6. References¶
David van der Spoel, Julián Marrades, Kristian Kříž, A. Najla Hosseini, Alfred T. Nordman, João Paulo Ataide Martins, Marie-Madeleine Walz, Paul J. van Maaren, and Mohammad M. Ghahremanpour. Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space. Digit. Discovery, 4:1925–1935, 2025. doi:10.1039/d5dd00178a.
David van der Spoel and Erik Lindahl. Brute-Force Molecular Dynamics Simulations of Villin Headpiece: Comparison with NMR Parameters. J. Phys. Chem. B, 107(40):11178–11187, 2003. doi:10.1021/jp034108n.
Oliver F Lange, David van der Spoel, and Bert L de Groot. Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data. Biophys. J., 99:647–655, 2010. doi:10.1016/j.bpj.2010.04.062.
Haiyang Zhang, Chunhua Yin, Yang Jiang, and David van der Spoel. Force field benchmark of amino acids: i. hydration and diffusion in different water models. J. Chem. Inf. Model., 58:1037–1052, 2018.
Zahedeh Bashardanesh and David van der Spoel. Impact of dispersion coefficient on simulations of proteins and organic liquids. J. Phys. Chem. B., 122:8018–8027, 2018. doi:10.1021/acs.jpcb.8b05770.
David van der Spoel. Systematic design of biomolecular force fields. Curr. Opin. Struct. Biol., 67:18–24, 2021. doi:10.1016/j.sbi.2020.08.006.
David van der Spoel, Jin Zhang, and Haiyang Zhang. Quantitative predictions from molecular simulations using explicit or implicit interactions. Wiley Interdiscip. Rev.-Comput. Mol. Sci., 12:e1560, 2022. doi:{10.1002/wcms.1560}.
Kristian Kříž, Lisa Schmidt, Alfred T. Andersson, Marie-Madeleine Walz, and David van der Spoel. An imbalance in the force: the need for standardised benchmarks for molecular simulation. J. Chem. Inf. Model., 63:412–431, 2023. doi:10.1021/acs.jcim.2c01127.
C Caleman, P J van Maaren, M Hong, J S Hub, L T Costa, and D van der Spoel. Force field benchmark of organic liquids: density, enthalpy of vaporization, heat capacities, surface tension, compressibility, expansion coefficient and dielectric constant. J. Chem. Theory Comput., 8:61–74, 2012. doi:10.1021/ct200731v.
Nina M. Fischer, Paul J. van Maaren, Jonas C. Ditz, Ahmet Yildirim, and David van der Spoel. Properties of liquids in molecular dynamics simulations with explicit long-range Lennard-Jones interactions. J. Chem. Theory Comput., 11:2938–2944, 2015. doi:10.1021/acs.jctc.5b00190.
Jin Zhang, Badamkhatan Tuguldur, and David van der Spoel. Force field benchmark II: Gibbs energy of solvation of organic molecules in organic liquids. J. Chem. Inf. Model., 55:1192–1201, 2015. doi:10.1021/acs.jcim.5b00106.
Jin Zhang, Badamkhatan Tuguldur, and David van der Spoel. Correction to force field benchmark II: Gibbs energy of solvation of organic molecules in organic liquids. J. Chem. Inf. Model., 56:819–820, 2016. doi:10.1021/acs.jcim.6b00081.
David van der Spoel, Mohammad Mehdi Ghahremanpour, and Justin Lemkul. Small molecule thermochemistry: a tool for empirical force field development. J. Phys. Chem. A, 122:8982–8988, 2018. doi:10.1021/acs.jpca.8b09867.
Lisa Schmidt, David van der Spoel, and Marie-Madeleine Walz. Probing phase transitions in organic crystals using atomistic md simulations. ACS Phys Chem Au, 3:84–93, 2023. doi:10.1021/acsphyschemau.2c00045.
A. Najla Hosseini and David van der Spoel. Simulations of amyloid-forming peptides in the crystal state. Prot. J., 42:192–204, 2023. doi:10.1007/s10930-023-10119-3.
