Glossary
Terms, in Plain Words
The words used on this site, defined once.
- Ab Initio
- A method built from the laws of quantum mechanics and physical constants, with no parameters fitted to experiment. Hartree-Fock and coupled cluster are examples.
- AiMolSim Knowledge
- The ranked library of papers, books and data behind every default in the engine.
- Auxiliary Basis Set
- A second, fitting basis used by density fitting (RI) to approximate the electron repulsion integrals faster.
- Basis Set
- The set of functions used to build molecular orbitals. Larger basis sets give answers closer to the exact limit at higher cost.
- Basis Set Superposition Error (BSSE)
- The artificial extra binding in a complex, because each part borrows the basis functions of its neighbour. The counterpoise correction estimates it.
- Checked
- Our badge for a method that reproduces printed values from its source paper.
- Checked (exact)
- Our badge for a method that no paper prints a value for: it is checked against exact mathematics or a brute-force recomputation, never against another program. It is counted separately from Checked.
- Chemistry Lab
- The browser workspace of AiMolSim, where Studies hold molecules, computations, results and notes.
- CIP Descriptors
- The labels R, S, r, s, E and Z from the Cahn-Ingold-Prelog Sequence Rules. They name the stereo configuration of a centre or double bond.
- Composite Method
- A recipe that adds several cheaper calculations to approach a much more expensive one, such as G3 or G4.
- Conical Intersection
- A geometry where two electronic states of the same spin have the same energy, so a molecule can cross from one to the other very fast.
- Continuum Solvation
- A model that treats the solvent as a polarisable medium around a molecular cavity, such as PCM or COSMO.
- COSMO-RS
- A statistical model that turns COSMO surface charges into activity coefficients, solubility and partition coefficients.
- Counterpoise Correction
- A correction for basis set superposition error in an interaction energy: each fragment is computed in the basis set of the whole complex.
- Coupled Cluster
- A family of accurate correlated methods. CCSD(T) is often called the gold standard for small molecules.
- Density Fitting (RI)
- A way to approximate the four-centre electron repulsion integrals with an auxiliary basis set. It makes large calculations much faster for a small error.
- Density Functional Theory (DFT)
- A method that computes the energy from the electron density. The functional sets its accuracy and cost.
- Dispersion Correction
- An added term for the weak attraction between atoms that most density functionals miss. D3 and D4 are common choices.
- Distributed SCF
- One self-consistent field calculation split over several processes or servers.
- Double Hybrid
- A density functional that adds a second-order perturbation (MP2-like) correlation term to a hybrid functional, such as B2PLYP.
- Effective Core Potential (ECP)
- A potential that replaces the inner electrons of a heavy atom, which also brings in scalar relativistic effects.
- Embedding
- A way to treat a chosen part of a system at a higher level of theory while the rest is described more cheaply.
- Force Field
- A classical energy model with bonds, angles, torsions and nonbonded terms, used for large systems and long dynamics.
- Franck-Condon and Herzberg-Teller
- Two ways to compute the vibrational structure of an electronic band. Franck-Condon uses fixed transition moments; Herzberg-Teller adds their change with geometry.
- Free Energy Perturbation (FEP)
- A way to compute free energy differences by gradually changing one system into another.
- Generalized Gradient Approximation (GGA)
- A density functional that depends on the electron density and its gradient. PBE and BLYP are examples. Hybrid functionals add a share of exact exchange.
- GIAO
- Gauge-including atomic orbitals, the usual way to compute NMR shielding so that the result does not depend on the origin of the magnetic gauge.
- Hartree-Fock (HF)
- The basic wavefunction method in which each electron moves in the average field of the others.
- Hybrid Functional
- A density functional that mixes a share of Hartree-Fock exchange with density functional exchange. Range-separated hybrids change that share with distance.
- Intersystem Crossing (ISC)
- A radiationless jump between states of different spin, made possible by spin-orbit coupling.
- Intrinsic Reaction Coordinate (IRC)
- The steepest-descent path from a transition state to the minima on either side.
- Machine-Learned Potential
- A neural network trained on quantum results that predicts energies and forces much faster.
- Meta-GGA
- A density functional that also uses the kinetic energy density of the orbitals, such as SCAN and M06-2X.
- Minimum-Energy Crossing Point (MECP)
- The lowest-energy geometry where two states of different spin have the same energy; it controls intersystem crossing.
- MM/GBSA
- An end-point estimate of binding energy that combines a force field energy with Generalized Born solvation and a surface area term.
- MP2
- Second-order Moller-Plesset perturbation theory, the simplest correlated wavefunction method.
- Natural Transition Orbitals (NTO)
- The pair of orbitals, hole and particle, that best describes an electronic excitation. It shows where the electron leaves and where it goes.
- Nudged Elastic Band (NEB)
- A way to find a reaction path between two minima by relaxing a chain of geometries. The climbing-image version also finds the saddle point.
- Partial
- Our badge for a method whose code exists and whose unchecked parts are badged in the app.
- Provenance
- The record kept with every result: method, basis, engine version, inputs and the server that ran it.
- QM/MM
- A model with a small quantum region inside a larger classical region.
- Real-Time TDDFT
- Time-dependent DFT solved by following the density through time after a small kick, which gives a whole spectrum from one run.
- RRKM Theory
- A theory for the rate of a unimolecular reaction as a function of the energy of the molecule, and with collisions as a function of pressure.
- Self-Consistent Field (SCF)
- The iteration in which orbitals and the field they create are repeated until they no longer change. Hartree-Fock and Kohn-Sham DFT both use it.
- Spin-Orbit Coupling
- The interaction between an electron's spin and its orbital motion, important for heavy atoms and intersystem crossing.
- Surface Hopping
- A way to simulate dynamics that moves between electronic states, used for photochemistry.
- TDDFT
- Time-dependent DFT, used for excitation energies and UV-Vis spectra.
- Transition State
- The highest point on the lowest path between reactant and product; it has exactly one imaginary frequency.
- Transition State Theory (TST)
- A theory that gives a reaction rate from the free energy of the transition state relative to the reactants.
- Unverified
- Our badge for a method that is built but has no printed check yet.
- VPT2
- Second-order vibrational perturbation theory, which adds anharmonicity to harmonic frequencies.
- VYROX Math Kernel
- Our own C++ and CUDA code for dense linear algebra and GPU integral kernels, used by the engine with no third-party math library.
- Wannier Function
- A localised orbital built from the delocalised bands of a periodic solid, used for bonding analysis and band interpolation.
- Zero-Field Splitting (ZFS)
- The splitting of the spin levels of a molecule with two or more unpaired electrons without any magnetic field.
Run Your Next Molecule Through AiMolSim
Describe a molecule and your question; the assistant drafts the plan and you approve it. Or see it first in a 30 minute demo.