Q-Chem is a general-purpose electronic structure package[1][2][3][4] 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, HPCC, and cloud computing 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[5] community, Q-Chem also provides a versatile code development platform.
Q-Chem software is maintained and distributed by Q-Chem, Inc.,[6] located in Pleasanton, California, USA. It was founded in 1993 as a result of disagreements within the Gaussian company that led to the departure (and subsequent "banning") of John Pople and a number of his students and postdocs (see Gaussian License Controversy[7]).[6][8]
The first lines of the Q-Chem code were written by Peter Gill, at that time a postdoc of Pople, during a winter vacation (December 1992) in Australia. Gill was soon joined by Benny Johnson (a Pople graduate student) and Carlos Gonzalez (another Pople postdoc), but the latter left the company shortly thereafter. In mid-1993, Martin Head-Gordon, formerly a Pople student, but at that time on the Berkeley tenure track, joined the growing team of academic developers.[6][8]
Postcard advertising the release of Q-Chem 1.0.
In preparation for the first commercial release, the company hired Eugene Fleischmann as marketing director and acquired its URL www.q-chem.com in January 1997. The first commercial product, Q-Chem 1.0, was released in March 1997. Advertising postcards celebrated the release with the proud headline, "Problems which were once impossible are now routine"; however, version 1.0 had many shortcomings, and a wit once remarked that the words "impossible" and "routine" should probably be interchanged![8] However, vigorous code development continued, and by the following year Q-Chem 1.1 was able to offer most of the basic quantum chemical functionality as well as a growing list of features (the continuous fast multipole method, J-matrix engine, COLD PRISM for integrals, and G96 density functional, for example) that were not available in any other package.[6][8]
Following a setback when Johnson left, the company became more decentralized, establishing and cultivating relationships with an ever-increasing circle of research groups in universities around the world. In 1998, Fritz Schaefer accepted an invitation to join the Board of Directors and, early in 1999, as soon as his non-compete agreement with Gaussian had expired, John Pople joined as both a Director and code developer.[6][8]
In 2000, Q-Chem established a collaboration with Wavefunction Inc., which led to the incorporation of Q-Chem as the ab initio engine in all subsequent versions of the Spartan package. The Q-Chem Board was expanded in March 2003 with the addition of Anna Krylov and Jing Kong. In 2012, John Herbert joined the Board and Fritz Schaefer became a Member Emeritus. The following year, Shirin Faraji joined the Board; Peter Gill, who had been President of Q-Chem since 1988, stepped down; and Anna Krylov became the new president. In 2022-23 Yuezhi Mao and Joonho Lee joined the board. The active Board of Directors currently consists of Lee, Mao, Faraji, Gill (past-President), Herbert, Krylov (President), and Hilary Pople (John's daughter). Martin Head-Gordon remains a Scientific Advisor to the Board.[6][8]
Currently, there are thousands of Q-Chem licenses in use, and Q-Chem's user base is expanding, as illustrated by citation records for releases 2.0, 3.0, and 4.0, which reached 400 per year in 2016 (see Figure 2).[8]
Fig. 2. Citations to Q-Chem: 2001 to 2019.
Q-Chem has been used as an engine in high-throughput studies, such as the Harvard Clean Energy Project,[9] in which about 350,000 calculations were performed daily on the IBM World Community Grid.
Figure 3. Statistics of Q-Chem developer activity since 2006. Top chart: Total number of code commits (height of bars) and number of developers contributing (color of bar) by month. Bottom chart: Growth of developer base, showing existing and new developers each month. A steady growth of the developer base can be seen. The inset depicts the total number of commits by the 50 most-prolific developers, showing contributions by full-time team (> 2000 commits), the core developer team (500–2000 commits), and non-core developers (< 500 commits).
Innovative algorithms and new approaches to electronic structure have been enabling cutting-edge scientific discoveries. This transition, from in-house code to major electronic structure engine, has become possible due to contributions from numerous scientific collaborators; the Q-Chem business model encourages broad developer participation. Q-Chem defines its genre as open-teamware:[8] its source code is open to a large group of developers. In addition, some Q-Chem modules are distributed as open source.[8] Since 1992, over 400 man- (and woman-) years have been devoted to code development. Q-Chem 5.2.2, released in December 2019, consists of 7.5 million lines of code, which includes contributions by more than 300 active developers (current estimate is 312).[6][8] See Figure 3.
Features
Q-Chem can perform a number of general quantum chemistry calculations, such as Hartree–Fock, density functional theory (DFT) including time-dependent DFT (TDDFT), Møller–Plesset perturbation theory (MP2), coupled cluster (CC), equation-of-motion coupled-cluster (EOM-CC),[10][11][12]configuration interaction (CI), algebraic diagrammatic construction (ADC), and other advanced electronic structure methods. Q-Chem also includes QM/MM functionality. Q-Chem 4.0 and higher releases come with the graphical user interface, IQMol, which includes a hierarchical input generator, a molecular builder, and general visualization capabilities (MOs, densities, molecular vibrations, reaction pathways, etc.). IQMol is developed by Andrew Gilbert (in coordination with Q-Chem) and is distributed as free open-source software. IQmol is written using the Qt libraries, enabling it to run on a range of platforms, including OS X, Widows, and Linux. It provides an intuitive environment to set up, run, and analyze Q-Chem calculations. It can also read and display a variety of file formats, including the widely available formatted checkpoint format. A complete, up-to-date list of features is published on the Q-Chem website and in the user manual.[6]
In addition, Q-Chem is interfaced with WebMO and is used as the computing engine in Spartan, or as a back-end to CHARMM, GROMACS, NAMD, and ChemShell. Other popular visualization programs such as Jmol and Molden can also be used.
