text:
@article{.zuchowski2003,
  title = {Dispersion Interaction of High-Spin Open-Shell Complexes in the Random Phase Approximation},
  author = {{\textbackslash}.Zuchowski, Piotr S and {Bussery-Honvault}, B{\'e}atrice and Moszynski, Robert and Jeziorski, Bogumil},
  year = {2003},
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  number = {20},
  pages = {10497--16},
  doi = {10.1063/1.1620496},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/3BJIEJUN/C98E9288-CD31-40EE-85C3-280ACC4D97CC.pdf}
}

@article{1983,
  title = {Full {{CI}} Calculations on {{BH}}, {{H2O}}, {{NH3}}, and {{HF}}},
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  number = {4-5},
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  publisher = {{North-Holland}},
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  abstract = {Full CI calculations are reported on BH (double-zeta plus polarisation basis), H2O (double-zeta, three geometries). NH3 (double-zeta, frozen core and \textbackslash ldots},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/U9FGPZCS/31AC49BF-1F69-48A3-B093-93B88C240A2E.pdf;/Users/dasirianni/Zotero/storage/ZFMIVFVJ/31AC49BF-1F69-48A3-B093-93B88C240A2E.pdf}
}

@book{1991,
  title = {Complex {{Chemistry}}},
  year = {1991},
  publisher = {{Springer Berlin Heidelberg}},
  address = {{Berlin, Heidelberg}},
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}

@book{2005,
  title = {Complex {{Chemistry}}},
  year = {2005},
  month = mar,
  publisher = {{Springer Berlin Heidelberg}},
  address = {{Berlin, Heidelberg}},
  issn = {0081-5993},
  isbn = {978-3-540-53499-0}
}

@article{2005a,
  title = {Calibrating Quantum Chemistry: {{A}} Multi-Teraflop, Parallel-Vector, Full-Configuration Interaction Program for the {{Cray-X1}}},
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}

@book{2009,
  title = {Reviews in {{Computational Chemistry}}},
  year = {2009},
  publisher = {{John Wiley \& Sons, Ltd}},
  isbn = {978-0-470-39954-5}
}

@book{2016,
  title = {Many-{{Body Effects}} and {{Electrostatics}} in {{Biomolecules}}},
  year = {2016},
  month = mar,
  publisher = {{Pan Stanford}},
  isbn = {978-981-4613-92-7}
}

@book{2017,
  title = {Non-{{Covalent Interactions}} in {{Quantum Chemistry}} and {{Physics}}},
  year = {2017},
  publisher = {{Elsevier}},
  isbn = {978-0-12-809835-6},
  file = {/Users/dasirianni/Zotero/storage/AE5FL9KI/402B9064-E94D-4A2E-9470-A6C327726096.pdf}
}

@misc{2017a,
  title = {The {{Many Guises}} of {{Aromaticity}}},
  year = {2017},
  month = feb,
  journal = {American Scientist},
  urldate = {2022-04-06},
  abstract = {Is hype debasing a core chemical concept?},
  howpublished = {https://www.americanscientist.org/article/the-many-guises-of-aromaticity},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/VA6BQ3HM/the-many-guises-of-aromaticity.html}
}

@article{2023,
  title = {For Chemists, the {{AI}} Revolution Has yet to Happen},
  year = {2023},
  month = may,
  journal = {Nature},
  volume = {617},
  number = {7961},
  pages = {438--438},
  publisher = {{Nature Publishing Group}},
  doi = {10.1038/d41586-023-01612-x},
  urldate = {2023-05-22},
  abstract = {Machine-learning systems in chemistry need accurate and accessible training data. Until they get it, they won't achieve their potential.},
  copyright = {2023 Springer Nature Limited},
  langid = {english},
  keywords = {Biological techniques,Chemistry,Computational biology and bioinformatics,Drug discovery,Structural biology},
  annotation = {Bandiera\_abtest: a Cg\_type: Editorial Subject\_term: Chemistry, Structural biology, Computational biology and bioinformatics, Biological techniques, Drug discovery},
  file = {/Users/dasirianni/Zotero/storage/KJRD5TYS/2023 - For chemists, the AI revolution has yet to happen.pdf}
}

@article{adamo1999,
  title = {Toward Reliable Density Functional Methods without Adjustable Parameters: {{The PBE0}} Model},
  author = {Adamo, Carlo and Barone, Vincenzo},
  year = {1999},
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  volume = {110},
  number = {13},
  pages = {6158},
  doi = {10.1063/1.478522},
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}

@article{addison-smith2023,
  title = {Accurate {{Boundary Integral Formulations}} for the {{Calculation}} of {{Electrostatic Forces}} with an {{Implicit-Solvent Model}}},
  author = {{Addison-Smith}, Ian and Guzman, Horacio V. and Cooper, Christopher D.},
  year = {2023},
  month = may,
  journal = {J. Chem. Theory Comput.},
  volume = {19},
  number = {10},
  pages = {2996--3006},
  publisher = {{American Chemical Society}},
  issn = {1549-9618},
  doi = {10.1021/acs.jctc.3c00021},
  urldate = {2023-07-06},
  abstract = {An accurate force calculation with the Poisson\textendash Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here we present a calculation of the electric field on the solute\textendash solvent interface that is exact for piecewise linear variations of the potential and analyze four different alternatives to compute the force using a boundary element method. We performed a verification exercise for two cases: the isolated and two interacting molecules. Our results suggest that the boundary element method outperforms the finite difference method, as the latter needs a much finer mesh than in solvation energy calculations to get acceptable accuracy in the force, whereas the same surface mesh as in a standard energy calculation is appropriate for the boundary element method. Among the four evaluated alternatives of force calculation, we saw that the most accurate one is based on the Maxwell stress tensor. However, for a realistic application, like the barnase\textendash barstar complex, the approach based on variations of the energy functional, which is less accurate, gives equivalent results. This analysis is useful toward using the Poisson\textendash Boltzmann equation for force calculations in applications where high accuracy is key, for example, to feed molecular dynamics models or to enable the study of the interaction between large molecular structures, like viruses adsorbed onto substrates.},
  file = {/Users/dasirianni/Zotero/storage/A8YWWGQ5/Addison-Smith et al. - 2023 - Accurate Boundary Integral Formulations for the Ca.pdf}
}

@article{adler2007,
  title = {A Simple and Efficient {{CCSD}}({{T}})-{{F12}} Approximation},
  author = {Adler, Thomas B and Knizia, Gerald and Werner, Hans-Joachim},
  year = {2007},
  journal = {J. Chem. Phys.},
  volume = {127},
  number = {22},
  pages = {221106},
  doi = {10.1063/1.2817618},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/QIL3EB4I/J. Chem. Phys. 2007 Adler.pdf;/Users/dasirianni/Zotero/storage/QKYD8X4A/J. Chem. Phys. 2007 Adler.pdf}
}

@article{aguado2011,
  title = {Melting and {{Freezing}} of {{Metal Clusters}}},
  author = {Aguado, Andr{\'e}s and Jarrold, Martin F},
  year = {2011},
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  volume = {62},
  number = {1},
  pages = {151--172},
  doi = {10.1146/annurev-physchem-032210-103454},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/22FUD928/7C0E6FEC-EA30-4CA8-9D58-0BFD45BA4AA3.pdf;/Users/dasirianni/Zotero/storage/F8FB4H9S/7C0E6FEC-EA30-4CA8-9D58-0BFD45BA4AA3.pdf}
}

@article{ahmed2014,
  title = {Next-{{Generation Epigenetic Detection Technique}}: {{Identifying Methylated Cytosine Using Graphene Nanopore}}},
  author = {Ahmed, Towfiq and Haraldsen, Jason T and Zhu, Jian-Xin and Balatsky, Alexander V},
  year = {2014},
  month = jul,
  journal = {J. Phys. Chem. Lett.},
  pages = {2601--2607},
  doi = {10.1021/jz501085e},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/2AE7HENX/J. Phys. Chem. Lett. 2014 Ahmed.pdf;/Users/dasirianni/Zotero/storage/UI4J9X42/J. Phys. Chem. Lett. 2014 Ahmed.pdf}
}

@article{aidas2013,
  title = {The {{Dalton}} Quantum Chemistry Program System},
  author = {Aidas, Kestutis and Angeli, Celestino and Bak, Keld L and Bakken, Vebj{\o}rn and Bast, Radovan and Boman, Linus and Christiansen, Ove and Cimiraglia, Renzo and Coriani, Sonia and Dahle, P{\aa}l and Dalskov, Erik K and Ekstr{\"o}m, Ulf and Enevoldsen, Thomas and Eriksen, Janus J and Ettenhuber, Patrick and Fern{\'a}ndez, Berta and Ferrighi, Lara and Fliegl, Heike and Frediani, Luca and Hald, Kasper and Halkier, Asger and H{\"a}ttig, Christof and Heiberg, Hanne and Helgaker, Trygve and Hennum, Alf Christian and Hettema, Hinne and Hjertenaes, Eirik and H{\o}st, Stinne and H{\o}yvik, Ida-Marie and Iozzi, Maria Francesca and Jans{\'i}k, Branislav and Jensen, Hans Jo{$\not$}rgen Aa and Jonsson, Dan and J{\o}rgensen, Poul and Kauczor, Joanna and Kirpekar, Sheela and Kj{\ae}rgaard, Thomas and Klopper, Wim and Knecht, Stefan and Kobayashi, Rika and Koch, Henrik and Kongsted, Jacob and Krapp, Andreas and Kristensen, Kasper and Ligabue, Andrea and Lutnaes, Ola B and Melo, Juan I and Mikkelsen, Kurt V and Myhre, Rolf H and Neiss, Christian and Nielsen, Christian B and Norman, Patrick and Olsen, Jeppe and Olsen, J{\'o}gvan Magnus H and Osted, Anders and Packer, Martin J and Pawlowski, Filip and Pedersen, Thomas B and Provasi, Patricio F and Reine, Simen and Rinkevicius, Zilvinas and Ruden, Torgeir A and Ruud, Kenneth and Rybkin, Vladimir V and Sa{\textbackslash}lek, Pawel and Samson, Claire C M and {de Mer{\'a}s}, Alfredo S{\'a}nchez and Saue, Trond and Sauer, Stephan P A and Schimmelpfennig, Bernd and Sneskov, Kristian and Steindal, Arnfinn H and {Sylvester-Hvid}, Kristian O and Taylor, Peter R and Teale, Andrew M and Tellgren, Erik I and Tew, David P and Thorvaldsen, Andreas J and Th{\o}gersen, Lea and Vahtras, Olav and Watson, Mark A and Wilson, David J D and Ziolkowski, Marcin and {\AA}gren, Hans},
  year = {2013},
  month = sep,
  journal = {WIREs Comput. Mol. Sci.},
  volume = {4},
  number = {3},
  pages = {269--284},
  doi = {10.1002/wcms.1172},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/66ZNTJ5N/3F8F4E0B-6912-4587-B03A-2A6438F6E308.pdf}
}

@article{aikens2003,
  title = {A Derivation of the Frozen-Orbital Unrestricted Open-Shell and Restricted Closed-Shell Second-Order Perturbation Theory Analytic Gradient Expressions},
  author = {Aikens, Christine M and Webb, Simon P and Bell, Rob L and Fletcher, Graham D and Schmidt, Michael W and Gordon, Mark S},
  year = {2003},
  month = nov,
  journal = {Theor. Chem. Acc.},
  volume = {110},
  number = {4},
  pages = {233--253},
  doi = {10.1007/s00214-003-0453-3},
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}

@article{alenaizan2020,
  title = {Python Implementation of the Restrained Electrostatic Potential Charge Model},
  author = {Alenaizan, Asem and Burns, Lori A. and Sherrill, C. David},
  year = {2020},
  journal = {International Journal of Quantum Chemistry},
  volume = {120},
  number = {2},
  pages = {e26035},
  issn = {1097-461X},
  doi = {10.1002/qua.26035},
  urldate = {2022-03-09},
  abstract = {The restrained electrostatic potential (RESP) charge model is widely used in molecular dynamics simulations, especially for the AMBER and GAFF force fields. We have implemented the RESP scheme using the accessible and widely used Python language and the NumPy numerical library. This article provides a programming-oriented introduction to the RESP scheme and highlights some of the features of NumPy that are useful in scientific computing.},
  langid = {english},
  keywords = {atomic charges,NumPy,RESP,restrained electrostatic potential},
  file = {/Users/dasirianni/Zotero/storage/7X54HLSW/Alenaizan et al. - 2020 - Python implementation of the restrained electrosta.pdf;/Users/dasirianni/Zotero/storage/PRX643ZE/qua.html}
}

