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A Spectroscopic Validation of the Improved Lennard-Jones Model.

ABSTRACT: The Lennard-Jones (LJ) and Improved Lennard-Jones (ILJ) potential models have been deeply tested on the most accurate CCSD(T)/CBS electronic energies calculated for some weakly bound prototype systems. These results are important to plan the correct application of such models to systems at increasing complexity. CCSD(T)/CBS ground state electronic energies were determined for 21 diatomic systems composed by the combination of the noble gas atoms. These potentials were employed to calculate the rovibrational spectroscopic constants, and the results show that for 20 of the 21 pairs the ILJ predictions agree more effectively with the experimental data than those of the LJ model. The CCSD(T)/CBS energies were also used to determine the β parameter of the ILJ form, related to the softness/hardness of the interacting partners and controlling the shape of the potential well. This information supports the experimental finding that suggests the adoption of β≈9 for most of the systems involving noble gas atoms. The He-Ne and He-Ar molecules have a lifetime of less than 1ps in the 200-500 K temperature range, indicating that they are not considered stable under thermal conditions of gaseous bulks. Furthermore, the controversy concerning the presence of a "virtual" or a "real" vibrational state in the He2 molecule is discussed.

SUBMITTER: de Oliveira RM

PROVIDER: S-EPMC8271504 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Molecular dynamics (MD) simulations based on atomic models play an important role in the drug-discovery process to screen molecules, estimate binding free energies, and optimize lead compounds in chemical space. Accurate computations of thermodynamic and kinetic properties using MD simulations are highly dependent on the accuracy of the underlying atomic force field. In this context, going beyond the nonpolarizable fixed-charge model by accounting explicitly for induced polarization is highly desirable. The CHARMM polarizable force field based on classical Drude oscillators, in which an auxiliary charged particle is attached via a harmonic spring to its parent nucleus, offers both a computationally convenient and rigorous framework to model explicitly induced electronic polarization in MD simulations. For any molecule of interest, electrostatic partial charges, atomic polarizabilities, and Thole shielding factors, as well as bonded parameters can either be determined from ab initio calculations or ascribed from the knowledge-based library of the CHARMM Generalized force field. While this approach is fairly reliable in general, it is well understood that the overall accuracy of the models with respect to thermodynamic properties such as bulk density, enthalpies, and solvation free energies is particularly sensitive to the nonbonded Lennard-Jones (LJ) parameters. In the present study, we systematically refined the set of LJ parameters for the atom types available in the Drude force field to best match the experimental thermodynamic properties for 416 small druglike organic molecules. To further test the transferability of the optimized parameters, the hydration free energy of 372 molecules was computed. The calculations resulted in a small average error of 0.46 kcal/mol and a Pearson R of 0.9, representing a significant improvement over the additive GAFF force field in our previous study, where an average error of ∼2 kcal/mol was obtained. Such an improvement is consistent with the ability of the polarizable Drude model to more accurately model interactions in different environments. The effort provides a roadmap for the global optimization of force field parameters using experimental data. It is hoped that the present effort will further the application of the Drude polarizable force field in molecular simulations including drug design and discovery.

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A Spectroscopic Validation of the Improved Lennard-Jones Model.

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