text:
c.6b00304},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/B936Z26D/19B005C2-021A-49CC-B293-BAB87080A878.pdf}
}

@article{dafermos2017,
  title = {The Interior of Dynamical Vacuum Black Holes {{I}}: {{The C0-stability}} of the {{Kerr Cauchy}} Horizon},
  author = {Dafermos, M and Luk, J},
  year = {2017},
  month = oct,
  journal = {arXiv},
  pages = {1--217},
  abstract = {We initiate a series of works where we study the interior of dynamical rotating vacuum black holes without symmetry. In the present paper, we take up the problem starting from appropriate Cauchy data for the Einstein vacuum equations defined on a hypersurface already within the black hole interior, representing the expected geometry just inside the event horizon. We prove that for all such data, the maximal Cauchy evolution can be extended across a non-trivial piece of Cauchy horizon as a Lorentzian manifold with continuous metric. In subsequent work, we will retrieve our assumptions on data assuming only that the black hole event horizon geometry suitably asymptotes to a rotating Kerr solution. In particular, if the exterior region of the Kerr family is proven to be dynamically stable\textemdash as is widely expected\textemdash then it will follow that the C0-inextendibility formulation of Penrose's celebrated strong cosmic censorship conjecture is in fact false. The proof suggests, however, that the C0-metric Cauchy horizons thus arising are generically singular in an essential way, representing so-called ``weak null singularities'', and thus that a revised version of strong cosmic censorship holds.},
  file = {/Users/dasirianni/Zotero/storage/5NSQYKTC/06A6DE33-6813-4122-9C3C-85ADC9C6C806.pdf}
}

@article{damjanovic1999,
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  urldate = {2023-02-14},
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}

@article{damjanovic2002,
  title = {Excitons in a Photosynthetic Light-Harvesting System: {{A}} Combined Molecular Dynamics, Quantum Chemistry, and Polaron Model Study},
  shorttitle = {Excitons in a Photosynthetic Light-Harvesting System},
  author = {Damjanovi{\'c}, Ana and Kosztin, Ioan and Kleinekath{\"o}fer, Ulrich and Schulten, Klaus},
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  urldate = {2023-02-14},
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}

@article{dayou2010,
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}

@article{delange2011,
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}

@book{delaroza2017,
  title = {Non-Covalent {{Interactions}} in {{Quantum Chemistry}} and {{Physics}}: {{Theory}} and {{Applications}}},
  author = {{de la Roza}, A O and DiLabio, G A},
  year = {2017},
  publisher = {{Elsevier Science}},
  isbn = {978-0-12-809836-3}
}

@article{deluca1974,
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  urldate = {2023-04-09},
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}

@article{demarco2016,
  title = {Differences in the {{Vibrational Dynamics}} of {{H 2O}} and {{D 2O}}: {{Observation}} of {{Symmetric}} and {{Antisymmetric Stretching Vibrations}} in {{Heavy Water}}},
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}

@article{deshmukh2011,
  title = {Binding Energy of Gas Molecule with Two Pyrazine Molecules as Organic Linker in Metal\textendash Organic Framework: Its Theoretical Evaluation and Understanding of Determining Factors},
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}

@article{dexter1953,
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  doi = {10.1063/1.1699044},
  urldate = {2023-02-14},
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}

@book{diercksen1983,
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  address = {{Dordrecht}},
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}

@article{diffenderfer1982,
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}

@article{dion2004,
  title = {Van Der {{Waals Density Functional}} for {{General Geometries}}},
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@article{dirac1929,
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@article{dobson2006,
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}

@article{dolfi2014,
  title = {Matrix Product State Applications for the {{ALPS}} Project},
  author = {Dolfi, Michele and Bauer, Bela and Keller, Sebastian and Kosenkov, Alexandr and Ewart, Timoth{\'e}e and Kantian, Adrian and Giamarchi, Thierry and Troyer, Matthias},
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}

@article{dolgounitcheva2016,
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}

@article{domingo2009,
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}

@article{dontgen2020,
  title = {Atomic {{Partial Charges}} as {{Descriptors}} for {{Barrier Heights}}},
  author = {D{\"o}ntgen, Malte and Fenard, Yann and Heufer, K. Alexander},
  year = {2020},
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  number = {12},
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  publisher = {{American Chemical Society}},
  issn = {1549-9596},
  doi = {10.1021/acs.jcim.0c00787},
  urldate = {2022-05-09},
  abstract = {Atomic partial charges are found to be valuable descriptors for barrier heights of unimolecular reactions due to the considerable information about the electronic structure embedded in them. If the chemical changes of the reactions are somewhat centralized at a single atom, the respective partial charge is a potentially meaningful descriptor and might outperform bond dissociation energies as descriptors. We propose that atomic partial charges should be considered as barrier height descriptors in future research.},
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}

@article{doran2012,
  title = {Rotational Spectrum and Structure of the Pyridine\textendash{{CO}}{\textsubscript{2}} van Der {{Waals}} Complex},
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  abstract = {The rotational spectrum of the pyridine\textendash CO2 van der Waals complex has been recorded in a cold supersonic jet using pulsed-nozzle Fourier transform microwave s.},
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}

@article{dresselhaus2014,
  title = {Self-{{Consistent Embedding}} of {{Density-Matrix Renormalization Group Wavefunctions}} in a {{Density Fucntional Environment}}},
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  abstract = {We present the first implementation of a density matrix renormalization group algorithm embedded in an environment described by density functional theory. The frozen density embedding scheme is used with a freeze-and-thaw strategy for a self-consistent polarization of the orbital-optimized wavefunction and the environmental densities with respect to each other.},
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}

@article{dubecky2016,
  title = {Noncovalent {{Interactions}} by {{Quantum Monte Carlo}}},
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}

@article{dunlap1979,
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@article{dunning1989,
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@article{durell2017,
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  abstract = {The process of protein folding is obviously driven by forces exerted on the atoms of the amino-acid chain. These forces arise from interactions with other parts of the protein itself (direct forces), as...},
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@article{dutta2014,
  title = {Enhanced {{Gas Adsorption}} on {{Graphitic Substrates}} via {{Defects}} and {{Local Curvature}}: {{A Density Functional Theory Study}}},
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@article{eckart1926,
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  abstract = {Abstract A formal calculus is developed which includes the Born and Jordan matrix dynamics, and also the remarkable quantum condition of Schroedinger. A method for the calculation of the matrices which is in close analogy to the classical Hamilton-Jacobi ...},
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}

