MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR

Miguel Díaz; David Coll; David Vega

doi:10.15446/rev.fac.cienc.v13n1.109657

Publicado

2024-01-01

MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR

MODELS OF ATOMIC INTERACTIONS IN MOLECULAR MECHANICS

DOI:

https://doi.org/10.15446/rev.fac.cienc.v13n1.109657

Palabras clave:

mecánica molecular, modelos matemáticos, interacciones atómicas (es)
molecular mechanics, mathematical models, atomic interactions (en)

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Autores/as

Miguel Díaz Instituto Venezolano de Investigaciones Científicas, Venezuela https://orcid.org/0000-0001-6276-2156
David Coll Instituto Venezolano de Investigaciones Científicas, Venezuela https://orcid.org/0000-0001-7276-7049
David Vega Universidad de Carabobo

Resumen (es)
Resumen (en)

Esta revisión describe modelos de interacciones atómicas utilizados en la mecánica molecular, enfatizando consideraciones que se deben tener en cuenta para su implementación computacional. Estos modelos constituyen los términos de una función que aproxima la superficie de energía potencial de un sistema molecular, conocida como campo de fuerzas. Existen dos grupos de interacciones: enlazantes y no enlazantes. La primera categoría contempla potenciales estiramiento de enlace, flexión de enlaces, torsión de enlace y flexión respecto a un plano molecular. La segunda categoría contempla potenciales electrostáticos y de van der Waals. Las interacciones electrostáticas son descritas mediante la ley de Coulomb, requiriendo una metodología de asignación de cargas. Las interacciones de van der Waals son modeladas mediante términos de largo alcance asociados a la interacción entre dipolos inducidos, y mediante términos de corto alcance asociados a la improbabilidad de encontrar electrones con el mismo espín en el mismo lugar del espacio.

This review describes models of atomic interactions used in molecular mechanics, with an emphasis on considerations in their computational implementation. These models form a function approximating the potential energy surface of a molecular system, known as the force field. There are two groups of interactions: bonding and non-bonding. The former includes bond stretching, bending, torsion and out-of-plane bending potentials. The latter consists of electrostatic and van der Waals potentials. Electrostatic interactions are modeled by Coulomb's law and require a charge assignment method. Van der Waals interactions are modeled with long-range terms related to induced dipole interactions and short-range terms related to the improbability of finding electrons with the same spin state at the same location in space.

Referencias

Allinger, N. L. (1976). Calculation of molecular structure and energy by force-field methods. In: Advances in physical organic chemistry. Gold, V.; Bethell, D. eds. Academic Press. 1-82. DOI: https://doi.org/10.1016/S0065-3160(08)60212-9

Allured, V. S., Kelly, C. M. & Landis, C. R. (1991). SHAPES empirical force field: new treatment of angular potentials and its application to square-planar transition-metal complexes. J. Am. Chem. Soc. 113 1-12. DOI: https://doi.org/10.1021/ja00001a001

Anandakrishnan, R., Baker, C., Izadi, S. & Onufriev, A. V. (2013). Point charges optimally placed to represent the multipole expansion of charge distributions. PLOS ONE, 8, e67715. DOI: https://doi.org/10.1371/journal.pone.0067715

Anisimov, V. M., Lamoreux, G., Vorobyov, I. V., Huang, N., Roux, B. & MacKerell, A. D. (2005). Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator. J. Chem. Theory Comput., 1, 153-168. DOI: https://doi.org/10.1021/ct049930p

Applequist, J. (1985). A multipole interaction theory of electric polarization of atomic molecular assemblies. J. Chem. Phys., 83, 809-826. DOI: https://doi.org/10.1063/1.449496

Applequist, J., Carl, J. R. & Fung, K. K. (1972). An atom dipole interaction model for molecular polarizability. Application to polyatomic molecules and determination of atom polarizabilities. J. Am. Chem. Soc., 94, 2952-2960. DOI: https://doi.org/10.1021/ja00764a010

Aranha, M. P., Spooner, C., Demerdash, O., Czejdo, B., Smith & J. C., Mitchell, J. C. (2020). Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets. Biochim. Biophys. Acta, Gen. Subj., 1864, 129535. DOI: https://doi.org/10.1016/j.bbagen.2020.129535

Artemova, S., Jaillet, L. & Redon, S. (2016). Automatic molecular structure perception for the universal force field. J. Comput. Chem., 37, 1191-1205. DOI: https://doi.org/10.1002/jcc.24309

Bader, R. F. W. (1994). Atoms in molecules: a quantum theory. Oxford University Press. 438 p.

Bayly, C I., Ciepak, P., Cornell, W. D. & Kollman, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem., 97, 10269-10280. DOI: https://doi.org/10.1021/j100142a004

Berendsen, H. J. C., Grigera, J. R. & Straatsma, T. P. (1987). The missing term in effective pair potentials. J. Phys. Chem., 91, 6269-6271. DOI: https://doi.org/10.1021/j100308a038

Berthelot, D. (1898). On the gas mixture. Comptes Rendus Acad. Sci., 126, 1703-1706.

