This is an initial library of BibTex references for the lammps_step plug-in for SEAMM,
generated automatically by the cookiecutter. You may wish to edit the first entry to correct some
of the information.

Add other references to the end of the file and add code in the plug-in to cite the references as
appropriate. This is done with code like this:

        self.references.cite(
            raw=self._bibliography['doi:10.1002/jcc.21224'],
            alias='packmol',
            module='packmol_step',
            level=1,
            note='The principle PACKMOL citation.'
        )

which is typically in the run() method of the plug-in.

The base node class in SEAMM automatically reads this list of references into a dictionary in
self._bibliography with the key being the key of the BibTex entry -- usually the name on the
first line of the entry after the 'article' or 'misc' (for software) keyword.

See the documentation for the Reference Handler for the other arguments to cite().

# End of initial comments #

@Misc{mopac_step,
	author = {Paul Saxe},
	title = {MOPAC plug-in for SEAMM},
	month = {$month},
	year = {$year},
	organization = {The Molecular Sciences Software Institute (MolSSI)},
	url = {https://github.com/molssi-seamm/mopac_step},
	address = {Virginia Tech, Blacksburg, VA, USA},
	version = {$version}
}
@Misc{Stewart_2016,
	key = {MOPAC_2016},
	author = {Stewart, J. J. P.},
	title = {$release},
	month = {$month},
	year = {$year},
	organization = {Stewart Computational Chemistry},
	url = {http://OpenMOPAC.net},
	address = {Colorado Springs, CO, USA},
	version = {$version},
}
@article{Stewart_2012,
	doi = {10.1007/s00894-012-1667-x},
	url = {https://doi.org/10.1007%2Fs00894-012-1667-x},
	year = 2012,
	month = {nov},
	publisher = {Springer Science and Business Media {LLC}},
	volume = {19},
	number = {1},
	pages = {1--32},
	author = {James J. P. Stewart},
	title = {Optimization of parameters for semiempirical methods {VI}: more modifications to the {NDDO} approximations and re-optimization of parameters},
	journal = {Journal of Molecular Modeling}
}
@article{Stewart_2007,
	doi = {10.1007/s00894-007-0233-4},
	url = {https://doi.org/10.1007%2Fs00894-007-0233-4},
	year = 2007,
	month = {sep},
	publisher = {Springer Science and Business Media {LLC}},
	volume = {13},
	number = {12},
	pages = {1173--1213},
	author = {James J. P. Stewart},
	title = {Optimization of parameters for semiempirical methods V: Modification of {NDDO} approximations and application to 70 elements},
	journal = {Journal of Molecular Modeling}
}
@article{Stewart_1989,
	doi = {10.1002/jcc.540100208},
	url = {https://doi.org/10.1002%2Fjcc.540100208},
	year = 1989,
	month = {mar},
	publisher = {Wiley},
	volume = 10,
	number = 2,
	pages = {209--220},
	author = {James J. P. Stewart},
	title = {Optimization of parameters for semiempirical methods I. Method},
	journal = {Journal of Computational Chemistry}
}
@article{Stewart_1991,
	doi = {10.1002/jcc.540120306},
	url = {https://doi.org/10.1002%2Fjcc.540120306},
	year = 1991,
	month = {apr},
	publisher = {Wiley},
	volume = 12,
	number = 3,
	pages = {320--341},
	author = {James J. P. Stewart},
	title = {Optimization of parameters for semiempirical methods. {III} Extension of {PM}3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi},
	journal = {Journal of Computational Chemistry}
}
@article{Anders_1993,
	doi = {10.1002/jcc.540141106},
	url = {https://doi.org/10.1002%2Fjcc.540141106},
