Q-Chem

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Q-Chem
Developer(s) Q-Chem Inc.
Operating system Linux, FreeBSD, Unix and like operating systems, Microsoft Windows, Mac OS X
Type Computational Chemistry
License Commercial
Website http://www.q-chem.com/

Q-Chem is a general-purpose electronic structure package[1][2] featuring a variety of established and new methods implemented using innovative algorithms that enable fast calculations of large systems on regular lab workstations using density functional and wave-function based approaches. It offers an integrated graphical interface and input generator, large selection of functionals and correlation methods including methods for electronically excited states and open-shell systems. In addition to serving the computational chemistry[3] community, Q-Chem also provides a versatile code development platform.

History[edit]

Fig. 1. A snapshot of the code submitted by John Pople to Q-Chem in August 2003. The code is written elegantly in C++, and significantly improves the efficiency of the original Head-Gordon-Pople integral code, facilitating speed-up of the Hartree–Fock and hybrid density functional theory calculations.

Q-Chem software is distributed by Q-Chem, Inc.,[4] 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[5]).[4][6]

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.[4][6]

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 that "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![6] 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.[4][6]

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.[4][6]

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 the promotion of Jing Kong (who had joined the company as a postdoc seven years earlier). In 2012, John Herbert joined the Board and Fritz Schaefer became a Member Emeritus. The active Board of Directors currently consists of Gill (President), Herbert, Krylov, and Hilary Pople (John's daughter). Martin Head-Gordon remains a Scientific Advisor to the Board.[4][6]

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 and 3.0, which reached 200 per year in 2010 (see Figure 2).[6]

Fig. 2. Citations to Q-Chem: 2001 to 2011.

As part of the IBM World Community Grid, about 350,000 Q-Chem calculations are performed every day by the Harvard Clean Energy Project,[7] which is powered by Q-Chem.

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 a broad developer participation. Since 1992, well over 300 man (and woman) years have been devoted to code development. Q-Chem 4.0, which was released in January 2012, consists of 3.3 million lines of code (of which 1.5 million is machine-generated) and includes contributions from more than 150 developers (current estimate is 169).[4][6]

Features[edit]

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),[8][9][10] configuration interaction (CI), and other advanced electronic structure methods. Q-Chem also includes QM/MM functionality. Q-Chem 4.0 comes with the new graphical interface, IQMol which includes hierarchical input generator, molecular builder, and general visualization capabilities (MOs, molecular vibrations, etc.). In addition, Q-Chem is interfaced with WebMO and is used as the computing engine in Spartan, or as a back-end to CHARMM and ChemShell. Other popular visualization programs such as Jmol and Molden can also be used.

A complete, up-to-date list of features is published on the Q-Chem website and in the user manual.[4]

Ground State Self-Consistent Field Methods[edit]

  • Restricted, unrestricted, and restricted open-shell formulations
  • Analytical first and second derivatives for geometry optimizations and harmonic frequency analysis
  • Efficient algorithms for fast convergence
  • Variety of guess options (including MOM)

Density functional theory[edit]

  • Variety of local, GGA, hybrid, double-hybrid, dispersion-corrected, range separated functionals (energies and analytic first and second derivatives)
  • TDDFT and spin-flip-TDDFT formulations (energies and gradients)
  • Constrained DFT

Innovative algorithms for faster performance and reduced scaling of integral calculations and HF/DFT[edit]

  • Dual basis
  • Resolution of identity
  • Continuous Fast Multipole Method (CFMM)
  • Fast numerical integration of exchange-correlation with mrXC (multiresolution exchange-correlation)
  • Linear-scaling HF-exchange method (LinK)
  • Fourier transform Coulomb method (FTC)
  • COLD PRISM and J-matrix engine

Post Hartree–Fock methods[edit]