Bondi, A. (1964). Van der Waals volumes and radii. J. Phys. Chem., 68, 441-451. DOI: https://doi.org/10.1021/j100785a001

Born, M. & Mayer, J. E. (1932). On the lattice theory of ion crystals. Z. Physik, 75, 1-18. DOI: https://doi.org/10.1007/BF01340511

Bowen, J. P. & Allinger, N. L. (1991). Molecular mechanics: the art and science of parametrization. In: Reviews in Computational Chemistry. Lipkowitz, K. B., Boyd, D. B. eds. Wiley-VCH Inc. 81-97. DOI: https://doi.org/10.1002/9780470125793.ch3

Buckingham, R. A. (1938), The classical equation of state of gaseous helium, neon and argon. Proc. R. Soc. Lond. A, 168, 264-283. DOI: https://doi.org/10.1098/rspa.1938.0173

Burden, R. L. & Faires, J. D. (2011). Numerical analysis. Brooks/Cole, Cengage Learning. Boston, USA. 872 p.

Cardamone, S., Hughes, T. J. & Popelier, P. L. A. (2014). Multipolar electrostatics. Phys. Chem. Chem. Phys., 16, 10367-10387. DOI: https://doi.org/10.1039/c3cp54829e

Chen, J., Hundertmark, D. & Martínez, T. J. (2008). A unified theoretical framework for fluctuating-charge models in atom-space and bond-space. J. Chem. Phys., 129, 214113. DOI: https://doi.org/10.1063/1.3021400

Chen, T., Li, M.& Liu, J. (2018). $pi-pi$ stacking interaction: a nondestructive and facile means in material engineering for bioapplications. Cryst. Growth Des., 18, 2765-2783. DOI: https://doi.org/10.1021/acs.cgd.7b01503

Chen, J. & Martínez, T. J. (2007). QTPIE: charge transfer with polarization current equalization. A fluctuating charge model with correct asymptotics. Chem. Phys. Lett., 438, 315-320. DOI: https://doi.org/10.1016/j.cplett.2007.02.065

Chen, J. & Martínez, T. J. (2009). The dissociation catastrophe in fluctuating charge models and its implications for the concept of atomic electronegativity. In: Progress in theoretical chemistry and physics. Piecuch, P., Maruani, J., Delgado-Barrio, G., Wilson S. eds. Springer. 397-415. DOI: https://doi.org/10.1007/978-90-481-2596-8_19

Choi, H., Kang, H. & Park, H. (2009). New angle-dependent potential energy function for backbone-backbone hydrogen bond protein-protein interactions. J. Comput. Chem., 31, 897-903. DOI: https://doi.org/10.1002/jcc.21378

Cohen, E. R., Cvitas, T., Frey, J. G., Holmstr" o m, B., Kuchitsu, K., Marquardt, R., Mills, I., Pavese, F., Quack, M., Stohner, J., Strauss, H. L., Takami, M. & Thor, A. J. (2008). Quantities, units and symbols in physical chemistry. IUPAC Green Book. IUPAC & RSC Publishing. 233 p.

Coulomb, C. A. (1884). First memoir on electricity and magnetism. Construction & use of an electrical balance, based on the property of the metal wires, to have a torsion reaction force proportional to the twist angle. In: Collection de Mémoires relatifs a la Physique. La Société Franc c aise de Physique. Paris. 107-115.

Cox, S. R. & Williams, D. E. (1981). Representation of the molecular electrostatic potential by a net atomic charge model. J. Comput. Chem., 2, 304-323. DOI: https://doi.org/10.1002/jcc.540020312

Dahiyat, B., Gordon, D. B. & Mayo, S. L. (1997). Automated desing of the surface points of protein helices. Protein Sci., 6, 1333-1337. DOI: https://doi.org/10.1002/pro.5560060622

Dans, P. D., Zeida, A., Machado, M. R. & Pantano, S. (2010). A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics. J. Chem. Theory Comput., 6, 1711-1725. DOI: https://doi.org/10.1021/ct900653p

Darré, L., Machado, M. R., Brandner, A. F., González, H. C., Ferreira, S. & Panatano, S. (2015). SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics. J. Chem. Theory Comput., 11, 723-739. DOI: https://doi.org/10.1021/ct5007746

Demerdash, O. N. A. & Mitchell, J. C. (2013). Using physical potentials and learned models to distinguish native binding interfaces from de novo designed interfaces that do not bind. Proteins, 81, 1919-1930. DOI: https://doi.org/10.1002/prot.24337

Denning, E. J., Priyakumar, U. D., Nilsson, L. & MacKerell Jr., A. D. (2011). Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J. Comput. Chem., 32, 1929-1943. DOI: https://doi.org/10.1002/jcc.21777

Dickson, C. J., Walker, R. C. & Gould, I. R. (2022). Lipid21: complex lipid membrane simulations with AMBER. J. Chem. Theory Comput., 18, 1726-1736. DOI: https://doi.org/10.1021/acs.jctc.1c01217