Mohammad Mehdi Ghahremanpour, Paul J. van Maaren, Jonas Ditz, Roland Lindh, and David van der Spoel. Large-scale calculations of gas phase thermochemistry: enthalpy of formation, standard entropy and heat capacity. J. Chem. Phys., 145:114305, 2016. doi:10.1063/1.4962627.
Mohammad Mehdi Ghahremanpour, Paul J. van Maaren, and David van der Spoel. The Alexandria library: a quantum chemical database of molecular properties for force field development. Sci. Data, 5:180062, 2018. doi:10.1038/sdata.2018.62.
Mohammad Mehdi Ghahremanpour, Paul J. van Maaren, and David van der Spoel. Alexandria library [data set]. Zenodo. 2017. URL: https://dx.doi.org/10.5281/zenodo.1004711.
Marie Madeleine Walz, Mohammad M. Ghahremanpour, Paul J. van Maaren, and David van der Spoel. Phase-transferable force field for alkali halides. J. Chem. Theory Comput., 14:5933–5948, 2018. doi:10.1021/acs.jctc.8b00507.
Marie-Madeleine Walz and David van der Spoel. Molten alkali halides - temperature dependence of structure, dynamics and thermodynamics. Phys. Chem. Chem. Phys., 21:8516–18524, 2019. doi:10.1039/C9CP03603B.
Marie-Madeleine Walz and David van der Spoel. Systematically improved melting point prediction: a detailed physical simulation model is required. Chem. Comm., 55:12044–12047, 2019. doi:10.1039/C9CC06177K.
Marie-Madeleine Walz and David van der Spoel. Direct link between structure, dynamics and thermodynamics in molten salts. J. Phys. Chem. C., 123:25596–25602, 2019. doi:10.1021/acs.jpcc.9b07756.
Marie-Madeleine Walz and David van der Spoel. Microscopic origin of conductivity in molten salts unraveled by computer simulations. Commun. Chem., 4(9):1–10, 2021. doi:10.1038/s42004-020-00446-2.
David van der Spoel, Henning Henschel, Paul J. van Maaren, Mohammad M. Ghahremanpour, and Luciano T. Costa. A potential for molecular simulation of compounds with linear moieties. J. Chem. Phys., 153(8):084503, 2020. doi:10.1063/5.0015184.
Kristian Kříž, Paul J. van Maaren, and David van der Spoel. Impact of combination rules, level of theory and potential function on the modelling of gas and condensed phase properties of noble gases. J. Chem. Theory Comput., 20:2362–2376, 2024. doi:10.1021/acs.jctc.3c01257.
Kristian Kříž and David van der Spoel. Quantification of anisotropy in exchange and dispersion interactions: a simple model for physics-based force fields. J. Phys. Chem. Lett., 15:9974–9978, 2024. doi:10.1021/acs.jpclett.4c02034.
Paul J. van Maaren and David van der Spoel. Quantitative evaluation of anharmonic bond potentials for molecular simulations. Digit. Discov., 4:824–830, 2025. doi:10.1039/D4DD00344F.
Alexander G. Donchev, Andrew G. Taube, Elizabeth Decolvenaere, Cory Hargus, Robert T. McGibbon, Ka-Hei Law, Brent A. Gregersen, Je-Luen Li, Kim Palmo, Karthik Siva, Michael Bergdorf, John L. Klepeis, and David E. Shaw. Quantum chemical benchmark databases of gold-standard dimer interaction energies. Sci. Data, 8(1):55, 2021. doi:10.1038/s41597-021-00833-x.
Peter Eastman, Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu, Stephen E. Farr, Emilio Gallicchio, Anton Gorenko, Michael M. Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A. Mitchell, Vijay S. Pande, João PGLM Rodrigues, Jaime Rodriguez-Guerra, Andrew C. Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D. Chodera, Gianni De Fabritiis, and Thomas E. Markland. Openmm 8: molecular dynamics simulation with machine learning potentials. J. Phys. Chem. B., 128:109–116, 2024. doi:10.1021/acs.jpcb.3c06662.
