GPU-Accelerated Pipeline

High-throughput DFT
descriptors

Normally, DFT-level descriptor calculation requires coordinating numerous packages, debugging academic code, and weeks on HPC clusters. We automated this process, reduced the time to hours, and created a simple interface for harnessing it.

Platform benchmarks

100x

Faster than traditional DFT

GPU acceleration + neural network potentials vs. CPU-only HPC cluster workflows.

100s

Physics-based descriptors

3D-geometry and quantum-chemistry computed descriptors. Orbital energies, charges, steric parameters, and more.

Weeks → hrs

Library featurization

Full molecular library DFT featurization that took months on HPC clusters.

How It Works

From flat molecules to quantum descriptors

Our structure-agnostic pipeline transforms 2D molecular representations into DFT-level electronic properties, fully automated, no HPC cluster required.

DFT pipeline: 2D phosphine ligand structure, 3D conformer ensemble, and electrostatic potential surface
Step 1

Diverse Structure Input Formats

Start from SMILES strings, CDXML, or 3D coordinates. Upload MOL2, XYZ, CSV, or SDF files — the pipeline handles everything from flat molecular representations to full 3D geometries.

SMILESCDXMLMOL2 / XYZCSV / SDF
Step 2

3D Geometry Optimization

Generate conformer ensembles using CREST or GPU-accelerated RDKit/nvMolKit ETKDG. Further optimize geometries using neural network potentials like Meta's UMA to access DFT-level molecular geometries.

CREST / xTBnvMolKitMeta UMA
Step 3

Electronic Structure & Descriptors

GPU-accelerated DFT followed by automated extraction of descriptors provides you with an organized dataset of whole-molecule, atom-level, and bond-level descriptors ready for modeling.

PBE/SVP → ωB97M-V/QZP200+ descriptors100+ solvents
Why Chemetrian

No queue management

Submit thousands of molecules and walk away. No SLURM scripts, no HPC allocation requests, no babysitting jobs.

vs. weeks configuring HPC clusters

Automatic error recovery

Failed geometries retry with alternate methods. Problematic molecules get flagged, not silently dropped.

vs. manual debugging per molecule

Exported descriptors are ready for machine learning

Download as CSV. Column-level descriptor selection before export.

vs. parsing custom output files

Reproducible by default

Every job logs its full configuration — basis set, solvent model, conformer method, software versions.

vs. undocumented lab scripts

See it in action

From upload to ML-ready in three steps

A fully automated pipeline accessible through a simple interface — no HPC cluster required.

1

Upload

Drop in your molecular library

Upload SMILES, SDF, CDXML, MOL2, or XYZ files. The molecule editor validates structures and flags issues before compute begins.

app.chemetrian.com/dft/upload
Molecule editor and file upload interface
2

Configure

Pick your functional, basis set, and solvent

Four tiers of theory. Choose your accuracy-speed tradeoff, select solvation models, and configure output descriptors.

app.chemetrian.com/dft/configure
DFT Level of Theory selector panel
3

Results

ML-ready descriptors

Browse bond lengths, Sterimol parameters, Fukui indices, buried volumes, and dozens more — all computed per molecule and ready to export as CSV.