Dykstra, C. E. (1988). Efficient calculation of electrically based intermolecular potentials of weakly bonded clusters. J. Comput. Chem., 9, 476-487. DOI: https://doi.org/10.1002/jcc.540090506

Dykstra, C. E. (1993). Electrostatic interaction potentials in molecular force fields. Chem. Rev., 93, 2339-2353. DOI: https://doi.org/10.1021/cr00023a001

Ermer O. (1976). Calculation of molecular properties using force fields. Applications in organic chemistry. In: Bonding Forces. Springer. Heidelberg. 161-211. DOI: https://doi.org/10.1007/3-540-07671-9_3

Fuji, H., Qi, F., Qu, L., Takaesu, Y. & Hoshino, T. (2017). Prediction of ligand binding affinity to target proteins by molecular mechanics theoretical calculation. Chem. Phar. Bull., 65, 461-468. DOI: https://doi.org/10.1248/cpb.c16-00913

Gao, J., Habibollazadeh, D. & Shao, L. (1995). A polarizable intermolecular potential function for simulation of liquid alcohols. J. Phys. Chem., 99, 16460. DOI: https://doi.org/10.1021/j100044a039

Gasteiger, J. & Marsili, M. (1980a). Iterative partial equalization of orbital electronegativity -- A rapid access to atomic charges. Tetrahedron, 36, 3219-3228. DOI: https://doi.org/10.1016/0040-4020(80)80168-2

Gasteiger, J. & Marsili, M. (1980b). $pi$ charge distribution from molecular topology and $pi$ orbital electronegativity. Croat. Chem. Acta, 53, 601-614.

Gresh, N., Cisneros, A., Darden, T. A. & Piquemal, J-P. (2007). Anisotropic, polarizable molecular mechanics studies of inter- and intramolecular interactions and ligand-macromolecule complexes. A bottom-up strategy. J. Chem. Theory Comput., 3, 1960-1986. DOI: https://doi.org/10.1021/ct700134r

Halgren, T. A. (1996). Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem., 17, 490-519. DOI: https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P

Harder, E., Anisimov, V. M., Vorobyov, I. V., Lopes, P. E. M., Noskov, S. Y., MacKerell Jr., A. D. & Roux, B. (2006). Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical Drude oscillator. J. Chem. Theory Comput., 2, 1587-1597. DOI: https://doi.org/10.1021/ct600180x

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. (2015). OPLS3: a force field providing broad coverage of drug-like small molecules and proteins. J. Chem. Theory Comput., 12, 281-296. DOI: https://doi.org/10.1021/acs.jctc.5b00864

Hart, K., Foloppe, N., Baker, C. M., Denning, E. J., Nilsson, L. & MacKerell Jr., A. D. (2012). Optimization of the CHARMM additive force field for DNA: improved treatment of the BI/BII conformational equilibrium. J. Chem. Theory Comput., 8, 348-362. DOI: https://doi.org/10.1021/ct200723y

Hill, T. L. (1948). Steric effects. I. Van der Waals potential energy curves. J. Chem. Phys., 16, 399-404. DOI: https://doi.org/10.1063/1.1746902

Hinze, J. & Jaffé, H. H. (1962). Electronegativity. I. Orbital electronegativity of neutral atoms. J. Am. Chem. Soc., 84, 540-546. DOI: https://doi.org/10.1021/ja00863a008

Hinze, J., Whitehead, M. A. & Jaffé, H. H. (1963). Electronegativity. II. Bond and orbital electronegativities. J. Am. Chem. Soc., 85, 148-154. DOI: https://doi.org/10.1021/ja00885a008

Hooke, R. (1678). Lectures de potentia restitutiva, or of spring, explaining the power of springing bodies. [En línea]. Carnegie Mellon University. Digital Collections. [Consultada en Julio de 2022]. Disponible en: https://digitalcollections.library.cmu.edu/node/68323

Horn, H. W., Swope, W. C., Pitera, J. W., Madura, J. D., Dick, T. J., Hura, G. L. & Head-Gordon, T. (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J. Chem. Phys., 120, 9665-9678. DOI: https://doi.org/10.1063/1.1683075

Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., L de Groot, B., Grubm" u ller, H. & MacKerell Jr., A. D. (2017). CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods, 14, 71-73. DOI: https://doi.org/10.1038/nmeth.4067

Izadi, S., Anandakrishnan, R.& Onufriev, A. V. (2014). Building water models: a different approach. J. Phys. Chem. Lett., 5, 3863-3871. DOI: https://doi.org/10.1021/jz501780a

Izadi, S., Anandakrishnan, R. & Onufriev, A. V. (2016). Implicit solvent model for million-atom atomistic simulations: insights into the organization of 30-nm chromatin fiber. J. Chem. Theory Comput., 12, 5946-5959. DOI: https://doi.org/10.1021/acs.jctc.6b00712

Artemova, S. & Redon, S. (2017). IM-UFF: extending the universal force field for interactive molecular modeling. J. Mol. Graph. Model., 77, 350-362. DOI: https://doi.org/10.1016/j.jmgm.2017.08.023

Jensen, F. (2017). Introduction to computational chemistry. John Wiley & Sons, Ltd. Chichester, UK. 638 p.

