Periodic Reporting for period 1 - A-TO-B (A Theory of Organic Bioelectronics Materials)
Reporting period: 2021-10-01 to 2023-03-31
Bioelectronics materials are used as interface between human-made electronic devices and biological cells, tissues or fluids for applications such as diagnostics/sensing or monitoring/stimulating neural activity. Organic (often polymeric) materials able to conduct both ionic and electronic current are emerging as the ideal choice for bioelectronics because of an enhanced biocompatibility, flexibility and, most of all, the ability to fine tune their property through the control of their chemical composition. However, despite the excellent proof of concepts available, there is no systematic approach to improve this class of materials because there is no approach currently available to model and design them. No existing methodology enables the study of electronic motion in soft-materials concurrently with the motion of ions: the timescales of the relevant phenomena are very different and a new approach should be constructed drawing elements from different areas of modelling science.
Developing a methodology that establishes a link between the chemical composition and the behaviour of organic bioelectronics materials will accelerate their development and bring to fruition the benefits of this technology in terms of improved healthcare. The areas of proposed applications are ever growing and, in addition to diagnostics, they now include controlled drug delivery and tissue reparation to treat, for example, spinal cord injuries or certain types of blindness.
The overall goal of this proposal is (i) to lay the foundations for atomistic modelling of organic bioelectronics materials, (ii) to derive structure-property relationship from the study a range of experimentally relevant systems and (iii) to address some of the most pressing scientific questions on the physics of bioelectronics devices.
Developing a methodology that establishes a link between the chemical composition and the behaviour of organic bioelectronics materials will accelerate their development and bring to fruition the benefits of this technology in terms of improved healthcare. The areas of proposed applications are ever growing and, in addition to diagnostics, they now include controlled drug delivery and tissue reparation to treat, for example, spinal cord injuries or certain types of blindness.
The overall goal of this proposal is (i) to lay the foundations for atomistic modelling of organic bioelectronics materials, (ii) to derive structure-property relationship from the study a range of experimentally relevant systems and (iii) to address some of the most pressing scientific questions on the physics of bioelectronics devices.
The work performed follows closely the original work-plan with the high risk components of the first 2 workpackage now successfully completed. Eight publications already appeared in literature.
WP1: Ion-electron coupled dynamics
The original goal reported in the proposal was to develop a new methodology to study the coupled ion-electron dynamics in organic bioelectronics polymers. The dynamics was to be studied in timescales relevant for describing ion diffusion (~50 ns) using a novel quantum/classical Hamiltonian that retains the essential system-specific information on the quantum nature of the excess charge in the polymer and treats the remaining degrees of freedom classically. The method has been developed, tested and published in literature as [J. Mater. Chem. C, DOI: 10.1039/D2TC05103F 2023]. This is a key milestone for this proposal, underpinning the work of the next 3.5 years.
The method referred to as QM/MD proved to be very powerful to study different kinds of interface as demonstrated by a work co-authored by the PI investigating aqueous mono- and divalent salt electrolytes in contact with charged carbon-based electrodes [Carbon, DOI: 10.1016/j.carbon.2023.03.019 2023].
WP2: Rapid polymer and polymer composite simulation
This WP had two fairly distinct aspects already in the original proposal (a) accelerating the generation of classical models and (b) accelerating the computation of electronic properties. Important progress has been made on both aspects:
(a.1) A method was developed to rapidly equilibrate semiconducting polymers using a hybrid resolution where the side chains are described with a coarse representation and the backbone is described atomistically. This method is fast do implement and deploy, it has been published as [Mol. Sys. Des. Eng., DOI: 10.1039/D1ME00165E 2022] and will be one of the tools to be used in the reminder of this project.
(a.2) A separate aspects that needs to be accelerated is the generation of the classical model and it parametrization. A workflow has been designed and implemented by Hesam Makki to do exactly this. It has been used to create models of several polymers (IDT-BT, IDT-BTPT) and will be disseminated later in the project as these methodologies need to be studied on larger data sets before public dissemination.
(b.1) To accelerate the screening of polymers for their electronic properties we proposed a method where the only input is the polymer sequence [J. Mater. Chem. C, DOI: 10.1039/D2TC02527B , 2022]. The approach proved to be powerful and revealed a good number unanticipated features (e.g. that shorter repeat sequences of monomers are desirable).
(b.2) A challenging step is the connection between electronic structure calculation (done in b.1) and charge mobility. This was achieved in a recently published work [Adv. Funct. Mater, DOI: 10.1002/adfm.202303234 2023] via model reduction, i.e. by building a simplified model that retains the essential chemical characteristics but is suitable to predict the charge mobility with any desirable model.
WP3: Bioelectronics Interfaces & WP4: Device Modelling.
These two WPs were due to start later in the project but two preliminary activities took place, leading to important publications.
(a) One of the benchmark materials in organic bioelectronics is the composited PDOT:PSS, the natural choice to study interface with biomolecules in WP3. However, this material has a complex two-phase microstructure which had to be characterized before any study of further interfaces. We built such model, reported in [J. Mater. Chem. C, DOI: 10.1039/D2TC03158B 2022] where we show that both PEDOT-rich and PSS-rich phases consist of PEDOT lamellae embedded in PSS chains.
(b) We have supported the group of A. Salleo (Stanford) in the interpretation of unexpected experimental observation on the charge transport of PDOT:PSS film [J. Am. Chem. Soc., 10.1021/jacs.2c02139 2022].