@article{eggert1997,
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  abstract = {A common need in machine vision is to compute the 3-D rigid body transformation that aligns two sets of points for which correspondence is known. A comparative analysis is presented here of four popular and efficient algorithms, each of which computes the translational and rotational components of the transform in closed form, as the solution to a least squares formulation of the problem. They differ in terms of the transformation representation used and the mathematical derivation of the solution, using respectively singular value decomposition or eigensystem computation based on the standard [R,T] representation, and the eigensystem analysis of matrices derived from unit and dual quaternion forms of the transform. This comparison presents both qualitative and quantitative results of several experiments designed to determine (1) the accuracy and robustness of each algorithm in the presence of different levels of noise, (2) the stability with respect to degenerate data sets, and (3) relative computation time of each approach under different conditions. The results indicate that under ``ideal'' data conditions (no noise) certain distinctions in accuracy and stability can be seen. But for ``typical, real-world'' noise levels, there is no difference in the robustness of the final solutions (contrary to certain previously published results). Efficiency, in terms of execution time, is found to be highly dependent on the computer system setup.},
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}

@article{eriksen2015,
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}

@article{ernzerhof1999,
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}

@article{fales2015,
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}

@article{faver2011,
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}

@article{fedorov2011,
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@article{fernandez-ramos2006,
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}

@book{fernandez2021,
  title = {Aromaticity: Modern Computational Methods and Applications},
  shorttitle = {Aromaticity},
  editor = {Fernandez, Israel},
  year = {2021},
  edition = {First},
  publisher = {{Elsevier}},
  address = {{Cambridge}},
  isbn = {978-0-12-822723-7}
}

@book{fleming2010,
  title = {Molecular {{Orbitals}} and {{Organic Chemical Reactions}}},
  author = {Fleming, Ian},
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  urldate = {2023-06-01},
  isbn = {978-0-470-74658-5 978-0-470-68949-3},
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  file = {/Users/dasirianni/Zotero/storage/ITMPWQ3S/Fleming - 2010 - Molecular Orbitals and Organic Chemical Reactions.pdf}
}

@article{fliegl2005,
  title = {Coupled-Cluster Theory with Simplified Linear-r[Sub 12] Corrections: {{The CCSD}}({{R12}}) Model},
  author = {Fliegl, Heike and Klopper, Wim and H{\"a}ttig, Christof},
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}

@article{fosso-tande2016,
  title = {Large-{{Scale Variational Two-Electron Reduced-Density-Matrix-Driven Complete Active Space Self-Consistent Field Methods}}},
  author = {{Fosso-Tande}, Jacob and Nguyen, Truong-Son and Gidofalvi, Gergely and DePrince III, A Eugene},
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}

@article{fowler1990,
  title = {C6 Dispersion Coefficients in Multiconfiguration Self-Consistent Field Linear Response Theory},
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}

@incollection{francisco2017,
  title = {Chapter 2 - {{Energy Partition Analyses}}: {{Symmetry-Adapted Perturbation Theory}} and {{Other Techniques}}},
  booktitle = {Non-{{Covalent Interactions}} in {{Quantum Chemistry}} and {{Physics}}},
  author = {Francisco, E and Pend{\'a}s, A Mart{\'i}n},
  editor = {{de la Roza}, Alberto Otero and DiLabio, Gino A},
  year = {2017},
  pages = {27--64},
  publisher = {{Elsevier}},
  doi = {10.1016/B978-0-12-809835-6.00003-7},
  isbn = {978-0-12-809835-6},
  file = {/Users/dasirianni/Zotero/storage/KI699DCV/2732721C-8731-44E7-89F4-77D72D19AD51.pdf}
}

@article{fransson,
  title = {{{eChem}}: {{A}} Notebook Exploration of Quantum Chemistry},
  author = {Fransson, Thomas and Delcey, Mickael G and Brumboiu, Iulia Emilia and Hodecker, Manuel and Li, Xin and Rinkevicius, Zilvinas and Dreuw, Andreas and Rhee, Young Min and Norman, Patrick},
  pages = {12},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/58FZ46HM/Fransson et al. - eChem A notebook exploration of quantum chemistry.pdf}
}

@article{fransson2016,
  title = {Four-{{Component Damped Density Functional Response Theory Study}} of {{UV}}/{{Vis Absorption Spectra}} and {{Phosphorescence Parameters}} of {{Group}} 12 {{Metal-Substituted Porphyrins}}},
  author = {Fransson, Thomas and Saue, Trond and Norman, Patrick},
  year = {2016},
  month = apr,
  journal = {J. Chem. Theory Comput.},
  pages = {acs.jctc.6b00030--11},
  doi = {10.1021/acs.jctc.6b00030},
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  file = {/Users/dasirianni/Zotero/storage/ZCZEYLCP/4183F4A9-6587-45F3-9613-B1057C8D9D69.pdf}
}

@article{frederickrmanby2012,
  title = {A {{Simple}}, {{Exact Density-Functional-Theory Embedding Scheme}}},
  author = {Frederick R Manby, Martina Stella Jason D Goodpaster and Miller, Thomas F.},
  year = {2012},
  month = aug,
  pages = {1--5},
  doi = {10.1021/ct300544e},
  abstract = {J. Chem. Theory Comput. 2012.8:2564-2568},
  file = {/Users/dasirianni/Zotero/storage/AI94PW5M/F008F7C7-9849-42C1-B794-1668B562642C.pdf}
}

@article{frey2016,
  title = {Experimental and {{Theoretical Determination}} of {{Dissociation Energies}} of {{Dispersion-Dominated Aromatic Molecular Complexes}}},
  author = {Frey, Jann A and Holzer, Christof and Klopper, Wim and Leutwyler, Samuel},
  year = {2016},
  month = apr,
  journal = {Chem. Rev.},
  pages = {acs.chemrev.5b00652--28},
  doi = {10.1021/acs.chemrev.5b00652},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/JKIHZFQ6/38ABC6A9-C533-4CEF-ADED-32EB42E0FB70.pdf}
}

@article{fukui1981,
  title = {The Path of Chemical Reactions - the {{IRC}} Approach},
  author = {Fukui, Kenichi},
  year = {1981},
  journal = {Accounts of Chemical Research},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/L3I2BH97/Fukui - 1981 - The path of chemical reactions - the IRC approach.pdf}
}

@article{furche2016,
  title = {Accelerating {{Molecular Property Calculations}} with {{Nonorthonormal Krylov Space Methods}}},
  author = {Furche, Filipp and Krull, Brandon T and Nguyen, Brian D and Kwon, Jake},
  year = {2016},
  month = may,
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  number = {17},
  pages = {174105--16},
  doi = {10.1063/1.4947245},
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}