app.chemetrian.com/dft/results
DFT Descriptors63 features
r2SCAN-D4 / def2-TZVP
↓ CSV
DescriptorValue
Bond Length A–E
1.61
Bond Length A–F
1.59
Bond Length B–C
0.97
Bond Length F–G
1.39
Bond Length G–H
1.39
Bond Length H–I
1.88
Bond Angle A–E–F
109.47
Bond Angle E–F–G
121.33
Dihedral A–E–F–G
-14.82
Electrophilicity
0.51
Chemical Hardness
12.68
Chemical Potential
-3.60
Nucleophilicity
-7.14
HOMO (eV)
-7.14
LUMO (eV)
0.52
HOMO–LUMO Gap (eV)
7.66
HOMO−1 (eV)
-7.89
LUMO+1 (Hartree)
-0.05
Ionization Potential
7.14
Electron Affinity
0.54
Convex Hull Volume
1611.11
Geometric Diameter
23.96
Radius of Gyration
6.09
Molecular Span
12.34
SASA
482.71
Asphericity
0.38
Eccentricity
0.91
NPR1
0.12
NPR2
0.54
Van der Waals Volume
1203.44
Sterimol L Atoms A–B
7.64
Sterimol L Atoms A–D
8.42
Sterimol L Atoms A–E
10.65
Sterimol L Atoms A–F
9.18
Sterimol B1 Atoms A–B
3.21
Sterimol B5 Atoms A–B
6.78
Wiberg Bond A–E
0.94
Wiberg Bond E–F
1.07
Buried Volume A 3.0
0.61
Buried Volume A 3.5
0.53
Buried Volume A 4.5
0.34
Buried Volume B 3.0
0.65
Buried Volume B 3.5
0.50
Buried Volume B 4.5
0.28
Mulliken Charge A
-0.42
Mulliken Charge B
0.18
Mulliken Charge C
-0.31
NPA Charge A
-0.55
NPA Charge B
0.24
NPA Charge C
-0.38
Fukui f⁺ Atom A
0.12
Fukui f⁻ Atom A
0.08
Fukui f⁰ Atom A
0.10
Fukui Dual Atom A
0.04
Fukui f⁺ Atom B
0.06
Fukui f⁻ Atom B
0.15
Fukui f⁰ Atom B
0.11
Fukui Dual Atom B
-0.09
Fukui f⁺ Atom F
-0.06
Fukui f⁰ Atom F
-0.01
Fukui f⁻ Atom G
-0.17
Fukui f⁰ Atom G
-0.04
Fukui f⁻ Atom H
-0.07
Bond Length A–E
1.61
Bond Length A–F
1.59
Bond Length B–C
0.97
Bond Length F–G
1.39
Bond Length G–H
1.39
Bond Length H–I
1.88
Bond Angle A–E–F
109.47
Bond Angle E–F–G
121.33
Dihedral A–E–F–G
-14.82
Electrophilicity
0.51
Chemical Hardness
12.68
Chemical Potential
-3.60
Nucleophilicity
-7.14
HOMO (eV)
-7.14
LUMO (eV)
0.52
HOMO–LUMO Gap (eV)
7.66
HOMO−1 (eV)
-7.89
LUMO+1 (Hartree)
-0.05
Ionization Potential
7.14
Electron Affinity
0.54
Convex Hull Volume
1611.11
Geometric Diameter
23.96
Radius of Gyration
6.09
Molecular Span
12.34
SASA
482.71
Asphericity
0.38
Eccentricity
0.91
NPR1
0.12
NPR2
0.54
Van der Waals Volume
1203.44
Sterimol L Atoms A–B
7.64
Sterimol L Atoms A–D
8.42
Sterimol L Atoms A–E
10.65
Sterimol L Atoms A–F
9.18
Sterimol B1 Atoms A–B
3.21
Sterimol B5 Atoms A–B
6.78
Wiberg Bond A–E
0.94
Wiberg Bond E–F
1.07
Buried Volume A 3.0
0.61
Buried Volume A 3.5
0.53
Buried Volume A 4.5
0.34
Buried Volume B 3.0
0.65
Buried Volume B 3.5
0.50
Buried Volume B 4.5
0.28
Mulliken Charge A
-0.42
Mulliken Charge B
0.18
Mulliken Charge C
-0.31
NPA Charge A
-0.55
NPA Charge B
0.24
NPA Charge C
-0.38
Fukui f⁺ Atom A
0.12
Fukui f⁻ Atom A
0.08
Fukui f⁰ Atom A
0.10
Fukui Dual Atom A
0.04
Fukui f⁺ Atom B
0.06
Fukui f⁻ Atom B
0.15
Fukui f⁰ Atom B
0.11
Fukui Dual Atom B
-0.09
Fukui f⁺ Atom F
-0.06
Fukui f⁰ Atom F
-0.01
Fukui f⁻ Atom G
-0.17
Fukui f⁰ Atom G
-0.04
Fukui f⁻ Atom H
-0.07
BOX ligands · 29 molecules
bond
electronic
geometric
steric
charge
fukui

Applications

Physics-informed features for every domain

Drug Discovery

Generate QSAR-ready descriptors for hit-to-lead optimization. Predict pIC50, solubility, and ADMET properties with physics-informed features that capture electronic structure beyond fingerprints.

Catalyst Design

Compute Sterimol parameters, buried volumes, and electronic properties for ligand optimization in asymmetric catalysis, cross-coupling, and other reaction classes.

Materials Science

Characterize polymer building blocks and functional materials with atom-level electronic descriptors at DFT accuracy. Model structure-property relationships for novel material design.

Atom Label Editor

Label atoms for bond- and atom-level descriptors

Upload CDXML molecules with bond and atom labels, or upload SMILES or 3D structures and label atoms in browser with our labeling tool. Our common-substructure algorithm identifies shared scaffolds across your library and auto-assigns consistent labels to atoms of interest. Edit any label to match your naming convention and the same labels propagate to every matching molecule.

app.chemetrian.com/molecule-editor
Click atom to select
3D2D
8 common atoms highlighted · MCS match: full · 29 / 29 molecules
Atom Labels
8
N
A

Atom 19 · N (C, C)

N
B

Atom 9 · N (C, C)

O
C

Atom 6 · O (C, C)

O
D

Atom 18 · O (C, C)

C
E

Atom 4 · C (O, C, N)

C
F

Atom 5 · C (C, N, O)

C
G

Atom 7 · C (C, N, H)

C
H

Atom 10 · C (N, C, C, H)

Matched molecules29 / 29
Apply to Active
Apply to All (29)

Automatic MCS detection

Finds the maximum common substructure across your library — no manual alignment needed.

Consistent labeling

Deterministic atom ordering guarantees the same label set regardless of upload order.

Bond & atom descriptors

Labels enable per-bond and per-atom descriptor extraction from DFT or GFN2-xTB calculations.

Ready to compute descriptors?

Upload your molecular library and get ML-ready DFT descriptors in hours, not weeks.