Mohammad Mehdi Ghahremanpour, Paul J. van Maaren, Carl Caleman, Geoffrey R. Hutchison, and David van der Spoel. Polarizable drude model with s-type gaussian or slater charge density for general molecular mechanics force fields. J. Chem. Theory Comput., 14:5553–5566, 2018. doi:10.1021/acs.jctc.8b00430.
Daniel S D Larsson and David van der Spoel. Screening for the location of RNA using the chloride ion distribution in simulations of virus capsids. J. Chem. Theory Comput., 8:2474–2483, 2012. doi:10.1021/ct3002128.
B G Dick and A W Overhauser. Theory of the dielectric constants of alkali halide crystals. Phys. Rev., 112:90–103, 1958. doi:10.1103/PhysRev.112.90.
P C Jordan, P J van Maaren, J Mavri, D van der Spoel, and H J C Berendsen. Towards Phase Transferable Potential Functions: Methodology and Application to Nitrogen. J. Chem. Phys., 103:2272–2285, 1995. doi:10.1063/1.469703.
P J van Maaren and D van der Spoel. Molecular dynamics simulations of water with a novel shell-model potential. J. Phys. Chem. B., 105:2618–2626, 2001. doi:10.1021/jp003843l.
P. Dauber-Osguthorpe and A.T. Hagler. Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there? J. Comput. Aid. Mol. Des., 33:133–203, 2019. doi:10.1007/s10822-018-0111-4.
A.T. Hagler. Force field development phase II: relaxation of physics-based criteria... or inclusion of more rigorous physics into the representation of molecular energetics. J. Comput. Aided Mol. Des., 33:205–264, 2019. doi:10.1007/s10822-018-0134-x.
Zhifeng Jing, Chengwen Liu, Sara Y. Cheng, Rui Qi, Brandon D. Walker, Jean-Philip Piquemal, and Pengyu Ren. Polarizable force fields for biomolecular simulations: recent advances and applications. Ann. Rev. Biophys., 48(1):371–394, 2019. doi:10.1146/annurev-biophys-070317-033349.
A. Najla Hosseini, Kristian Kříž, and David van der Spoel. Beyond partitioning: using force field science to evaluate electrostatics models. J. Chem. Theory Comput., 22: , 2026. doi:10.1021/acs.jctc.6c00039.
Herman J. C. Berendsen. Simulating the physical world. Cambridge University Press, Cambridge, 2007.
Frank Jensen. Introduction to computational chemistry. John Wiley & Sons Ltd, West Sussex, UK, 2007.
P Calaminici, K Jug, and M Köster. Density funtional calculations of molecular polarizabilities anf hyperpolarizabilities. J. Chem. Phys., 109(18):7756, 1998. doi:10.1063/1.477421.
A. J Stone. The Theory of Intermolecular Forces. Oxford University Press, Great Clarendon Street, Oxford, ox2 6dp, UK, 2013.
Henning Henschel, Alfred T. Andersson, Willem Jespers, Mohammad Mehdi Ghahremanpour, and David van der Spoel. Theoretical infrared spectra: quantitative similarity measures and force fields. J. Chem. Theory Comput., 16(5):3307–3315, 2020. doi:10.1021/acs.jctc.0c00126.
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin, V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox. Gaussian 16 Revision A.03. 2016. Gaussian Inc. Wallingford CT.
A D Becke. Density-functional exchange-energy approximation with correct asymptotic-behavior. Phys. Rev. A, 38:3098–3100, 1988. doi:10.1103/PhysRevA.38.3098.
R A Kendall, T H Dunning, Jr., and R J Harrison. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J. Chem. Phys., 96:6796–6806, 1992. URL: http://dx.doi.org/10.1063/1.462569.