	year = 1993,
	month = {nov},
	publisher = {Wiley},
	volume = {14},
	number = {11},
	pages = {1301--1312},
	author = {Ernst Anders and Rainer Koch and Peter Freunscht},
	title = {Optimization and application of lithium parameters for {PM}3},
	journal = {Journal of Computational Chemistry}
}
@article{Stewart_2004,
	doi = {10.1007/s00894-004-0183-z},
	url = {https://doi.org/10.1007%2Fs00894-004-0183-z},
	year = 2004,
	month = {apr},
	publisher = {Springer Science and Business Media {LLC}},
	volume = {10},
	number = {2},
	pages = {155--164},
	author = {James J. P. Stewart},
	title = {Optimization of parameters for semiempirical methods {IV}: extension of {MNDO}, {AM}1, and {PM}3 to more main group elements},
	journal = {Journal of Molecular Modeling}
}
@article{Dewar_1977,
	doi = {10.1021/ja00457a004},
	url = {https://doi.org/10.1021%2Fja00457a004},
	year = 1977,
	month = {jun},
	publisher = {American Chemical Society ({ACS})},
	volume = {99},
	number = {15},
	pages = {4899--4907},
	author = {Michael J. S. Dewar and Walter Thiel},
	title = {Ground states of molecules. 38. The {MNDO} method. Approximations and parameters},
	journal = {Journal of the American Chemical Society}
}
@article{Dewar_1978,
	doi = {10.1021/ja00471a020},
	url = {https://doi.org/10.1021%2Fja00471a020},
	year = 1978,
	month = {feb},
	publisher = {American Chemical Society ({ACS})},
	volume = {100},
	number = {3},
	pages = {777--784},
	author = {Michael J. S. Dewar and Henry S. Rzepa},
	title = {Ground states of molecules. 45. {MNDO} results for molecules containing beryllium},
	journal = {Journal of the American Chemical Society}
}
@article{Davis_1981,
	doi = {10.1002/jcc.540020412},
	url = {https://doi.org/10.1002%2Fjcc.540020412},
	year = 1981,
	publisher = {Wiley},
	volume = {2},
	number = {4},
	pages = {433--445},
	author = {L. P. Davis and R. M. Guidry and J. R. Williams and M. J. S. Dewar and H. S. Rzepa},
	title = {{MNDO} calculations for compounds containing aluminum and boron},
	journal = {Journal of Computational Chemistry}
}
@article{Dewar_1978b,
	doi = {10.1021/ja00469a010},
	url = {https://doi.org/10.1021%2Fja00469a010},
	year = 1978,
	month = {jan},
	publisher = {American Chemical Society ({ACS})},
	volume = {100},
	number = {1},
	pages = {58--67},
	author = {Michael J. S. Dewar and Henry S. Rzepa},
	title = {Ground states of molecules. 40. {MNDO} results for molecules containing fluorine},
	journal = {Journal of the American Chemical Society}
}
@article{Dewar_1986,
	doi = {10.1021/om00133a029},
	url = {https://doi.org/10.1021%2Fom00133a029},
	year = 1986,
	month = {feb},
	publisher = {American Chemical Society ({ACS})},
	volume = {5},
	number = {2},
	pages = {375--379},
	author = {Michael J. S. Dewar and Eamonn F. Healy and James J. P. Stewart and James. Friedheim and Gilbert. Grady},
	title = {Revised {MNDO} parameters for silicon},
	journal = {Organometallics}
}
@article{Dewar_1978c,
	doi = {10.1021/ja00479a058},
	url = {https://doi.org/10.1021%2Fja00479a058},
	year = 1978,
	month = {may},
	publisher = {American Chemical Society ({ACS})},
	volume = {100},
	number = {11},
	pages = {3607--3607},
	author = {Michael J. S. Dewar and Michael L. McKee and Henry S. Rzepa},
	title = {{MNDO} parameters for third period elements},
	journal = {Journal of the American Chemical Society}
}
@article{Dewar_1986b,
	doi = {10.1002/jcc.540070206},
	url = {https://doi.org/10.1002%2Fjcc.540070206},