@article{amabilino2017,
  title = {{{DFT Analysis}} of {{Spin Crossover}} in {{Mn}}({{III}}) {{Complexes}}: {{Is}} a {{Two-Electron S}}= 2 to {{S}}= 0 {{Spin Transition Feasible}}?},
  author = {Amabilino, Silvia and Deeth, Robert J},
  year = {2017},
  month = mar,
  journal = {Inorg. Chem.},
  volume = {56},
  number = {5},
  pages = {2602--2613},
  doi = {10.1021/acs.inorgchem.6b02793},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/77MYI8DJ/C14C65A0-1C96-4A05-8AD1-8EB2013BB6F9.pdf}
}

@article{ambrosetti2014,
  title = {Long-Range Correlation Energy Calculated from Coupled Atomic Response Functions},
  author = {Ambrosetti, Alberto and Reilly, Anthony M and DiStasio Jr., Robert A and Tkatchenko, Alexandre},
  year = {2014},
  month = may,
  journal = {J. Chem. Phys.},
  volume = {140},
  number = {18},
  pages = {18A508},
  doi = {10.1063/1.4865104},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/ITEJBUZV/346AC5AA-061E-4E16-9C0A-AF8C7E8B8C37.pdf}
}

@article{ambrosetti2014a,
  title = {Hard {{Numbers}} for {{Large Molecules}}: {{Toward Exact Energetics}} for {{Supramolecular Systems}}},
  author = {Ambrosetti, Alberto and Alf{\`e}, Dario and DiStasio Jr., Robert A and Tkatchenko, Alexandre},
  year = {2014},
  month = feb,
  journal = {J. Phys. Chem. Lett.},
  volume = {5},
  number = {5},
  pages = {849--855},
  doi = {10.1021/jz402663k},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/8I7QKXM6/2512E7F9-D5F3-454B-BEDF-0AB02CC72ED7.pdf;/Users/dasirianni/Zotero/storage/WST4V96Y/2512E7F9-D5F3-454B-BEDF-0AB02CC72ED7.pdf}
}

@article{ambrosetti2014b,
  title = {Hard {{Numbers}} for {{Large Molecules}}: {{Toward Exact Energetics}} for {{Supramolecular Systems}}},
  author = {Ambrosetti, Alberto and Alf{\`e}, Dario and DiStasio Jr., Robert A and Tkatchenko, Alexandre},
  year = {2014},
  month = feb,
  journal = {J. Phys. Chem. Lett.},
  pages = {849--855},
  doi = {10.1021/jz402663k},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/8LSR2ZK5/J. Phys. Chem. Lett. 2014 Ambrosetti.pdf;/Users/dasirianni/Zotero/storage/TFKABT9J/J. Phys. Chem. Lett. 2014 Ambrosetti.pdf}
}

@article{ambrosetti2016,
  title = {Wavelike Charge Density Fluctuations and van Der {{Waals}} Interactions at the Nanoscale},
  author = {Ambrosetti, Alberto and Ferri, Nicola and DiStasio Jr., Robert A and Tkatchenko, Alexandre},
  year = {2016},
  month = mar,
  journal = {Science},
  volume = {351},
  number = {6278},
  pages = {1171--1176},
  doi = {10.1126/science.aae0509},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/K2KZYUPW/39A0D63C-66C5-4340-9FF2-7F19F7938191.pdf}
}

@article{aquilante2008,
  title = {Accurate Ab Initio Density Fitting for Multiconfigurational Self-Consistent Field Methods},
  author = {Aquilante, Francesco and Pedersen, Thomas Bondo and Lindh, Roland and Roos, Bj{\"o}rn Olof and {S{\'a}nchez de Mer{\'a}s}, Alfredo and Koch, Henrik},
  year = {2008},
  journal = {J. Chem. Phys.},
  volume = {129},
  number = {2},
  pages = {024113--8},
  doi = {10.1063/1.2953696},
  langid = {english},
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}

@article{aquilante2015,
  title = {Molcas8: {{New}} Capabilities for Multiconfigurational Quantum Chemical Calculations across the Periodic Table},
  author = {Aquilante, Francesco and Autschbach, Jochen and Carlson, Rebecca K and Chibotaru, Liviu F and Delcey, Micka{\"e}l G and De Vico, Luca and Fdez Galv{\'a}n, Ignacio and Ferr{\'e}, Nicolas and Frutos, Luis Manuel and Gagliardi, Laura and Garavelli, Marco and Giussani, Angelo and Hoyer, Chad E and Li Manni, Giovanni and Lischka, Hans and Ma, Dongxia and Malmqvist, Per {\AA}ke and M{\"u}ller, Thomas and Nenov, Artur and Olivucci, Massimo and Pedersen, Thomas Bondo and Peng, Daoling and Plasser, Felix and Pritchard, Ben and Reiher, Markus and Rivalta, Ivan and Schapiro, Igor and {Segarra-Mart{\'i}}, Javier and Stenrup, Michael and Truhlar, Donald G and Ungur, Liviu and Valentini, Alessio and Vancoillie, Steven and Veryazov, Valera and Vysotskiy, Victor P and Weingart, Oliver and Zapata, Felipe and Lindh, Roland},
  year = {2015},
  month = nov,
  journal = {J. Comput. Chem.},
  volume = {37},
  number = {5},
  pages = {506--541},
  doi = {10.1002/jcc.24221},
  abstract = {In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin...},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/EGZ5PIIT/1392F397-BB31-46CE-A86C-95264CC6DF61.pdf;/Users/dasirianni/Zotero/storage/QJUMTNJ2/1392F397-BB31-46CE-A86C-95264CC6DF61.pdf}
}

@article{arun1987,
  title = {Least-{{Squares Fitting}} of {{Two}} 3-{{D Point Sets}}},
  author = {Arun, K S and Huang, T S and Blostein, S D},
  year = {1987},
  journal = {IEEE Trans. Pattern Anal. Machine Intell.},
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  abstract = {Two points sets p\_i and p'\_i; i=1, 2, ..., N, are related by p'\_i = Rp\_i + T + N\_i, where R is a rotation matrix, T a translation vector, and N\_i a noise vector. Given p\_i and p'\_i, we present an algorithm for finding the least-squares solution of R and T, which is based on the singular value decomposition of a 3x3 matrix. This new algorithm is compared to two earlier algorithms with respect to computer time requirements.},
  file = {/Users/dasirianni/Zotero/storage/L68AGE9F/F5590AD7-56C8-47E8-B0F6-0C00B6E7F6C8.pdf}
}

@article{ashley2017,
  title = {Ironing out the Photochemical and Spin-Crossover Behavior of {{Fe}}({{II}}) Coordination Compounds with Computational Chemistry},
  author = {Ashley, Daniel C and Jakubikova, Elena},
  year = {2017},
  month = apr,
  journal = {Coordination Chemistry Reviews},
  volume = {337},
  pages = {97--111},
  publisher = {{Elsevier B.V.}},
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  abstract = {Coordination Chemistry Reviews, 337 (2017) 97-111. doi:10.1016/j.ccr.2017.02.005},
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}

@book{attig2004,
  title = {Computational {{Soft Matter}}: From {{Synthetic Polymers}} to {{Proteins}}: {{Lecture}} Notes. ...},
  author = {Attig, N},
  year = {2004},
  series = {{{NIC}} Series},
  publisher = {{NIC}},
  isbn = {978-3-00-012641-3}
}

@article{babin2014,
  title = {Development of a ``{{First Principles}}'' {{Water Potential}} with {{Flexible Monomers}}. {{II}}: {{Trimer Potential Energy Surface}}, {{Third Virial Coefficient}}, and {{Small Clusters}}},
  author = {Babin, Volodymyr and Medders, Gregory R and Paesani, Francesco},
  year = {2014},
  month = mar,
  journal = {J. Chem. Theory Comput.},
  pages = {140321071122009},
  doi = {10.1021/ct500079y},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/ACX5NJ2Z/J. Chem. Theory Comput. 2014 Babin.pdf;/Users/dasirianni/Zotero/storage/BJPHDWQB/J. Chem. Theory Comput. 2014 Babin.pdf}
}

@article{bakr2013,
  title = {Highly Accurate Potential Energy Surface for the {{He-H2}} Dimer},
  author = {Bakr, Brandon W and Smith, Daniel G A and Patkowski, Konrad},
  year = {2013},
  journal = {J. Chem. Phys.},
  volume = {139},
  number = {14},
  pages = {144305},
  doi = {10.1063/1.4824299},
  langid = {english},
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}

@article{barber2021,
  title = {Chemistry of {{Functionalized Reactive Organic Intermediates}} in the {{Earth}}'s {{Atmosphere}}: {{Impact}}, {{Challenges}}, and {{Progress}}},
  shorttitle = {Chemistry of {{Functionalized Reactive Organic Intermediates}} in the {{Earth}}'s {{Atmosphere}}},
  author = {Barber, Victoria P. and Kroll, Jesse H.},
  year = {2021},
  month = dec,
  journal = {J. Phys. Chem. A},
  volume = {125},
  number = {48},
  pages = {10264--10279},
  publisher = {{American Chemical Society}},
  issn = {1089-5639},
  doi = {10.1021/acs.jpca.1c08221},
  urldate = {2023-06-29},
  abstract = {The gas-phase oxidation of organic compounds is an important chemical process in the Earth's atmosphere. It governs oxidant levels and controls the production of key secondary pollutants, and hence has major implications for air quality and climate. Organic oxidation is largely controlled by the chemistry of a few reactive intermediates, namely, alkyl (R) radicals, alkoxy (RO) radicals, peroxy (RO2) radicals, and carbonyl oxides (R1R2COO), which may undergo a number of unimolecular and bimolecular reactions. Our understanding of these intermediates, and the reaction pathways available to them, is based largely on studies of unfunctionalized intermediates, formed in the first steps of hydrocarbon oxidation. However, it has become increasingly clear that intermediates with functional groups, which are generally formed later in the oxidation process, can exhibit fundamentally different reactivity than unfunctionalized ones. In this Perspective, we explore the unique chemistry available to functionalized organic intermediates in the Earth's atmosphere. After a brief review of the canonical chemistry available to unfunctionalized intermediates, we discuss how the addition of functional groups can introduce new reactions, either by changing the energetics or kinetics of a given reaction or by opening up new chemical pathways. We then provide examples of atmospheric reaction classes that are available only to functionalized intermediates. Some of these, such as unimolecular H-shift reactions of RO2 radicals, have been elucidated only relatively recently, and can have important impacts on atmospheric chemistry (e.g., on radical cycling or organic aerosol formation); it seems likely that other, as-yet undiscovered reactions of (multi)functional intermediates may also exist. We discuss the challenges associated with the study of the chemistry of such intermediates and review novel experimental and theoretical approaches that have recently provided (or hold promise for providing) new insights into their atmospheric chemistry. The continued use and development of such techniques and the close collaboration between experimentalists and theoreticians are necessary for a complete, detailed understanding of the chemistry of functionalized intermediates and their impact on major atmospheric chemical processes.}
}

