Research Accomplishments

Direct observation of migration pathways of ions and a quantitative dissection of their energetics in
solid polymer electrolytes (SPEs) are essential to understand the molecular origins of barriers
limiting the conductivity of SPEs. SPEs are ion-conducting polymers obtained by dissolving alkali
salts in high molecular weight solid polymers. Depending upon the interplay between molecular
packing and dynamics, SPEs exhibit a wide range of conductivity (10 -9-10-4 S/cm) at room
temperature despite their common polymer matrix. A detailed molecular studies are needed to
establish a precise correlation between the nature of polymer packing, dynamics, energetics, and ion
conduction for rational design of SPE-based fast ion conductors. The principal driving forces
controlling the degree of conductivity of SPEs including the nature of macromolecular packing, ion-
polymer interactions, ion coordination structure, conformational order and mobility of polymers are
significantly different among the SPEs.

However, the precise correlations between these molecular factors and the ion transport in SPEs are
not well established. It remains unclear whether disordered amorphous or ordered crystalline
structures promote conduction of ions in SPEs. The other important challenges that remain in SPE-
related research are the identification of low-energy ion conduction pathways, characterization of
the free energy profiles and the structural and dynamical contributions to the favorable (stable
energy wells) and unfavorable (activation energy barriers) ion sites along these conduction
pathways.

Detailed molecular-level studies are needed to establish a precise correlation between the nature of
polymer packing, dynamics, energetics and ion conduction in SPEs. In this regard, molecular
dynamics (MD) simulations and enhanced sampling free energy methods play an important role in
elucidating the atomistic details of ion transport and the critical ion-ion and ion-polymer
interactions in SPEs. In my doctoral thesis, I have employed molecular dynamics simulation,
enhanced sampling methods (for example, the adaptive biasing force method, well-tempered
metadynamics simulation, and nudged elastic band method) and normal mode analysis to
investigate the structure, dynamics and energetics of crystalline and amorphous phases of
poly(ethylene oxide) (PEO) and PEO-based SPEs. The schematic representations of the different
modeled PEO-based SPEs is shown in Figure 1.
Figure 1 Structures of different poly(ethylene oxide) (PEO)-based SPEs investigated. (a) Pristine
PEO, (b) PEO3:NaI, (c) PEO6:LiPF6, (d) PEO8:NaAsF6

A detailed report of my research work is as follows:

Project 1: Thermal Evolution of Conformation, Structure, and Dynamics of Crystalline

Poly(Ethylene Oxide)

The lack of a clear understanding of the conduction mechanism of ions in solid polymer electrolytes
(SPEs) has spurred a large amount of research. It is widely believed that the conduction of ions in
SPEs is mainly driven by the mobility of the host polymer. Moreover, with increase in the
temperature, the ionic conductivity increases due presumably to thermally induced changes in the
polymer dynamics. Therefore, it is essential to characterize the thermal behavior of polymer host in
pristine and salt-complexed crystalline states. We have used large-scale atomistic molecular
dynamics simulations of a model of crystalline poly(ethylene oxide) at various temperatures to
characterize the thermal variation of volume of simulation cell, intra-molecular radial distribution
functions, radius of gyration (Rg), and percentage of conformational defects as a function of
temperature. The calculations have revealed a premelting transition leading to a state intermediate
to the crystal and melt.

Project 2: Accurate Determination of the Melting Point of a Helical Polymer Crystal Using
Pseudo-Supercritical Path Method

The most direct computational approach to determine the melting point of a polymer crystal is to
perform brute MD simulations of the crystal at different temperatures and identify the temperature
at which abrupt changes in the density and polymer conformations occur. However, the heating
rates employed in MD simulations are many orders of magnitude higher than the experimental
heating rates leading to the super-heating of the polymer crystal. Since the superheated crystals melt
at higher temperatures than the equilibrium crystals, this computational approach results in
overestimation of the melting point (Tm) of the crystal. The pseudo-supercritical path (PSCP)
approach is a recently proposed MD-based computational method to accurately determine the
precise melting points of simulated crystals. We have investigated the melting of a pristine PEO
crystal using all-atom MD simulations and the free energy-based PSCP method. The T m computed
from the direct heating simulations was a factor of more than two higher than the experimental
value whereas Tm computed from the PSCP method is 346 K, which is in good agreement with the
experimental melting point of 340 K.