	year = 1986,
	month = {apr},
	publisher = {Wiley},
	volume = {7},
	number = {2},
	pages = {140--143},
	author = {Michael J. S. Dewar and Charles H. Reynolds},
	title = {An improved set of mndo parameters for sulfur},
	journal = {Journal of Computational Chemistry}
}
@article{Dewar_1983,
	doi = {10.1002/jcc.540040207},
	url = {https://doi.org/10.1002%2Fjcc.540040207},
	year = 1983,
	publisher = {Wiley},
	volume = {4},
	number = {2},
	pages = {158--169},
	author = {Michael J. S. Dewar and Henry S. Rzepa},
	title = {Ground states of molecules. 53.{MNDO} calculations for molecules containing chlorine},
	journal = {Journal of Computational Chemistry}
}
@article{Dewar_1986c,
	doi = {10.1021/om00138a033},
	url = {https://doi.org/10.1021%2Fom00138a033},
	year = 1986,
	month = {jul},
	publisher = {American Chemical Society ({ACS})},
	volume = {5},
	number = {7},
	pages = {1494--1496},
	author = {Michael J. S. Dewar and Kenneth M. Merz},
	title = {Ground states of molecules. Part 84. {MNDO} calculations for compounds containing zinc},
	journal = {Organometallics}
}
@article{Dewar_1987,
	doi = {10.1021/om00144a034},
	url = {https://doi.org/10.1021%2Fom00144a034},
	year = 1987,
	month = {jan},
	publisher = {American Chemical Society ({ACS})},
	volume = {6},
	number = {1},
	pages = {186--189},
	author = {Michael J. S. Dewar and Gilbert L. Grady and Eamonn F. Healy},
	title = {Ground states of molecules. 73. {MNDO} calculations for compounds containing germanium},
	journal = {Organometallics}
}
@article{Dewar_1983b,
	doi = {10.1002/jcc.540040412},
	url = {https://doi.org/10.1002%2Fjcc.540040412},
	year = 1983,
	publisher = {Wiley},
	volume = {4},
	number = {4},
	pages = {542--551},
	author = {Michael J. S. Dewar and Eamonn Healy},
	title = {Ground states of molecules. 64.{MNDO} Calculations for compounds containing bromine},
	journal = {Journal of Computational Chemistry}
}
@article{Dewar_1984,
	doi = {10.1021/ja00334a051},
	url = {https://doi.org/10.1021%2Fja00334a051},
	year = 1984,
	month = {oct},
	publisher = {American Chemical Society ({ACS})},
	volume = {106},
	number = {22},
	pages = {6771--6773},
	author = {Michael J. S. Dewar and Gilbert L. Grady and James J. P. Stewart},
	title = {{MNDO} Calculations for Compounds Containing Tin},
	journal = {Journal of the American Chemical Society}
}
@article{Dewar_1984b,
	doi = {10.1002/jcc.540050413},
	url = {https://doi.org/10.1002%2Fjcc.540050413},
	year = 1984,
	month = {aug},
	publisher = {Wiley},
	volume = {5},
	number = {4},
	pages = {358--362},
	author = {Michael J. S. Dewar and Eamonn F. Healy and James J. P. Stewart},
	title = {Ground states of molecules. 67.{MNDO} Calculations for compounds containing iodine},
	journal = {Journal of Computational Chemistry}
}
@article{Dewar_1985,
	doi = {10.1021/om00130a008},
	url = {https://doi.org/10.1021%2Fom00130a008},
	year = 1985,
	month = {nov},
	publisher = {American Chemical Society ({ACS})},
	volume = {4},
	number = {11},
	pages = {1964--1966},
	author = {Michael J. S. Dewar and Gilbert L. Grady and Kenneth M. Merz and James J. P. Stewart},
	title = {{MNDO} calculations for compounds containing mercury},
	journal = {Organometallics}
}
@article{Dewar_1985b,
	doi = {10.1021/om00130a010},
	url = {https://doi.org/10.1021%2Fom00130a010},
	year = 1985,
	month = {nov},
	publisher = {American Chemical Society ({ACS})},
	volume = {4},
	number = {11},
	pages = {1973--1980},