@article{barber2021a,
  title = {Chemistry of {{Functionalized Reactive Organic Intermediates}} in the {{Earth}}'s {{Atmosphere}}: {{Impact}}, {{Challenges}}, and {{Progress}}},
  shorttitle = {Chemistry of {{Functionalized Reactive Organic Intermediates}} in the {{Earth}}'s {{Atmosphere}}},
  author = {Barber, Victoria P. and Kroll, Jesse H.},
  year = {2021},
  month = dec,
  journal = {J. Phys. Chem. A},
  volume = {125},
  number = {48},
  pages = {10264--10279},
  issn = {1089-5639, 1520-5215},
  doi = {10.1021/acs.jpca.1c08221},
  urldate = {2023-06-29},
  abstract = {The gas-phase oxidation of organic compounds is an important chemical process in the Earth's atmosphere. It governs oxidant levels and controls the production of key secondary pollutants, and hence has major implications for air quality and climate. Organic oxidation is largely controlled by the chemistry of a few reactive intermediates, namely, alkyl (R) radicals, alkoxy (RO) radicals, peroxy (RO2) radicals, and carbonyl oxides (R1R2COO), which may undergo a number of unimolecular and bimolecular reactions. Our understanding of these intermediates, and the reaction pathways available to them, is based largely on studies of unfunctionalized intermediates, formed in the first steps of hydrocarbon oxidation. However, it has become increasingly clear that intermediates with functional groups, which are generally formed later in the oxidation process, can exhibit fundamentally different reactivity than unfunctionalized ones. In this Perspective, we explore the unique chemistry available to functionalized organic intermediates in the Earth's atmosphere. After a brief review of the canonical chemistry available to unfunctionalized intermediates, we discuss how the addition of functional groups can introduce new reactions, either by changing the energetics or kinetics of a given reaction or by opening up new chemical pathways. We then provide examples of atmospheric reaction classes that are available only to functionalized intermediates. Some of these, such as unimolecular H-shift reactions of RO2 radicals, have been elucidated only relatively recently, and can have important impacts on atmospheric chemistry (e.g., on radical cycling or organic aerosol formation); it seems likely that other, as-yet undiscovered reactions of (multi)functional intermediates may also exist. We discuss the challenges associated with the study of the chemistry of such intermediates and review novel experimental and theoretical approaches that have recently provided (or hold promise for providing) new insights into their atmospheric chemistry. The continued use and development of such techniques and the close collaboration between experimentalists and theoreticians are necessary for a complete, detailed understanding of the chemistry of functionalized intermediates and their impact on major atmospheric chemical processes.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/VR9EV7E4/Barber and Kroll - 2021 - Chemistry of Functionalized Reactive Organic Inter.pdf}
}

@article{barnes2013,
  title = {Accurate Basis Set Truncation for Wavefunction Embedding},
  author = {Barnes, Taylor A and Goodpaster, Jason D and Manby, Frederick R and Miller III, Thomas F},
  year = {2013},
  month = jul,
  journal = {J. Chem. Phys.},
  volume = {139},
  number = {2},
  pages = {024103--12},
  doi = {10.1063/1.4811112},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/RJAKS95T/5CC7A41C-A09D-48EF-AAD5-E847F72B93EC.pdf}
}

@article{barone2023,
  title = {Reliable {{Gas Phase Reaction Rates}} at {{Affordable Cost}} by {{Means}} of the {{Parameter-Free JunChS-F12 Model Chemistry}}},
  author = {Barone, Vincenzo and Lupi, Jacopo and Salta, Zoi and Tasinato, Nicola},
  year = {2023},
  month = jun,
  journal = {J. Chem. Theory Comput.},
  volume = {19},
  number = {12},
  pages = {3526--3537},
  publisher = {{American Chemical Society}},
  issn = {1549-9618},
  doi = {10.1021/acs.jctc.3c00343},
  urldate = {2023-06-28},
  abstract = {A recently developed strategy for the computation at affordable cost of reliable barrier heights ruling reactions in the gas phase (junChS, [Barone, V.; J. Chem. Theory Comput. 2021, 17, 4913-4928]) has been extended to the employment of explicitly correlated (F12) methods. A thorough benchmark based on a wide range of prototypical reactions shows that the new model (referred to as junChS-F12), which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries, has an improved performance with respect to its conventional counterpart and outperforms the most well-known model chemistries without the need of any empirical parameter and at an affordable computational cost. Several benchmarks show that revDSD-PBEP86-D3(BJ) structures and force fields provide zero point energies and thermal contributions, which can be confidently used, together with junChS-F12 electronic energies, for obtaining accurate reaction rates in the framework of the master equation approach based on the ab initio transition-state theory.}
}

@article{bartolomei2013,
  title = {Global {{Potentials}} for the {{Interaction Between Rare Gases}} and {{Graphene-based Surfaces}}: {{An Atom-bond Pairwise Additive Representation}}},
  author = {Bartolomei, Massimiliano and {Carmona-Novillo}, E and Pirani, Fernando and Hernandez, Marta I and {Campos-Martinez}, Jose},
  year = {2013},
  journal = {J. Supercrit. Fluids.},
  volume = {117},
  number = {117},
  pages = {10512--10522},
  doi = {10.1021/jp401635t},
  abstract = {Global potentials for the physisorption of rare- gas atoms on graphene and graphite, amenable for a variety of dynamics simulations, are reported. An atom\textbackslash textminusbond pairwise additive form of the potential is used, where the interaction pairs, represented by proper analytical functions, are constituted by the Rg atom (Rg = He, Ne, Ar, Kr) and the C\textbackslash textminusC bonds of the graphene sheet(s). The parameters of the atom\textbackslash textminusbond pair potential, derived from the polarizability of the interacting partners, are fine-tuned, exploiting calculations of the prototypical Rg\textbackslash textminuscoronene system using high-level electronic structure methods and large basis sets. The atom\textbackslash textminusgraphene/graphite potential is further expanded in a Fourier series, and it is found that for an accurate representation of the interaction only a small number of corrugation terms need to be added to the laterally averaged potential. Furthermore, this corrugation part of the potential is both identical for Rg\textbackslash textminusgraphene and Rg\textbackslash textminus graphite; in other words, inner layers of graphite only play a role in the laterally averaged Rg\textbackslash textminusgraphite potential. For all systems, the hollow at the center of the carbon ring is the preferred adsorption site, although diffusion barriers are low. The present results compare well with previous data regarding well depths and equilibrium distances at different adsorption sites and, for graphite, the long-range dispersion coefficient C3. In addition, binding energies (eigenvalues of the laterally averaged potentials) are in a fairly good agreement with experimental determinations, providing further support for the reliability of the potentials.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/E6ZYPAD4/J. Phys. Chem. C 2013 Bartolomei.pdf;/Users/dasirianni/Zotero/storage/HH2L4YEG/J. Phys. Chem. C 2013 Bartolomei.pdf}
}

@article{bayly1993,
  title = {A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The {{RESP}} Model},
  shorttitle = {A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges},
  author = {Bayly, Christopher I. and Cieplak, Piotr and Cornell, Wendy and Kollman, Peter A.},
  year = {1993},
  month = oct,
  journal = {J. Phys. Chem.},
  volume = {97},
  number = {40},
  pages = {10269--10280},
  issn = {0022-3654, 1541-5740},
  doi = {10.1021/j100142a004},
  urldate = {2022-03-09},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/5T3S6B3N/Bayly et al. - A well-behaved electrostatic potential based metho.pdf}
}

@article{becke1988,
  title = {Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior},
  author = {Becke, A D},
  year = {1988},
  journal = {Phys. Rev. A.},
  volume = {38},
  number = {6},
  pages = {3098--3100},
  doi = {10.1103/PhysRevA.38.3098},
  abstract = {Current gradient-corrected density-functional approximations for the exchange energies of atom- ic and molecular systems fail to reproduce the correct 1/r asymptotic behavior of the exchange- energy density. Here we report a gradient-corrected exchange-energy functional with the proper asymptotic limit. Our functional, containing only one parameter, fits the exact Hartree-Fock ex- change energies of a wide variety of atomic systems with remarkable accuracy, surpassing the per- formance of previous functionals containing two parameters or more},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/NWNVNPE9/1988 Becke.pdf;/Users/dasirianni/Zotero/storage/WLBQCKBQ/1988 Becke.pdf}
}

@article{becke1993,
  title = {Density-Functional Thermochemistry. {{III}}. {{The}} Role of Exact Exchange},
  author = {Becke, Axel D},
  year = {1993},
  journal = {J. Chem. Phys.},
  volume = {98},
  number = {7},
  pages = {5648},
  doi = {10.1063/1.464913},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/VD2Q38SF/J. Chem. Phys. 1993 Becke.pdf;/Users/dasirianni/Zotero/storage/ZNY6TZH6/J. Chem. Phys. 1993 Becke.pdf}
}

@article{becke1997,
  title = {Density-Functional Thermochemistry. {{V}}. {{Systematic}} Optimization of Exchange-Correlation Functionals},
  author = {Becke, Axel D},
  year = {1997},
  journal = {J. Chem. Phys.},
  volume = {107},
  number = {20},
  pages = {8554--8560},
  doi = {10.1063/1.475007},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/SMBPT4CN/J. Chem. Phys. 1997 Becke.pdf;/Users/dasirianni/Zotero/storage/STSD7L2Y/J. Chem. Phys. 1997 Becke.pdf}
}

@article{becke2005,
  title = {Exchange-Hole Dipole Moment and the Dispersion Interaction},
  author = {Becke, Axel D and Johnson, Erin R},
  year = {2005},
  journal = {J. Chem. Phys.},
  volume = {122},
  number = {15},
  pages = {154104},
  doi = {10.1063/1.1884601},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/G5V4UYML/J. Chem. Phys. 2005 Becke.pdf;/Users/dasirianni/Zotero/storage/MN35B7WK/J. Chem. Phys. 2005 Becke.pdf}
}

@article{becke2007,
  title = {A Unified Density-Functional Treatment of Dynamical, Nondynamical, and Dispersion Correlations},
  author = {Becke, Axel D and Johnson, Erin R},
  year = {2007},
  journal = {J. Chem. Phys.},
  volume = {127},
  number = {12},
  pages = {124108},
  doi = {10.1063/1.2768530},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/BM6G77LN/J. Chem. Phys. 2007 Becke.pdf;/Users/dasirianni/Zotero/storage/XLDXP7JR/J. Chem. Phys. 2007 Becke.pdf}
}

@article{behn2011,
  title = {Efficient Exploration of Reaction Paths via a Freezing String Method},
  author = {Behn, Andrew and Zimmerman, Paul M and Bell, Alexis T and {Head-Gordon}, Martin},
  year = {2011},
  journal = {J. Chem. Phys.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/GDYVF59C/Behn et al. - 2011 - Efﬁcient exploration of reaction paths via a freez.pdf}
}

@article{bennie2015,
  title = {Accelerating Wavefunction in Density-Functional-Theory Embedding by Truncating the Active Basis Set},
  author = {Bennie, Simon J and Stella, Martina and Miller III, Thomas F and Manby, Frederick R},
  year = {2015},
  month = jul,
  journal = {J. Chem. Phys.},
  volume = {143},
  number = {2},
  pages = {024105--8},
  doi = {10.1063/1.4923367},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/MABJGYDD/CD98041B-0F1F-4060-83E5-C0E0343D861A.pdf}
}

@article{bernard2012,
  title = {General Formulation of Spin-Flip Time-Dependent Density Functional Theory Using Non-Collinear Kernels: {{Theory}}, Implementation, and Benchmarks},
  shorttitle = {General Formulation of Spin-Flip Time-Dependent Density Functional Theory Using Non-Collinear Kernels},
  author = {Bernard, Yves A. and Shao, Yihan and Krylov, Anna I.},
  year = {2012},
  month = may,
  journal = {J. Chem. Phys.},
  volume = {136},
  number = {20},
  pages = {204103},
  publisher = {{American Institute of Physics}},
  issn = {0021-9606},
  doi = {10.1063/1.4714499},
  urldate = {2022-03-28},
  abstract = {We report an implementation of the spin-flip (SF) variant of time-dependent density functional theory (TD-DFT) within the Tamm-Dancoff approximation and non-collinear (NC) formalism for local, generalized gradient approximation, hybrid, and range-separated functionals. The performance of different functionals is evaluated by extensive benchmark calculations of energy gaps in a variety of diradicals and open-shell atoms. The benchmark set consists of 41 energy gaps. A consistently good performance is observed for the Perdew-Burke-Ernzerhof (PBE) family, in particular PBE0 and PBE50, which yield mean average deviations of 0.126 and 0.090 eV, respectively. In most cases, the performance of original (collinear) SF-TDDFT with 50-50 functional is also satisfactory (as compared to non-collinear variants), except for the same-center diradicals where both collinear and non-collinear SF variants that use LYP or B97 exhibit large errors. The accuracy of NC-SF-TDDFT and collinear SF-TDDFT with 50-50 and BHHLYP is very similar. Using PBE50 within collinear formalism does not improve the accuracy.},
  file = {/Users/dasirianni/Zotero/storage/AJXDH4EZ/suppl.pdf;/Users/dasirianni/Zotero/storage/UCAPY229/Bernard et al. - 2012 - General formulation of spin-flip time-dependent de.pdf}
}