@article{furmanuniversity2020,
  title = {The {{Molecular Education}} and {{Research Consortium}} in {{Undergraduate Computational Chemistry}} ({{MERCURY}}): {{Twenty Years}} of {{Exceptional Success Supporting Undergraduate Research}} and {{Inclusive Excellence}}},
  shorttitle = {The {{Molecular Education}} and {{Research Consortium}} in {{Undergraduate Computational Chemistry}} ({{MERCURY}})},
  author = {{Furman University} and Shields, George},
  year = {2020},
  month = feb,
  journal = {SPUR},
  volume = {3},
  number = {2},
  pages = {5--15},
  issn = {2476101X},
  doi = {10.18833/spur/3/2/1},
  urldate = {2022-07-31},
  abstract = {The author discusses the history of the Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY), which has made significant contributions benefiting science faculty and undergraduates. The peer review publication rate of 1.7 for MERCURY faculty is 3.4 times the average rate for physical science faculty at primarily undergraduate institutions. Since 2001, 888 students have worked on research projects; 75 percent of them have come from underrepresented populations, such as female students or students of color. Approximately half of all graduates have pursued advanced degrees in STEM fields; two-thirds of this group have been female and/or students of color. More than 1,600 people have attended the 18 MERCURY conferences that have hosted 111 speakers, including 61 who were faculty members of color or female.},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/AQ29GF93/Furman University and Shields - 2020 - The Molecular Education and Research Consortium in.pdf}
}

@article{galikov2010,
  title = {{{SORRISO}}: {{Quantum}} Chemistry Tool for Visualization of Electron Transfer Processes},
  author = {Galikov, I and Gruodis, A},
  year = {2010},
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  number = {9},
  pages = {11--16},
  file = {/Users/dasirianni/Zotero/storage/WVQ97LTQ/74588658-94B5-4679-8299-54D12823DBFA.pdf}
}

@article{gauss1991,
  title = {Analytic Energy Gradients for Open-Shell Coupled-Cluster Singles and Doubles ({{CCSD}}) Calculations Using Restricted Open-Shell {{Hartree}}\textemdash{{Fock}} ({{ROHF}}) Reference \textbackslash ldots},
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  abstract = {Abstract The theory of analytic energy gradients for the open-shell single and double excitation coupled-cluster (CCSD) method based on restricted open-shell Hartree\textemdash Fock (ROHF) reference functions is presented. The new CCSD gradient method is applied to ...},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/4GH256Z7/5D0D550E-711A-4D61-B8B7-EC1A2A390534.pdf;/Users/dasirianni/Zotero/storage/7N2AM4LX/5D0D550E-711A-4D61-B8B7-EC1A2A390534.pdf}
}

@article{geertsen1989,
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}

@article{georgakilas2012,
  title = {Functionalization of {{Graphene}}: {{Covalent}} and {{Non-Covalent Approaches}}, {{Derivatives}} and {{Applications}}},
  author = {Georgakilas, Vasilios and Otyepka, Michal and Bourlinos, Athanasios B and Chandra, Vimlesh and Kim, Namdong and Kemp, K Christian and Hobza, Pavel and Zboril, Radek and Kim, Kwang S},
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  file = {/Users/dasirianni/Zotero/storage/KXVKLFBY/Chem. Rev. 2012 Georgakilas.pdf}
}

@incollection{gershoni-poranne2021,
  title = {{{NICS}} \textendash{} {{Nucleus Independent Chemical Shift}}},
  booktitle = {Aromaticity: Modern Computational Methods and Applications},
  author = {{Gershoni-Poranne}, Renana and Stanger, Amnon},
  editor = {Fernandez, Israel},
  year = {2021},
  edition = {First},
  publisher = {{Elsevier}},
  address = {{Cambridge}},
  isbn = {978-0-12-822723-7},
  file = {/Users/dasirianni/Zotero/storage/SUL39VSC/Gershoni-Poranne and Stanger - 2021 - NICS – Nucleus Independent Chemical Shift.pdf}
}

@article{giacinto2014,
  title = {Cl (\textbackslash textminus){{Exchange S N2 Reaction}} inside {{Carbon Nanotubes}}: {{C}}\textendash{{H}}{$\cdot\cdot\cdot\pi$} and {{Cl}}{$\cdot\cdot\cdot\pi$} {{Interactions Govern}} the {{Course}} of the {{Reaction}}},
  author = {Giacinto, Pietro and Bottoni, Andrea and Calvaresi, Matteo and Zerbetto, Francesco},
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  journal = {J. Phys. Chem. C},
  volume = {118},
  number = {9},
  pages = {5032--5040},
  doi = {10.1021/jp412456q},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/UAFATMDH/J. Phys. Chem. C 2014 Giacinto-2.pdf}
}

@article{giner2016,
  title = {A Simple Approach to the State-Specific {{MR-CC}} Using the Intermediate {{Hamiltonian}} Formalism},
  author = {Giner, E and David, G and Scemama, A and Malrieu, J P},
  year = {2016},
  month = feb,
  journal = {J. Chem. Phys.},
  volume = {144},
  number = {6},
  pages = {064101--13},
  doi = {10.1063/1.4940781},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/JVRZPK6U/FB19CE2C-41A3-4729-9E34-9890D8F4D001.pdf}
}

@article{goel2017,
  title = {Variation in {{Free Radical Yields}} from {{U}}.{{S}}. {{Marketed Cigarettes}}},
  author = {Goel, Reema and Bitzer, Zachary and Reilly, Samantha M. and Trushin, Neil and Foulds, Jonathan and Muscat, Joshua and Liao, Jason and Elias, Ryan J. and Richie, John P.},
  year = {2017},
  month = apr,
  journal = {Chem. Res. Toxicol.},
  volume = {30},
  number = {4},
  pages = {1038--1045},
  issn = {0893-228X, 1520-5010},
  doi = {10.1021/acs.chemrestox.6b00359},
  urldate = {2022-02-21},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/2Q6P3T7G/acs.chemrestox.6b00359.pdf;/Users/dasirianni/Zotero/storage/GCR63S7T/Goel et al. - 2017 - Variation in Free Radical Yields from U.S. Markete.pdf}
}

@article{goerigk2015,
  title = {Treating {{London-Dispersion Effects}} with the {{Latest Minnesota Density Functionals}}: {{Problems}} and {{Possible Solutions}}},
  author = {Goerigk, Lars},
  year = {2015},
  month = oct,
  journal = {J. Phys. Chem. Lett.},
  volume = {6},
  number = {19},
  pages = {3891--3896},
  doi = {10.1021/acs.jpclett.5b01591},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/EEECNIKJ/C20E5834-26BC-4F3F-BA07-954D2DD24A9E.pdf}
}