	author = {Michael J. S. Dewar and Mary K. Holloway and Gilbert L. Grady and James J. P. Stewart},
	title = {Ground states of molecules. Part 79. {MNDO} calculations for compounds containing lead},
	journal = {Organometallics}
}
@article{Dewar_1985c,
	doi = {10.1021/ja00299a024},
	url = {https://doi.org/10.1021%2Fja00299a024},
	year = 1985,
	month = {jun},
	publisher = {American Chemical Society ({ACS})},
	volume = {107},
	number = {13},
	pages = {3902--3909},
	author = {Michael J. S. Dewar and Eve G. Zoebisch and Eamonn F. Healy and James J. P. Stewart},
	title = {Development and use of quantum mechanical molecular models. 76. {AM}1: a new general purpose quantum mechanical molecular model},
	journal = {Journal of the American Chemical Society}
}
@article{Dewar_1988,
	doi = {10.1016/0166-1280(88)80074-5},
	url = {https://doi.org/10.1016%2F0166-1280%2888%2980074-5},
	year = 1988,
	month = {nov},
	publisher = {Elsevier {BV}},
	volume = {180},
	pages = {1--21},
	author = {Michael J.S. Dewar and Eve G. Zoebisch},
	title = {Extension of {AM}1 to the halogens},
	journal = {Journal of Molecular Structure: {THEOCHEM}}
}
@article{Dewar_1990,
	doi = {10.1021/om00116a031},
	url = {https://doi.org/10.1021%2Fom00116a031},
	year = 1990,
	month = {feb},
	publisher = {American Chemical Society ({ACS})},
	volume = {9},
	number = {2},
	pages = {508--511},
	author = {Michael J. S. Dewar and Andrew J. Holder},
	title = {{AM}1 parameters for aluminum},
	journal = {Organometallics}
}
@article{Dewar_1987b,
	doi = {10.1021/om00150a020},
	url = {https://doi.org/10.1021%2Fom00150a020},
	year = 1987,
	month = {jul},
	publisher = {American Chemical Society ({ACS})},
	volume = {6},
	number = {7},
	pages = {1486--1490},
	author = {Michael J. S. Dewar and Caoxian. Jie},
	title = {{AM}1 calculations for compounds containing silicon},
	journal = {Organometallics}
}
@article{Dewar_1989,
	doi = {10.1016/0166-1280(89)85145-0},
	url = {https://doi.org/10.1016%2F0166-1280%2889%2985145-0},
	year = 1989,
	month = {may},
	publisher = {Elsevier {BV}},
	volume = {187},
	pages = {1--13},
	author = {Michael J.S. Dewar and Caoxion Jie},
	title = {{AM}1 parameters for phosphorus},
	journal = {Journal of Molecular Structure: {THEOCHEM}}
}
@article{Dewar_1990b,
	doi = {10.1021/ic00344a045},
	url = {https://doi.org/10.1021%2Fic00344a045},
	year = 1990,
	month = {sep},
	publisher = {American Chemical Society ({ACS})},
	volume = {29},
	number = {19},
	pages = {3881--3890},
	author = {Michael J. S. Dewar and Yate Ching Yuan},
	title = {{AM}1 parameters for sulfur},
	journal = {Inorganic Chemistry}
}
@article{Dewar_1988b,
	doi = {10.1021/om00092a044},
	url = {https://doi.org/10.1021%2Fom00092a044},
	year = 1988,
	month = {feb},
	publisher = {American Chemical Society ({ACS})},
	volume = {7},
	number = {2},
	pages = {522--524},
	author = {Michael J. S. Dewar and Kenneth M. Merz},
	title = {{AM}1 parameters for zinc},
	journal = {Organometallics}
}
@article{Dewar_1989b,
	doi = {10.1021/om00108a028},
	url = {https://doi.org/10.1021%2Fom00108a028},
	year = 1989,
	month = {jun},
	publisher = {American Chemical Society ({ACS})},
	volume = {8},
	number = {6},
	pages = {1544--1547},
	author = {Michael J. S. Dewar and Caoxian. Jie},
	title = {{AM}1 calculations for compounds containing germanium},
	journal = {Organometallics}
}
@article{Voityuk_2000,
	doi = {10.1021/jp994394w},
	url = {https://doi.org/10.1021%2Fjp994394w},
	year = 2000,
	month = {may},
