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Add more method and software references for semiempirical models
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paper.bib

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%% This BibTeX bibliography file was created using BibDesk.
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%% https://bibdesk.sourceforge.io/
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%% Created for Jonathan Moussa at 2025-02-22 00:58:58 -0500
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%% Created for Jonathan Moussa at 2025-05-23 12:55:02 -0400
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@misc{Gaussian,
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address = {Wallingford, CT %! Gaussian 16},
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author = {Frisch, M. J. and Trucks, G. W. and Schlegel, H. B. and Scuseria, G. E. and Robb, M. A. and Cheeseman, J. R. and Scalmani, G. and Barone, V. and Petersson, G. A. and Nakatsuji, H. and Li, X. and Caricato, M. and Marenich, A. V. and Bloino, J. and Janesko, B. G. and Gomperts, R. and Mennucci, B. and Hratchian, H. P. and Ortiz, J. V. and Izmaylov, A. F. and Sonnenberg, J. L. and Williams and Ding, F. and Lipparini, F. and Egidi, F. and Goings, J. and Peng, B. and Petrone, A. and Henderson, T. and Ranasinghe, D. and Zakrzewski, V. G. and Gao, J. and Rega, N. and Zheng, G. and Liang, W. and Hada, M. and Ehara, M. and Toyota, K. and Fukuda, R. and Hasegawa, J. and Ishida, M. and Nakajima, T. and Honda, Y. and Kitao, O. and Nakai, H. and Vreven, T. and Throssell, K. and Montgomery Jr., J. A. and Peralta, J. E. and Ogliaro, F. and Bearpark, M. J. and Heyd, J. J. and Brothers, E. N. and Kudin, K. N. and Staroverov, V. N. and Keith, T. A. and Kobayashi, R. and Normand, J. and Raghavachari, K. and Rendell, A. P. and Burant, J. C. and Iyengar, S. S. and Tomasi, J. and Cossi, M. and Millam, J. M. and Klene, M. and Adamo, C. and Cammi, R. and Ochterski, J. W. and Martin, R. L. and Morokuma, K. and Farkas, O. and Foresman, J. B. and Fox, D. J.},
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date = {2016},
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date-added = {2025-05-23 12:54:38 -0400},
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date-modified = {2025-05-23 12:54:57 -0400},
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title = {Gaussian 16 Rev. C.01},
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year = {2016}}
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@misc{SQM_perspective,
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archiveprefix = {arXiv},
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author = {Jonathan E. Moussa},
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date-added = {2025-05-23 12:46:55 -0400},
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date-modified = {2025-05-23 12:47:11 -0400},
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eprint = {2505.13424},
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primaryclass = {physics.chem-ph},
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title = {The Enduring Relevance of Semiempirical Quantum Mechanics},
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url = {https://arxiv.org/abs/2505.13424},
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year = {2025},
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bdsk-url-1 = {https://arxiv.org/abs/2505.13424}}
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@article{ULYSSES,
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annote = {doi: 10.1021/acs.jcim.2c00757},
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author = {Menezes, Filipe and Popowicz, Grzegorz M.},
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date = {2022/08/22},
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date-added = {2025-05-23 12:46:13 -0400},
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date-modified = {2025-05-23 12:46:29 -0400},
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doi = {10.1021/acs.jcim.2c00757},
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isbn = {1549-9596},
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journal = {Journal of Chemical Information and Modeling},
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journal1 = {Journal of Chemical Information and Modeling},
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journal2 = {J. Chem. Inf. Model.},
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month = {08},
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number = {16},
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pages = {3685--3694},
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publisher = {American Chemical Society},
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title = {ULYSSES: An Efficient and Easy to Use Semiempirical Library for C++},
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type = {doi: 10.1021/acs.jcim.2c00757},
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url = {https://doi.org/10.1021/acs.jcim.2c00757},
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volume = {62},
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year = {2022},
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year1 = {2022},
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bdsk-url-1 = {https://doi.org/10.1021/acs.jcim.2c00757}}
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@article{Sparrow,
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abstract = {Semi-empirical quantum chemical approaches are known to compromise accuracy for the feasibility of calculations on huge molecules. However, the need for ultrafast calculations in interactive quantum mechanical studies, high-throughput virtual screening, and data-driven machine learning has shifted the emphasis toward calculation runtimes recently. This comes with new constraints for the software implementation as many fast calculations would suffer from a large overhead of the manual setup and other procedures that are comparatively fast when studying a single molecular structure, but which become prohibitively slow for high-throughput demands. In this work, we discuss the effect of various well-established semi-empirical approximations on calculation speed and relate this to data transfer rates from the raw-data source computer to the results of the visualization front end. For the former, we consider desktop computers, local high performance computing, and remote cloud services in order to elucidate the effect on interactive calculations, for web and cloud interfaces in local applications, and in world-wide interactive virtual sessions. The models discussed in this work have been implemented into our open-source software SCINE Sparrow.},
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author = {Bosia, Francesco and Zheng, Peikun and Vaucher, Alain and Weymuth, Thomas and Dral, Pavlo O. and Reiher, Markus},
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date-added = {2025-05-23 12:44:59 -0400},
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date-modified = {2025-05-23 12:45:07 -0400},
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doi = {10.1063/5.0136404},
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eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0136404/16703358/054118\_1\_online.pdf},
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issn = {0021-9606},
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journal = {The Journal of Chemical Physics},
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month = {02},
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number = {5},
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pages = {054118},
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title = {Ultra-fast semi-empirical quantum chemistry for high-throughput computational campaigns with Sparrow},
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url = {https://doi.org/10.1063/5.0136404},
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volume = {158},
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year = {2023},
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bdsk-url-1 = {https://doi.org/10.1063/5.0136404}}
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@article{CP2K,