@article{besnard2008,
  title = {Raman Spectroscopy and Ab Initio Investigations of Transient Complex Formation in {{CO}}[Sub 2]-Benzene Mixtures},
  author = {Besnard, M and Caba{\c c}o, M Isabel and Talaga, D and Danten, Y},
  year = {2008},
  journal = {J. Chem. Phys.},
  volume = {129},
  number = {22},
  pages = {224511},
  doi = {10.1063/1.3037025},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/5X5489KY/J. Chem. Phys. 2008 Besnard.pdf}
}

@article{bhattacharya2018,
  title = {Photochemical {{Activation}} of {{Enediyne Warheads}}: {{A Potential Tool}} for {{Targeted Antitumor Therapy}}},
  shorttitle = {Photochemical {{Activation}} of {{Enediyne Warheads}}},
  author = {Bhattacharya, Prabuddha and Basak, Amit and Campbell, Adam and Alabugin, Igor V.},
  year = {2018},
  month = mar,
  journal = {Mol. Pharmaceutics},
  volume = {15},
  number = {3},
  pages = {768--797},
  issn = {1543-8384, 1543-8392},
  doi = {10.1021/acs.molpharmaceut.7b00911},
  urldate = {2022-02-21},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/5LBIXIPB/Bhattacharya et al. - 2018 - Photochemical Activation of Enediyne Warheads A P.pdf}
}

@article{binkley1974,
  title = {The Calculation of Spin-Restricted Single-Determinant Wavefunctions},
  author = {Binkley, J S and Pople, John A},
  year = {1974},
  journal = {Mol. Phys.},
  volume = {28},
  number = {6},
  pages = {1423},
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}

@article{bizzarro2019,
  title = {Nature of {{Halide}}\textendash{{Water Interactions}}: {{Insights}} from {{Many-Body Representations}} and {{Density Functional Theory}}},
  author = {Bizzarro, Brandon B and Egan, Colin K and {ORCID: 0000-0002-4451-1203}, Francesco Paesani},
  year = {2019},
  month = mar,
  journal = {J. Chem. Theory Comput.},
  pages = {1--13},
  publisher = {{American Chemical Society}},
  doi = {10.1021/acs.jctc.9b00064},
  file = {/Users/dasirianni/Zotero/storage/BZKX279T/E8CACE0A-5469-4A12-9B6E-6C01B0B528B1.pdf}
}

@article{blazhynska2023,
  title = {Improving {{Speed}} and {{Affordability}} without {{Compromising Accuracy}}: {{Standard Binding Free-Energy Calculations Using}} an {{Enhanced Sampling Algorithm}}, {{Multiple-Time Stepping}}, and {{Hydrogen Mass Repartitioning}}},
  shorttitle = {Improving {{Speed}} and {{Affordability}} without {{Compromising Accuracy}}},
  author = {Blazhynska, Marharyta and {Goulard Coderc de Lacam}, Emma and Chen, Haochuan and Chipot, Christophe},
  year = {2023},
  month = may,
  journal = {J. Chem. Theory Comput.},
  publisher = {{American Chemical Society}},
  issn = {1549-9618},
  doi = {10.1021/acs.jctc.3c00141},
  urldate = {2023-05-22},
  abstract = {Accurate evaluation of protein\textendash ligand binding free energies in silico is of paramount importance for understanding the mechanisms of biological regulation and providing a theoretical basis for drug design and discovery. Based on a series of atomistic molecular dynamics simulations in an explicit solvent, using well-tempered metadynamics extended adaptive biasing force (WTM-eABF) as an enhanced sampling algorithm, the so-called ``geometrical route'' offers a rigorous theoretical framework for binding affinity calculations that match experimental values. However, although robust, this strategy remains expensive, requiring substantial computational time to achieve convergence of the simulations. Improving the efficiency of the geometrical route, while preserving its reliability through improved ergodic sampling, is, therefore, highly desirable. In this contribution, having identified the computational bottleneck of the geometrical route, to accelerate the calculations we combine (i) a longer time step for the integration of the equations of motion with hydrogen-mass repartitioning (HMR), and (ii) multiple time-stepping (MTS) for collective-variable and biasing-force evaluation. Altogether, we performed 50 independent WTM-eABF simulations in triplicate for the ``physical'' separation of the Abl kinase-SH3 domain:p41 complex, following different HMR and MTS schemes, while tuning, in distinct protocols, the parameters of the enhanced-sampling algorithm. To demonstrate the consistency and reliability of the results obtained with the best-performing setups, we carried out quintuple simulations. Furthermore, we demonstrated the transferability of our method to other complexes by triplicating a 200 ns separation simulation of nine chosen protocols for the MDM2-p53:NVP-CGM097 complex. [Holzer et al. J. Med. Chem. 2015, 58, 6348-6358.] Our results, based on an aggregate simulation time of 14.4 {$\mu$}s, allowed an optimal set of parameters to be identified, able to accelerate convergence by a factor of three without any noticeable loss of accuracy.}
}

@article{blazhynska2023a,
  title = {Improving {{Speed}} and {{Affordability}} without {{Compromising Accuracy}}: {{Standard Binding Free-Energy Calculations Using}} an {{Enhanced Sampling Algorithm}}, {{Multiple-Time Stepping}}, and {{Hydrogen Mass Repartitioning}}},
  shorttitle = {Improving {{Speed}} and {{Affordability}} without {{Compromising Accuracy}}},
  author = {Blazhynska, Marharyta and Goulard Coderc De Lacam, Emma and Chen, Haochuan and Chipot, Christophe},
  year = {2023},
  month = may,
  journal = {J. Chem. Theory Comput.},
  pages = {acs.jctc.3c00141},
  issn = {1549-9618, 1549-9626},
  doi = {10.1021/acs.jctc.3c00141},
  urldate = {2023-05-22},
  abstract = {Accurate evaluation of protein-ligand binding free energies in silico is of paramount importance for understanding the mechanisms of biological regulation and providing a theoretical basis for drug design and discovery. Based on a series of atomistic molecular dynamics simulations in an explicit solvent, using well-tempered metadynamics extended adaptive biasing force (WTMeABF) as an enhanced sampling algorithm, the so-called ``geometrical route'' offers a rigorous theoretical framework for binding affinity calculations that match experimental values. However, although robust, this strategy remains expensive, requiring substantial computational time to achieve convergence of the simulations. Improving the efficiency of the geometrical route, while preserving its reliability through improved ergodic sampling, is, therefore, highly desirable. In this contribution, having identified the computational bottleneck of the geometrical route, to accelerate the calculations we combine (i) a longer time step for the integration of the equations of motion with hydrogen-mass repartitioning (HMR), and (ii) multiple time-stepping (MTS) for collective-variable and biasing-force evaluation. Altogether, we performed 50 independent WTM-eABF simulations in triplicate for the ``physical'' separation of the Abl kinase-SH3 domain:p41 complex, following different HMR and MTS schemes, while tuning, in distinct protocols, the parameters of the enhanced-sampling algorithm. To demonstrate the consistency and reliability of the results obtained with the best-performing setups, we carried out quintuple simulations. Furthermore, we demonstrated the transferability of our method to other complexes by triplicating a 200 ns separation simulation of nine chosen protocols for the MDM2-p53:NVP-CGM097 complex. [Holzer et al. J. Med. Chem. 2015, 58, 6348-6358.] Our results, based on an aggregate simulation time of 14.4 {$\mu$}s, allowed an optimal set of parameters to be identified, able to accelerate convergence by a factor of three without any noticeable loss of accuracy.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/QDV5MX9S/Blazhynska et al. - 2023 - Improving Speed and Affordability without Compromi.pdf}
}

@article{bochevarov2013,
  title = {Jaguar: {{A}} High-Performance Quantum Chemistry Software Program with Strengths in Life and Materials Sciences},
  author = {Bochevarov, Art D and Harder, Edward and Hughes, Thomas F and Greenwood, Jeremy R and Braden, Dale A and Philipp, Dean M and Rinaldo, David and Halls, Mathew D and Zhang, Jing and Friesner, Richard A},
  year = {2013},
  month = jul,
  journal = {Int. J. Quantum Chem.},
  volume = {113},
  number = {18},
  pages = {2110--2142},
  doi = {10.1002/qua.24481},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/K4J6MMR9/6F6CB6C3-D993-400D-90A3-87D524676DE3.pdf}
}

@article{boese2011,
  title = {Effects of Counterpoise Correction and Basis Set Extrapolation on the {{MP2}} Geometries of Hydrogen Bonded Dimers of Ammonia, Water, and Hydrogen Fluoride},
  author = {Boese, A Daniel and Jansen, Georg and Torheyden, Martin and H{\"o}fener, Sebastian and Klopper, Wim},
  year = {2011},
  journal = {Phys. Chem. Chem. Phys.},
  volume = {13},
  number = {3},
  pages = {1230--1238},
  doi = {10.1039/C0CP01493A},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/5K4YH36S/E192505A-2F7D-4E97-9BBE-7C11AA63A174.pdf}
}

@article{boese2015,
  title = {Basis Set Limit Coupled-Cluster Studies of Hydrogen-Bonded Systems},
  author = {Boese, A Daniel},
  year = {2015},
  month = mar,
  journal = {Mol. Phys.},
  volume = {113},
  number = {13-14},
  pages = {1618--1629},
  doi = {10.1080/00268976.2014.1001806},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/A5DFCKIQ/12476A22-05C4-4E1C-8677-045004714D29.pdf}
}

@article{borca2019,
  title = {{{CrystaLattE}}: {{Automated}} Computation of Lattice Energies of Organic Crystals Exploiting the Many-Body Expansion to Achieve Dual-Level Parallelism},
  author = {Borca, Carlos H and Bakr, Brandon W and Burns, Lori A and Sherrill, C David},
  year = {2019},
  month = oct,
  journal = {J. Chem. Phys.},
  pages = {144103},
  publisher = {{AIP Publishing, LLC}},
  doi = {10.1063/1.5120520},
  abstract = {J. Chem. Phys. 2019.151:144103},
  file = {/Users/dasirianni/Zotero/storage/8QAU5FCC/B7A144C0-AE3B-4E57-B343-8F2D3DFF7759.pdf}
}

@article{borca2023,
  title = {Benchmark Coupled-Cluster Lattice Energy of Crystalline Benzene and Assessment of Multi-Level Approximations in the Many-Body Expansion},
  author = {Borca, Carlos H. and Glick, Zachary L. and Metcalf, Derek P. and Burns, Lori A. and Sherrill, C. David},
  year = {2023},
  month = jun,
  journal = {The Journal of Chemical Physics},
  volume = {158},
  number = {23},
  pages = {234102},
  issn = {0021-9606, 1089-7690},
  doi = {10.1063/5.0159410},
  urldate = {2023-06-16},
  abstract = {The many-body expansion (MBE) is promising for the efficient, parallel computation of lattice energies in organic crystals. Very high accuracy should be achievable by employing coupled-cluster singles, doubles, and perturbative triples at the complete basis set limit [CCSD(T)/CBS] for the dimers, trimers, and potentially tetramers resulting from the MBE, but such a brute-force approach seems impractical for crystals of all but the smallest molecules. Here, we investigate hybrid or multi-level approaches that employ CCSD(T)/CBS only for the closest dimers and trimers and utilize much faster methods like M\o ller\textendash Plesset perturbation theory (MP2) for more distant dimers and trimers. For trimers, MP2 is supplemented with the Axilrod\textendash Teller\textendash Muto (ATM) model of three-body dispersion. MP2(+ATM) is shown to be a very effective replacement for CCSD(T)/CBS for all but the closest dimers and trimers. A limited investigation of tetramers using CCSD(T)/CBS suggests that the four-body contribution is entirely negligible. The large set of CCSD(T)/CBS dimer and trimer data should be valuable in benchmarking approximate methods for molecular crystals and allows us to see that a literature estimate of the core-valence contribution of the closest dimers to the lattice energy using just MP2 was overbinding by 0.5 kJ mol-1, and an estimate of the three-body contribution from the closest trimers using the T0 approximation in local CCSD(T) was underbinding by 0.7 kJ mol-1. Our CCSD(T)/CBS best estimate of the 0 K lattice energy is -54.01 kJ mol-1, compared to an estimated experimental value of -55.3 {$\pm$} 2.2 kJ mol-1.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/UM8HXXHB/Borca et al. - 2023 - Benchmark coupled-cluster lattice energy of crysta.pdf}
}

