Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion, the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials.
In solid-state physics, the electronic band structure of a solid describes the range of energy levels that electrons may have within it, as well as the ranges of energy that they may not have.
The Wannier functions are a complete set of orthogonal functions used in solid-state physics. They were introduced by Gregory Wannier in 1937. Wannier functions are the localized molecular orbitals of crystalline systems.
The Vienna Ab initio Simulation Package, better known as VASP, is a package for performing ab initio quantum mechanical calculations using either Vanderbilt pseudopotentials, or the projector augmented wave method, and a plane wave basis set. The basic methodology is density functional theory (DFT), but the code also allows use of post-DFT corrections such as hybrid functionals mixing DFT and Hartree–Fock exchange, many-body perturbation theory and dynamical electronic correlations within the random phase approximation (RPA) and MP2.
In theoretical and computational chemistry, a basis set is a set of functions that is used to represent the electronic wave function in the Hartree–Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer.
Local-density approximations (LDA) are a class of approximations to the exchange–correlation (XC) energy functional in density functional theory (DFT) that depend solely upon the value of the electronic density at each point in space. Many approaches can yield local approximations to the XC energy. However, overwhelmingly successful local approximations are those that have been derived from the homogeneous electron gas (HEG) model. In this regard, LDA is generally synonymous with functionals based on the HEG approximation, which are then applied to realistic systems.
PQS is a general purpose quantum chemistry program. Its roots go back to the first ab initio gradient program developed in Professor Peter Pulay's group but now it is developed and distributed commercially by Parallel Quantum Solutions. There is a reduction in cost for academic users and a site license. Its strong points are geometry optimization, NMR chemical shift calculations, and large MP2 calculations, and high parallel efficiency on computing clusters. It includes many other capabilities including Density functional theory, the semiempirical methods, MINDO/3, MNDO, AM1 and PM3, Molecular mechanics using the SYBYL 5.0 Force Field, the quantum mechanics/molecular mechanics mixed method using the ONIOM method, natural bond orbital (NBO) analysis and COSMO solvation models. Recently, a highly efficient parallel CCSD(T) code for closed shell systems has been developed. This code includes many other post Hartree–Fock methods: MP2, MP3, MP4, CISD, CEPA, QCISD and so on.
Atomistix Virtual NanoLab (VNL) is a commercial point-and-click software for simulation and analysis of physical and chemical properties of nanoscale devices. Virtual NanoLab is developed and sold commercially by QuantumWise A/S. QuantumWise was then acquired by Synopsys in 2017.
Ab initio quantum chemistry methods are computational chemistry methods based on quantum chemistry. The term ab initio was first used in quantum chemistry by Robert Parr and coworkers, including David Craig in a semiempirical study on the excited states of benzene. The background is described by Parr. Ab initio means "from first principles" or "from the beginning", implying that the only inputs into an ab initio calculation are physical constants. Ab initio quantum chemistry methods attempt to solve the electronic Schrödinger equation given the positions of the nuclei and the number of electrons in order to yield useful information such as electron densities, energies and other properties of the system. The ability to run these calculations has enabled theoretical chemists to solve a range of problems and their importance is highlighted by the awarding of the Nobel prize to John Pople and Walter Kohn.
Atomistix A/S was a software company developing tools for atomic scale modelling. It was headquartered in Copenhagen, Denmark, with a subsidiary for Asia Pacific in Singapore and for the Americas in California. In September 2008 Atomistix A/S went bankrupt, but in December 2008 the newly founded company QuantumWise announced that they had acquired all assets from the Atomistix estate and would continue the development and marketing of the products Atomistix ToolKit and Atomistix Virtual NanoLab. QuantumWise was then acquired by Synopsys in 2017.
Car–Parrinello molecular dynamics or CPMD refers to either a method used in molecular dynamics or the computational chemistry software package used to implement this method.
Atomistix ToolKit (ATK) is a commercial software for atomic-scale modeling and simulation of nanosystems. The software was originally developed by Atomistix A/S, and was later acquired by QuantumWise following the Atomistix bankruptcy. QuantumWise was then acquired by Synopsys in 2017.
The hybrid QM/MM approach is a molecular simulation method that combines the strengths of ab initio QM calculations (accuracy) and MM (speed) approaches, thus allowing for the study of chemical processes in solution and in proteins. The QM/MM approach was introduced in the 1976 paper of Warshel and Levitt. They, along with Martin Karplus, won the 2013 Nobel Prize in Chemistry for "the development of multiscale models for complex chemical systems".
In quantum chemistry, a natural bond orbital or NBO is a calculated bonding orbital with maximum electron density. The NBOs are one of a sequence of natural localized orbital sets that include "natural atomic orbitals" (NAO), "natural hybrid orbitals" (NHO), "natural bonding orbitals" (NBO) and "natural (semi-)localized molecular orbitals" (NLMO). These natural localized sets are intermediate between basis atomic orbitals (AO) and molecular orbitals (MO):
TeraChem is a computational chemistry software program designed for CUDA-enabled Nvidia GPUs. The initial development started at the University of Illinois at Urbana-Champaign and was subsequently commercialized. It is currently distributed by PetaChem, LLC, located in Silicon Valley. As of 2020, the software package is still under active development.
BigDFT is a free software package for physicists and chemists, distributed under the GNU General Public License, whose main program allows the total energy, charge density, and electronic structure of systems made of electrons and nuclei to be calculated within density functional theory (DFT), using pseudopotentials, and a wavelet basis.
FHI-aims is a software package for computational molecular and materials science written in Fortran. It uses density functional theory and many-body perturbation theory to simulate chemical and physical properties of atoms, molecules, nanostructures, solids, and surfaces. Originally developed at the Fritz Haber Institute in Berlin, the ongoing development of the FHI-aims source code is now driven by a worldwide community of collaborating research institutions.
Qbox is an open-source software package for atomic-scale simulations of molecules, liquids and solids. It implements first principles molecular dynamics, a simulation method in which inter-atomic forces are derived from quantum mechanics. Qbox is released under a GNU General Public License (GPL) with documentation provided at http://qboxcode.org. It is available as a FreeBSD port.
The linearized augmented-plane-wave method (LAPW) is an implementation of Kohn-Sham density functional theory (DFT) adapted to periodic materials. It typically goes along with the treatment of both valence and core electrons on the same footing in the context of DFT and the treatment of the full potential and charge density without any shape approximation. This is often referred to as the all-electron full-potential linearized augmented-plane-wave method (FLAPW). It does not rely on the pseudopotential approximation and employs a systematically extendable basis set. These features make it one of the most precise implementations of DFT, applicable to all crystalline materials, regardless of their chemical composition. It can be used as a reference for evaluating other approaches.
The FLEUR code is an open-source scientific software package for the simulation of material properties of crystalline solids, thin films, and surfaces. It implements Kohn-Sham density functional theory (DFT) in terms of the all-electron full-potential linearized augmented-plane-wave method. With this, it is a realization of one of the most precise DFT methodologies. The code has the common features of a modern DFT simulation package. In the past, major applications have been in the field of magnetism, spintronics, quantum materials, e.g. in ultrathin films, complex magnetism like in spin spirals or magnetic Skyrmion lattices, and in spin-orbit related physics, e.g. in graphene and topological insulators.