	publisher = {American Chemical Society ({ACS})},
	volume = {104},
	number = {17},
	pages = {4089--4094},
	author = {Alexander A. Voityuk and Notker Rösch},
	title = {{AM}1/d Parameters for Molybdenum},
	journal = {The Journal of Physical Chemistry A}
}
@article{Dewar_1989c,
	doi = {10.1021/om00108a029},
	url = {https://doi.org/10.1021%2Fom00108a029},
	year = 1989,
	month = {jun},
	publisher = {American Chemical Society ({ACS})},
	volume = {8},
	number = {6},
	pages = {1547--1549},
	author = {Michael J. S. Dewar and Caoxian. Jie},
	title = {{AM}1 calculations for compounds containing mercury},
	journal = {Organometallics}
}
@article{Rocha_2006,
	doi = {10.1002/jcc.20425},
	url = {https://doi.org/10.1002%2Fjcc.20425},
	year = 2006,
	month = {jul},
	publisher = {Wiley},
	volume = {27},
	number = {10},
	pages = {1101--1111},
	author = {Gerd B. Rocha and Ricardo O. Freire and Alfredo M. Simas and James J. P. Stewart},
	title = {{RM}1: A reparameterization of {AM}1 for H, C, N, O, P, S, F, Cl, Br, and I},
	journal = {Journal of Computational Chemistry}
}
@article{Thiel_1996,
	doi = {10.1021/jp952148o},
	url = {https://doi.org/10.1021%2Fjp952148o},
	year = 1996,
	month = {jan},
	publisher = {American Chemical Society ({ACS})},
	volume = {100},
	number = {2},
	pages = {616--626},
	author = {Walter Thiel and Alexander A. Voityuk},
	title = {Extension of {MNDO} to d Orbitals:~ Parameters and Results for the Second-Row Elements and for the Zinc Group},
	journal = {The Journal of Physical Chemistry}
}
@article{Thiel_1992,
	doi = {10.1007/bf01134863},
	url = {https://doi.org/10.1007%2Fbf01134863},
	year = 1992,
	publisher = {Springer Science and Business Media {LLC}},
	volume = {81},
	number = {6},
	pages = {391--404},
	author = {Walter Thiel and Alexander A. Voityuk},
	title = {Extension of the {MNDO} formalism tod orbitals: Integral approximations and preliminary numerical results},
	journal = {Theoretica Chimica Acta}
}
@article{Grimme_2010,
	doi = {10.1063/1.3382344},
	url = {https://doi.org/10.1063%2F1.3382344},
	year = 2010,
	month = {apr},
	publisher = {{AIP} Publishing},
	volume = {132},
	number = {15},
	pages = {154104},
	author = {Stefan Grimme and Jens Antony and Stephan Ehrlich and Helge Krieg},
	title = {A consistent and accurate ab initio parametrization of density functional dispersion correction ({DFT}-D) for the 94 elements H-Pu},
	journal = {The Journal of Chemical Physics}
}
@article{Korth_2010,
	doi = {10.1021/ct100408b},
	url = {https://doi.org/10.1021%2Fct100408b},
	year = 2010,
	month = {nov},
	publisher = {American Chemical Society ({ACS})},
	volume = {6},
	number = {12},
	pages = {3808--3816},
	author = {Martin Korth},
	title = {Third-Generation Hydrogen-Bonding Corrections for Semiempirical {QM} Methods and Force Fields},
	journal = {Journal of Chemical Theory and Computation}
}
@article{Korth_2009,
	doi = {10.1021/ct900541n},
	url = {https://doi.org/10.1021%2Fct900541n},
	year = 2009,
	month = {dec},
	publisher = {American Chemical Society ({ACS})},
	volume = {6},
	number = {1},
	pages = {344--352},
	author = {Martin Korth and Michal Pito{\v{n}}{\'{a}}k and Jan {\v{R}}ez{\'{a}}{\v{c}} and Pavel Hobza},
	title = {A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods},
	journal = {Journal of Chemical Theory and Computation}
}
@article{Rezac_2009,
	doi = {10.1021/ct9000922},
	url = {https://doi.org/10.1021%2Fct9000922},
	year = 2009,
	month = {may},