@incollection{goerigk2017,
  title = {Chapter 6 - {{A Comprehensive Overview}} of the {{DFT-D3 London-Dispersion Correction}}},
  booktitle = {Non-{{Covalent Interactions}} in {{Quantum Chemistry}} and {{Physics}}},
  author = {Goerigk, Lars},
  editor = {{de la Roza}, Alberto Otero and DiLabio, Gino A},
  year = {2017},
  pages = {195--219},
  publisher = {{Elsevier}},
  doi = {10.1016/B978-0-12-809835-6.00007-4},
  isbn = {978-0-12-809835-6},
  file = {/Users/dasirianni/Zotero/storage/G63EHNNB/B5AD841D-4195-4190-8F3B-89821FA99022.pdf}
}

@incollection{goerigk2017a,
  title = {Chapter 6 - {{A Comprehensive Overview}} of the {{DFT-D3 London-Dispersion Correction}}},
  booktitle = {Non-{{Covalent Interactions}} in {{Quantum Chemistry}} and {{Physics}}},
  author = {Goerigk, Lars},
  editor = {{de la Roza}, Alberto Otero and DiLabio, Gino A},
  year = {2017},
  pages = {195--219},
  publisher = {{Elsevier}},
  doi = {10.1016/B978-0-12-809835-6.00007-4},
  isbn = {978-0-12-809835-6},
  file = {/Users/dasirianni/Zotero/storage/7JD3WBK4/8B44478A-888C-451A-BAD8-7235FCD31BC1.pdf}
}

@article{golubeva2007,
  title = {Performance of the {{Spin-Flip}} and {{Multireference Methods}} for {{Bond Breaking}} in {{Hydrocarbons}}:\, {{A Benchmark Study}}},
  shorttitle = {Performance of the {{Spin-Flip}} and {{Multireference Methods}} for {{Bond Breaking}} in {{Hydrocarbons}}},
  author = {Golubeva, Anna A. and Nemukhin, Alexandr V. and Klippenstein, Stephen J. and Harding, Lawrence B. and Krylov, Anna I.},
  year = {2007},
  month = dec,
  journal = {J. Phys. Chem. A},
  volume = {111},
  number = {50},
  pages = {13264--13271},
  publisher = {{American Chemical Society}},
  issn = {1089-5639},
  doi = {10.1021/jp0764079},
  urldate = {2022-05-25},
  abstract = {Benchmark results for spin-flip (SF) coupled-cluster and multireference (MR) methods for bond-breaking in hydrocarbons are presented. The nonparallelity errors (NPEs), which are defined as an absolute value of the difference between the maximum and minimum values of the errors in the potential energy along bond-breaking curves, are analyzed for (i) the entire range of nuclear distortions from equilibrium to the dissociation limit and (ii) in the intermediate range (2.5-4.5 \AA ), which is the most relevant for kinetics modeling. For methane, the spin-flip and MR results are compared against full configuration interaction (FCI). For the entire potential energy curves, the NPEs for the SF model with single and double substitutions (SF-CCSD) are slightly less than 3 kcal/mol. Inclusion of triple excitations reduces the NPEs to 0.32 kcal/mol. The corresponding NPEs for the MR-CI are less than 1 kcal/mol, while those of multireference perturbation theory are slightly larger (1.2 kcal/mol). The NPEs in the intermediate range are smaller for all of the methods. The largest errors of 0.35 kcal/mol are observed, surprisingly, for a spin-flip approach that includes triple excitations, while MR-CI, CASPT2, and SF-CCSD curves are very close to each other and are within 0.1-0.2 kcal/mol of FCI. For a larger basis set, the difference between MR-CI and CASPT2 is about 0.2 kcal/mol, while SF-CCSD is within 0.4 kcal/mol of MR-CI. For the C-C bond breaking in ethane, the results of the SF-CCSD are within 1 kcal/mol of MR-CI for the entire curve and within 0.4 kcal/mol in the intermediate region. The corresponding NPEs for CASPT2 are 1.8 and 0.4 kcal/mol, respectively. Including the effect of triples by energy-additivity schemes is found to be insignificant for the intermediate region. For the entire range of nuclear separations, sufficiently large basis sets are required to avoid artifacts at small internuclear separations.},
  file = {/Users/dasirianni/Zotero/storage/IJR4GRU9/Golubeva et al. - 2007 - Performance of the Spin-Flip and Multireference Me.pdf;/Users/dasirianni/Zotero/storage/D5HVHCBS/jp0764079.html}
}

@article{goodpaster2014,
  title = {Accurate and Systematically Improvable Density Functional Theory Embedding for Correlated Wavefunctions},
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}

@article{goodpaster2016,
  title = {Identification of {{Possible Pathways}} for {{C}}\textendash{{C Bond Formation}} during {{Electrochemical Reduction}} of {{CO}} 2: {{New Theoretical Insights}} from an {{Improved Electrochemical Model}}},
  author = {Goodpaster, Jason D and Bell, Alexis T and {Head-Gordon}, Martin},
  year = {2016},
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  number = {8},
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}

@article{gordon2012,
  title = {Fragmentation {{Methods}}: {{A Route}} to {{Accurate Calculations}} on {{Large Systems}}},
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}

@book{gower2004,
  title = {Procrustes {{Problems}}},
  author = {Gower, J C and Dijksterhuis, G B},
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  publisher = {{OUP Oxford}},
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}

@article{grafova2010,
  title = {Comparative {{Study}} of {{Selected Wave Function}} and {{Density Functional Methods}} for {{Noncovalent Interaction Energy Calculations Using}} the {{Extended S22 Data Set}}},
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@article{grason2016,
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@article{grimme2003,
  title = {Improved Second-Order {{M\o ller}}\textendash{{Plesset}} Perturbation Theory by Separate Scaling of Parallel- and Antiparallel-Spin Pair Correlation Energies},
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}

@article{grimme2004,
  title = {Accurate Description of van Der {{Waals}} Complexes by Density Functional Theory Including Empirical Corrections},
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}

@article{grimme2006,
  title = {Semiempirical Hybrid Density Functional with Perturbative Second-Order Correlation},
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}

@article{grimme2006a,
  title = {Semiempirical {{GGA-type}} Density Functional Constructed with a Long-Range Dispersion Correction},
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  pages = {1787--1799},
  publisher = {{Wiley Subscription Services, Inc., A Wiley Company}},
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}

