak Ridge National Laboratory (ORNL). The computing resources for INS simulations were
made available through the VirtuES and the ICE-MAN projects, funded by Laboratory Directed Research and
Development (LDRD) Program and Compute and Data Environment for Science (CADES) at ORNL. The
research is also sponsored by the Artificial Intelligence Initiative as part of the LDRD program of ORNL, managed
by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725.

Author contributions
Y.C. designed the project, performed the simulations, created the database, and drafted the manuscript. M.B.S.
and A.J.R.C. contributed to the data validation. All authors discussed and revised the manuscript.

Competing interests
The authors declare no competing interests.

Additional information
Supplementary information The online version contains supplementary material available at https://doi.
org/10.1038/s41597-022-01926-x.
Correspondence and requests for materials should be addressed to Y.C.
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