	publisher = {American Chemical Society ({ACS})},
	volume = {5},
	number = {7},
	pages = {1749--1760},
	author = {Jan {\v{R}}ez{\'{a}}{\v{c}} and Jind{\v{r}}ich Fanfrl{\'{\i}}k and Dennis Salahub and Pavel Hobza},
	title = {Semiempirical Quantum Chemical {PM}6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes},
	journal = {Journal of Chemical Theory and Computation}
}
@article{Rezac_2011,
	doi = {10.1016/j.cplett.2011.03.009},
	url = {https://doi.org/10.1016%2Fj.cplett.2011.03.009},
	year = 2011,
	month = {apr},
	publisher = {Elsevier {BV}},
	volume = {506},
	number = {4-6},
	pages = {286--289},
	author = {Jan {\v{R}}ez{\'{a}}{\v{c}} and Pavel Hobza},
	title = {A halogen-bonding correction for the semiempirical {PM}6 method},
	journal = {Chemical Physics Letters}
}
@article{Rezac_2011,
	doi = {10.1021/ct200751e},
	url = {https://doi.org/10.1021%2Fct200751e},
	year = 2011,
	month = {dec},
	publisher = {American Chemical Society ({ACS})},
	volume = {8},
	number = {1},
	pages = {141--151},
	author = {Jan {\v{R}}ez{\'{a}}{\v{c}} and Pavel Hobza},
	title = {Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods},
	journal = {Journal of Chemical Theory and Computation}
}
@article{Vorlova_2015,
	doi = {10.1016/j.ejmech.2014.10.043},
	url = {https://doi.org/10.1016%2Fj.ejmech.2014.10.043},
	year = 2015,
	month = {jan},
	publisher = {Elsevier {BV}},
	volume = {89},
	pages = {189--197},
	author = {Barbora Vorlov{\'{a}} and Dana Nachtigallov{\'{a}} and Jana Jir{\'{a}}skov{\'{a}}-Van{\'{\i}}{\v{c}}kov{\'{a}} and Haresh Ajani and Petr Jansa and Jan {\v{R}}ez{\'{a}}{\v{c}} and Jind{\v{r}}ich Fanfrl{\'{\i}}k and Michal Otyepka and Pavel Hobza and Jan Konvalinka and Martin Lep{\v{s}}{\'{\i}}k},
	title = {Malonate-based inhibitors of mammalian serine racemase: Kinetic characterization and structure-based computational study},
	journal = {European Journal of Medicinal Chemistry}
}
@article{Brahmkshatriya_2013,
	doi = {10.2174/1573409911309010011},
	url = {https://doi.org/10.2174%2F1573409911309010011},
	year = 2013,
	month = {jan},
	publisher = {Bentham Science Publishers Ltd.},
	volume = {9},
	number = {1},
	pages = {118--129},
	author = {Pathik S. Brahmkshatriya and Petr Dobes and Jindrich Fanfrlik and Jan Rezac and Kamil Paruch and Agnieszka Bronowska and Martin Leps{\'{\i}}k and Pavel Hobza},
	title = {Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines},
	journal = {Current Computer Aided-Drug Design}
}
@article{Baker_1986,
	doi = {10.1002/jcc.540070402},
	url = {https://doi.org/10.1002%2Fjcc.540070402},
	year = 1986,
	month = {aug},
	publisher = {Wiley},
	volume = {7},
	number = {4},
	pages = {385--395},
	author = {Jon Baker},
	title = {An algorithm for the location of transition states},
	journal = {Journal of Computational Chemistry}
}
@article{Broyden_1970,
	doi = {10.1093/imamat/6.3.222},
	url = {https://doi.org/10.1093%2Fimamat%2F6.3.222},
	year = 1970,
	publisher = {Oxford University Press ({OUP})},
	volume = {6},
	number = {3},
	pages = {222--231},
	author = {C. G. BROYDEN},
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@TechReport{Bartels_1972,
  author = 	 {R. H. Bartels},
  title = 	 {Nonlinear least squares without derivatives: An application of the QR matrix decomposition.},
  institution =  {Center for Numerical Analysis, University of Texas at Austin},
  year = 	 1972,
  number = 	 {CNA-44},
  month = 	 {apr},
  url = 	 {ftp://ftp.ma.utexas.edu/pub/CNA/cna44.pdf}
}