In 2018, Q-Chem established a partnership with BrianQC, produced by StreamNovation, Ltd., a new integral engine exploiting the computational power of GPUs. The BrianQC plug-in speeds up Q-Chem calculations by taking advantage of GPUs on mixed architectures, which is highly efficient for simulating large molecules and extended systems. BrianQC is the first GPU Quantum Chemistry software capable of calculating high angular momentum orbitals.
Ground State Self-Consistent Field Methods
Restricted, unrestricted, and restricted open-shell formulations
Analytical first and second derivatives for geometry optimizations, harmonic frequency analysis, and ab initio molecular dynamics
Efficient algorithms for fast convergence
Variety of guess options (including MOM)
Density functional theory
Variety of local, GGA, mGGA, hybrid, double-hybrid, dispersion-corrected, range separated functionals (energies and analytic first and second derivatives)
TDDFT and spin-flip-TDDFT formulations (energies, gradients, and frequencies)
Constrained DFT
Innovative algorithms for faster performance and reduced scaling of integral calculations, HF/DFT and many-body methods
EOM-XX-CCSD methods for open-shell and electronically excited species (XX=EE, SF, IP, EA, DIP, DEA, 2SF; energies, properties, and gradients for most methods),[10][11][12] including complex-valued variants for treating resonances (states metastable with respect to electron detachment)[13]
Extensions of DFT and many-body methods to treat core-level states and related spectroscopies[19]
ADC methods
CIS, TDDFT, CIS(D), and SOS-CIS(D) methods for excited states
Variety of implicit solvent models
Wave-function analysis tools enabled by libwfa developed by Felix Plasser and co-workers[20]
Sir John Anthony Pople was a British theoretical chemist who was awarded the Nobel Prize in Chemistry with Walter Kohn in 1998 for his development of computational methods in quantum chemistry.
In computational chemistry and molecular physics, Gaussian orbitals are functions used as atomic orbitals in the LCAO method for the representation of electron orbitals in molecules and numerous properties that depend on these.
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.
Gaussian is a general purpose computational chemistry software package initially released in 1970 by John Pople and his research group at Carnegie Mellon University as Gaussian 70. It has been continuously updated since then. The name originates from Pople's use of Gaussian orbitals to speed up molecular electronic structure calculations as opposed to using Slater-type orbitals, a choice made to improve performance on the limited computing capacities of then-current computer hardware for Hartree–Fock calculations. The current version of the program is Gaussian 16. Originally available through the Quantum Chemistry Program Exchange, it was later licensed out of Carnegie Mellon University, and since 1987 has been developed and licensed by Gaussian, Inc.
Møller–Plesset perturbation theory (MP) is one of several quantum chemistry post-Hartree–Fock ab initio methods in the field of computational chemistry. It improves on the Hartree–Fock method by adding electron correlation effects by means of Rayleigh–Schrödinger perturbation theory (RS-PT), usually to second (MP2), third (MP3) or fourth (MP4) order. Its main idea was published as early as 1934 by Christian Møller and Milton S. Plesset.
Vibronic coupling in a molecule involves the interaction between electronic and nuclear vibrational motion. The term "vibronic" originates from the combination of the terms "vibrational" and "electronic", denoting the idea that in a molecule, vibrational and electronic interactions are interrelated and influence each other. The magnitude of vibronic coupling reflects the degree of such interrelation.
In computational chemistry, post–Hartree–Fock (post-HF) methods are the set of methods developed to improve on the Hartree–Fock (HF), or self-consistent field (SCF) method. They add electron correlation which is a more accurate way of including the repulsions between electrons than in the Hartree–Fock method where repulsions are only averaged.
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.
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-UK) is a computer software program for computational chemistry. The original code split in 1981 into GAMESS-UK and GAMESS (US) variants, which now differ significantly. Many of the early developments in the UK version arose from the earlier UK based ATMOL program, which, unlike GAMESS, lacked analytical gradients for geometry optimisation.
Spartan is a molecular modelling and computational chemistry application from Wavefunction. It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models, post-Hartree–Fock models, and thermochemical recipes including G3(MP2) and T1. Quantum chemistry calculations in Spartan are powered by Q-Chem.
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 be used to calculate very large molecular systems with thousands of atoms using ab initio quantum-chemical wave functions.
Martin Philip Head-Gordon is a professor of chemistry at the University of California, Berkeley, and Lawrence Berkeley National Laboratory working in the area of computational quantum chemistry. He is a member of the International Academy of Quantum Molecular Science.
