Dataset Information

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be₆B₁₁^- Flux-Ional Cluster.

ABSTRACT: The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be₆B₁₁^- clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be₆B₁₁^- clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations' temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer's infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.

SUBMITTER: Buelna-Garcia CE

PROVIDER: S-EPMC7796227 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Publications

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11- Flux-Ional Cluster.

Buelna-Garcia Carlos Emilano CE Cabellos José Luis JL Quiroz-Castillo Jesus Manuel JM Martinez-Guajardo Gerardo G Castillo-Quevedo Cesar C de-Leon-Flores Aned A Anzueto-Sanchez Gilberto G Martin-Del-Campo-Solis Martha Fabiola MF

Materials (Basel, Switzerland) 20201229 1

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11- clusters and the effect of temperature on thei ...[more]

PMID: 33383889

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Project description:A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein-ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters). Recent advances in sampling methods and force fields coupled with vast increases in computational resources have made FEP a viable technology to drive hit-to-lead and lead optimization, allowing for more efficient cycles of medicinal chemistry and the possibility to explore much larger chemical spaces. However, previous FEP applications have focused on systems with high-resolution crystal structures of the target as starting points-something that is not always available in drug discovery projects. As such, the ability to apply FEP on homology models would greatly expand the domain of applicability of FEP in drug discovery. In this work we apply a particular implementation of FEP, called FEP+, on congeneric ligand series binding to four diverse targets: a kinase (Tyk2), an epigenetic bromodomain (BRD4), a transmembrane GPCR (A2A), and a protein-protein interaction interface (BCL-2 family protein MCL-1). We apply FEP+ using both crystal structures and homology models as starting points and find that the performance using homology models is generally on a par with the results when using crystal structures. The robustness of the calculations to structural variations in the input models can likely be attributed to the conformational sampling in the molecular dynamics simulations, which allows the modeled receptor to adapt to the "real" conformation for each ligand in the series. This work exemplifies the advantages of using all-atom simulation methods with full system flexibility and offers promise for the general application of FEP to homology models, although additional validation studies should be performed to further understand the limitations of the method and the scenarios where FEP will work best.

Dataset Information

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be₆B₁₁^- Flux-Ional Cluster.

Publications

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be<sub>6</sub>B<sub>11</sub><sup>-</sup> Flux-Ional Cluster.

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