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abstract = {CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post--Hartree--Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.},
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author = {K{\"u}hne, Thomas D. and Iannuzzi, Marcella and Del Ben, Mauro and Rybkin, Vladimir V. and Seewald, Patrick and Stein, Frederick and Laino, Teodoro and Khaliullin, Rustam Z. and Sch{\"u}tt, Ole and Schiffmann, Florian and Golze, Dorothea and Wilhelm, Jan and Chulkov, Sergey and Bani-Hashemian, Mohammad Hossein and Weber, Val{\'e}ry and Bor{\v s}tnik, Urban and Taillefumier, Mathieu and Jakobovits, Alice Shoshana and Lazzaro, Alfio and Pabst, Hans and M{\"u}ller, Tiziano and Schade, Robert and Guidon, Manuel and Andermatt, Samuel and Holmberg, Nico and Schenter, Gregory K. and Hehn, Anna and Bussy, Augustin and Belleflamme, Fabian and Tabacchi, Gloria and Gl{\"o}{\ss}, Andreas and Lass, Michael and Bethune, Iain and Mundy, Christopher J. and Plessl, Christian and Watkins, Matt and VandeVondele, Joost and Krack, Matthias and Hutter, J{\"u}rg},
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date-added = {2025-05-23 12:43:43 -0400},
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date-modified = {2025-05-23 12:44:09 -0400},
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doi = {10.1063/5.0007045},
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eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0007045/16718133/194103\_1\_online.pdf},
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issn = {0021-9606},
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journal = {The Journal of Chemical Physics},
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month = {05},
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number = {19},
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pages = {194103},
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title = {CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations},
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url = {https://doi.org/10.1063/5.0007045},
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volume = {152},
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year = {2020},
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bdsk-url-1 = {https://doi.org/10.1063/5.0007045}}
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@inbook{QCPE,
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author = {Boyd, Donald B.},
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booktitle = {Pioneers of Quantum Chemistry},
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pages = {154},
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title = {An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin},
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volume = {23},
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year = {2017}}
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year = {2017},
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bdsk-url-1 = {https://doi.org/10.1007/s00894-017-3326-8}}
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@article{MOZYME,
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author = {J. J. P. Stewart},
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pages = {133--146},
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title = {Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations},
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volume = {58},
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year = {1996}}
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year = {1996},
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bdsk-url-1 = {https://doi.org/10.1002/(SICI)1097-461X(1996)58:2%3C133::AID-QUA2%3E3.0.CO;2-Z}}
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@article{PM6ORG,
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author = {J. J. P. Stewart and A. C. Stewart },
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author = {J. J. P. Stewart and A. C. Stewart},
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date-added = {2025-02-21 19:36:42 -0500},
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date-modified = {2025-02-21 19:38:06 -0500},
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doi = {10.1007/s00894-023-05695-1},
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journal = {Journal of Molecular Modeling},
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pages = {284},
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title = {A semiempirical method optimized for modeling proteins},
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volume = {29},
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year = {2023}}
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year = {2023},
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bdsk-url-1 = {https://doi.org/10.1007/s00894-023-05695-1}}
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@article{INDO,
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author = {R. L. M. Gieseking},
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pages = {365--378},
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title = {A new release of MOPAC incorporating the INDO/S semiempirical model with CI excited states},
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volume = {42},
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year = {2021}}
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year = {2021},
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bdsk-url-1 = {https://doi.org/10.1002/jcc.26455}}
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@article{PM6,
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author = {J. J. P. Stewart},
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pages = {1173--1213},
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title = {Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements},
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volume = {13},
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year = {2007}}
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year = {2007},
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bdsk-url-1 = {https://doi.org/10.1007/s00894-007-0233-4}}
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@article{solvent,
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author = {A. Klamt and G. Sch\"{u}\"{u}rmann},
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journal = {Journal of the Chemical Society, Perkin Transactions 2},
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pages = {799--805},
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title = {COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient},
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year = {1993}}
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year = {1993},
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bdsk-url-1 = {https://doi.org/10.1039/P29930000799}}
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@article{solids,
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author = {J. J. P. Stewart},
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pages = {59--67},
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title = {A practical method for modeling solids using semiempirical methods},
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volume = {556},
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year = {2000}}
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year = {2000},
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bdsk-url-1 = {https://doi.org/10.1016/S0022-2860(00)00651-7}}
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@article{interactive,
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author = {T. Weymuth and M. Reiher},
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pages = {45--49},
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title = {Immersive Interactive Quantum Mechanics for Teaching and Learning Chemistry},
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volume = {75},
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year = {2021},
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bdsk-url-1 = {https://doi.org/10.2533/chimia.2021.45}}
