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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.
Coupled cluster (CC) is a numerical technique used for describing many-body systems. Its most common use is as one of several post-Hartree–Fock ab initio quantum chemistry methods in the field of computational chemistry, but it is also used in nuclear physics. Coupled cluster essentially takes the basic Hartree–Fock molecular orbital method and constructs multi-electron wavefunctions using the exponential cluster operator to account for electron correlation. Some of the most accurate calculations for small to medium-sized molecules use this method.
MOLPRO is a software package used for accurate ab initio quantum chemistry calculations. It is developed by Peter Knowles at Cardiff University and Hans-Joachim Werner at Universität Stuttgart in collaboration with other authors.
GAMESS is a computational chemistry software program and stands for General Atomic and Molecular Electronic Structure System. The original Quantum Chemistry Program Exchange (QCPE) code of GAMESS split in 1981 and now the three version differ considerably:
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.
Psi is an ab initio computational chemistry package originally written by the research group of Henry F. Schaefer, III. Utilizing Psi, one can perform a calculation on a molecular system with various kinds of methods such as Hartree-Fock, Post-Hartree–Fock electron correlation methods, and density functional theory. The program can compute energies, optimize molecular geometries, and compute vibrational frequencies. The major part of the program is written in C++, while Python API is also available, which allows users to perform complex computations or automate tasks easily.
NWChem is an ab initio computational chemistry software package which includes quantum chemical and molecular dynamics functionality. It was designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Theory, Modeling & Simulation program of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). The early implementation was funded by the EMSL Construction Project.
MNDO, or Modified Neglect of Diatomic Overlap is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the Neglect of Diatomic Differential Overlap integral approximation. Similarly, this method replaced the earlier MINDO method. It is part of the MOPAC program and was developed in the group of Michael Dewar. It is also part of the AMPAC, GAMESS (US), PC GAMESS, GAMESS (UK), Gaussian, ORCA and CP2K programs.
Austin Model 1, or AM1, is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the Neglect of Differential Diatomic Overlap integral approximation. Specifically, it is a generalization of the modified neglect of differential diatomic overlap approximation. Related methods are PM3 and the older MINDO.
Modern valence bond theory is the application of valence bond theory (VBT) with computer programs that are competitive in accuracy and economy with programs for the Hartree–Fock or post-Hartree-Fock methods. The latter methods dominated quantum chemistry from the advent of digital computers because they were easier to program. The early popularity of valence bond methods thus declined. It is only recently that the programming of valence bond methods has improved. These developments are due to and described by Gerratt, Cooper, Karadakov and Raimondi (1997); Li and McWeeny (2002); Joop H. van Lenthe and co-workers (2002); Song, Mo, Zhang and Wu (2005); and Shaik and Hiberty (2004)
Valence bond (VB) computer programs for modern valence bond calculations:-
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.
General Atomic and Molecular Electronic Structure System (GAMESS (US)) is computer software for computational chemistry program. The original code started on October 1, 1977 as a National Resources for Computations in Chemistry project. In 1981, the code base split into GAMESS (US) and GAMESS (UK) variants, which now differ significantly. GAMESS (US) is maintained by the members of the Gordon Research Group at Iowa State University. GAMESS (US) source code is available as source-available freeware, but is not open-source software, due to license restrictions.
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.
The fragment molecular orbital method (FMO) is a computational method that can compute very large molecular systems with thousands of atoms using ab initio quantum-chemical wave functions.
Quantum chemistry composite methods are computational chemistry methods that aim for high accuracy by combining the results of several calculations. They combine methods with a high level of theory and a small basis set with methods that employ lower levels of theory with larger basis sets. They are commonly used to calculate thermodynamic quantities such as enthalpies of formation, atomization energies, ionization energies and electron affinities. They aim for chemical accuracy which is usually defined as within 1 kcal/mol of the experimental value. The first systematic model chemistry of this type with broad applicability was called Gaussian-1 (G1) introduced by John Pople. This was quickly replaced by the Gaussian-2 (G2) which has been used extensively. The Gaussian-3 (G3) was introduced later.
Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2).
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.
References
- Guest *, Martyn F.; Bush, Ian J.; Van Dam, Huub J. J.; Sherwood, Paul; Thomas, Jens M. H.; Van Lenthe, Joop H.; Havenith, Remco W. A.; Kendrick, John (2005). "The GAMESS-UK structure package: algorithms, developments and applications". Molecular Physics. 103 (6–8): 719–747. arXiv: 1506.05421 . Bibcode:2005MolPh.103..719G. doi:10.1080/00268970512331340592. This is one of the most cited chemistry papers