@incollection{borden2015,
  title = {Diradicals \textendash{} {{A Fifty Year Fascination}}},
  booktitle = {{{ACS Symposium Series}}},
  author = {Borden, Weston Thatcher},
  editor = {Strom, E. Thomas and Mainz, Vera V.},
  year = {2015},
  month = jan,
  volume = {1209},
  pages = {251--303},
  publisher = {{American Chemical Society}},
  address = {{Washington, DC}},
  doi = {10.1021/bk-2015-1209.ch011},
  urldate = {2022-07-10},
  isbn = {978-0-8412-3071-2 978-0-8412-3072-9},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/SHZRBJ7J/Borden - 2015 - Diradicals – A Fifty Year Fascination.pdf}
}

@article{borden2017,
  title = {Dioxygen: {{What Makes This Triplet Diradical Kinetically Persistent}}?},
  shorttitle = {Dioxygen},
  author = {Borden, Weston Thatcher and Hoffmann, Roald and Stuyver, Thijs and Chen, Bo},
  year = {2017},
  month = jul,
  journal = {J. Am. Chem. Soc.},
  volume = {139},
  number = {26},
  pages = {9010--9018},
  publisher = {{American Chemical Society}},
  issn = {0002-7863},
  doi = {10.1021/jacs.7b04232},
  urldate = {2023-06-16},
  abstract = {Experimental heats of formation and enthalpies obtained from G4 calculations both find that the resonance stabilization of the two unpaired electrons in triplet O2, relative to the unpaired electrons in two hydroxyl radicals, amounts to 100 kcal/mol. The origin of this huge stabilization energy is described within the contexts of both molecular orbital (MO) and valence-bond (VB) theory. Although O2 is a triplet diradical, the thermodynamic unfavorability of both its hydrogen atom abstraction and oligomerization reactions can be attributed to its very large resonance stabilization energy. The unreactivity of O2 toward both these modes of self-destruction maintains its abundance in the ecosphere and thus its availability to support aerobic life. However, despite the resonance stabilization of the {$\pi$} system of triplet O2, the weakness of the O\textendash O {$\sigma$} bond makes reactions of O2, which eventually lead to cleavage of this bond, very favorable thermodynamically.},
  file = {/Users/dasirianni/Zotero/storage/7JMMD6AN/Borden et al. - 2017 - Dioxygen What Makes This Triplet Diradical Kineti.pdf}
}

@article{borden2017a,
  title = {Dioxygen: {{What Makes This Triplet Diradical Kinetically Persistent}}?},
  author = {Borden, Weston Thatcher and Hoffmann, Roald and Stuyver, Thijs and Chen, Bo},
  year = {2017},
  journal = {J. Am. Chem. Soc.},
  abstract = {Experimental heats of formation and enthalpies obtained from G4 calculations both find that the resonance stabilization of the two unpaired electrons in triplet O2, relative to the unpaired electrons in two hydroxyl radicals, amounts to 100 kcal/mol. The origin of this huge stabilization energy is described within the contexts of both molecular orbital (MO) and valence-bond (VB) theory. Although O2 is a triplet diradical, the thermodynamic unfavorability of both its hydrogen atom abstraction and oligomerization reactions can be attributed to its very large resonance stabilization energy. The unreactivity of O2 toward both these modes of self-destruction maintains its abundance in the ecosphere and thus its availability to support aerobic life. However, despite the resonance stabilization of the {$\pi$} system of triplet O2, the weakness of the O-O {$\sigma$} bond makes reactions of O2, which eventually lead to cleavage of this bond, very favorable thermodynamically.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/U5F6F8XH/Borden et al. - 2017 - Dioxygen What Makes This Triplet Diradical Kineti.pdf}
}

@article{born1927,
  title = {{Zur Quantentheorie der Molekeln}},
  author = {Born, M and Oppenheimer, R},
  year = {1927},
  journal = {Annalen der Physik},
  volume = {389},
  number = {20},
  pages = {457--484},
  publisher = {{John Wiley \& Sons, Ltd}},
  doi = {10.1002/andp.19273892002},
  abstract = {Click on the article title to read more.},
  langid = {german},
  file = {/Users/dasirianni/Zotero/storage/8SQMYIQE/4BFC35C0-01FF-47AC-8D5F-D4CEC0EE1178.pdf;/Users/dasirianni/Zotero/storage/LKXPNUK6/4BFC35C0-01FF-47AC-8D5F-D4CEC0EE1178.pdf}
}

@article{bousseksou1993,
  title = {Two-{{Level Models}} for the {{Two-Step Spin Crossovers}}},
  author = {Bousseksou, A and Nasser, J and Linares, J and Boukheddaden, K and Varret, F},
  year = {1993},
  journal = {Molecular Crystals and Liquid Crystals Science and Technology. Section A. Molecular Crystals and Liquid Crystals},
  volume = {234},
  number = {1},
  pages = {269--274},
  doi = {10.1080/10587259308042926},
  langid = {english}
}

@article{bousseksou1995,
  title = {A {{Simple Ising-Like Model}} for {{Spin Conversion Including Molecular Vibrations}}},
  author = {Bousseksou, A and {Constant-Machado}, H and Varret, F},
  year = {1995},
  journal = {Journal de Physique I},
  volume = {5},
  number = {6},
  pages = {747--760},
  doi = {10.1051/jp1:1995165>},
  abstract = {An Ising-type model for spin conversion, explicitly accounting for intramolecular vibrations has been studied. Each two level system is associated with p harmonic oscillators having two possible frequencies w\_LS, w\_HS. The major advantage of this model is that it provides an excellent agreement with both the conversion curve and calorimetric data, in particular the entropy change upon spin conversion. With the help of Arrhenius plots, the predictions of the model are accurately compared to the literature experimental data on the spin equilibrium curves. A very accurate M\"ossbauer investigation by Jacobi, Spiering and G\"utlich, provides evidence for a small effect typical for vibrations. A novel example is given where the conversion curve is essentially monitored by vibrations; this originates from the extremely small value of the energy gap between HS and LS electrovibrational groundstates. However, in most cases, as a first approach, the low freqeuncy approximation of the model can be used. Then the model reduces to a simple two-level model with additional degeneracies implicitely accounting for intramolecular vibrations.},
  file = {/Users/dasirianni/Zotero/storage/9TT6IKY9/C114E8E3-0A03-4FE8-B71E-13DB720FED42.pdf}
}

@article{boys1970,
  title = {The Calculation of Small Molecular Interactions by the Differences of Separate Total Energies. {{Some}} Procedures with Reduced Errors},
  author = {Boys, S F and Bernardi, F},
  year = {1970},
  journal = {Mol. Phys.},
  volume = {19},
  number = {4},
  pages = {553--566},
  doi = {10.1080/00268977000101561},
  langid = {english}
}

@article{braess2005,
  title = {Approximation of 1/x by Exponential Sums in [1, )},
  author = {Braess, D},
  year = {2005},
  month = feb,
  journal = {IMA Journal of Numerical Analysis},
  volume = {25},
  number = {4},
  pages = {685--697},
  doi = {10.1093/imanum/dri015},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/GFW2H8GY/2704BF80-B57D-46C0-AD70-AFDC558688F0.pdf}
}

@article{brauer2014,
  title = {Some {{Observations}} on {{Counterpoise Corrections}} for {{Explicitly Correlated Calculations}} on {{Noncovalent Interactions}}},
  author = {Brauer, Brina and Kesharwani, Manoj K and Martin, Jan M L},
  year = {2014},
  month = jul,
  journal = {J. Chem. Theory Comput.},
  volume = {10},
  number = {9},
  pages = {3791--3799},
  doi = {10.1021/ct500513b},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/9IWXSYK3/J. Chem. Theory Comput. 2014 Brauer.pdf;/Users/dasirianni/Zotero/storage/VNSMXNA8/J. Chem. Theory Comput. 2014 Brauer.pdf}
}

@article{brehm2002,
  title = {Estimation of the {{Vibrational Contribution}} to the {{Entropy Change Associated}} with the {{Low-}} to {{High-Spin Transition}} in {{Fe}}(Phen) 2({{NCS}}) {{2Complexes}}: {{Results Obtained}} by {{IR}} and {{Raman Spectroscopy}} and {{DFT Calculations}}},
  author = {Brehm, G and Reiher, M and Schneider, S},
  year = {2002},
  month = dec,
  journal = {J. Phys. Chem. A},
  volume = {106},
  number = {50},
  pages = {12024--12034},
  doi = {10.1021/jp026586o},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/8UIK5F7M/3A8C653F-CB81-4C9F-BA80-A8DDDD397BCF.pdf}
}

@article{brehm2002a,
  title = {Estimation of the {{Vibrational Contribution}} to the {{Entropy Change Associated}} with the {{Low-}} to {{High-Spin Transition}} in {{Fe}}(Phen) 2({{NCS}}) {{2Complexes}}: {{Results Obtained}} by {{IR}} and {{Raman Spectroscopy}} and {{DFT Calculations}}},
  author = {Brehm, G and Reiher, M and Schneider, S},
  year = {2002},
  month = dec,
  journal = {J. Phys. Chem. A},
  volume = {106},
  number = {50},
  pages = {12024--12034},
  doi = {10.1021/jp026586o},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/7S69JG23/CA13D5D8-D384-4A0A-B9BD-9772E465697F.pdf;/Users/dasirianni/Zotero/storage/SU5X9KIB/CA13D5D8-D384-4A0A-B9BD-9772E465697F.pdf}
}

@article{brehm2021,
  title = {Optimized {{Atomic Partial Charges}} and {{Radii Defined}} by {{Radical Voronoi Tessellation}} of {{Bulk Phase Simulations}}},
  author = {Brehm, Martin and Thomas, Martin},
  year = {2021},
  month = mar,
  journal = {Molecules},
  volume = {26},
  number = {7},
  pages = {1875},
  issn = {1420-3049},
  doi = {10.3390/molecules26071875},
  urldate = {2022-05-09},
  abstract = {We present a novel method for the computation of well-defined optimized atomic partial charges and radii from the total electron density. Our method is based on a two-step radical Voronoi tessellation of the (possibly periodic) system and subsequent integration of the total electron density within each Voronoi cell. First, the total electron density is partitioned into the contributions of each molecule, and subsequently the electron density within each molecule is assigned to the individual atoms using a second set of atomic radii for the radical Voronoi tessellation. The radii are optimized on-the-fly to minimize the fluctuation (variance) of molecular and atomic charges. Therefore, our method is completely free of empirical parameters. As a by-product, two sets of optimized atomic radii are produced in each run, which take into account many specific properties of the system investigated. The application of an on-the-fly interpolation scheme reduces discretization noise in the Voronoi integration. The approach is particularly well suited for the calculation of partial charges in periodic bulk phase systems. We apply the method to five exemplary liquid phase simulations and show how the optimized charges can help to understand the interactions in the systems. Well-known effects such as reduced ion charges below unity in ionic liquid systems are correctly predicted without any tuning, empiricism, or rescaling. We show that the basis set dependence of our method is very small. Only the total electron density is evaluated, and thus, the approach can be combined with any electronic structure method that provides volumetric total electron densities\textemdash it is not limited to Hartree\textendash Fock or density functional theory (DFT). We have implemented the method into our open-source software tool TRAVIS.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/36FZ6TLI/Brehm and Thomas - 2021 - Optimized Atomic Partial Charges and Radii Defined.pdf}
}