D E Woon and T H Dunning, Jr. Benchmark calculations with correlated molecular wave functions. I. Multireference configuration interaction calculations for the second row diatomic hydrides. J. Chem. Phys., 99:1914–1929, 1993. doi:10.1063/1.464303.
D E Woon and T H Dunning, Jr. Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon. J. Chem. Phys., 98:1358–1371, 1993.
William L. Jorgensen, Mohammad M. Ghahremanpour, Anastasia Saar, and Julian Tirado-Rives. OPLS/2020 force field for unsaturated hydrocarbons, alcohols, and ethers. J. Phys. Chem. B., 128:250–262, 2023. doi:10.1021/acs.jpcb.3c06602.
John Rumble. CRC Handbook of Chemistry and Physics 103rd edition. CRC Press, Gaitherburg, MD, 2022. URL: http://hbcp.chemnetbase.com/.
I. Amdur and E. A. Mason. Properties of gases at very high temperatures. Phys. Fluids, 1:370–383, 09 1958. doi:10.1063/1.1724353.
W L Jorgensen, J Chandrasekhar, J D Madura, R W Impey, and M L Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79:926–935, 1983. doi:10.1063/1.445869.
Brian J. Kirby and Pavel Jungwirth. Charge scaling manifesto: a way of reconciling the inherently macroscopic and microscopic natures of molecular simulations. J. Phys. Chem. Lett., 10:7531–7536, 2019. doi:10.1021/acs.jpclett.9b02652.
S W Rick, S J Stuart, and B J Berne. Dynamical fluctuating charge force fields: Application to liquid water. J. Chem. Phys., 101:6141–6156, 1994. doi:10.1063/1.468398.
R Hentschke, E M Aydt, B Fodi, and E Schöckelmann. Molekulares Modellieren mit Kraftfeldern. Bergische Universität Wuppertal, Wuppertal, Germany, 2004. URL: http://constanze.materials.uni-wuppertal.de.
Anders Öhrn, Jose M. Hermida-Ramon, and Gunnar Karlström. Method for slater-type density fitting for intermolecular electrostatic interactions with charge overlap. i. the model. J. Chem. Theory Comput., 12(5):2298–2311, 2016.
I I Guseinov. Analytical evaluation of two-centre coulomb, hybrid and one-electron integrals for slater-type orbitals. J. Phys. B: Atom. Molec. Phys., 3(11):1399, 1970. doi:10.1088/0022-3700/3/11/001.
D van der Spoel and P J van Maaren. The origin of layer structure artifacts in simulations of liquid water. J. Chem. Theory Comput., 2:1–11, 2006. doi:10.1021/ct0502256.
T Darden, D York, and L Pedersen. Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. J. Chem. Phys., 98:10089–10092, 1993. doi:10.1063/1.464397.
U Essmann, L Perera, M L Berkowitz, T Darden, H Lee, and L G Pedersen. A smooth particle mesh Ewald method. J. Chem. Phys., 103:8577–8592, 1995. doi:10.1063/1.470117.
Jesse G. McDaniel and J.R. Schmidt. Physically-motivated force fields from symmetry-adapted perturbation theory. J. Phys. Chem. A., 117(10):2053–2066, 2013. doi:10.1021/jp3108182.
Thomas A Halgren. The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters. J. Amer. Chem. Soc., 114:7827–7843, 1992. doi:10.1021/ja00046a032.
Jasper C Werhahn, Evangelos Miliordos, and Sotiris S Xantheas. A new variation of the buckingham exponential-6 potential with a tunable, singularity-free short-range repulsion and an adjustable long-range attraction. Chem. Phys. Lett., 619:133–138, 2015. doi:10.1016/j.cplett.2014.11.051.
Lee-Ping Wang, Jiahao Chen, and Troy Van Voorhis. Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data. J. Chem. Theory Comput., 9(1):452–460, 2013. doi:10.1021/ct300826t.
R A Buckingham. The Classical Equation of State of Gaseous Helium, Neon and Argon. Proc. R. Soc. London Ser. A, 168:264–283, 1938. doi:10.1098/rspa.1938.0173.