  • MP2[11][12] (including RI-MP2,[13][14][15] energies and analytic gradients)
  • SCS and SOS MP2
  • CCD, QCISD, CCSD, OOCCD, VOOCCD
  • (T), (2), (dT), and (fT) corrections
  • EOM-XX-CCSD methods for open-shell and electronically excited species (XX=EE, SF, *IP, EA, DIP, 2SF; energies and gradients)[8][9][10]
  • ADC methods
  • CIS, TDDFT, CIS(D), and SOS-CIS(D) methods for excited states

QM/MM and QM/EFP methods for extended systems[edit]

  • Janus QM/MM interface
  • YinYang Atom model without linked atoms
  • ONIOM model
  • EFP method (including library of effective fragments, EFP interface with CC/EOM, DFT/TDDFT, and other methods)[16][17][18][19]

Version history[edit]

  • Q-Chem 1.0: March 1997
  • Q-Chem 1.1: 1997[20]
  • Q-Chem 1.2 1998[21]
  • Q-Chem 2.0: 2000[1]
  • Q-Chem 3.0: 2006[2]
  • Q-Chem 4.0: February 2012 [22]
  • Q-Chem 4.1: July 2013 [23]

Outlook[edit]

Q-Chem views its mission as facilitating scientific breakthroughs and catalyzing innovation in computational and theoretical chemistry by bringing robust, fast, and accurate tools to the scientific community. It also strives to provide strong support for method developers. These two goals synergistically enhance each other: while users benefit from the latest methods and algorithms, developers maximize the impact of their research by bringing new methods to the broad community of users. However, these goals also pose the unique challenge of maintaining a robust code while enabling experimentation. Q-Chem continues to cultivate close relationships with universities and to develop and maintain an infrastructure for scientific contributors. Communication between developers is facilitated by a Trac site, whereas users can exchange information on the Q-Chem users' forum, hosted by iOpenShell.[24] Recent educational initiatives include workshops for users and developers.[4][6]

Q-Chem is an open-source platform for its developers. It welcomes new contributions and recognizes them through acknowledgments on its website and inclusion on the author list of Q-Chem papers,[1][2] and also distributes more than 15% of its income as royalties.[4][6]

See also[edit]

References[edit]