@article{britz2006,
  title = {Noncovalent Interactions of Molecules with Single Walled Carbon Nanotubes},
  author = {Britz, David A and Khlobystov, Andrei N},
  year = {2006},
  journal = {Chem. Soc. Rev.},
  volume = {35},
  number = {7},
  pages = {637--659},
  publisher = {{The Royal Society of Chemistry}},
  doi = {10.1039/B507451G},
  abstract = {... DOI:10.1039/B507451G (Critical Review) Chem . Soc . Rev ., 2006 , 35 , 637 - 659 . ... David A. Britz ab and Andrei N. Khlobystov *c. a Department of Materials, University of Oxford, Parks Road, Oxford, UK OX1 3PH. b Eikos Inc., 2 Master Drive, Franklin, MA 02038, USA. ...},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/5G4XJ5HY/Chem. Soc. Rev. 2006 Britz.pdf}
}

@article{bucior2012,
  title = {Porous {{Carbon Nanotube Membranes}} for {{Separation}} of {{H}} 2/{{CH}} 4and {{CO}} 2/{{CH 4Mixtures}}},
  author = {Bucior, Benjamin J and Chen, De-Li and Liu, Jinchen and Johnson, J Karl},
  year = {2012},
  month = dec,
  journal = {J. Phys. Chem. C},
  volume = {116},
  number = {49},
  pages = {25904--25910},
  doi = {10.1021/jp3098022},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/HSZ2RY42/J. Phys. Chem. C 2012 Bucior.pdf}
}

@article{bukowski2005,
  title = {Efficient Calculation of Coupled {{Kohn}}\textendash{{Sham}} Dynamic Susceptibility Functions and Dispersion Energies with Density Fitting},
  author = {Bukowski, Robert and Podeszwa, Rafa{\textbackslash}l and Szalewicz, Krzysztof},
  year = {2005},
  month = oct,
  journal = {Chem. Phys. Lett.},
  volume = {414},
  number = {1-3},
  pages = {111--116},
  doi = {10.1016/j.cplett.2005.08.048},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/HJAWTZKT/25A60973-E754-4CB0-9149-4B3C01B85579.pdf}
}

@article{bukowski2006,
  title = {Portable Parallel Implementation of Symmetry-Adapted Perturbation Theory Code},
  author = {Bukowski, Robert and Cencek, Wojciech and Patkowski, Konrad and Jankowski, Piotr and Jeziorska, Ma{\textbackslash}lGorzata and Ko{\textbackslash}laski, Maciej and Szalewicz, Krzysztof},
  year = {2006},
  month = jul,
  journal = {Mol. Phys.},
  volume = {104},
  number = {13-14},
  pages = {2241--2262},
  doi = {10.1080/00268970600693395},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/VD3HSJDA/Mol. Phys. 2006 Bukowski.pdf}
}

@article{bukowski2008,
  title = {Polarizable Interaction Potential for Water from Coupled Cluster Calculations. {{I}}. {{Analysis}} of Dimer Potential Energy Surface},
  author = {Bukowski, Robert and Szalewicz, Krzysztof and Groenenboom, Gerrit C and {van der Avoird}, Ad},
  year = {2008},
  journal = {J. Chem. Phys.},
  volume = {128},
  number = {9},
  pages = {094313},
  doi = {10.1063/1.2832746},
  file = {/Users/dasirianni/Zotero/storage/IRXITZAW/711E44E8-B1B6-480B-AEE2-D22E75C4EC82.pdf}
}

@article{bultinck2007,
  title = {Critical Analysis and Extension of the {{Hirshfeld}} Atoms in Molecules},
  author = {Bultinck, Patrick and Van Alsenoy, Christian and Ayers, Paul W and {Carb{\'o}-Dorca}, Ramon},
  year = {2007},
  journal = {J. Chem. Phys.},
  volume = {126},
  number = {14},
  pages = {144111--10},
  doi = {10.1063/1.2715563},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/QWYLV29T/3016FA99-598C-4A63-A0F4-9C757D2EE022.pdf}
}

@article{burke2016,
  title = {Locality of Correlation in Density Functional Theory},
  author = {Burke, Kieron and Cancio, Antonio and Gould, Tim and Pittalis, Stefano},
  year = {2016},
  month = aug,
  journal = {J. Chem. Phys.},
  volume = {145},
  number = {5},
  pages = {054112--16},
  doi = {10.1063/1.4959126},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/I8KKKSTP/765ACE64-70EC-44CC-8B33-1DA2E996BA61.pdf}
}

@article{burns2011,
  title = {Density-Functional Approaches to Noncovalent Interactions: {{A}} Comparison of Dispersion Corrections ({{DFT-D}}), Exchange-Hole Dipole Moment ({{XDM}}) Theory, and Specialized Functionals},
  author = {Burns, Lori A and Mayagoitia, {\'A}lvaro V{\'a}zquez and Sumpter, Bobby G and Sherrill, C David},
  year = {2011},
  journal = {J. Chem. Phys.},
  volume = {134},
  number = {8},
  pages = {084107},
  doi = {10.1063/1.3545971},
  abstract = {A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmarkquality evaluations of binding strength compiled for molecular ...},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/6ECU5NR3/J. Chem. Phys. 2011 Burns.pdf;/Users/dasirianni/Zotero/storage/PRSC8FZZ/J. Chem. Phys. 2011 Burns.pdf}
}

@article{burns2014,
  title = {Comparing {{Counterpoise-Corrected}}, {{Uncorrected}}, and {{Averaged Binding Energies}} for {{Benchmarking Noncovalent Interactions}}},
  author = {Burns, Lori A and Marshall, Michael S and Sherrill, C David},
  year = {2014},
  month = jan,
  journal = {J. Chem. Theory Comput.},
  volume = {10},
  number = {1},
  pages = {49--57},
  doi = {10.1021/ct400149j},
  abstract = {High-quality benchmark computations are critical for the development and assessment of approximate methods to describe noncovalent interactions . Recent advances in the treatment of dispersion by density functional theory and also the development of more ...},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/L86FPB8S/J. Chem. Theory Comput. 2014 Burns.pdf;/Users/dasirianni/Zotero/storage/XX52UM4P/J. Chem. Theory Comput. 2014 Burns.pdf}
}

@article{burns2014a,
  title = {Appointing Silver and Bronze Standards for Noncovalent Interactions: {{A}} Comparison of Spin-Component-Scaled ({{SCS}}), Explicitly Correlated ({{F12}}), and Pecialized Wavefunction Approaches Specialized \textbackslash ldots},
  author = {Burns, Lori A and Marshall, Michael S and Sherrill, C David},
  year = {2014},
  journal = {J. Chem. Phys.},
  volume = {141},
  number = {23},
  pages = {234111},
  doi = {10.1063/1.4903765},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/6TADEUHD/2014 Burns.pdf}
}

@article{burns2017,
  title = {The {{BioFragment Database}} ({{BFDb}}): {{An}} Open-Data Platform for Computational Chemistry Analysis of Noncovalent Interactions},
  author = {Burns, Lori A and Faver, John C and Zheng, Zheng and Marshall, Michael S and Smith, Daniel G A and Vanommeslaeghe, Kenno and MacKerell Jr., Alexander D and Merz Jr., Kenneth M and Sherrill, C David},
  year = {2017},
  month = oct,
  journal = {J. Chem. Phys.},
  volume = {147},
  number = {16},
  pages = {161727--16},
  doi = {10.1063/1.5001028},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/ECHGDX8G/C242AF14-B8F8-481C-B88C-67B8D8AE600B.pdf;/Users/dasirianni/Zotero/storage/W59KSJN5/C242AF14-B8F8-481C-B88C-67B8D8AE600B.pdf}
}

@article{bykov2015,
  title = {Efficient Implementation of the Analytic Second Derivatives of {{Hartree}}\textendash{{Fock}} and Hybrid {{DFT}} Energies: A Detailed Analysis of Different Approximations},
  author = {Bykov, Dmytro and Petrenko, Taras and Izs{\'a}k, R{\'o}bert and Kossmann, Simone and Becker, Ute and Valeev, Edward and Neese, Frank},
  year = {2015},
  month = mar,
  journal = {Mol. Phys.},
  volume = {113},
  number = {13-14},
  pages = {1961--1977},
  doi = {10.1080/00268976.2015.1025114},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/3MSR7EQD/97728339-19A0-499B-80E2-289220F233A8.pdf;/Users/dasirianni/Zotero/storage/ATH4F79L/97728339-19A0-499B-80E2-289220F233A8.pdf}
}

@article{carlson1993,
  title = {Accuracy of Free Energies of Hydration for Organic Molecules from 6-31g*-Derived Partial Charges},
  author = {Carlson, Heather A. and Nguyen, Toan B. and Orozco, Modesto and Jorgensen, William L.},
  year = {1993},
  journal = {Journal of Computational Chemistry},
  volume = {14},
  number = {10},
  pages = {1240--1249},
  issn = {1096-987X},
  doi = {10.1002/jcc.540141013},
  urldate = {2022-03-09},
  abstract = {Absolute free energies of hydration have been computed for 13 diverse organic molecules using partial charges derived from ab initio 6-31G* wave functions. Both Mulliken charges and charges fit to the electrostatic potential surface (EPS) were considered in conjunction with OPLS Lennard\textendash Jones parameters for the organic molecules and the TIP4P model of water. Monte Carlo simulations with statistical perturbation theory yielded relative free energies of hydration. These were converted to absolute quantities through perturbations to reference molecules for which absolute free energies of hydration had been obtained previously in TIP4P water. The average errors in the computed absolute free energies of hydration are 1.1 kcal/mol for the 6-31G* EPS charges and 4.0 kcal/mol for the Mulliken charges. For the EPS charges, the largest individual errors are under 2 kcal/mol except for acetamide, in which case the error is 3.7 kcal/mol. The hydrogen bonding between the organic solutes and water has also been characterized. \textcopyright{} John Wiley \& Sons, Inc.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/MECSAYVF/jcc.html}
}

@article{casanova2008,
  title = {The Spin-Flip Extended Single Excitation Configuration Interaction Method},
  author = {Casanova, David and {Head-Gordon}, Martin},
  year = {2008},
  month = aug,
  journal = {J. Chem. Phys.},
  volume = {129},
  number = {6},
  pages = {064104},
  publisher = {{American Institute of Physics}},
  issn = {0021-9606},
  doi = {10.1063/1.2965131},
  urldate = {2022-06-09},
  abstract = {An extension of the spin-flip single excitation configuration interaction (SF-CIS) method is introduced. The extension, abbreviated as SF-XCIS, includes all configurations in which no more than one virtual level of the high spin triplet reference becomes occupied and no more than one doubly occupied level becomes vacant. The number of such configurations is quadratic with molecule size, and the method is implemented in a direct algorithm whose cost scales in the same way with molecule size as CIS itself, thus permitting applications to large systems. Starting from a spin restricted triplet determinant, SF-XCIS yields spin-pure singlet, triplet, and quintet states, and treats both half-occupied reference orbitals in a fully balanced way to allow application to strongly correlated problems. Tests on bond dissociation in the HF molecule, the torsional potential of ethylene, and excited states of polyenes show encouraging improvements using SF-XCIS compared to SF-CIS and a previously suggested extension, the spin-complete CIS model.}
}

@article{case2005,
  title = {The {{Amber}} Biomolecular Simulation Programs},
  author = {Case, David A and Cheatham, Thomas E and Darden, Tom and Gohlke, Holger and Luo, Ray and Merz, Kenneth M and Onufriev, Alexey and Simmerling, Carlos and Wang, Bing and Woods, Robert J},
  year = {2005},
  journal = {J. Comput. Chem.},
  volume = {26},
  number = {16},
  pages = {1668--1688},
  publisher = {{Wiley-Blackwell}},
  doi = {10.1002/jcc.20290},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/2U2IUDMM/A30156C5-77C5-443F-BE16-50EAAB6410A6.pdf;/Users/dasirianni/Zotero/storage/3XYZSP9Q/A30156C5-77C5-443F-BE16-50EAAB6410A6.pdf}
}