Edward A. Mason. Transport Properties of Gases Obeying a Modified Buckingham (Exp-Six) Potential. J. Chem. Phys., 22:169–186, 2004. doi:10.1063/1.1740026.
K T Tang and J P Toennies. An improved simple-model for the vanderwaals potential based on universal damping functions for the dispersion coefficients. J. Chem. Phys., 80:3726–3741, 1984. doi:10.1063/1.447150.
K. T. Tang and J. P. Toennies. The van der Waals potentials between all the rare gas atoms from He to Rn. J. Chem. Phys., 118(11):4976–4983, 03 2003. URL: https://doi.org/10.1063/1.1543944, arXiv:https://pubs.aip.org/aip/jcp/article-pdf/118/11/4976/19209973/4976\_1\_online.pdf, doi:10.1063/1.1543944.
Xiaowei Sheng, J. Peter Toennies, and K. T. Tang. Conformal analytical potential for all the rare gas dimers over the full range of internuclear distances. Phys. Rev. Lett., 125:253402, 2020. doi:10.1103/PhysRevLett.125.253402.
Mary J. Van Vleet, Alston J. Misquitta, Anthony J. Stone, and J. R. Schmidt. Beyond born-mayer: improved models for short-range repulsion in ab initio force fields. J. Chem. Theory Comput., 12(8):3851–3870, 2016. doi:10.1021/acs.jctc.6b00209.
Mary J. Van Vleet, Alston J. Misquitta, and J. R. Schmidt. New angles on standard force fields: toward a general approach for treating atomic-level anisotropy. J. Chem. Theory Comput., 14(2):739–758, 2018. PMID: 29266931. doi:10.1021/acs.jctc.7b00851.
J E Jones. On the determination of molecular fields. -II. From the equation of state of a gas. Proc. Royal Soc. Lond. Ser. A, 106:463–477, 1924. doi:10.1098/rspa.1924.0082.
Christian L. Wennberg, Teemu Murtola, Berk Hess, and Erik Lindahl. Lennard-Jones lattice summation in bilayer simulations has critical effects on surface tension and lipid properties. J. Chem. Theory Comput., 9:3527–3537, 2013. doi:10.1021/ct400140n.
Chang Lyoul Kong and Manoj R Chakrabarty. Combining rules for intermolecular potential parameters. iii. application to the exp 6 potential. J. Phys. Chem., 77(22):2668–2670, 1973. doi:10.1021/j100640a019.
D Berthelot. Sur le mélange des gaz. C. R. Hebd. Seances Acad. Sci., 126:1703–1855, 1898.
H. A. Lorentz. Ueber die anwendung des satzes vom virial in der kinetischen theorie der gase. Annalen der Physik, 248(1):127–136, 1881. doi:10.1002/andp.18812480110.
W Hogervorst. Transport and equilibrium properties of simple gases and forces between like and unlike atoms. Physica, 51(1):77–89, 1971. doi:10.1016/0031-8914(71)90138-8.
Li Yang, Lei Sun, and Wei-Qiao Deng. Combination Rules for Morse-Based van der Waals Force Fields. J. Phys. Chem. A, 122:1672–1677, 2018. doi:10.1021/acs.jpca.7b11252.
P M Morse. Diatomic molecules according to the wave mechanics. II. Vibrational levels. Phys. Rev., 34:57–64, 1929. doi:10.1103/PhysRev.34.57.
Edward A. Mason. Forces between Unlike Molecules and the Properties of Gaseous Mixtures. J. Chem. Phys., 23:49–56, 1955. doi:10.1063/1.1740561.
M Waldman and A T Hagler. New combining rules for rare gas van der waals parameters. J. Comput. Chem., 14:1077–1084, 1993. doi:10.1002/jcc.540140909.
Rui Qi, Qiantao Wang, and Pengyu Ren. General van der Waals potential for common organic molecules. Bioorg. Med. Chem., 24:4911–4919, 2016. doi:10.1016/j.bmc.2016.07.062.
