Bibliography

1
Cacelli, I.; Prampolini, G. Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations J. Chem. Theory Comput. 2007, 3, 1803-1817.

2
Prampolini, G.; Livotto, P. R.; Cacelli, I. Accuracy of Quantum Mechanically Derived Force-Fields Parameterized from Dispersion-Corrected DFT Data: The Benzene Dimer as a Prototype for Aromatic Interactions. J. Chem. Theory Comput. 2015, 11, 5182-96.

3
Vilhena, J. G.; Greff da Silveira, L.; Livotto, P. R.; Cacelli, I.; Prampolini, G. Automated Parameterization of Quantum Mechanically Derived Force Fields for Soft Materials and Complex Fluids: Development and Validation J. Chem. Theory Comput. 2021, 17, 4449-4464.

4
Prampolini, G.; Silveira, L. G. D.; Vilhena, J. G.; Livotto, P. R. Predicting Spontaneous Orientational Self-Assembly: In Silico Design of Materials with Quantum Mechanically Derived Force Fields J. Phys. Chem. Lett. 2022, 13, 243-250.

5
Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon: Oxford, 1987.

6
Frenkel, D.; Smith, B. Understanding Molecular Simulations; Academic Press: San Diego, 1996.

7
Maier, J. A.; Martinez, C.; Kasavajhala, K.; Wickstrom, L.; Hauser, K. E.; Simmerling, C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB J. Chem. Theory Comput. 2015, 11, 3696-3713; PMID: 26574453.

8
Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174.

9
Jorgensen, W. L.; Maxwell, D. S.; Tirado-rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236.

10
Jorgensen, W. L.; Tirado-Rives, J. Potential Energy Functions for Atomic-Level Simulations of Water and Organic and Biomolecular Systems. Proc. Natl. Acad. Sci. USA 2005, 102, 6665-70.

11
Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The biomolecular simulation program J. Comp. Chem. 2009, 30, 1545-1614.

12
Prampolini, G.; Cerezo, J.; Giannni; De Mitri, N.; Cacelli, I.; JOYCE3.0, intra-molecular force field parameterization software, available free of charge at http://www.iccom.cnr.it/en/joyce-2/; 2024.

13
Martinez, P. M.; Piras, A.; Cerezo, J.; Galvez, J. P.; Giannini, S.; A., L.; Padula, D.; Semmeq, A.; Vilhena, J. G.; Prampolini, G.; JOYCE website, visit: https://joyce-documentation.gitlab.io/; 2024.

14
Wang, J.; Wang, W.; P. A., K.; D. A., C.; Tirado-Rives, J. Automatic atom type and bond type perception in molecular mechanical calculations J. Mol. Graph. Model. 2006, 25, 247260.

15
Dodda, L. S.; Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands Nucleic Acids Res. 2017, 45, W331-W336.

16
Procacci, P. PrimaDORAC: A Free Web Interface for the Assignment of Partial Charges, Chemical Topology, and Bonded Parameters in Organic or Drug Molecules J. Chem. Inf. Mod. 2017, 57, 1240-1245.

17
Morado, J.; Mortenson, P. N.; Verdonk, M. L.; Ward, R. A.; Essex, J. W.; Skylaris, C.-K. ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields J. Chem. Inf. Mod. 2021, 61, 2026-2047.

18
Abraham, M. J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J. C.; Hess, B.; Lindahl, E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers SoftwareX 2015, 1-2, 19 - 25.

19
Santoro, F.; Cerezo, J.; $ \mathcal{FC}classes$3, a code for vibronic calculations. Available from http://www.iccom.cnr.it/en/fcclasses; 2019.

20
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; Zakrzewski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J.; GAUSSIAN16 Revision D.02; 2016; Gaussian Inc. Wallingford CT.

21
Cerezo, J.; Prampolini, G.; Cacelli, I. Developing accurate intramolecular force fields for conjugated systems through explicit coupling terms Theor. Chem. Accounts 2018, 137, 80.

22
Cacelli, I.; Cimoli, A.; Livotto, P. R.; Prampolini, G. An Automated Approach for the Parameterization of Accurate Intermolecular Force-Fields: Pyridine as a Case Study. J. Comp. Chem. 2012, 33, 1055.