@article{chaban1997,
  title = {Approximate Second Order Method for Orbital Optimization of {{SCF}} and {{MCSCF}} Wavefunctions},
  author = {Chaban, Galina and Schmidt, Michael W and Gordon, Mark S},
  year = {1997},
  month = oct,
  journal = {Theor. Chem. Acc.},
  volume = {97},
  number = {1-4},
  pages = {88--95},
  publisher = {{Springer-Verlag}},
  doi = {10.1007/s002140050241},
  abstract = {Abstract. A quasi-Newton method involving a diagonal guess orbital hessian with iterative updates has been proposed recently by Almlof for the optimization of closed shell self- consistent field ( SCF ) wavefunctions . The technique is extended in the present work to ...},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/745UQGVG/Theor. Chem. Acc. 1997 Chaban.pdf;/Users/dasirianni/Zotero/storage/FQQUV8ZV/Theor. Chem. Acc. 1997 Chaban.pdf}
}

@article{chai2008,
  title = {Long-Range Corrected Hybrid Density Functionals with Damped Atom\textendash Atom Dispersion Corrections},
  author = {Chai, Jeng-Da and {Head-Gordon}, Martin},
  year = {2008},
  journal = {Phys. Chem. Chem. Phys.},
  volume = {10},
  number = {44},
  pages = {6615--6620},
  publisher = {{The Royal Society of Chemistry}},
  doi = {10.1039/b810189b},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/BWDREW2D/Phys. Chem. Chem. Phys. 2008 Chai.pdf;/Users/dasirianni/Zotero/storage/G8QTRJHQ/Phys. Chem. Chem. Phys. 2008 Chai.pdf}
}

@article{chai2008a,
  title = {Long-Range Corrected Hybrid Density Functionals with Damped Atom\textendash Atom Dispersion Corrections},
  author = {Chai, Jeng-Da and {Head-Gordon}, Martin},
  year = {2008},
  journal = {Phys. Chem. Chem. Phys.},
  volume = {10},
  number = {44},
  pages = {6615},
  issn = {1463-9076, 1463-9084},
  doi = {10.1039/b810189b},
  urldate = {2022-07-09},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/498XD6Z5/Chai and Head-Gordon - 2008 - Long-range corrected hybrid density functionals wi.pdf}
}

@article{chai2009,
  title = {Long-Range Corrected Double-Hybrid Density Functionals},
  author = {Chai, Jeng-Da and {Head-Gordon}, Martin},
  year = {2009},
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  volume = {131},
  number = {17},
  pages = {174105},
  doi = {10.1063/1.3244209},
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  file = {/Users/dasirianni/Zotero/storage/6QJZEH2Z/J. Chem. Phys. 2009 Chai.pdf;/Users/dasirianni/Zotero/storage/IUS7KJDI/J. Chem. Phys. 2009 Chai.pdf}
}

@incollection{chalmers2019,
  title = {Atomism from the 17th to the 20th {{Century}}},
  booktitle = {The {{Stanford Encyclopedia}} of {{Philosophy}}},
  author = {Chalmers, Alan},
  editor = {Zalta, Edward N},
  year = {2019},
  publisher = {{Metaphysics Research Lab, Stanford University}}
}

@article{chan2002,
  title = {Highly Correlated Calculations with a Polynomial Cost Algorithm: {{A}} Study of the Density Matrix Renormalization Group},
  author = {Chan, Garnet Kin-Lic and {Head-Gordon}, Martin},
  year = {2002},
  month = mar,
  journal = {J. Chem. Phys.},
  volume = {116},
  number = {11},
  pages = {4462--4476},
  doi = {10.1063/1.1449459},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/7YAE5RQY/BF1678AC-0C6C-4271-AD44-1DC042918FA9.pdf}
}

@article{chan2004,
  title = {An Algorithm for Large Scale Density Matrix Renormalization Group Calculations},
  author = {Chan, Garnet Kin-Lic},
  year = {2004},
  month = feb,
  journal = {J. Chem. Phys.},
  volume = {120},
  number = {7},
  pages = {3172--3178},
  doi = {10.1063/1.1638734},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/PBWG4R23/246FDCDA-6010-4C80-923B-164A2B94B3C2.pdf}
}

@incollection{chan2008,
  title = {An {{Introduction}} to the {{Density Matrix Renormalization Group Ansatz}} in {{Quantum Chemistry}}},
  booktitle = {Frontiers in {{Quantum Systems}} in {{Chemistry}} and {{Physics}}},
  author = {Chan, Garnet Kin-Lic and Dorando, Jonathan J and Ghosh, Debashree and Hachmann, Johannes and Neuscamman, Eric and Wang, Haitao and Yanai, Takeshi},
  year = {2008},
  pages = {49--65},
  publisher = {{Springer Netherlands}},
  address = {{Dordrecht}},
  doi = {10.1007/978-1-4020-8707-3_4},
  abstract = {The Density Matrix Renormalisation Group (DMRG) is an electronic structure method that has recently been applied to ab-initio quantum chemistry. Even at this early stage, it has enabled the solution of many problems that would previously have been intractable with any other method, in particular, multireference problems with very large active spaces. Historically, the DMRG was not originally formulated from a wavefunction perspective, but rather in a Renormalisation Group (RG) language. However, it is now realised that a wavefunction view of the DMRG provides a more convenient, and in some cases more powerful, paradigm. Here we provide an expository introduction to the DMRG ansatz in the context of quantum chemistry.},
  isbn = {978-1-4020-8706-6},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/PYTBG4EF/F284D833-C522-4FB6-BB3F-16472BF402BB.pdf;/Users/dasirianni/Zotero/storage/ZVH2TGYM/F284D833-C522-4FB6-BB3F-16472BF402BB.pdf}
}

@article{chattopadhyay2009,
  title = {Investigation of {{Low-Lying States}} of {{Oxygen Molecule}} via {{Second-Order Multireference Perturbation Theory}}: {{A State-Specific Approach}}},
  author = {Chattopadhyay, Sudip and Mahapatra, Uttam Sinha and Chaudhuri, Rajat K},
  year = {2009},
  month = may,
  journal = {J. Phys. Chem. A},
  volume = {113},
  number = {20},
  pages = {5972--5984},
  doi = {10.1021/jp810910n},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/4SAJ99VI/57B3E429-1F8C-4B60-9641-0AD038F85C7C.pdf}
}

@article{chen2005,
  title = {Nucleus-{{Independent Chemical Shifts}} ({{NICS}}) as an {{Aromaticity Criterion}}},
  author = {Chen, Zhongfang and Wannere, Chaitanya S. and Corminboeuf, Cl{\'e}mence and Puchta, Ralph and Schleyer, Paul von Ragu{\'e}},
  year = {2005},
  month = oct,
  journal = {Chem. Rev.},
  volume = {105},
  number = {10},
  pages = {3842--3888},
  issn = {0009-2665, 1520-6890},
  doi = {10.1021/cr030088+},
  urldate = {2022-02-21},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/YYLTPAK3/Chen et al. - 2005 - Nucleus-Independent Chemical Shifts (NICS) as an A.pdf}
}

@article{chen2013,
  title = {Ab Initiostudy of the {$\pi$}-{$\pi$} Interactions between {{CO}} 2and Benzene, Pyridine, and Pyrrole},
  author = {Chen, Long and Cao, Fenglei and Sun, Huai},
  year = {2013},
  month = may,
  journal = {Int. J. Quantum Chem.},
  volume = {113},
  number = {20},
  pages = {2261--2266},
  doi = {10.1002/qua.24444},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/6254KYEW/Int. J. Quantum Chem. 2013 Chen.pdf;/Users/dasirianni/Zotero/storage/WYFSJKR7/Int. J. Quantum Chem. 2013 Chen.pdf}
}

@article{cho2020,
  title = {The {{Atomic Partial Charges Arboretum}}: {{Trying}} to {{See}} the {{Forest}} for the {{Trees}}},
  shorttitle = {The {{Atomic Partial Charges Arboretum}}},
  author = {Cho, Minsik and Sylvetsky, Nitai and Eshafi, Sarah and Santra, Golokesh and Efremenko, Irena and Martin, Jan M. L.},
  year = {2020},
  journal = {ChemPhysChem},
  volume = {21},
  number = {8},
  pages = {688--696},
  issn = {1439-7641},
  doi = {10.1002/cphc.202000040},
  urldate = {2022-03-09},
  abstract = {Atomic partial charges are among the most commonly used interpretive tools in quantum chemistry. Dozens of different `population analyses' are in use, which are best seen as proxies (indirect gauges) rather than measurements of a `general ionicity'. For the GMTKN55 benchmark of nearly 2,500 main-group molecules, which span a broad swathe of chemical space, some two dozen different charge distributions were evaluated at the PBE0 level near the 1-particle basis set limit. The correlation matrix between the different charge distributions exhibits a block structure; blocking is, broadly speaking, by charge distribution class. A principal component analysis on the entire dataset suggests that nearly all variation can be accounted for by just two `principal components of ionicity': one has all the distributions going in sync, while the second corresponds mainly to Bader QTAIM vs. all others. A weaker third component corresponds to electrostatic charge models in opposition to the orbital-based ones. The single charge distributions that have the greatest statistical similarity to the first principal component are iterated Hirshfeld (Hirshfeld-I) and a minimal-basis projected modification of Bickelhaupt charges. If three individual variables, rather than three principal components, are to be identified that contain most of the information in the whole dataset, one representative for each of the three classes of Corminboeuf et al. is needed: one based on partitioning of the density (such as QTAIM), a second based on orbital partitioning (such as NPA), and a third based on the molecular electrostatic potential (such as HLY or CHELPG).},
  langid = {english},
  keywords = {atoms in molecules,charge distributions,molecular modelling,population analysis,principal components of ionicity},
  file = {/Users/dasirianni/Zotero/storage/TACAAAM4/Cho et al. - 2020 - The Atomic Partial Charges Arboretum Trying to Se.pdf}
}

@article{choi2016,
  title = {Performance of Heterogeneous Computing with Graphics Processing Unit and Many Integrated Core for Hartree Potential Calculations on a Numerical Grid},
  author = {Choi, Sunghwan and Kwon, Oh-Kyoung and Kim, Jaewook and Kim, Woo Youn},
  year = {2016},
  month = jul,
  journal = {J. Comput. Chem.},
  pages = {1--9},
  doi = {10.1002/jcc.24443},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/8WHD3C2N/03C88CAC-C077-41A5-9F75-3C204B157552.pdf;/Users/dasirianni/Zotero/storage/GDY4PUCB/03C88CAC-C077-41A5-9F75-3C204B157552.pdf}
}

@article{christensen2016,
  title = {Semiempirical {{Quantum Mechanical Methods}} for {{Noncovalent Interactions}} for {{Chemical}} and {{Biochemical Applications}}},
  author = {Christensen, Anders S and Kuba{\v r}, Tom{\'a}{\v s} and Cui, Qiang and Elstner, Marcus},
  year = {2016},
  month = apr,
  journal = {Chem. Rev.},
  pages = {acs.chemrev.5b00584--37},
  doi = {10.1021/acs.chemrev.5b00584},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/GHTG4769/33166105-EFF0-4AA2-8512-1BC4AF103BF6.pdf}
}

@article{christiansen1995,
  title = {The Second-Order Approximate Coupled Cluster Singles and Doubles Model {{CC2}}},
  author = {Christiansen, Ove and Koch, Henrik and J{\o}rgensen, Poul},
  year = {1995},
  journal = {Chem. Phys. Lett.},
  volume = {243},
  number = {5},
  pages = {409--418},
  doi = {10.1016/0009-2614(95)00841-Q},
  abstract = {An approximate coupled cluster singles and doubles model is presented, denoted CC2. The CC2 total energy is of second-order M\o ller-Plesset perturbation theory (MP2) quality. The CC2 linear response function is derived. Unlike MP2, excitation energies and transition moments can be obtained in CC2. A hierarchy of coupled cluster models, CCS, CC2, CCSD, CC3, CCSDT etc., is presented where CC2 and CC3 are approximate coupled cluster models defined by similar approximations. Higher levels give increased accuracy at increased computational effort. The scaling of CCS, CC2, CCSD, CC3 and CCSDT is N4, N5, N6, N7 and N8, respectively where N is th the number of orbitals. Calculations on Be, N2 and C2H4 are performed and results compared with those obtained in the second-order polarization propagator approach SOPPA.}
}