Uwe Hohm. A continuous description of different means with application to mixing rules. ACS Omega, 11:10641–10648, 2026. doi:10.1021/acsomega.5c12377.
W Hua. 4-parameter exactly solvable potential for diatomic-molecules. Phys. Rev. A, 42(5):2524–2529, SEP 1 1990. doi:10.1103/PhysRevA.42.2524.
Wei Hua. Four-parameter potential and its bound-state matrix elements. J. Phys. B: Atom., Molec. Opt. Phys., 23:2521, aug 1990. doi:10.1088/0953-4075/23/15/019.
J P Ryckaert and A Bellemans. Molecular Dynamics of Liquid n-Butane near its Boiling Point. Chem. Phys. Lett., 30:123–125, 1975. doi:10.1016/0009-2614(75)85513-8.
David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, and Herman J C Berendsen. GROMACS: Fast, Flexible and Free. J. Comput. Chem., 26:1701–1718, 2005. doi:10.1002/jcc.20291.
Peter Eastman and Vijay S Pande. Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit. J. Comput. Chem., 31:1268–1272, 2010. doi:10.1002/jcc.21413.
David van der Spoel and A. Najla Hosseini. Point + Gaussian charge model for electrostatic interactions derived by machine learning. Phys. Chem. Chem. Phys., 27:13817–13820, 2025. doi:10.1039/D5CP01254F.
M W Mahoney and W L Jorgensen. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys., 112:8910–8922, 2000. doi:10.1063/1.481505.
Shuyi Qin. Sensitivity analysis in high-dimensional space. Master's thesis, Uppsala University, Dept. of Information Technology, 2021. URL: https://uu.diva-portal.org/smash/record.jsf?pid=diva2%3A1614100&dswid=6669.
Steven F. van Dijk. Genetic Algorithms for Map Labeling. PhD thesis, Utrecht University, Dept. of Mathematics and Computer Science, 2001. URL: https://dspace.library.uu.nl/bitstream/handle/1874/864/full.pdf?sequence=1.
G Lamoureux, A D MacKerell, and B Roux. A simple polarizable model of water based on classical Drude oscillators. J. Chem. Phys., 119:5185–5197, 2003. doi:10.1063/1.1598191.
Greg Landrum and RDKit contributors. Rdkit/rdkit: 2025_09_4 (q3 2025) release. 2025. doi:10.5281/zenodo.18098214.
Daylight Chemical Information Systems, Inc. Smarts — a language for describing molecular patterns. Accessed: 2026-01-26. URL: https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html.
Brent H Besler, Kenneth M Merz Jr., and Peter A Kollman. Atomic charges derived from semiempirical methods. J. Comput. Chem., 11:431–439, 1990. doi:10.1002/jcc.540110404.
Toon Verstraelen, Veronique Van Speybroeck, and Michel Waroquier. The electronegativity equalization method and the split charge equilibration applied to organic systems: Parametrization, validation, and comparison. J. Chem. Phys., 131:044127, 2009. doi:10.1063/1.3187034.
A K Rappé and W A Goddard III. Charge Equillibration for Molecular Dynamics Simulations. J. Phys. Chem., 95:3358–3363, 1991. doi:10.1021/j100161a070.
Razvan A. Nistor, Jeliazko G. Polihronov, Martin H. Müser, and Nicholas J. Mosey. A generalization of the charge equilibration method for nonmetallic materials. J. Chem. Phys., 125(9):094108, 2006. doi:10.1063/1.2346671.
Chunhua Yin, Ziheng Cui, Yang Jiang, David van der Spoel, and Haiyang Zhang. Role of host-guest charge transfer in cyclodextrin complexation: a computational study. J. Phys. Chem. C., 123:17745–17756, 2019. doi:10.1021/acs.jpcc.9b05399.
Frank Jensen. Unifying charge-flow polarization models. J. Chem. Theory Comput., 19:4047–4073, 2023. doi:10.1021/acs.jctc.3c00341.