Jones, J. E. (1924a). On the determination of molecular fields.--I. From the variation of the viscosity of a gas with temperature. Prod. R. Soc. Lond. A, 106, 441-462. DOI: https://doi.org/10.1098/rspa.1924.0081

Jones, J. E. (1924b). On the determination of molecular fields.--II. From the equation of state of a gas. Prod. R. Soc. Lond. A, 106, 463-477. DOI: https://doi.org/10.1098/rspa.1924.0082

Jorgensen, W. L., Chandrasekhar, J., Madura, J. & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935. DOI: https://doi.org/10.1063/1.445869

Joung, S. & Cheatham, T. E. (2008). Determination of alkali and halide ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B, 112, 9020-9041. DOI: https://doi.org/10.1021/jp8001614

Kirschner, K. N., Yongye, A. B., Tschampel, S. M., González-Outeiriño, J., Daniels, C. R., Foley, B. L. & Woods, R. J. (2007). GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J. Comput. Chem., 29, 622-655. DOI: https://doi.org/10.1002/jcc.20820

Klauda, J. B,, Venable, R. M., Freites, J. A., O'Connor, J. W., Tobias, D. J., Mondragon-Ramirez, C., Vorobyov, I., MacKerell Jr., A. D. & Pastor, R. W. (2010). Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B, 114, 7830-7843. DOI: https://doi.org/10.1021/jp101759q

Klein, F., Soñora, M., Santos, L. H., Frigini, E. N., Ballesteros-Casallas, A., Machado, M. R. & Panatano, S. (2023). The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels. J. Struct. Biol., 215, 107985. DOI: https://doi.org/10.1016/j.jsb.2023.107985

Lacava, F. (2016). Classical electrodynamics. From image charges to the photon mass and magnetic monopoles. Springer International Publishing. Switzerland. 195 p. DOI: https://doi.org/10.1007/978-3-319-39474-9

Leach, A. R. (2001). Molecular modelling: principles and applications. Pearson Education Limited. England. 744 p.

Levine, I. N. (2014). Quantum chemistry. Pearson Educaction, Inc. USA. 714 p.

Lewards, E. G. (2016). Computational chemistry. Introduction to the theory and applications of molecular and quantum mechanics. Springer International Publishing. Switzerland. 739 p.

Li, Z., Song, F., Li, P. & Merz Jr., K. M. (2014). Taking into account the ion-induced dipole interaction in the nonbonded model of ions. J. Chem. Theory Comput., 10, 289-297. DOI: https://doi.org/10.1021/ct400751u

Li, Z., Song, F., Li, P. & Merz Jr., K. M. (2015). Parametrization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water. J. Chem. Phys. B, 119, 883-895. DOI: https://doi.org/10.1021/jp505875v

Li, Z., Song, F., Li, P. & Merz Jr., K. M. (2015). Systematic parametrization of monovalent ions using the nonbonded model. J. Chem. Theory Comput., 11, 1645-1657. DOI: https://doi.org/10.1021/ct500918t

Li, Z., Song, F., Li, P. & Merz Jr., K. M. (2020). Systematic parametrization of divalent metal ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models. J. Chem. Theory Comput., 16, 4429-4442. DOI: https://doi.org/10.1021/acs.jctc.0c00194

Li, Z., Song, F., Li, P. & Merz Jr., K. M. (2021). Parametrization of monovalent ions for the OPC3, OPC, TIP3P-FB and TIP4P-FB water models. J. Chem. Inf. Model., 61, 869-880.

Li, Z., Song, F., Li, P. & Merz Jr., K. M. (2021). Parametrization of trivalent and tetravalent metal ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models. J. Chem. Inf. Model., 17, 2342-2354. DOI: https://doi.org/10.1021/acs.jctc.0c01320

Lin, F.-Y., Huang, J., Pandey, P., Rupakheti, C., Li, J., Roux, B.& MacKerell Jr., A. D. (2020). Further optimization and validation of the classical Drude polarizable protein force field. J. Chem. Theory Comput., 16, 3221-3239. DOI: https://doi.org/10.1021/acs.jctc.0c00057

Lindan, P. J. D. & Gillan, M. J. (1993). Shell-model molecular dynamics simulation of superionic conduction in CaF2. J. Phys.: Condens. Matter, 5, 1019. DOI: https://doi.org/10.1088/0953-8984/5/8/005

Liu, C., Piquemal, J.-P. & Ren, P. (2019). AMOEBA+ classical potential for molecular interactions. J. Chem. Theory Comput., 15, 4122-4139. DOI: https://doi.org/10.1021/acs.jctc.9b00261

