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CBE Research Opportunities

Research Opportunities in Chemical and Biomolecular Engineering for Undergraduates

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Nanostructured Polysulfone Polyelectrolyte Copolymer Membranes for Fuel Cells

Sulfonated polysulfone copolymers with controlled nanophase-separated morphology hold great potential
as alternatives to benchmark Nafion® for polyelectrolyte membrane fuel cells (PEMFCs), due to their much
better proton conductivity at low relative humidity (RH) levels and thermal stability. Previous research have
shown that long hydrophilic (ionic) sequences or high degree of sulfonation are needed to form wellconnected
proton conducting nanochannels that enables high proton conductivity at low RH. However, it invariably comes at the expense of high water uptake and excessive membrane swelling resulting in deterioration of the dimensional stability and mechanical robustness. This project aims to exploiting an innovative supramolecular strategy to address this water management challenge in PEM membranes via introducing triptycene-based building blocks into polymer backbones. It is expected that supramolecular interactions of chain threading and interlocking induced by triptycene units can effectively suppress water swelling while maintaining high water uptake, which is critical to provide high proton conductivity under low RH conditions. Specifically, both random and multiblock copolymers of systematically varied compositions will be developed in this project to investigate how supramolecular interactions of triptycene units govern the formation of proton-conducting nanochannels as well as proton transport properties. The project will start with the synthesis of triptycene diol monomer, which will be copolymerized with commercial sulfonated monomer to produce both random and multiblock copolymers. Comprehensive characterizations of the copolymers will be conducted to confirm the chemical structure (NMR ad FTIR) and access their thermal and mechanical properties (DSC, TGA, tensile test, etc.). Membrane fabrication and acidification will then follow to prepare free standing, defect-free films for water swelling measurement, morphology characterization (AFM, TEM) and proton conductivity measurements (Impedance spectroscopy).

Preferred disciplines: A student in materials science, chemical engineering, or chemistry is preferred, and having previous experience in a chemical laboratory would be helpful.

Contact: Assistant Professor Ruilan Guo, 205E McCourtney Hall, 574 631-3453 (rguo@nd.edu)
Department of Chemical and Biomolecular Engineering

Polymer Membranes with Tunable Microporosity for Gas Separations

Polymers with well-defined microporosity are highly desired for gas separation membranes, wherein high
microporosity enables fast gas transport while the finely tuned pore size regulates selective transport via
size sieving. Recently there have been markedly increasing research interests in developing microporous
polymers for gas separation membranes, such as polymers with intrinsic microporosity (PIMs). However,
the reportedly super high gas permeability of microporous polymers always accompanies with low selectivity, mainly due to the lack of precise control over pore size distribution in these polymers. Moreover, physical aging induced deterioration of permeability remains as one of the biggest challenges for microporous polymer membranes. This project will focus on constructing highly rigid ladder-like polymers using a shape-persistent building block based on pentiptycene-containing structural units. The novelty of this new type of microporous polymers lies in the truly intrinsic microporosity defined configurationally by the shape of the pentiptycene units, which offers unique opportunity to tailor the microcavity architecture in the membranes and simultaneously provide superior resistance towards physical aging by taking advantage of the rigid framework of pentiptycene moieties. The project will involve the synthesis of pentiptycene-based monomers with various bridgehead substituent groups, polymerization of tetrafunctional pentiptycene monomers with commercial comonomers, membrane fabrication/characterization, and pure-gas permeation tests.

Preferred disciplines: A student in materials science, chemical engineering, or chemistry is preferred, and having previous experience in a chemical laboratory would be helpful.

Contact:
Assistant Professor Ruilan Guo, 205E McCourtney Hall, 574 631-3453 (rguo@nd.edu)
Department of Chemical and Biomolecular Engineering

Polymer Electrolytes for Advanced Rechargeable Batteries

The objective of the research is to investigate solid polymer electrolytes for use in lithium and/or magnesium rechargeable batteries. Such electrolytes have to potential for increase battery safety due to their lower volatility and higher thermal stability compared with commercial electrolytes. Current polymer electrolytes suffer from low ionic conductivities that result in low battery charge/discharge rates, which preclude their use in commercial devices.

This project will investigate the use of novel salts and/or additives in polymer electrolyte formulations.

Student Involvement: The REU student will prepare polymer electrolyte films and characterize the electrochemical and thermal properties of these films.

Preferred Disciplines: chemical engineering, not required, though greater levels of experience in a chemical laboratory are preferred.