WP1: Ion-electron coupled dynamics
The original goal reported in the proposal was to develop a new methodology to study the coupled ion-electron dynamics in organic bioelectronics polymers. The dynamics was to be studied in timescales relevant for describing ion diffusion (~50 ns) using a novel quantum/classical Hamiltonian that retains the essential system-specific information on the quantum nature of the excess charge in the polymer and treats the remaining degrees of freedom classically. The method has been developed, tested and published in literature as [J. Mater. Chem. C, DOI: 10.1039/D2TC05103F 2023]. This is a key milestone for this proposal, underpinning the work of the next 3.5 years.
The method referred to as QM/MD proved to be very powerful to study different kinds of interface as demonstrated by a work co-authored by the PI investigating aqueous mono- and divalent salt electrolytes in contact with charged carbon-based electrodes [Carbon, DOI: 10.1016/j.carbon.2023.03.019 2023].
WP2: Rapid polymer and polymer composite simulation
This WP had two fairly distinct aspects already in the original proposal (a) accelerating the generation of classical models and (b) accelerating the computation of electronic properties. Important progress has been made on both aspects:
(a.1) A method was developed to rapidly equilibrate semiconducting polymers using a hybrid resolution where the side chains are described with a coarse representation and the backbone is described atomistically. This method is fast do implement and deploy, it has been published as [Mol. Sys. Des. Eng., DOI: 10.1039/D1ME00165E 2022] and will be one of the tools to be used in the reminder of this project.
(a.2) A separate aspects that needs to be accelerated is the generation of the classical model and it parametrization. A workflow has been designed and implemented by Hesam Makki to do exactly this. It has been used to create models of several polymers (IDT-BT, IDT-BTPT) and will be disseminated later in the project as these methodologies need to be studied on larger data sets before public dissemination.
(b.1) To accelerate the screening of polymers for their electronic properties we proposed a method where the only input is the polymer sequence [J. Mater. Chem. C, DOI: 10.1039/D2TC02527B , 2022]. The approach proved to be powerful and revealed a good number unanticipated features (e.g. that shorter repeat sequences of monomers are desirable).
(b.2) A challenging step is the connection between electronic structure calculation (done in b.1) and charge mobility. This was achieved in a recently published work [Adv. Funct. Mater, DOI: 10.1002/adfm.202303234 2023] via model reduction, i.e. by building a simplified model that retains the essential chemical characteristics but is suitable to predict the charge mobility with any desirable model.
WP3: Bioelectronics Interfaces & WP4: Device Modelling.
These two WPs were due to start later in the project but two preliminary activities took place, leading to important publications.
(a) One of the benchmark materials in organic bioelectronics is the composited PDOT:PSS, the natural choice to study interface with biomolecules in WP3. However, this material has a complex two-phase microstructure which had to be characterized before any study of further interfaces. We built such model, reported in [J. Mater. Chem. C, DOI: 10.1039/D2TC03158B 2022] where we show that both PEDOT-rich and PSS-rich phases consist of PEDOT lamellae embedded in PSS chains.
(b) We have supported the group of A. Salleo (Stanford) in the interpretation of unexpected experimental observation on the charge transport of PDOT:PSS film [J. Am. Chem. Soc., 10.1021/jacs.2c02139 2022].
First 18 months:
(1) It is now possible to build a model of charged semiconducting polymer mixed with water and electrolytes and study the concurrent time evolution of ionic and electronic charge.
(2) It is now possible to generate rapidly and accurately classical models of bulk semiconducting polymers thanks to an automated procedure to generate the model parameters and a novel hybrid-resolution method that enables a rapid equilibration of the model.
(3) A model to link the monomer sequence to the charge mobility has been developed. The cost for performing such prediction is marginal with respect to cost of performing the experiments.
(4) An atomistic model of the two-phase PDOT:PSS material has been developed and used to describe the charge transport mechanism in this benchmark class of composite materials.
By the conclusion of the project:
(5) A large number of chemical compositions are studied and the relation between key parameters (charge and ionic mobility, volumetric capacitance) and chemical composition is derived.
(6) Dynamic processes currently not well understood (e.g. the reversible charging and uncharging of the active materials, microstructure changes) can be modelled.
(7) The parameters dictating the device operation (charge and ionic mobility, ion injection barrier) can be computed and used to derive a consistent description of the device operations.
(8) Models describing the interaction between the material and aqueous interface (including biomolecules and cell walls) are developed to describe the sensing mechanism.
(9) The software tools developed by this project are made available (i.e. publically accessible and with good documentation) to the community.
(1) It is now possible to build a model of charged semiconducting polymer mixed with water and electrolytes and study the concurrent time evolution of ionic and electronic charge.
(2) It is now possible to generate rapidly and accurately classical models of bulk semiconducting polymers thanks to an automated procedure to generate the model parameters and a novel hybrid-resolution method that enables a rapid equilibration of the model.
(3) A model to link the monomer sequence to the charge mobility has been developed. The cost for performing such prediction is marginal with respect to cost of performing the experiments.
(4) An atomistic model of the two-phase PDOT:PSS material has been developed and used to describe the charge transport mechanism in this benchmark class of composite materials.
By the conclusion of the project:
(5) A large number of chemical compositions are studied and the relation between key parameters (charge and ionic mobility, volumetric capacitance) and chemical composition is derived.
(6) Dynamic processes currently not well understood (e.g. the reversible charging and uncharging of the active materials, microstructure changes) can be modelled.
(7) The parameters dictating the device operation (charge and ionic mobility, ion injection barrier) can be computed and used to derive a consistent description of the device operations.
(8) Models describing the interaction between the material and aqueous interface (including biomolecules and cell walls) are developed to describe the sensing mechanism.
(9) The software tools developed by this project are made available (i.e. publically accessible and with good documentation) to the community.