Liu, C., Piquemal, J.-P. & Ren, P. (2020). Implementation of geometry-dependent charge flux into the polarizable AMOEBA+ potential. J. Phys. Chem. Lett., 11, 419-426. DOI: https://doi.org/10.1021/acs.jpclett.9b03489

London, F. (1937). The general theory of molecular forces. Trans. Faraday Soc., 33, 8b-26. DOI: https://doi.org/10.1039/tf937330008b

Lopes, P. E. M., Huang, J., Shim, J., Luo, Y., Roux, B. & MacKerell, Jr., A. D. (2013). Polarizable force field for peptides and proteins based on the classical Drude oscillator. J. Chem. Theory Comput., 12, 5430-5449. DOI: https://doi.org/10.1021/ct400781b

Lorentz, H. A. (1880). On the relationship between the rate of light propagation and body density. Ann. Phys., 245, 641-665. DOI: https://doi.org/10.1002/andp.18802450406

Lorentz, H. A. (1881). On the application of the virial theorem in the kinetic theory of gases. Ann. Phys., 248, 127-136. DOI: https://doi.org/10.1002/andp.18812480110

Lorenz, L. (1880). On the refraction constant. Ann. Phys., 247, 70-103. DOI: https://doi.org/10.1002/andp.18802470905

Maerzke, K. A. & Siepmann, J. I. (2011). Transferable potentials for phase equilibria--coarse-grain description for linear alkanes. J. Phys. Chem. B, 115, 3452-3465. DOI: https://doi.org/10.1021/jp1063935

Mallajosyula, S. S., Guvench, O., Hatcher, E. & MacKerell, Jr., A. D. (2012). CHARMM additive all-atom force field for phosphate and sulfate linked to carbohydrates. J. Chem. Theory Comput., 8, 759-776. DOI: https://doi.org/10.1021/ct200792v

Martin, M. G. & Siepmann, J. I. (1998). Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes. J. Phys. Chem. B, 102, 2569-2577. DOI: https://doi.org/10.1021/jp972543+

Mayo, S. L., Olafson, B. D. & Goddard III, W. A. (1990). DREIDING: a generic force field for molecular simulations. J. Am. Chem. Soc., 94, 8897-8909. DOI: https://doi.org/10.1021/j100389a010

Maple, J. R., Hwang, M.-J., Stockfisch, T. P., Dinur, U., Waldman, M., Ewig, C. S. & Hagler, T. (1994). Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules. J. Comput. Chem., 15, 162-182. DOI: https://doi.org/10.1002/jcc.540150207

Mauger, N., Plé, T., Lagard` e re, L., Huppert, S. & Piquemal, J.-P. (2022). Improving condensed-phase water dynamics with explicit nuclear quantum effects: the polarizable Q-AMOEBA force field. J. Comput. Chem., 15, 162-182. DOI: https://doi.org/10.1021/acs.jpcb.2c04454

Meister, J. & Schwarz, W. H. E. (1994). Principal components of ionicity. J. Phys. Chem., 98, 8245-8252. DOI: https://doi.org/10.1021/j100084a048

Momany, F. A. (1978). Determination of partial atomic charges from ab initio electrostatic potentials. Application to formamide, methanol and formic acid. J. Phys. Chem., 82, 592-601. DOI: https://doi.org/10.1021/j100494a019

Morse, P. M. (1929). Diatomic molecules according to the wave mechanics. II. Vibrational levels. Phys. Rev., 34, 57-64. DOI: https://doi.org/10.1103/PhysRev.34.57

Mulliken, R. S. (1934). A new electroaffinity scale, together with data on valence states and on valence ionization potentials and electron affinities. J. Chem. Phys., 2, 782-793. DOI: https://doi.org/10.1063/1.1749394

Mulliken, R. S. (1955). Electronic population analysis on LCAO-MO molecular wave functions. I. J. Chem. Phys., 23, 1833-1840. DOI: https://doi.org/10.1063/1.1740588

Naseem-Khan, S., Lagard` e re, L., Narth, C., Cisneros, G. A., Ren, P., Gresh, N. & Piquemal, J.-P. (2022). Development of the quantum-inspired SIBFA many-body polarizable force field: enabling condensed-phase molecular dynamics simulations. J. Chem. Theory Comput., 18, 3607-3621. DOI: https://doi.org/10.1021/acs.jctc.2c00029

Nesse, F. (2012). The ORCA program system. WIREs Comput. Mol. Sci., 2, 73-78. DOI: https://doi.org/10.1002/wcms.81

Nocedal, J. & Wright, S. J. (2006). Numerical optimization. Springer Science+Business Media, LLC. New York, USA. 664 p.

