Single Point Energy
GPU-accelerated density functional theory methods using Gaussian orbital basis sets.
Features:
- Density functional approximations including LDA, GGA, Meta-GGA, hybrid (full exchange and range-separated exchange).
- Empirical and non-local dispersion corrections available.
- Support for basis sets with arbitrary angular momentum.
- Support for effective core potentials.
- Continuum solvent available via PCM.
- Excited state calculations possible with time-dependent density functional theory.
- Population analysis, reactivity indices, ESP maps, and electron density maps.
Geometry Optimization
Locate equilibrium geometries of molecules in their ground or excited states.
Did you know?
- Analytic gradients are available for all methods.
- Many types of constraints are supported.
- Input structure doesn't need to satisfy constraints.
Method:
Locate equilibrium geometries of molecules in their ground or excited states.
Outputs:
- Optimized equilibrium structure.
- Vibrational and thermodynamic analysis.
- IR and Raman spectra.
Types of questions you can answer:
- What shape is the molecule?
Conformer Search
Find the energies of all low-lying equilibrium structures.
Did you know?
- Multiple input formats supported including SMILES strings.
- Highly customizable range of conformer generation and refinement methods, including molecular mechanics, machine-learned force fields, xTB, and density functional theory.
Method:
Molecular mechanics and neural network potentials for initial screening of conformers. DFT optimization and single points for accurate final energies and structures.
Outputs:
- Equilibrium structures for each conformer.
- Relative energies and Boltzmann populations.
Types of questions you can answer:
- Find distribution of effective molecule shapes and corresponding energies.
Torsion Scan
Compute the potential energy of rotations about bonds in molecules.
Did you know?
- Bond selection is available through our GUI.
- Calculation of the torsional potential is automatically parallelized over many GPUs.
Method:
A series of constrained optimizations is performed using DFT to obtain the torsional potential.
Outputs:
- Potential energy curve along the torsion.
- Optimized geometries at each value of the torsion.
- Torsion profiles can be exported to Transition State Optimization and Reaction Path Optimization workflows for barrier estimation and reaction analysis.
Types of questions you can answer:
- Find active conformation of molecules.
- Quantify rates of interconversion between conformers.
InteractionMap
InteractionMap utilizes F-SAPT to provide a quantum-accurate, functional-group-level breakdown of non-covalent interactions. With InteractionMap, medicinal chemists now have a direct line of sight into why ligands bind the way they do. It moves beyond heuristics and docking scores, offering quantitative, interpretable insights that accelerate lead optimization.
Did you know?
- You can use InteractionMap to explore
pi-pi stacking - You can explore differences in potency with Interaction Difference Map
- Analyze transition states to understand reaction selectivity and guide catalyst optimization
- InteractionMap can be applied to covalent ligands using heterolytic partitioning.
Method:
Interaction energy is computed using symmetry-adapted perturbation theory (SAPT), with functional-group SAPT (F-SAPT) used to partition interactions at the chemical group level.
Why use InteractionMap:
- Promethium’s proprietary InteractionMap workflow utilizes F-SAPT methodology to provide a quantum-accurate, functional group level breakdown of non-covalent interactions.
With InteractionMap, medicinal chemists now have a direct line of sight into why ligands bind the way they do. It moves beyond heuristics and docking scores, offering quantitative, interpretable insights that accelerate lead optimization.
Types of questions you can answer:
- Discover which functional groups drive binding and which hinder it, based on
quantitative interaction energies in kcal/mol, broken down into:
- Electrostatics
- Exchange (steric repulsion)
- Polarization
- Dispersion - Automated Protein-Ligand Setup
- Promethium automates sample preparation for protein-ligand complexes, reducing setup time and eliminating fragmentation errors. - Comparative Analysis across Ligand Series
- Evaluate how interaction patterns change across congeneric series, essential for understanding SAR and guiding R-group modifications. - Visual, Color-Coded Insights
- Promethium provides intuitive visualization and full access to rich, downloadable numerical data, making it easy to communicate findings across teams. - Understanding Intermolecular Interactions
- Determine which intermolecular forces drive molecular recognition, binding, and selectivity.
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Interaction Energy
Compute the interaction energy between two non-bonded molecules.
Did you know?
- Basis set superposition error is automatically removed.
- Highly accurate results can be obtained with the ωB97M-V functional.
Method:
Interaction energies are computed using the Boys-Bernardi counterpoise correction.
Outputs:
- Interaction energy of a non-covalent dimer.
- Quantification of the basis set superposition error in that interaction energy.
Types of questions you can answer:
- Quantify the strength of interactions within non-bonded complexes.
- Test the effect of chemical substitutions on non-bonded interactions.
Relaxed Potential Energy Surface Scan
Explore geometric changes in molecules.
Did you know?
- Relaxed potential scans can be performed on any combination of bond distances, bond angles, torsion angles and out-of-plane angles.
- A bond distance difference coordinate is provided to scan over reactive coordinates.
- Scans can start from reactant-state geometries and optionally use product-state geometries to define the end of the scan.
- Optimization of the starting and ending structures is automated within the workflow.
Method:
The potential energy surface is explored by performing a series of constrained geometry optimizations over user-specified coordinates.
Outputs:
- Energies and geometries along the scanned coordinates
- Geometries of critical points along the path
Types of questions you can answer:
- Compare different reaction mechanisms
- Search for reaction intermediates and products
- Estimate reaction barriers and transition states
Transition State Optimization
Locate transition state structures.
Transition state optimization is available through the following workflows:
- Transition State Optimization: Starts from a user-supplied guess of the transition state geometry.
- Reactant-Product Transition State Optimization: Starts from user-supplied guesses of the reactant and product geometries.
Did you know?
- A secondary lower level of theory can be selected by the user to accelerate the calculation.
- Vibrational frequencies can be calculated at the optimized transition state.
- A transition state optimization can be started from the reactant and product geometries.
- A guess of the transition state geometry can be obtained from reaction path optimization using the Reactant-Product Transition State Optimization workflow.
Method:
Transition state is optimized by partitioned rational function optimization using an exact eigenvector following algorithm.
Outputs:
- Energy and geometry of the transition state.
- (Optionally) Vibrational frequencies at the transition state.
Types of questions you can answer:
- Find energetic barriers to chemical reactions.
- Compute reaction rate constants.
- Identify chemical reaction mechanisms.
Reaction Path Optimization
Identify the minimum energy path connecting reactants and products.
Did you know?
- Optimization of the endpoints can be performed as part of this workflow.
- Interpolation of the reaction path is performed automatically.
- The result of a reaction path optimization can be used to initiate a transition state optimization.
Methods:
Promethium's proprietary method for determining intrinsic reaction coordinates based on Chebyshev splines can be used to optimize the reaction path. This method is more stable and efficient than existing alternatives.
The nudged elastic band (NEB) method can be used to define the reaction path. NEB force constants are adjustable to provide increased resolution near the transition state. A purpose-built optimization algorithm ensures robust convergence.
The nudged elastic band (NEB) method can be used to define the reaction path. NEB force constants are adjustable to provide increased resolution near the transition state. A purpose-built optimization algorithm ensures robust convergence.
Outputs:
- Reaction energy and barriers, with reaction path optimization results that provide more realistic activation barrier estimates.
- Approximate transition state geometry.
- Optimized structures along the path.
Types of questions you can answer:
- Find reaction energies and energetic barriers to chemical reactions.
- Compute reaction rate constants.
- Identify chemical reaction mechanisms.