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@article{screening,
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author = {E. O. Pyzer-Knapp and C. Suh and R. G\'{o}mez-Bombarelli and J. Aguilera-Iparraguirre and A. Aspuru-Guzik},
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pages = {195--216},
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title = {What Is High-Throughput Virtual Screening? A Perspective from Organic Materials Discovery},
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volume = {45},
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year = {2015}}
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year = {2015},
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bdsk-url-1 = {https://doi.org/10.1146/annurev-matsci-070214-020823}}
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@article{MOPAC2,
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author = {J. J. P. Stewart},
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pages = {1--103},
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title = {MOPAC: A semiempirical molecular orbital program},
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volume = {4},
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year = {1990}}
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year = {1990},
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bdsk-url-1 = {https://doi.org/10.1007/BF00128336}}
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@article{MOPAC1,
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author = {J. J. P. Stewart},
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pages = {3902--3909},
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title = {Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model},
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volume = {107},
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year = {1985}}
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year = {1985},
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bdsk-url-1 = {https://doi.org/10.1021/ja00299a024}}
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@article{MNDO,
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author = {Michael J. S. Dewar and Walter Thiel},
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pages = {4899--4907},
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title = {Ground states of molecules. 38. The MNDO method. Approximations and parameters},
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volume = {99},
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year = {1977}}
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year = {1977},
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bdsk-url-1 = {https://doi.org/10.1021/ja00457a004}}
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@article{Dewar,
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author = {Michael J. S. Dewar},
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pages = {1037--1044},
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title = {Quantum Organic Chemistry},
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volume = {187},
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year = {1975}}
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year = {1975},
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bdsk-url-1 = {https://doi.org/10.1126/science.187.4181.1037}}
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@article{Pople2,
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author = {J. A. Pople and D. P. Santry and G. A. Segal},
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pages = {S129--S135},
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title = {Approximate Self‐Consistent Molecular Orbital Theory. I. Invariant Procedures},
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volume = {43},
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year = {1965}}
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year = {1965},
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bdsk-url-1 = {https://doi.org/10.1063/1.1701475}}
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@article{Pople1,
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author = {J. A. Pople},
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pages = {1375--1385},
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title = {Electron interaction in unsaturated hydrocarbons},
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volume = {49},
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year = {1953},
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bdsk-url-1 = {https://doi.org/10.1039/TF9534901375}}
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@article{PM7,
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author = {J. J. P. Stewart},
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pages = {1--32},
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title = {Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters},
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volume = {19},
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year = {2012}}
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year = {2012},
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bdsk-url-1 = {https://doi.org/10.1007/s00894-012-1667-x}}
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@misc{mopactools,
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author = {Jonathan E. Moussa},
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publisher = {GitHub},
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title = {mopactools},
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url = {https://github.com/openmopac/mopactools},
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year = {2025},
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bdsk-url-1 = {https://github.com/arfon/fidgit}}
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year = {2025}}

paper.md

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Semiempirical models of thermochemistry were pioneered by Pople [@Pople1; @Pople2] and later
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championed by Dewar [@Dewar], culminating in the development of the Modified Neglect of Diatomic
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Overlap (MNDO) model form [@MNDO], the Austin Model 1 (AM1) parameterization [@AM1], and the
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MOPAC program [@MOPAC1].
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MOPAC program [@MOPAC1]. Historically, MOPAC has been the development platform for the MNDO-family
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semiempirical models, but these models are also implemented in other software such as
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Gaussian [@Gaussian], CP2K [@CP2K], Sparrow [@Sparrow], and ULYSSES [@ULYSSES].
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In the four decades since MOPAC was first released, the computing power of personal computers
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has increased a million fold. As a result, the practical cost considerations of quantum chemistry
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it is useful to perform calculations at a semiempirical level to estimate results and check for
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problems before committing to a much more expensive calculation at an *ab initio* level. For some
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expensive applications such as protein modeling, only the semiempirical level may be affordable to
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quantum chemistry users who do not have access to supercomputers.
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quantum chemistry users who do not have access to supercomputers. Semiempirical quantum mechanical
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models continue to be a middle ground in atomistic simulation between *ab initio* quantum mechanics
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and molecular mechanics based on classical force fields [@SQM_perspective].
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# Features
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