O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T. & Hutchison, G. R. (2011). Open babel: an open chemical toolbox. J. Cheminformatics, 3, 33. DOI: https://doi.org/10.1186/1758-2946-3-33

Oda, A. & Irono, S. (2003). Geometry-dependent atomic charge calculations using charge equilibration method with empirical two-center Coulombic terms. J. Mol. Struct.: TEOCHEM, 634, 159-170. DOI: https://doi.org/10.1016/S0166-1280(03)00338-5

Ongari, D., Boyd, P. G., Kadioglu, O., Mace, A. K., Keshin, S. & Smit, B. (2019). Evaluating charge equilibration methods to generate electrostatic fields in nanoporous materials. J. Chem. Theory Comput., 15, 382-401. DOI: https://doi.org/10.1021/acs.jctc.8b00669

Pauli, W. (1925). On the connection between the completion of electron groups in an atom with the complex structure of spectra. Z. Physik, 31, 765-783. DOI: https://doi.org/10.1007/BF02980631

Pauling, L. (1931). The nature of the chemical bond. Application of results obtained from the quantum mechanics and from a theory of paramagnetic susceptibility to the structure of molecules. J. Am. Chem. Soc., 53, 1367-1400. DOI: https://doi.org/10.1021/ja01355a027

Pearson, R. (1988). Absolute electronegativity and hardness: application to inorganic chemistry. Inorg. Chem., 27, 734-740. DOI: https://doi.org/10.1021/ic00277a030

Press, W. H., Teukolsky, S. A., Vetterling, W. T. & Flannery, B. P. (2007). Numerical recipes: the art of scientific computing. Cambridge University Press. Cambridge, UK. 1235 p.

Ramachandran, S., Lenz, T. G., Skiff, W. M. & Rappé, A. K. (1996). Toward an understanding of zeolite Y as a cracking catalyst with the use of periodic charge equilibration. J. Phys. Chem., 100, 5898-5907. DOI: https://doi.org/10.1021/jp952864q

Rappé, A. K., Bormann-Rochotte, L. M., Wiser, D. C., Hart, J. R., Pietsch, M. A., Casewit, C. J. & Skiff, W. M. (2007). APT a next genereration QM-based reactive force field. Mol. Phys., 105, 301-324. DOI: https://doi.org/10.1080/00268970701201106

Rappé, A. K., Casewit, C. J., Cowell, K. S., Goddard III, W. A. & Skiff, W. M. (1992). UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc., 114, 10024-10035. DOI: https://doi.org/10.1021/ja00051a040

Rappé, A. K. & Goddard III, W. A. (1991). Charge equilibration for molecular dynamics simulations. J. Phys. Chem., 95, 3358-3363. DOI: https://doi.org/10.1021/j100161a070

Rappé, A. K., Pietsch, M. A., Wiser, D. C., Hart, J. R. & Bormann-Rochotte, L. M. (1997). RFF, conceptual development of a full periodic table force field for studying reaction potential surfaces. Mol. Eng., 7, 385-400. DOI: https://doi.org/10.1023/A:1008264127580

Ren P. & Ponder, J. W. (2003). Polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B, 107, 5933-5947. DOI: https://doi.org/10.1021/jp027815+

Ren, P., Wu, C. & Ponder, J. W. (2011). Polarizable atomic multipole-based molecular mechanics for organic molecules. J. Chem. Theory Comput., 7, 3143-3161. DOI: https://doi.org/10.1021/ct200304d

Rick, S. W. & Stuart, S. J. (2002). Potentials and algorithms for incorporating polarizability in computer simulations. In: Reviews in Computational Chemistry. Lipkowitz, K. B., Boyd, D. B. eds. John Wiley & Sons, Inc. 89-146. DOI: https://doi.org/10.1002/0471433519.ch3

Rick, S. W., Stuart, S. J. & Berne, B. J. (1994). Dynamical fluctuating charge force fields: application to liquid water. J. Chem. Phys., 101, 6141-6156. DOI: https://doi.org/10.1063/1.468398

Robertson, M. J., Tirado-Rives, J. & Jorgensen, W. L. (2015). Improved peptide and protein torsional energetics with the OPLS-AA force field. J. Chem. Theory Comput., 11, 3499-3509. DOI: https://doi.org/10.1021/acs.jctc.5b00356

Robertson, M. J., Qian, Y., Robinson, M. C., Tirado-Rives, J. & Jorgensen, W. L. (2019). Development and testing of the OPLS-AA/M force field for RNA. J. Chem. Theory Comput., 15, 2734-2742. DOI: https://doi.org/10.1021/acs.jctc.9b00054

Root, D. M., Landis, C. R. & Cleveland, T. (1993). Valence bond concepts applied to the molecular mechanics description of molecular shapes. 1. Application to nonhypervalent molecules of the P-block. J. Am. Chem. Soc., 115, 4201-4209. DOI: https://doi.org/10.1021/ja00063a043

Sanderson, R. T. (1955). Partial charges on atoms in organic compounds. Science, 121, 207-208. DOI: https://doi.org/10.1126/science.121.3137.207

Scherer, P. O. J. (2017). Computational physics: simulation of classical and quantum systems. Springer. Germany. 633 p.