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@article{grimme2010,
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@article{grimme2011,
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}

@article{grimme2016,
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}

@article{grimme2017,
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@article{grimsley2019,
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  address = {{Berlin [u.a.] :}}
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@article{gyorffy2013,
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@article{hagfeldt2010,
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@article{handy1993,
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@article{hattig2012,
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@article{hawkins2007,
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@article{hedegard2016,
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@article{hegely2016,
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@book{helgaker2000,
  title = {Molecular Electronic-Structure Theory},
  author = {Helgaker, Trygve and J{\o}rgensen, Poul and Olsen, Jeppe},
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  publisher = {{John Wiley \& Sons Inc}},
  abstract = {Ab initio quantum chemistry has emerged as an important tool in chemical research and is appliced to a wide variety of problems in chemistry and molecular physics. Recent developments of computational methods have enabled previously intractable chemical problems to be solved using rigorous quantum-mechanical methods. This is the first comprehensive, up-to-date and technical work to cover all the important aspects of modern molecular electronic-structure theory. Topics covered in the book include: * Second quantization with spin adaptation * Gaussian basis sets and molecular-integral evaluation * Hartree-Fock theory * Configuration-interaction and multi-configurational self-consistent theory * Coupled-cluster theory for ground and excited states * Perturbation theory for single- and multi-configurational states * Linear-scaling techniques and the fast multipole method * Explicity correlated wave functions * Basis-set convergence and extrapolation * Calibration and benchmarking of computational methods, with applications to moelcular equilibrium structure, atomization energies and reaction enthalpies. Molecular Electronic-Structure Theory makes extensive use of numerical examples, designed to illustrate the strengths and weaknesses of each method treated. In addition, statements about the usefulness and deficiencies of the various methods are supported by actual examples, not just model calculations. Problems and exercises are provided at the end of each chapter, complete with hints and solutions. This book is a must for researchers in the field of quantum chemistry as well as for nonspecialists who wish to acquire a thorough understanding of ab initio molecular electronic-structure theory and its applications to problems in chemistry and physics. It is also highly recommended for the teaching of graduates and advanced undergraduates.},
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  langid = {english}
}

@article{helgaker2012,
  title = {Recent {{Advances}} in {{Wave Function-Based Methods}} of {{Molecular-Property Calculations}}},
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@article{herbert2021,
  title = {Neat, {{Simple}}, and {{Wrong}}: {{Debunking Electrostatic Fallacies Regarding Noncovalent Interactions}}},
  shorttitle = {Neat, {{Simple}}, and {{Wrong}}},
  author = {Herbert, John M.},
  year = {2021},
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  abstract = {Multipole moments such as charge, dipole, and quadrupole are often invoked to rationalize intermolecular phenomena, but a low-order multipole expansion is rarely a valid description of electrostatics at the length scales that characterize nonbonded interactions. This is illustrated by examining several common misunderstandings rooted in erroneous electrostatic arguments. First, the notion that steric repulsion originates in Coulomb interactions is easily disproved by dissecting the interaction potential for Ar2. Second, the Hunter-Sanders model of {$\pi-\pi$} interactions, which is based on quadrupolar electrostatics, is shown to have no basis in accurate calculations. Third, curved ``buckybowls'' exhibit unusually large dipole moments, but these are ancillary to the forces that control their intermolecular interactions, as illustrated by two examples involving corannulene. Finally, the assumption that interactions between water and small anions are dictated by the dipole moment of H2O is shown to be false in the case of binary halide-water complexes. These examples present a compelling case that electrostatic explanations based on low-order multipole moments are very often counterfactual for nonbonded interactions at close range and should not be taken seriously in the absence of additional justification.},
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  file = {/Users/dasirianni/Zotero/storage/XTDAQ6I5/Herbert - 2021 - Neat, Simple, and Wrong Debunking Electrostatic F.pdf}
}

@article{hesselmann2005,
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@article{hesselmann2008,
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}

@article{hesselmann2011,
  title = {On the Accuracy of {{DFT-SAPT}}, {{MP2}}, {{SCS-MP2}}, {{MP2C}}, and {{DFT}}+{{Disp}} Methods for the Interaction Energies of Endohedral Complexes of the {{C}} 60fullerene with a Rare Gas Atom},
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  volume = {13},
  number = {2},
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  publisher = {{The Royal Society of Chemistry}},
  doi = {10.1039/C0CP00968G},
  abstract = {Selected points on the potential energy surface for the complexes Rg@C60 (Rg = He, Ne, Ar, Kr) are calculated with various theoretical methods, like symmetry-adapted perturbation theory with monomers described by density functional theory (DFT-SAPT), supermolecular M\o ller\textendash Plesset theory truncated on the second order (MP2), spin-component-scaled MP2 (SCS-MP2), supermolecular density functional theory with empirical dispersion correction (DFT+Disp), and the recently developed MP2C method that improves the MP2 method for long-range electron correlation effects. A stabilization of the endohedral complex is predicted by all methods, but the depth of the potential energy well is overestimated by the DFT+Disp and MP2 approaches. On the other hand, the MP2C model agrees well with DFT-SAPT, which serves as the reference. The performance of SCS-MP2 is mixed: it produces too low interaction energies for the two heavier guests, while its accuracy for He@C60 and Ne@C60 is similar to that of MP2C. Fitting formulas for the main interaction energy components, i.e. the dispersion and first-order repulsion energies are proposed, which are applicable for both endo- and exohedral cases. For all examined methods density fitting is used to evaluate two-electron repulsion integrals, which is indispensable to allow studies of noncovalent complexes of this size. It has been found that density-fitting auxiliary basis sets cannot be used in a black-box fashion for the calculation of the first-order SAPT electrostatic energy, and that the quality of these basis sets should be always carefully examined in order to avoid an unphysical long-range behavior.},
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  file = {/Users/dasirianni/Zotero/storage/3D8R7AWY/3E712226-C573-4C76-9947-51596747B84A.pdf;/Users/dasirianni/Zotero/storage/GRUSUDX2/3E712226-C573-4C76-9947-51596747B84A.pdf}
}

@article{hesselmann2013,
  title = {On the {{Short-Range Behavior}} of {{Correlated Pair Functions}} from the {{Adiabatic-Connection Fluctuation}}\textendash{{Dissipation Theorem}} of {{Density-Functional Theory}}},
  author = {He{\ss}elmann, Andreas and G{\"o}rling, Andreas},
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}

@article{hesselmann2014,
  title = {Intermolecular Symmetry-Adapted Perturbation Theory Study of Large Organic Complexes},
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}

