Impact of solvent and local chemical environment on the binding of biologically relevant molecules with nanoparticles
EMSL Project ID
50637
Abstract
Motivation: This proposal is motivated by the need to assess the complex interactions between biological systems and nanoparticles in the environment when they come in contact with each other.Objective: The overarching goal of this proposed research is to perform theoretical investigation of binding of biologically relevant molecules such as proteins, nucleic acids (DNA), and lipids with model nanoparticles (for example, quantum dots). Specifically, the proposed research will investigate effect of solvent, and the local chemical environment such as pH on the binding of biomolecules to nanoparticles. The optical properties of quantum dots are strongly influenced by the chemistry of the surface ligands and the local electrostatic environment. The proposed research will calculate the binding energies, provide structures of the biomolecule-nano complexes, and will generate the spectral signature of the binding event by calculating the optical spectra of the bio-nano complexes.
Challenges: The central challenge in the computational treatment of the systems described above is the size of the overall system. Because of the large number of atoms, it is not possible to use density functional theory for performing electronic structure calculation on the quantum dots/rod. This problem is exacerbated by the presence of surface biomolecules such as proteins, DNA, and lipids. Moreover, these bio-nano systems exist in aqueous medium and therefore it is imperative to include solvent molecules in the calculations. All this factors highlight the need for developing new theoretical methods for treating these systems.
Intellectual merit and strategy: The proposed research addresses these challenges by developing a quantum mechanical/molecular mechanical (QM/MM) strategy for calculating the optical properties of the nanoparticle. The QM/MM approach has been used successfully for introducing quantum effects in enzymes and proteins. In the proposed research, the quantum dot is treated quantum mechanically and the electronic structure of the nanoparticle is obtained using atom-centered pseudopotential. Ground state calculations will be performed using density functional theory (DFT) and excited state calculations will be performed using the geminal screened electron-hole interaction kernel (GSIK) method and time-dependent density functional theory (TDDFT) methods. The protein on the surface of the nanoparticle and the surrounding water molecules is treated using molecular mechanics force field.
Relevance to the mission of the EMSL program: The proposed project has a strong overlap with the research interests of the EMSL program. More specifically, the proposed research will develop computation and theoretical methods that can be used as tools for predicting binding of biomolecules with semiconductor quantum dots. This information is the first step towards identification and categorization of level of nanotoxicity of these semiconductor nanoparticles. The result from this project will generate both binding-energy data and spectral signature of nanoparticles-biomolecule complexes which can be used with experimental techniques to identify, detect, and quantify binding events in the environment.
Project Details
Start Date
2018-12-01
End Date
2019-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Team Members