  1. ^ a b c Kong, Jing; White, Christopher A.; Krylov, Anna I.; Sherrill, David; Adamson, Ross D.; Furlani, Thomas R.; Lee, Michael S.; Lee, Aaron M.; Gwaltney, Steven R. (2000). "Q-Chem 2.0: a high-performance ab initio electronic structure program package". Journal of Computational Chemistry 21 (16): 1532. doi:10.1002/1096-987X(200012)21:16<1532::AID-JCC10>3.0.CO;2-W. 
  2. ^ a b c Y. Shao, L. F. Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S. Brown, A. T. B. Gilbert, L. V. Slipchenko, S. V. Levchenko, D. P. O'Neil, R. A. Distasio, Jr., R. C. Lochan, T. Wang, G. J. O. Beran, N. A. Besley, J. M. Herbert, C. Y. Lin, T. Van Voorhis, S. H. Chien, A. Sodt, R. P. Steele, V. A. Rassolov, P. Maslen, P. P. Korambath, R. D. Adamson, B. Austin, J. Baker, E. F. C. Bird, H. Daschel, R. J. Doerksen, A. Dreuw, B. D. Dunietz, A. D. Dutoi, T. R. Furlani, S. R. Gwaltney, A. Heyden, S. Hirata, C.-P. Hsu, G. S. Kedziora, R. Z. Khalliulin, P. Klunziger, A. M. Lee, W. Z. Liang, I. Lotan, N. Nair, B. Peters, E. I. Proynov, P. A. Pieniazek, Y. M. Rhee, J. Ritchie, E. Rosta, C. D. Sherrill, A. C. Simmonett, J. E. Subotnik, H. L. Woodcock III, W. Zhang, A. T. Bell, A. K. Chakraborty, D. M. Chipman, F. J. Keil, A. Warshel, W. J. Herhe, H. F. Schaefer III, J. Kong, A. I. Krylov, P. M. W. Gill, and M. Head-Gordon (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. PMID 16902710. 
  3. ^ 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. ISBN 978-0-471-33368-5. 
  4. ^ a b c d e f g h i j Quantum Computational Software; Molecular Modeling; Visualization
  5. ^ Banned By Gaussian
  6. ^ a b c d e f g h i j A.I. Krylov, P.M.W. Gill (2013). "Q-Chem: An engine for innovation". Invited software focus article. Wiley Interdisciplinary Reviews. WIREs Comput. Mol. Sci. 3:317–26 doi: 10.1002/wcms.1122, http://onlinelibrary.wiley.com/doi/10.1002/wcms.1122/full
  7. ^ The Clean Energy Project
  8. ^ a b A.I. Krylov (2008). "Equation-of-motion coupled-cluster methods for open-shell and electronically excited species: The hitchhiker's guide to Fock space". Annual Review of Physical Chemistry 59: 433–462. Bibcode:2008ARPC...59..433K. doi:10.1146/annurev.physchem.59.032607.093602. PMID 18173379. 
  9. ^ a b K. Sneskov, O. Christiansen (2011). "Excited state coupled cluster methods". Wiley Interdisciplinary Reviews: Computational Molecular Science. 
  10. ^ a b R.J. Bartlett (2012). "Coupled-cluster theory and its equation-of-motion extensions". Wiley Interdisciplinary Reviews: Computational Molecular Science 2 126. 
  11. ^ Chr. Møller and M. S. Plesset (October 1934). "Note on an Approximation Treatment form Many-Electron Systems". Physical Review (The American Physical Society) 46 (7): 618–622. Bibcode:1934PhRv...46..618M. doi:10.1103/PhysRev.46.618. 
  12. ^ Head-Gordon, Martin; Pople, John A.; Frisch, Michael J. (1988). "MP2 energy evaluation by direct methods". Chemical Physics Letters 153 (6): 503–506. Bibcode:1988CPL...153..503H. doi:10.1016/0009-2614(88)85250-3. 
  13. ^ Martin Feyereisena, George Fitzgeralda and Andrew Komornickib (May 10, 1993). "Scaled Second-Order Perturbation Corrections to Configuration Interaction Singles: Efficient and Reliable Excitation Energy Methods". Chemical Physics Letters (Elsevier). 208 (5-6) (5–6): 359–363. Bibcode:1993CPL...208..359F. doi:10.1016/0009-2614(93)87156-W. 
  14. ^ Florian Weigend and Marco Häser (October 13, 1997). "RI-MP2: first derivatives and global consistency". Theoretical Chemistry Accounts (Springer Berlin / Heidelberg). 97 (1-4): 331–340. doi:10.1007/s002140050269. 
  15. ^ Robert A. Distasio JR., Ryan P. Steele, Young Min Rhee, Yihan Shao, and 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 (Wiley InterScience) 28 (5): 839–856. doi:10.1002/jcc.20604. 
  16. ^ M.S. Gordon, M.A. Freitag, P. Bandyopadhyay, J.H. Jensen, V. Kairys, W.J. Stevens (2001). "The effective fragment potential method: A QM-based MM approach to modeling environmental effects in chemistry". Journal of Physical Chemistry A 105 (2): 203. doi:10.1021/jp002747h. 
  17. ^ 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. Volume 3 of Annual Reports in Computational Chemistry. Elsevier. pp. 177–193. 
  18. ^ 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. doi:10.1021/jp101797a. 
  19. ^ D. Ghosh, D. Kosenkov, V. Vanovschi, C. Williams, J. Herbert, M.S. Gordon, M. Schmidt, L.V. Slipchenko, A.I. Krylov (2010). "Non-covalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers". Journal of Physical Chemistry A 114 (48): 12739. doi:10.1021/jp107557p. 
  20. ^ 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. 
  21. ^ 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. 
  22. ^ http://www.q-chem.com/qchem-website/whatsNew4.html
  23. ^ http://www.q-chem.com/qchem-website/whatsNew4-1.html
  24. ^ Center for Computational Studies of Electronic Structure and Spectroscopy of Open-Shell and Electronically Excited Species - iOpenShell

External links[edit]