Peter Itskowitz and Max L Berkowitz. Chemical potential equalization principle: direct approach from density functional theory. J. Phys. Chem. A, 101(31):5687–5691, 1997. doi:10.1021/jp963962u.
W J Mortier, S K Ghosh, and S Shankar. Electronegativity-equalization method for the calculation of atomic charges in molecules. J. Amer. Chem. Soc., 108:4315–4320, 1986. doi:10.1021/ja00275a013.
Riccardo Chelli, Piero Procacci, Roberto Righini, and Salvatore Califano. Electrical response in chemical potential equalization schemes. J. Chem. Phys., 111(18):8569–8575, 1999. doi:10.1063/1.480198.
Jiahao Chen, Dirk Hundertmark, and Todd J. Martínez. A unified theoretical framework for fluctuating-charge models in atom-space and in bond-space. J. Chem. Phys., 129(21):214113, 2008. doi:10.1063/1.3021400.
T. Verstraelen, P. W. Ayers, V. Van Speybroeck, and M. Waroquier. Acks2: atom-condensed kohn-sham dft approximated to second order. J. Chem. Phys., 138:074108, 2013. doi:10.1063/1.4791569.
Bogumil Jeziorski, Robert Moszynski, and Krzysztof Szalewicz. Perturbation theory approach to intermolecular potential energy surfaces of van der waals complexes. Chem. Rev., 94(7):1887–1930, 1994. doi:10.1021/cr00031a008.
Trent M. Parker, Lori A. Burns, Robert M. Parrish, Alden G. Ryno, and C. David Sherrill. Levels of symmetry adapted perturbation theory (sapt). I. efficiency and performance for interaction energies. J. Chem. Phys., 140(9):094106, 2014. doi:10.1063/1.4867135.
Grzegorz Chałasiński and Małgorzata M Szcześniak. State of the art and challenges of the ab initio theory of intermolecular interactions. Chem. Rev., 100(11):4227–4252, 2000. doi:10.1021/cr990048z.
Jan Řezáč. Non-covalent interactions atlas benchmark data sets: hydrogen bonding. J. Chem. Theory Comput., 16:2355–2368, 2020. doi:10.1021/acs.jctc.9b01265.
Lori A. Burns, John C. Faver, Zheng Zheng, Michael S. Marshall, Daniel G. A. Smith, Kenno Vanommeslaeghe, Alexander D. MacKerell, Kenneth M. Merz, and C. David Sherrill. The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions. J. Chem. Phys., 147:161727, 2017. doi:10.1063/1.5001028.
Justin S. Smith, Olexandr Isayev, and Adrian E. Roitberg. ANI-1, a data set of 20 million calculated off-equilibrium conformations for organic molecules. Sci. Data, 4:170193, 2017. doi:10.1038/sdata.2017.193.
Justin M. Turney, Andrew C. Simmonett, Robert M. Parrish, Edward G. Hohenstein, Francesco A. Evangelista, Justin T. Fermann, Benjamin J. Mintz, Lori A. Burns, Jeremiah J. Wilke, Micah L. Abrams, Nicholas J. Russ, Matthew L. Leininger, Curtis L. Janssen, Edward T. Seidl, Wesley D. Allen, Henry F. Schaefer, Rollin A. King, Edward F. Valeev, C. David Sherrill, and T. Daniel Crawford. Psi4: an open-source ab initio electronic structure program. Wiley Interdiscip. Rev. Comput. Mol. Sci., 2:556–565, 2011. doi:10.1002/wcms.93.
J Wang, R M Wolf, J W Caldwell, P A Kollman, and D A Case. Development and testing of a general AMBER force field. J. Comput. Chem., 25:1157–1174, 2004. doi:10.1002/jcc.20035.
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R Shirts, Jeremy C Smith, Peter M Kasson, David van der Spoel, Berk Hess, and Erik Lindahl. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29:845–854, April 2013. doi:10.1093/bioinformatics/btt055.