Schlegel, H. B. (2011). Geometry optimization. WIREs Comput. Mol. Sci., 1, 790-809. DOI: https://doi.org/10.1002/wcms.34

Scott, W. R. P., H" u nenberg, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Kr" u ger, P. & Van Gunsteren, W. F. (1999). The GROMOS biomolecular simulation packacge. J. Phys. Chem. A, 103, 3596-3607. DOI: https://doi.org/10.1021/jp984217f

Sengupta, A., Li, Z., Song, L. F., Li, P. & Merz Jr., K. M. (2021). Parametrization of monovalent ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models. J. Chem. Inf. Model., 61, 869-880. DOI: https://doi.org/10.1021/acs.jcim.0c01390

Shah, M. S., Siepmann, J. I. & Tsapatsis, M. (2017). Transferble potentials for phase equilibria. Improved united-atom description of ethane and ethylene. AIChE J., 63, 5098-5110. DOI: https://doi.org/10.1002/aic.15816

Shi, S., Yan, L., Yang, Y., Fisher-Shaulsky, J. & Thacher, T. (2003). An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems. J. Comput. Chem., 24, 1059-1076. DOI: https://doi.org/10.1002/jcc.10171

Shi, Y., Zhang, J., Best, R., Wu, C., Ponder J. W. & Ren, P. (2013). Polarizable atomic multipole-based AMOEBA force field for proteins. J. Chem. Theory Comput., 9, 4046-4063. DOI: https://doi.org/10.1021/ct4003702

Silverman, R. A., Kolmogorov, A. N. & Fomin, S. V. (1970). Introductory real analysis. Dover Publications, Inc. New York, USA. 403 p.

Slater, J. C. (1930). Atomic shielding constants. Phys. Rev., 36, 57-64. DOI: https://doi.org/10.1103/PhysRev.36.57

Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Gr" u newald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., Kroon, P. C., Melcr, J., Nieto, V., Corradi, V., Khan, H. M., Doma' n ski, J., Javanainen, M., Martinez-Seara, H., Reuter, N., Best, R. B., Vattulainen, I., Monticelli, L., Periole, X., Tieleman, D. P., de Vries, A. H. & Marrink, S. J. (2021). Martini3: a general purpose force field for coarse-grained molecular dynamics. Nat. Methods, 18, 382-388. DOI: https://doi.org/10.1038/s41592-021-01098-3

Spicher, S. & Grimme, S. (2020). Robust atomistic modeling of materials, organometallic, and biochemical systems. Angew. Chem. Int. Ed., 59, 15665-15673. DOI: https://doi.org/10.1002/anie.202004239

Sun, H,, Jin, Z., Yang, C., Akkermans, R. L. C., Robertson, S. H., Spenley, N. A., Miller, S. & Todd, S. M. (2016). COMPASS II: extended coverage for polymer and drug-like molecule databases. J. Mol. Model., 22, 47. DOI: https://doi.org/10.1007/s00894-016-2909-0

Szabo, A. & Ostlund, N. S. (1996). Modern quantum chemistry. Introduction to advanced electronic structure theory. Dover Publications, Inc. Mineola, New York. 479 p.

Thakuria, R., Nath, N. K. & Saha, B. K. (2019). The nature and applications of $pi-pi$ interactions: a perspective. Cryst. Growth Des., 19, 523-528. DOI: https://doi.org/10.1021/acs.cgd.8b01630

Thole, B. T. (1981). Molecular polarizabilities calculated with a modified dipole interaction. Chem. Phys., 59, 341-350. DOI: https://doi.org/10.1016/0301-0104(81)85176-2

Tian, C., Kasavajhala, K., Belfon, K. A. A., Raguette, L., Huang, H., Migues, A. N., Bickel, J., Wang, Y., Pincay, J., Wu, Q. & Simmerling, C. (2020). ff19B: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. J. Chem. Theory Comput., 16, 528-552. DOI: https://doi.org/10.1021/acs.jctc.9b00591

Urey, H. C. & Bradley Jr., D. A. (1931). The vibrations of pentatonic tetrahedral molecules. Phys. Rev., 38, 1969-1978. DOI: https://doi.org/10.1103/PhysRev.38.1969

Van der Waals, J. D. (1873). On the continuity of the gas and liquid state [Doctoral thesis, University of Leiden]. Leiden.

Van Duijnen, P. Th. & Swart, M. (1998). Molecular and atomic polarizabilities: Thole's model revisited. J. Phys. Chem. A, 102, 2399-2407. DOI: https://doi.org/10.1021/jp980221f

Van Duin, A. C. T., Dasgupta, D., Lorant, F. & Goddard III, W. A. (2001). ReaxFF: a reactive force field for hydrocarbons. J. Phys. Chem. A, 105, 9396-9409. DOI: https://doi.org/10.1021/jp004368u

Vanommeslaeghe, K., Guvench, O. & MacKerell Jr., A. D. (2014). Molecular mechanics. Curr. Pharm. Des., 20, 3281-3292. DOI: https://doi.org/10.2174/13816128113199990600

Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I. & MacKerell Jr., A. D. (2009). CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem., 31, 671-690. DOI: https://doi.org/10.1002/jcc.21367

Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. (2004). Development and testing of a general amber force field. J. Comput. Chem., 25, 1157-1174. DOI: https://doi.org/10.1002/jcc.20035

Weels, B. A., De Bruin-Dickason, C. & Chaffe, A. L. (2015). Charge equilibration based on atomic ioinization in metal-organic frameworks. J. Phys. Chem. C, 119, 456-466. DOI: https://doi.org/10.1021/jp510415h

Westheimer, F. H. & Mayer, J. E. (1946). The theory of the racemization of optically active derivatives of diphenyl. J. Chem. Phys., 14, 733-738. DOI: https://doi.org/10.1063/1.1724095

Wilmer, C. E., Kim, K. C. & Snurr, R. Q. (2012). An extended charge equilibration method. J. Phys. Chem. Lett., 3, 2506-2511. DOI: https://doi.org/10.1021/jz3008485

Xie, W., Pu, J., Mackerell Jr., A. D. & Gao, J. (2007). Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J. Chem. Theory Comput., 3, 1878-1889. DOI: https://doi.org/10.1021/ct700146x

Xu, P., Guidez, E. B., Bertoni, C. & Gordon, M. S. (2018). Perspective: ab initio force field methods derived from quantum mechanics. J. Chem. Phys., 148, 090901. DOI: https://doi.org/10.1063/1.5009551

Yang, L., Sun, L. & Deng, W. (2020). Van der Waals function for molecular mechanics. J. Phys. Chem. A, 124, 2102-2107. DOI: https://doi.org/10.1021/acs.jpca.9b11222

Yuki, H., Tanaka, Y., Hata, M., Ishikawa, H., Neya, S. & Hoshino, T. (2007). Implementation of $pi-pi$ interactions in molecular dynamics simulation. J. Comput. Chem., 28, 1091-1099. DOI: https://doi.org/10.1002/jcc.20557

Zgarbová, M., Sponer, J. & Jurecka, P. (2021). Z-DNA as a touchstone for additive empirical force fields and refinement of the alpha/gamma DNA torsions for AMBER. J. Chem. Theory Comput., 17, 6292-6301. DOI: https://doi.org/10.1021/acs.jctc.1c00697

Zgarbová, M., Otyepka, M., Sponer, J., Mládek, A., Cheatham, T. E. & Jurecka, P. (2011). Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J. Chem. Theory Comput., 7, 2886-2902. DOI: https://doi.org/10.1021/ct200162x

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APA

Díaz, M., Coll, D. y Vega, D. (2024). MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR. Revista de la Facultad de Ciencias, 13(1), 73–127. https://doi.org/10.15446/rev.fac.cienc.v13n1.109657

ACM

[1]

Díaz, M., Coll, D. y Vega, D. 2024. MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR. Revista de la Facultad de Ciencias. 13, 1 (ene. 2024), 73–127. DOI:https://doi.org/10.15446/rev.fac.cienc.v13n1.109657.

ACS

(1)

Díaz, M.; Coll, D.; Vega, D. MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR. Rev. Fac. Cienc. 2024, 13, 73-127.

ABNT

DÍAZ, M.; COLL, D.; VEGA, D. MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR. Revista de la Facultad de Ciencias, [S. l.], v. 13, n. 1, p. 73–127, 2024. DOI: 10.15446/rev.fac.cienc.v13n1.109657. Disponível em: https://revistas.unal.edu.co/index.php/rfc/article/view/109657. Acesso em: 30 jul. 2024.

Chicago

Díaz, Miguel, David Coll, y David Vega. 2024. «MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR». Revista De La Facultad De Ciencias 13 (1):73-127. https://doi.org/10.15446/rev.fac.cienc.v13n1.109657.

Harvard

Díaz, M., Coll, D. y Vega, D. (2024) «MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR», Revista de la Facultad de Ciencias, 13(1), pp. 73–127. doi: 10.15446/rev.fac.cienc.v13n1.109657.

IEEE

[1]

M. Díaz, D. Coll, y D. Vega, «MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR», Rev. Fac. Cienc., vol. 13, n.º 1, pp. 73–127, ene. 2024.

MLA

Díaz, M., D. Coll, y D. Vega. «MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR». Revista de la Facultad de Ciencias, vol. 13, n.º 1, enero de 2024, pp. 73-127, doi:10.15446/rev.fac.cienc.v13n1.109657.

Turabian

Díaz, Miguel, David Coll, y David Vega. «MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR». Revista de la Facultad de Ciencias 13, no. 1 (enero 1, 2024): 73–127. Accedido julio 30, 2024. https://revistas.unal.edu.co/index.php/rfc/article/view/109657.

Vancouver

1.

Díaz M, Coll D, Vega D. MODELOS DE INTERACCIONES ATÓMICAS EN MECÁNICA MOLECULAR. Rev. Fac. Cienc. [Internet]. 1 de enero de 2024 [citado 30 de julio de 2024];13(1):73-127. Disponible en: https://revistas.unal.edu.co/index.php/rfc/article/view/109657

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