Project 3: Molecular Origins of Polymer-Coupled Helical Motion of Ions in a Crystalline

Polymer Electrolyte PEO3:NaI

Direct observation of migration pathways of ions and a quantitative dissection of their energetics in
solid polymer electrolytes (SPEs), for example PEO 3:NaI, are essential to understand the molecular
origins of barriers limiting the conductivity of these novel materials. Molecular dynamics and
enhanced sampling simulations were performed on different defected crystalline models of
PEO3:NaI. Two manuscripts were prepared based on the results obtained from these simulations.
The one with title, “Molecular Origins of Polymer-Coupled Helical Motion of Ions in a Crystalline
Polymer Electrolyte” has got published in Macromolecules (Macromolecules, 2016, 49 (2), pp 700–
707) and the second one, “Molecular Dynamics and Adaptive Biasing Force Investigation of
Crystalline 3:1 Polymer Electrolyte PEO3:NaI” is in pipeline.

Figure 2 summaries the key results obtained from our simulations. Free energy profiles for the
cation and anion transport, cation and anion migration pathways, and coupling between polymer
and ion dynamics are shown.
Figure 2 Free energy profiles for cation and anion transport, ion migration pathways, and coupling
between polymer and ion dynamics.

Project 4: Normal Mode Analysis of Low-frequency Collective Vibrations of Solid Polymer

Electrolytes

The role of low-frequency collective vibrational modes of polymer in ion transport and the nature of
transport-promoting polymer vibrations and salt-induced perturbations in the vibrational density of
states (VDOS) of PEO-based SPEs are poorly understood. It is believed that the conduction
pathways of ions in SPEs may follow the trajectories of one or a few low-frequency normal modes.
A comparison of the vibrational modes of PEO in crystalline PEO and PEO-salt complexes can help
us to understand the salt-induced changes in the low-frequency vibrational modes of PEO in SPEs.
A detailed characterization of the VDOS of different crystalline PEO:salt complexes provides clues
on the vibrational response of PEO to different salts and on the relationship between polymer
dynamics and ion transport in these systems.

Figure 3 Atomic displacements of representative normal mode of the PEO crystal.

Project 5: A Comparative Study of Ion Transport in Crystalline and Amorphous Solid
Polymer Electrolytes

The prevailing view of ion transport in SPEs is that the cation transport is facile in the amorphous
regions than in crystalline regions of SPEs but recent work by Bruce et al. supports the opposite
result. It remains unclear whether disordered amorphous or ordered crystalline structures promote
conduction of ions in SPEs. Molecular-level studies are needed to understand the differences
between the ion conduction in amorphous and crystalline SPEs. In this project, we have used all-
atom MD simulation and the adaptive biasing force (ABF) method to characterize the microscopic
differences in the structures and ion conduction mechanisms between the crystalline and amorphous
PEO3:NaI. In particular, the free energy profiles and activation energies for the cation hopping
between different coordinated states are estimated.

Figure 4 The free energy profiles as a function of the coordination of near neighbor OPEO,
coordination number distribution and geometry in crystalline and amorphous PEO3:NaI.
Project 6: Atomic-Scale Modeling of Interactions in Pore-Forming Toxins: Influence of
Membrane Composition and Cholesterol Concentration

Pore­forming   toxins   (PFTs)   are   membrane   disruptive   proteins,   which   undergo

oligomerization in the host­cell membrane by forming non­selective transmembrane
pores. PFTs are generally classified as  a­PFTs and  b­PFTs based on the dominant
secondary   structure   of   the   transmembrane   domain.   The   mechanism   of
oligomerization,   the   fate   of   lipids   during   pore   formation,   and   the   influence   of
cholesterol concentration on membrane­protein interactions in cholesterol dependent
cytolysins (CDCs) is rather poorly understood. Unraveling these membrane mediated
interactions not only has implications in bacterial resistance, but also enhances our
understanding of protein aggregation, implicated in neurodegenrative diseases such as
Alzheimers and Parkinsons. The lipid dynamics in the presence of PFT monomers and
intermediate arc like structures will enhance the understanding of oligomerization of
these toxins. However, challenges lie in deciphering these interactions experimentally.
Molecular dynamics (MD) simulations and enhanced sampling free energy methods
provide an elegant approach to investigate the atomistic details of protein­membrane
interactions. Here, we use all­atom MD simulations and the adaptive biasing force
(ABF) method to investigate the influence of membrane composition and cholesterol
concentration on membrane properties and to identify cholesterol retention sites on
the protein, respectively.