@article{hill2009,
  title = {Extrapolating {{MP2}} and {{CCSD}} Explicitly Correlated Correlation Energies to the Complete Basis Set Limit with First and Second Row Correlation Consistent Basis Sets},
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}

@article{hinze1973,
  title = {{{MC-SCF}}. {{I}}. {{The}} Multi-Configuration Self-Consistent-Field Method},
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}

@article{hofener2010,
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}

@article{hoffmann1968a,
  title = {Benzynes, Dehydroconjugated Molecules, and the Interaction of Orbitals Separated by a Number of Intervening Sigma Bonds},
  author = {Hoffmann, Roald and Imamura, Akira and Hehre, Warren J.},
  year = {1968},
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  publisher = {{American Chemical Society}},
  issn = {0002-7863},
  doi = {10.1021/ja01008a018},
  urldate = {2022-05-25},
  file = {/Users/dasirianni/Zotero/storage/TAZ7XB5Q/Hoffmann et al. - 1968 - Benzynes, dehydroconjugated molecules, and the int.pdf;/Users/dasirianni/Zotero/storage/ECD8TZ7D/ja01008a018.html}
}

@article{hoffmann1971,
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  year = {1971},
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  publisher = {{American Chemical Society}},
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  doi = {10.1021/ar50037a001},
  urldate = {2022-05-02},
  file = {/Users/dasirianni/Zotero/storage/U3FGXVU4/Hoffmann - 1971 - Interaction of orbitals through space and through .pdf;/Users/dasirianni/Zotero/storage/UJJWFS3F/ar50037a001.html}
}

@article{hoffmann2015,
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  author = {Hoffmann, Roald},
  year = {2015},
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  volume = {103},
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  pages = {18},
  issn = {0003-0996, 1545-2786},
  doi = {10.1511/2015.112.18},
  urldate = {2022-05-09}
}

@article{hohenstein2009,
  title = {Effects of {{Heteroatoms}} on {{Aromatic}} {$\Pi\backslash$}textminus{$\pi$} {{Interactions}}: {{Benzene}}\textbackslash{{textminusPyridine}} and {{Pyridine Dimer}}},
  author = {Hohenstein, Edward G and Sherrill, C David},
  year = {2009},
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  number = {5},
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  file = {/Users/dasirianni/Zotero/storage/54GIVX32/J. Phys. Chem. A 2009 Hohenstein.pdf}
}

@article{hohenstein2010,
  title = {Density Fitting and {{Cholesky}} Decomposition Approximations in Symmetry-Adapted Perturbation Theory: {{Implementation}} and Application to Probe the Nature of {$\pi$}-{$\pi$} Interactions in Linear Acenes},
  author = {Hohenstein, Edward G and Sherrill, C David},
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  volume = {132},
  number = {18},
  pages = {184111},
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  file = {/Users/dasirianni/Zotero/storage/CH9Q8JH3/J. Chem. Phys. 2010 Hohenstein.pdf;/Users/dasirianni/Zotero/storage/SIPVVTRZ/J. Chem. Phys. 2010 Hohenstein.pdf}
}

@article{hohenstein2011,
  title = {Wavefunction Methods for Noncovalent Interactions},
  author = {Hohenstein, Edward G and Sherrill, C David},
  year = {2011},
  month = jul,
  journal = {WIREs Comput. Mol. Sci.},
  volume = {2},
  number = {2},
  pages = {304--326},
  publisher = {{John Wiley \& Sons, Inc.}},
  doi = {10.1002/wcms.84},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/5YC5AD2A/WIREs Comput. Mol. Sci. 2011 Hohenstein.pdf;/Users/dasirianni/Zotero/storage/DRIKIU5T/WIREs Comput. Mol. Sci. 2011 Hohenstein.pdf}
}

@article{hohenstein2011a,
  title = {Large-Scale Symmetry-Adapted Perturbation Theory Computations via Density Fitting and {{Laplace}} Transformation Techniques: {{Investigating}} the Fundamental Forces of {{DNA-intercalator}} Interactions},
  author = {Hohenstein, Edward G and Parrish, Robert M and Sherrill, C David and Turney, Justin M and Schaefer, Henry F},
  year = {2011},
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  volume = {135},
  number = {17},
  pages = {174107--14},
  doi = {10.1063/1.3656681},
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}

@phdthesis{hohenstein2011b,
  title = {Implementation and {{Applications}} of {{Density-Fitted Symmetry-Adapted Perturbation Theory}}},
  author = {Hohenstein, Edward G},
  year = {2011},
  file = {/Users/dasirianni/Zotero/storage/9QJJPL5P/A9F3FCB6-1173-45B7-BAE9-97B5F77BA21C.pdf}
}

@article{hohenstein2012,
  title = {Wavefunction Methods for Noncovalent Interactions},
  author = {Hohenstein, Edward G and Sherrill, C David},
  year = {2012},
  journal = {WIREs Computational Molecular Science},
  volume = {2},
  number = {2},
  pages = {304--326},
  publisher = {{John Wiley \& Sons, Ltd}},
  doi = {10.1002/wcms.84},
  langid = {english}
}

@article{hohenstein2012a,
  title = {Communication: {{Tensor}} Hypercontraction. {{III}}. {{Least-squares}} Tensor Hypercontraction for the Determination of Correlated Wavefunctions},
  author = {Hohenstein, Edward G and Parrish, Robert M and Sherrill, C David and Mart{\'i}nez, Todd J},
  year = {2012},
  journal = {J. Chem. Phys.},
  volume = {137},
  number = {22},
  pages = {221101},
  doi = {10.1063/1.4768241},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/GG7HJ3YY/J. Chem. Phys. 2012 Hohenstein.pdf}
}

@article{hohenstein2015,
  title = {An Atomic Orbital-Based Formulation of the Complete Active Space Self-Consistent Field Method on Graphical Processing Units},
  author = {Hohenstein, Edward G and Luehr, Nathan and Ufimtsev, Ivan S and Mart{\'i}nez, Todd J},
  year = {2015},
  month = jun,
  journal = {J. Chem. Phys.},
  volume = {142},
  number = {22},
  pages = {224103--10},
  doi = {10.1063/1.4921956},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/ALZ5KMF9/146FBFF4-2774-475B-9EF4-D00E0ABD8438.pdf;/Users/dasirianni/Zotero/storage/IPLT8Z5K/146FBFF4-2774-475B-9EF4-D00E0ABD8438.pdf}
}