Anna Igorevna Krylov is the USC Associates Chair in Natural Sciences and Professor of Chemistry at the University of Southern California (USC). Working in the field of theoretical and computational quantum chemistry, she is the inventor of the spin-flip method. Krylov is the president of Q-Chem, Inc. and an elected member of the International Academy of Quantum Molecular Science, the Academia Europaea, and the American Academy of Sciences and Letters.
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.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
A Pople diagram or Pople's Diagram is a diagram which describes the relationship between various calculation methods in computational chemistry. It was initially introduced in January 1965 by Sir John Pople,, during the Symposium of Atomic and Molecular Quantum Theory in Florida. The Pople Diagram can be either 2-dimensional or 3-dimensional, with the axes representing ab initio methods, basis sets and treatment of relativity. The diagram attempts to balance calculations by giving all aspects of a computation equal weight.
References
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1 2 Shao, Y.; Molnar, L. F.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S. T.; Gilbert, A. T.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P.; Distasio Jr, R. A.; Lochan, R. C.; Wang, T.; Beran, G. J.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Van Voorhis, T.; Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E. F.; Dachsel, H.; etal. (2006). "Advances in methods and algorithms in a modern quantum chemistry program package". Physical Chemistry Chemical Physics. 8 (27): 3172–3191. Bibcode:2006PCCP....8.3172S. doi:10.1039/b517914a. PMID16902710.
↑ Young, David C. (2001). "Appendix A. A.2.7 Q-Chem". Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems. Wiley-Interscience. p.339. doi:10.1002/0471220655. ISBN978-0-471-33368-5.
1 2 K. Sneskov; O. Christiansen (2011). "Excited state coupled cluster methods". Wiley Interdisciplinary Reviews: Computational Molecular Science.
1 2 R.J. Bartlett (2012). "Coupled-cluster theory and its equation-of-motion extensions". Wiley Interdisciplinary Reviews: Computational Molecular Science. 2: 126. doi:10.1002/wcms.76. S2CID122135895.
1 2 Pokhilko, Pavel; Epifanovsky, Evgeny; Krylov, Anna I. (2018-08-14). "Double Precision Is Not Needed for Many-Body Calculations: Emergent Conventional Wisdom". Journal of Chemical Theory and Computation. 14 (8): 4088–4096. doi:10.1021/acs.jctc.8b00321. ISSN1549-9618. PMID29969560. S2CID49679144.
↑ Martin Feyereisena, George Fitzgeralda & Andrew Komornickib (May 10, 1993). "Scaled Second-Order Perturbation Corrections to Configuration Interaction Singles: Efficient and Reliable Excitation Energy Methods". Chemical Physics Letters. 208 (5–6): 359–363. Bibcode:1993CPL...208..359F. doi:10.1016/0009-2614(93)87156-W.
↑ Florian Weigend & Marco Häser (October 13, 1997). "RI-MP2: first derivatives and global consistency". Theoretical Chemistry Accounts. 97 (1–4): 331–340. doi:10.1007/s002140050269. S2CID97649855.
↑ Robert A. Distasio JR.; Ryan P. Steele; Young Min Rhee; Yihan Shao & Martin Head-Gordon (April 15, 2007). "An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis". Journal of Computational Chemistry. 28 (5): 839–856. doi:10.1002/jcc.20604. PMID17219361. S2CID8438511.
↑ M.S. Gordon, L. Slipchenko, H.Li, J.H. Jensen (2007). "The effective fragment potential: A general method for predicting intermolecular interactions". In D.C. Spellmeyer; R. Wheeler (eds.). Volume 3 of Annual Reports in Computational Chemistry. Elsevier. pp.177–193.{{cite book}}: CS1 maint: multiple names: authors list (link)
↑ L.V. Slipchenko (2010). "Solvation of the excited states of chromophores in polarizable environment: orbital relaxation versus polarization". Journal of Physical Chemistry A. 114 (33): 8824–30. Bibcode:2010JPCA..114.8824S. doi:10.1021/jp101797a. PMID20504011.
↑ B.G. Johnson; P.M.W. Gill; M. Head-Gordon; C.A. White; D.R. Maurice; T.R. Adams; J. Kong; M. Challacombe; E. Schwegler; M. Oumi; C. Ochsenfeld; N. Ishikawa; J. Florian; R.D. Adamson; J.P. Dombroski; R.L. Graham and A.Warshel (1997). Q-Chem, Version 1.1. Pittsburgh: Q-Chem, Inc.
↑ C.A. White; J. Kong; D.R. Maurice; T.R. Adams; J. Baker; M. Challacombe; E. Schwegler; J.P. Dombroski; C. Ochsenfeld; M. Oumi; T.R. Furlani; J. Florian; R.D. Adamson; N. Nair; A.M. Lee; N. Ishikawa; R.L. Graham; A. Warshel; B.G. Johnson; P.M.W. Gill; M. Head-Gordon (1998). Q-Chem, Version 1.2. Pittsburgh: Q-Chem, Inc.
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