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.
Computational physics is the study and implementation of numerical analysis to solve problems in physics. Historically, computational physics was the first application of modern computers in science, and is now a subset of computational science. It is sometimes regarded as a subdiscipline of theoretical physics, but others consider it an intermediate branch between theoretical and experimental physics — an area of study which supplements both theory and experiment.
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
Q-Chem is a general-purpose electronic structure package featuring a variety of established and new methods implemented using innovative algorithms that enable fast calculations of large systems on various computer architectures, from laptops and regular lab workstations to midsize clusters and HPCC, using density functional and wave-function based approaches. It offers an integrated graphical interface and input generator; a large selection of functionals and correlation methods, including methods for electronically excited states and open-shell systems; solvation models; and wave-function analysis tools. In addition to serving the computational chemistry community, Q-Chem also provides a versatile code development platform.
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.
MOLCAS is an ab initio computational chemistry program, developed as a joint project by a number of international institutes. MOLCAS is developed by scientists to be used by scientists. It is not primarily a commercial product and it is not sold in order to produce a fortune for its owner.
Jaguar is a computer software package used for ab initio quantum chemistry calculations for both gas and solution phases. It is commercial software marketed by the company Schrödinger. The program was originated in research groups of Richard Friesner and William Goddard and was initially called PS-GVB.
Semi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data. They are very important in computational chemistry for treating large molecules where the full Hartree–Fock method without the approximations is too expensive. The use of empirical parameters appears to allow some inclusion of electron correlation effects into the methods.
The fragment molecular orbital method (FMO) is a computational method that can be used to calculate very large molecular systems with thousands of atoms using ab initio quantum-chemical wave functions.
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.
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".
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
Roberto Car is an Italian physicist and the Ralph W. Dornte *31 Professor in Chemistry at Princeton University, where he is also a faculty member in the Princeton Institute for the Science and Technology of Materials. He conducts research on the simulation of molecular dynamics phenomena.
Metadynamics is a computer simulation method in computational physics, chemistry and biology. It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape. It was first suggested by Alessandro Laio and Michele Parrinello in 2002 and is usually applied within molecular dynamics simulations. MTD closely resembles a number of newer methods such as adaptively biased molecular dynamics, adaptive reaction coordinate forces and local elevation umbrella sampling. More recently, both the original and well-tempered metadynamics were derived in the context of importance sampling and shown to be a special case of the adaptive biasing potential setting. MTD is related to the Wang–Landau sampling.
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.
Michele Parrinello is an Italian physicist particularly known for his work in molecular dynamics. Parrinello and Roberto Car were awarded the Dirac Medal and the Sidney Fernbach Award in 2009 for their continuing development of the Car–Parrinello method, first proposed in their seminal 1985 paper, "Unified Approach for Molecular Dynamics and Density-Functional Theory". They have continued to receive awards for this breakthrough, most recently the Dreyfus Prize in the Chemical Sciences and the 2020 Benjamin Franklin Medal in Chemistry.
Newton-X is a general program for molecular dynamics simulations beyond the Born-Oppenheimer approximation. It has been primarily used for simulations of ultrafast processes in photoexcited molecules. It has also been used for simulation of band envelops of absorption and emission spectra.
Ursula Röthlisberger is a professor of computational chemistry at École Polytechnique Fédérale de Lausanne. She works on density functional theory using mixed quantum mechanical/molecular mechanical methods. She is an associate editor of the American Chemical Society Journal of Chemical Theory and Computation and a fellow of the American Association for the Advancement of Science.
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.