@article{hollett2011,
  title = {The Two Faces of Static Correlation},
  author = {Hollett, Joshua W and Gill, Peter M W},
  year = {2011},
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  volume = {134},
  number = {11},
  pages = {114111--6},
  doi = {10.1063/1.3570574},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/RX5TWBLA/98C6A481-237F-46B1-B4A8-BA0688C0BAFD.pdf}
}

@article{hollman2015,
  title = {A Tight Distance-Dependent Estimator for Screening Three-Center {{Coulomb}} Integrals over {{Gaussian}} Basis Functions},
  author = {Hollman, David S and Schaefer, Henry F and Valeev, Edward F},
  year = {2015},
  month = apr,
  journal = {J. Chem. Phys.},
  volume = {142},
  number = {15},
  pages = {154106--11},
  doi = {10.1063/1.4917519},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/7HQL77I6/12DA3D4B-08BA-4A13-9789-7A34FC200EDE.pdf}
}

@article{hopmann2019,
  title = {How {{To Make Your Computational Paper Interesting}} and {{Have It Published}}},
  author = {Hopmann, Kathrin H},
  year = {2019},
  month = feb,
  journal = {Organometallics},
  volume = {38},
  number = {3},
  pages = {603--605},
  publisher = {{American Chemical Society}},
  doi = {10.1021/acs.organomet.8b00942},
  file = {/Users/dasirianni/Zotero/storage/EJJ4UR6L/71C91A0C-E259-49DC-9D36-E2A606A33A42.pdf}
}

@article{horn1987,
  title = {Closed-Form Solution of Absolute Orientation Using Unit Quaternions},
  author = {Horn, B K P},
  year = {1987},
  journal = {J. Opt. Soc. Am. A},
  volume = {4},
  number = {4},
  pages = {629--642},
  abstract = {Finding the relationship between two coordinate systems using pairs of measurements of the coordinates of a number of points in both systems is a classic photogrammetric task. It finds applications in stereophotogrammetry and in robotics. I present here a closed-form solution to the least-squares problem for three or more points. Currently various empirical, graphical, and numerical iterative methods are in use. Derivation of the solution is simplified by use of unit quaternions to represent rotation. I emphasize a symmetry property that a solution to this problem ought to possess. The best translational offset is the difference between the centroid of the coordinates in one system and the rotated and scaled centroid of the coordinates in the other system. The best scale is equal to the ratio of the root-mean-square deviations of the coordinates in the two systems from their respective centroids. These exact results are to be preferred to approximate methods based on measurements of a few selected points. The unit quaternion representing the best rotation is the eigenvector associated with the most positive eigenvalue of a symmetric 4 \texttimes{} 4 matrix. The elements of this matrix are combinations of sums of products of corresponding coordinates of the points.},
  file = {/Users/dasirianni/Zotero/storage/NT4KSN3I/B6328058-3EE2-4EDB-8837-5A103CFE8AA3.pdf}
}

@article{horn1988,
  title = {Closed-Form Solution of Absolute Orientation Using Orthonormal Matrices},
  author = {Horn, B K P and Hilden, H M and Negahdaripour, S},
  year = {1988},
  journal = {J. Opt. Soc. Am. A},
  volume = {5},
  number = {7},
  pages = {1127--1135},
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}

@article{horn2016,
  title = {Probing Non-Covalent Interactions with a Second Generation Energy Decomposition Analysis Using Absolutely Localized Molecular Orbitals},
  author = {Horn, Paul and Mao, Yuezhi and {Head-Gordon}, Martin},
  year = {2016},
  journal = {Phys. Chem. Chem. Phys.},
  pages = {1--16},
  doi = {10.1039/C6CP03784D},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/M6264YJR/92078E5D-254B-4CD9-8DB1-531A7B0DD894.pdf}
}

@article{hsu2010,
  title = {{{ARTICLE IN PRESS}}},
  author = {Hsu, Shih-Chieh and Lu, Chungsying and Su, Fengsheng and Zeng, Wanting and Chen, Wenfa},
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  volume = {65},
  number = {4},
  pages = {1354--1361},
  publisher = {{Elsevier}},
  doi = {10.1016/j.ces.2009.10.005},
  langid = {english}
}

@article{hu2015,
  title = {Excited-{{State Geometry Optimization}} with the {{Density Matrix Renormalization Group}}, as {{Applied}} to {{Polyenes}}},
  author = {Hu, Weifeng and Chan, Garnet Kin-Lic},
  year = {2015},
  month = jul,
  journal = {J. Chem. Theory Comput.},
  volume = {11},
  number = {7},
  pages = {3000--3009},
  doi = {10.1021/acs.jctc.5b00174},
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  file = {/Users/dasirianni/Zotero/storage/J9NMESJ9/8C945137-53F5-493C-9124-965F5DCC5087.pdf}
}

@article{huang2007,
  title = {Simulations of {{Binary Mixture Adsorption}} of {{Carbon Dioxide}} and {{Methane}} in {{Carbon Nanotubes}}: {{Temperature}}, {{Pressure}}, and {{Pore Size Effects}}},
  author = {Huang, Liangliang and Zhang, Luzheng and Shao, Qing and Lu, Linghong and Lu, Xiaohua and Jiang, Shaoyi and Shen, Wenfeng},
  year = {2007},
  month = aug,
  journal = {J. Phys. Chem. C},
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  number = {32},
  pages = {11912--11920},
  doi = {10.1021/jp067226u},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/7KZR68JG/J. Phys. Chem. C 2007 Huang.pdf}
}

@article{huang2008,
  title = {Advances in {{Correlated Electronic Structure Methods}} for {{Solids}}, {{Surfaces}}, and {{Nanostructures}}},
  author = {Huang, Patrick and Carter, Emily A},
  year = {2008},
  month = may,
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  file = {/Users/dasirianni/Zotero/storage/F8MS5FCD/C364FA17-3E4D-439E-B0E0-AEB365777ADA.pdf}
}

@article{huang2011,
  title = {Quantum Mechanical Embedding Theory Based on a Unique Embedding Potential},
  author = {Huang, Chen and Pavone, Michele and Carter, Emily A},
  year = {2011},
  month = apr,
  journal = {J. Chem. Phys.},
  volume = {134},
  number = {15},
  pages = {154110--11},
  doi = {10.1063/1.3577516},
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  file = {/Users/dasirianni/Zotero/storage/YTK4CYLT/238399CA-5F4E-4499-A002-B1551D525CBE.pdf}
}

@article{huang2011a,
  title = {Quantum Mechanical Embedding Theory Based on a Unique Embedding Potential},
  author = {Huang, Chen and Pavone, Michele and Carter, Emily A},
  year = {2011},
  month = apr,
  journal = {J. Chem. Phys.},
  volume = {134},
  number = {15},
  pages = {154110--12},
  doi = {10.1063/1.3577516},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/X692F78I/8A08EB3E-14A9-4D0D-82AC-4A7DAE389A69.pdf}
}