@article{cinke2003,
  title = {{{CO}}{\textsubscript{2}} Adsorption in Single-Walled Carbon Nanotubes},
  author = {Cinke, Martin and Li, Jing and Bauschlicher Jr., Charles W and Ricca, Alessandra and Meyyappan, M},
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  month = jul,
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  volume = {376},
  number = {5-6},
  pages = {761--766},
  doi = {10.1016/S0009-2614(03)01124-2},
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  file = {/Users/dasirianni/Zotero/storage/TARCM5L6/Chem. Phys. Lett. 2003 Cinke.pdf}
}

@article{ck2011,
  title = {The Density-Matrix Renormalization Group in the Age of Matrix Product States},
  author = {{ck}, Ulrich Schollw{\~A}},
  year = {2011},
  month = jan,
  journal = {Annals of Physics},
  volume = {326},
  number = {1},
  pages = {96--192},
  publisher = {{Elsevier Inc.}},
  doi = {10.1016/j.aop.2010.09.012},
  abstract = {Annals of Physics, 326 (2011) 96-192. doi:10.1016/j.aop.2010.09.012},
  file = {/Users/dasirianni/Zotero/storage/5S3JF66U/E2961B4C-BE79-4188-89A1-78D522224C12.pdf}
}

@article{cogan2014,
  title = {Selective {{Suspension}} of {{Single-Walled Carbon Nanotubes Using}} {$\beta$}-{{Sheet Polypeptides}}},
  author = {Cogan, Nicole M B and Bowerman, Charles J and Nogaj, Lisa J and Nilsson, Bradley L and Krauss, Todd D},
  year = {2014},
  month = mar,
  journal = {J. Phys. Chem. C},
  pages = {140306063327003},
  doi = {10.1021/jp410870y},
  langid = {english},
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}

@book{coghill2006,
  title = {The {{ACS}} Style Guide: Effective Communication of Scientific Information},
  shorttitle = {The {{ACS}} Style Guide},
  editor = {Coghill, Anne M. and Garson, Lorrin R. and American Chemical Society},
  year = {2006},
  edition = {3rd ed},
  publisher = {{American Chemical Society ; Oxford University Press}},
  address = {{Washington, DC : Oxford ; New York}},
  isbn = {978-0-8412-3999-9 978-0-8412-7400-6},
  lccn = {QD8.5 .A25 2006},
  keywords = {Authorship,Chemistry,English language,{Handbooks, manuals, etc},Style,Style manuals,Technical writing},
  annotation = {OCLC: ocm62872860}
}

@article{cohen2012,
  title = {Challenges for {{Density Functional Theory}}},
  author = {Cohen, Aron J and {Mori-S{\'a}nchez}, Paula and Yang, Weitao},
  year = {2012},
  month = jan,
  journal = {Chem. Rev.},
  volume = {112},
  number = {1},
  pages = {289--320},
  doi = {10.1021/cr200107z},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/5UVP79F5/Chem. Rev. 2012 Cohen.pdf;/Users/dasirianni/Zotero/storage/9HSGYHPD/Chem. Rev. 2012 Cohen.pdf}
}

@article{collins2023,
  title = {Interpretable {{Graph-Network-Based Machine Learning Models}} via {{Molecular Fragmentation}}},
  author = {Collins, Eric M. and Raghavachari, Krishnan},
  year = {2023},
  month = may,
  journal = {J. Chem. Theory Comput.},
  volume = {19},
  number = {10},
  pages = {2804--2810},
  issn = {1549-9618, 1549-9626},
  doi = {10.1021/acs.jctc.2c01308},
  urldate = {2023-05-24},
  abstract = {Chemists have long benefitted from the ability to understand and interpret the predictions of computational models. With the current shift to more complex deep learning models, in many situations that utility is lost. In this work, we expand on our previously work on computational thermochemistry and propose an interpretable graph network, FragGraph(nodes), that provides decomposed predictions into fragment-wise contributions. We demonstrate the usefulness of our model in predicting a correction to density functional theory (DFT)-calculated atomization energies using {$\Delta$}-learning. Our model predicts G4(MP2)-quality thermochemistry with an accuracy of {$<$}1 kJ mol-1 for the GDB9 dataset. Besides the high accuracy of our predictions, we observe trends in the fragment corrections which quantitatively describe the deficiencies of B3LYP. Node-wise predictions significantly outperform our previous model predictions from a global state vector. This effect is most pronounced as we explore the generality by predicting on more diverse test sets indicating node-wise predictions are less sensitive to extending machine learning models to larger molecules.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/PXPUQSUN/Collins and Raghavachari - 2023 - Interpretable Graph-Network-Based Machine Learning.pdf}
}

@article{cook2015,
  title = {Spin State Behavior of Iron({{II}})/Dipyrazolylpyridine Complexes. {{New}} Insights from Crystallographic and Solution Measurements},
  author = {Cook, Laurence J Kershaw and Mohammed, Rufeida and Sherborne, Grant and Roberts, Thomas D and Alvarez, Santiago and Halcrow, Malcolm A},
  year = {2015},
  month = apr,
  journal = {Coordination Chemistry Reviews},
  volume = {289--290},
  pages = {2--12},
  publisher = {{Elsevier B.V.}},
  doi = {10.1016/j.ccr.2014.08.006},
  abstract = {Coordination Chemistry Reviews, 289-290 (2015) 2-12. doi:10.1016/j.ccr.2014.08.006},
  file = {/Users/dasirianni/Zotero/storage/5FPH6C2Q/Coordination Chemistry Reviews 2015 Cook.pdf;/Users/dasirianni/Zotero/storage/K5QFYBQ4/Coordination Chemistry Reviews 2015 Cook.pdf}
}

@article{cooper2017,
  title = {Core {{Ideas}} and {{Topics}}: {{Building Up}} or {{Drilling Down}}?},
  author = {Cooper, Melanie M and Posey, Lynmarie A and Underwood, Sonia M},
  year = {2017},
  month = mar,
  journal = {J. Chem. Educ.},
  pages = {acs.jchemed.6b00900--8},
  doi = {10.1021/acs.jchemed.6b00900},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/UTJKUUEU/DCE2D4EA-1A02-46FF-BDC7-A66E979DE748.pdf}
}

@article{cornell,
  title = {Application of {{RESP}} Charges to Calculate Conformational Energies, Hydrogen Bond Energies, and Free Energies of Solvation},
  author = {Cornell, Wendy D and Cieplak, Piotr and Bayly, Christopher I and Kollmann, Peter A},
  pages = {12},
  abstract = {We apply a new restrained electrostatic potential fit charge model (two-stage RESP) to conformational analysis and the calculation of intermolecular interactions. Specifically, we study conformational energies in butane, methyl ethyl thioether, three simple alcohols, three simple amines, and 1,2-ethanediol as a function of charge model (two-stage RESP vs standard ESP) and 1-4 electrostatic scale factor. We demonstrate that the two-stage RESP model with a 1-4 electrostatic scale factor of \textemdash 1/1.2 is a very good model, as evaluated by comparison with high-level ab initio calculations. For methanol and /V-methylacetamide interactions with TIP3P water, the two-stage RESP model leads to hydrogen bonds only slightly weaker than found with the standard ESP changes. In tests on DNA base pairs, the two-stage RESP model leads to hydrogen bonds which are \textasciitilde{} 1 kcal/mol weaker than those calculated with the standard ESP charges but closer in magnitude to the best current available ab initio calculations. Furthermore, the two-stage RESP charges, unlike the standard ESP charges, reproduce the result that Hoogsteen hydrogen bonding is stronger than Watson-Crick hydrogen bonding for adenine-thymine base pairs. The free energies of solvation of both methanol and f/ww-iV-methylacetamide were also calculated for the standard ESP and two-stage RESP models and both were in good agreement with experiment. We have combined the use of two-stage RESP charges with multiple conformational fitting\textemdash recently employed using standard ESP charges as described by Reynolds, et al. (J. Am. Chem. Soc. 1992, 114, 9075)\textemdash in studies of conformationally dependent dipole moments and energies of propylamine. We find that the combination of these approaches is synergistic in leading to useful charge distributions for molecular simulations. Two-stage RESP charges thus reproduce both intermolecular and intramolecular energies and structures quite well, making this charge model a critical advancement in the development of a general force field for modeling biological macromolecules and their ligands, both in the gas phase and in solution.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/SIKN37DD/Cornell et al. - Application of RESP charges to calculate conformat.pdf}
}

@article{cornell1993,
  title = {Application of {{RESP}} Charges to Calculate Conformational Energies, Hydrogen Bond Energies, and Free Energies of Solvation},
  author = {Cornell, Wendy D. and Cieplak, Piotr and Bayly, Christopher I. and Kollman, Peter A.},
  year = {1993},
  month = oct,
  journal = {J. Am. Chem. Soc.},
  volume = {115},
  number = {21},
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  doi = {10.1021/ja00074a030},
  urldate = {2022-03-09},
  langid = {english}
}

@article{cornell1995,
  title = {A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules},
  author = {Cornell, W D and Cieplak, P and Bayly, C I and Gould, I R and Merz Jr., Kenneth M and Ferguson, David M and Spellmeyer, David C and Fox, Thomas and Caldwell, James W and Kollman, Peter A},
  year = {1995},
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  volume = {117},
  number = {19},
  pages = {5179--5197},
  doi = {10.1021/ja00124a002},
  abstract = {Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force ...},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/3AKVCALS/68142F65-E9C5-4A1B-8E22-837A03D3FBE4.pdf;/Users/dasirianni/Zotero/storage/MG5ZLI6J/68142F65-E9C5-4A1B-8E22-837A03D3FBE4.pdf}
}

@article{coutsias2004,
  title = {Using Quaternions to Calculate {{RMSD}}},
  author = {Coutsias, Evangelos A and Seok, Chaok and Dill, Ken A},
  year = {2004},
  journal = {J. Comput. Chem.},
  volume = {25},
  number = {15},
  pages = {1849--1857},
  doi = {10.1002/jcc.20110},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/XISKTNBG/12794556-8125-4866-B76E-C59A3C5207B0.pdf}
}

@book{cramer2004,
  title = {Essentials of Computational Chemistry: Theories and Models},
  shorttitle = {Essentials of Computational Chemistry},
  author = {Cramer, Christopher J.},
  year = {2004},
  edition = {2nd ed},
  publisher = {{Wiley}},
  address = {{Chichester, West Sussex, England ; Hoboken, NJ}},
  isbn = {978-0-470-09182-1 978-0-470-09181-4},
  lccn = {QD455.3.E4 C73 2004},
  keywords = {{Chemistry, Physical and theoretical},Data processing,Mathematical models}
}

@article{crawford,
  title = {An {{Introduction}} to {{Coupled Cluster Theory}} for {{Computational Chemist}}},
  author = {Crawford, T Daniel and Schaefer, Henry F},
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}

@article{crawford1996,
  title = {On the Energy Invariance of Open-Shell Perturbation Theory with Respect to Unitary Transformations of Molecular Orbitals},
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}

@article{crawford2001,
  title = {Problematic P-Benzyne: {{Orbital}} Instabilities, Biradical Character, and Broken Symmetry},
  shorttitle = {Problematic {\emph{p}} -Benzyne},
  author = {Crawford, T. Daniel and Kraka, Elfi and Stanton, John F. and Cremer, Dieter},
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  journal = {The Journal of Chemical Physics},
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  doi = {10.1063/1.1373433},
  urldate = {2022-02-21},
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}

@article{cui2016,
  title = {Perspective: {{Quantum}} Mechanical Methods in Biochemistry and Biophysics},
  author = {Cui, Qiang},
  year = {2016},
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  number = {14},
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  doi = {10.1063/1.4964410},
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}

@article{cutini2016,
  title = {Assessment of {{Different Quantum Mechanical Methods}} for the {{Prediction}} of {{Structure}} and {{Cohesive Energy}} of {{Molecular Crystals}}},
  author = {Cutini, Michele and Civalleri, Bartolomeo and Corno, Marta and Orlando, Roberto and Brandenburg, Jan Gerit and Maschio, Lorenzo and Ugliengo, Piero},
  year = {2016},
  month = jun,
  journal = {J. Chem. Theory Comput.},
  pages = {acs.jctc.6b00304--13},
  doi = {10.1021/acs.jct

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