23
Prampolini, G.; Cimoli, A.; Cacelli, I.; PICKY3.0, a Fortran 77 code for inter-molecular force field parameterization, available free of charge of at http://www.iccom.cnr.it/en/picky-en/; 2020.

24
Cerezo, J.; Tools to interface $ \mathcal{FC}classes$3 with quantum chemistry codes, visit: https://github.com/jcerezochem/fcc_tools; 2022.

25
Padula, D.; A program to automatically select and group internal coordinates given a geometry. The output is a GROMACS topology ready to be used with the JOYCE program, to parameterise a Force Field., https://github.com/dpadula85/SelIntCoords; 2024.

26
Thompson, A. P.; Aktulga, H. M.; Berger, R.; Bolintineanu, D. S.; Brown, W. M.; Crozier, P. S.; in 't Veld, P. J.; Kohlmeyer, A.; Moore, S. G.; Nguyen, T. D.; Shan, R.; Stevens, M. J.; Tranchida, J.; Trott, C.; Plimpton, S. J. LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales Comp. Phys. Comm. 2022, 271, 108171.

27
Turner, P. XMGRACE, Version 5.1. 19 Center for coastal and land-margin research, Oregon Graduate Institute of Science and Technology, Beaverton, OR 2005, 2, 19.

28
Giannini, S.; Martinez, P.; Semmeq, A.; Galvez, J.; Piras, A.; Landi, A.; Padula, D.; Santoro, F.; Vilhena, J.; Cerezo, J.; Prampolini, G. JOYCE3.0: A General Purpose Protocol for the Specific Parameterization of Accurate Intramolecular Quantum Mechanically Derived Force-Fields J. Chem. Theory Comput. 2024, submitted.

29
Barone, V.; Cacelli, I.; De Mitri, N.; Licari, D.; Monti, S.; Prampolini, G. Joyce and Ulysses: Integrated and User-Friendly Tools for the Parameterization of Intramolecular Force Fields from Quantum Mechanical Data. Phys. Chem. Chem. Phys. 2013, 15, 3736-51.

30
Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J. Y.; Wang, L.; Lupyan, D.; Dahlgren, M. K.; Knight, J. L.; Kaus, J. W.; Cerutti, D. S.; Krilov, G.; Jorgensen, W. L.; Abel, R.; Friesner, R. A. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins J. Chem. Theory Comput. 2016, 12, 281-296.

31
Cerezo, J.; Gromacs version 4.5.5 with coupling terms, https://github.com/jcerezochem/gromacs455_couplings; 2020.

32
Cerezo, J.; Aranda, D.; Avila Ferrer, F. J.; Prampolini, G.; Santoro, F. Adiabatic-Molecular Dynamics Generalized Vertical Hessian Approach: A Mixed Quantum Classical Method to Compute Electronic Spectra of Flexible Molecules in the Condensed Phase J. Chem. Theory Comput. 2020, 16, 1215-1231.

33
Pulay, P.; Fogarasi, G. Geometry optimization in redundant internal coordinates J. Chem. Phys. 1992, 96, 2856.

34
Peng, C.; Ayala, P.; Shlegel, H.; Frisch, M. Using Redundant Internal Coordinates to Optimize Equilibrium Geometries and Transition States J. Comp. Chem. 1996, 17, 49.

35
Dasgupta, S.; Goddard III, W. Hessian biased force fields from combining theory and experiment J. Chem. Phys. 1989, 90, 7207.

36
Bakken, V.; Helgaker, T. The efficient optimization of molecular geometries using redundant internal coordinates J. Chem. Phys. 2002, 117, 9160.

37
Dasgupta, S.; Yamasaki, T.; Goddard III, W. The Hessian biased singular value decomposition method for optimization and analysis of force fields J. Chem. Phys. 1996, 104, 2898.

38
Press, W.; Teukolsky, S.; Vetterling, W.; Flannery, B. Numerical Recipies in Fortran 77; Cambridge University Press: Cambridge, 1992.

39
Maple, J.; Hwang, M.-J.; Stockfish, T.; Dinur, U.; Waldman, M.; Ewig, C.; Hagler, A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 J. Comp. Chem. 1994, 15, 162.