@article{huang2011b,
  title = {Potential-Functional Embedding Theory for Molecules and Materials},
  author = {Huang, Chen and Carter, Emily A},
  year = {2011},
  month = nov,
  journal = {J. Chem. Phys.},
  volume = {135},
  number = {19},
  pages = {194104--17},
  doi = {10.1063/1.3659293},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/EW8UHRUX/EE5A08CC-0705-4453-B50D-28BE7836B7E3.pdf}
}

@article{huang2013,
  title = {Accelerating {{MP2C}} Dispersion Corrections for Dimers and Molecular Crystals},
  author = {Huang, Yuanhang and Shao, Yihan and Beran, Gregory J O},
  year = {2013},
  journal = {J. Chem. Phys.},
  volume = {138},
  number = {22},
  pages = {224112--9},
  doi = {10.1063/1.4809981},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/ZQJZNNLY/2651EA13-24B9-4BA9-9346-2E27B6B8842E.pdf}
}

@article{huang2016,
  title = {Patching the {{Exchange-Correlation Potential}} in {{Density Functional Theory}}},
  author = {Huang, Chen},
  year = {2016},
  month = apr,
  journal = {J. Chem. Theory Comput.},
  pages = {acs.jctc.6b00051--10},
  doi = {10.1021/acs.jctc.6b00051},
  langid = {english},
  file = {/Users/dasirianni/Zotero/storage/WCSF3MQG/C301D968-63F5-4681-BA13-57D34A9187D9.pdf}
}

@article{hubert2016,
  title = {Investigation of {{Multiconfigurational Short-Range Density Functional Theory}} for {{Electronic Excitations}} in {{Organic Molecules}}},
  author = {Hubert, Micka{\"e}l and Hedeg{\aa}rd, Erik D and Jensen, Hans Jo{$\not$}rgen Aa},
  year = {2016},
  month = may,
  journal = {J. Chem. Theory Comput.},
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  number = {5},
  pages = {2203--2213},
  doi = {10.1021/acs.jctc.5b01141},
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  file = {/Users/dasirianni/Zotero/storage/J27MTSYD/56A7B55A-B1EE-4CE4-8C3A-613D787ED367.pdf;/Users/dasirianni/Zotero/storage/M6QMXDUD/56A7B55A-B1EE-4CE4-8C3A-613D787ED367.pdf}
}

@article{hundt2014,
  title = {Vibrational {{Activation}} of {{Methane Chemisorption}}: {{The Role}} of {{Symmetry}}},
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  journal = {J. Phys. Chem. Lett.},
  volume = {5},
  number = {11},
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  doi = {10.1021/jz500728d},
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  file = {/Users/dasirianni/Zotero/storage/EQA7AYCY/J. Phys. Chem. Lett. 2014 Hundt.pdf}
}

@article{hwang2018,
  title = {Tipping the {{Balance}} between {{S-$\pi$}} and {{O-$\pi$ Interactions}}},
  author = {Hwang, Jungwun and {ORCID: 0000-0001-9339-3111}, Ping Li and Smith, Mark D and Warden, Constance E and Sirianni, Dominic A and Vik, Erik C and Maier, Josef M and Yehl, Christopher J and Sherrill, C David and {ORCID: 0000-0002-0229-6541}, Ken D Shimizu},
  year = {2018},
  month = sep,
  journal = {J. Am. Chem. Soc.},
  pages = {1--7},
  publisher = {{American Chemical Society}},
  doi = {10.1021/jacs.8b07617},
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}

@article{igarashi2023,
  title = {Development of a {{GCN-based}} Model to Predict {\emph{in Vitro}} Phototoxicity from the Chemical Structure and {{HOMO-LUMO}} Gap},
  author = {Igarashi, Yoshinobu and Re, Suyong and Kojima, Ryosuke and Okuno, Yasushi and Yamada, Hiroshi},
  year = {2023},
  journal = {The Journal of Toxicological Sciences},
  volume = {48},
  number = {5},
  pages = {243--249},
  doi = {10.2131/jts.48.243},
  abstract = {The interaction between sunlight and drugs can lead to phototoxicity in patients who have received such drugs. Phototoxicity assessment is a regulatory requirement globally and one of the main toxicity screening steps in the early stages of drug discovery. An in silico-in vitro approach has been utilized mainly for toxicology assessments at these stages. Although several quantitative structure-activity relationship (QSAR) models for phototoxicity have been developed, in silico technology to evaluate phototoxicity has not been well established. In this study, we attempted to develop an artificial intelligence (AI) model to predict the in vitro Neutral Red Uptake Phototoxicity Test results from a chemical structure and its derived information. To accomplish this, we utilized an open-source software library, kMoL. kMoL employs a graph convolutional neural networks (GCN) approach, which allows it to learn the data for the specified chemical structure. kMoL also utilizes the integrated gradient (IG) method, enabling it to visually display the substructures contributing to any positive results. To construct this AI model, we used only the chemical structure as a basis, then added the descriptors and the HOMO-LUMO gap, which was obtained from quantum chemical calculations. As a result, the assortment of chemical structures and the HOMO-LUMO gap produced an AI model with high discrimination performance, and an F1 score of 0.857. Additionally, our AI model could visualize the substructures involved in phototoxicity using the IG method. Our AI model can be applied as a toxicity screening method and could enhance productivity in drug development.},
  keywords = {Deep learning,Explainable artificial intelligence,Graph convolutional neural networks,HOMO-LUMO gap,In vitro 3T3 NRU-PT,Phototoxicity},
  file = {/Users/dasirianni/Zotero/storage/6U96C3EP/Igarashi et al. - 2023 - Development of a GCN-based model to predict in .pdf;/Users/dasirianni/Zotero/storage/KLKLQQSA/_article.html}
}

@article{ilyin2019,
  title = {First-Principles\textendash Based Reaction Kinetics from Reactive Molecular Dynamics Simulations: {{Application}} to Hydrogen Peroxide Decomposition},
  shorttitle = {First-Principles\textendash Based Reaction Kinetics from Reactive Molecular Dynamics Simulations},
  author = {Ilyin, Daniil V. and Goddard, William A. and Oppenheim, Julius J. and Cheng, Tao},
  year = {2019},
  month = sep,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {116},
  number = {37},
  pages = {18202--18208},

license_type: permissive

branch_name: refs/heads/master

extension: bib