Contact: Assistant Professor Jennifer L. Schaefer, 205G McCourtney Hall, 574 631-5114 (Jennifer.L.Schaefer.43@nd.edu) Department of Chemical and Biomolecular Engineering

Effects of Acidity and Salinity on Polymer Drug-Delivery Complexes

Research description:
A host of interesting phenomena, both biological and technological, involve the complexation of charged
polymers; these may be long polymers with well-dened secondary structure, such as proteins1, linear
polyelectrolytes, or multi-branched species2. A particularly interesting phenomenon within polyelectrolyte
solutions is coacervation3,4, a liquid{liquid phase separation where polymer-enriched liquid droplets are
formed within a dilute phase5. Coacervation is a puzzling process where two primarily aqueous phases become immiscible6. Aggregates (coacervates) formed in mixtures of oppositely charged polyelectrolytes are known as complex coacervates5,7,8. Coacervates occur in many natural systems9,10, and have found application in microencapsulation11,12 and extraction13 processes, as their ultra-low surface tension allows them to readily assimilate nanoparticles or drug payloads within aqueous suspension. Coacervation is intimately related to the process of layer-by-layer deposition, where films up to micrometers in thickness are built by iterative surface adsorption of polyelectrolytes. Such films are of interest as solid electrolytes in lightweight
batteries14,15, fuel-cell electrodes14,16, protective coatings16, and drug micro-encapsulation17.

This topic inspires REU projects involving characterization of coacervates through molecular dynamics
simulation. These are focused on the use of complex coacervates in the delivery of therapeutic compounds to
specific biological targets, as the highly charged, condensed environments they facilitate can act to stabilize
and protect molecular and macromolecular species.

1. Using a customized version of the LAMMPS open-source molecular simulation package,LAMMPS25
the student will examine the role of pH in the complexation of long polyions in the presence of added
salt. Of particular note are the connections between molecular structure and effective pKa in dilute
and concentrated solutions, as this quantity determines the useful phase window for coacervates as a
host material for drug delivery applications.

2. A second project involves the influence of the highly charged environment provided by a complex coacervate in stabilizing drugs|in particular protein based therapies|against deactivation and degradation.
the student will explicitly determine how these environments affect the pKa and native structure of
therapeutic compounds using coarse-grained and fully atomistic models.

Student Involvement:
It is preferable (but not required) for students interested in this project to have prior experience with writing
computer code (C++ preferred) and with scripting languages such as python and bash to facilitate running
computations on the Whitmer group cluster and CRC machines.

References:
1. S. L. Perry, L. Leon, K. Q. Homann, et al. \Chirality-selected phase behavior in ionic polypeptide
complexes." Nature Communications, 6, 2015.

2. D. Priftis, X. Xia, K. O. Margossian, et al. \Ternary, tunable polyelectrolyte complex fluids driven by
complex coacervation." Macromolecules, 47(9):3076{3085, 2014.

3. S. L. Turgeon, C. Schmitt, and C. Sanchez. \Protein{polysaccharide complexes and coacervates." Curr.
Opin. Colloid Interface Sci., 12(4-5):166{178, 2007.

4. J. R. Nixon, A. H. Khalil, and J. E. Carless. \Phase relationships in the simple coacervating system
isoelectric gelatin : Ethanol : Water." J. Pharm. Pharmac., 18:409{416, 1966.

5. D. Priftis and M. Tirrell. \Phase behavior and complex coacervation of aqueous polypeptide solutions."
Soft Matter, 8(36):9396, 2012.

6. F. M. Menger and B. M. Sykes. \Anatomy of a coacervate." Langmuir, 14(15):4131{4137, 1998.

7. R. A. Riggleman, R. Kumar, and G. H. Fredrickson. \Investigation of the interfacial tension of complex
coacervates using eld-theoretic simulations." J. Chem. Phys., 136:024903, 2012.

8. C. G. de Kruif, F. Weinbreck, and R. de Vries. \Complex coacervation of proteins and anionic polysaccharides." Curr. Opin. Colloid Interface Sci., 9(5):340{349, 2004.

9. N. Pawar and H. B. Bohidar. \Statistical thermodynamics of liquid{liquid phase separation in ternary
systems during complex coacervation." Phys. Rev. E, 82(3):36107, 2010.

10. A. E. Smith, F. T. Bellware, and J. J. Silver. \Formation of nucleic acid coacervates by dehydration and
rehydration." Nature, 214(5092):1038{1040, 1967.

11. C. I. Onwulata. \Encapsulation of new active ingredients." Annu. Rev. Food. Sci. Technol., 3:183{202,
2012.

12. S. R. Bhatia, S. F. Khattak, and S. C. Roberts. \Polyelectrolytes for cell encapsulation." Curr. Opin.
Colloid Interface Sci., 10(1-2):45{51, 2005.

13. F.-J. Ruiz, S. Rubio, and D. Perez-Bendito. \Water-induced coacervation of alkyl carboxylic acide
reverse micelles: Phenomenon description and potential for the extraction of organic compounds." Anal.
Chem., 79:7473{7484, 2007.

14. J. L. Lutkenhaus and P. T. Hammond. \Electrochemically enabled polyelectrolyte multilayer devices:
from fuel cells to sensors." Soft Matter, 3(7):804, 2007.

15. D. M. DeLongchamp and P. T. Hammond. \Highly ion conductive poly(ethylene oxide)-based solid
polymer electrolytes from hydrogen bonding layer-by-layer assembly." Langmuir, 20(13):5403{11, 2004.

16. P. R. Van Tassel. \Polyelectrolyte adsorption and layer-by-layer assembly: Electrochemical control."
Curr. Opin. Colloid Interface Sci., 17(2):106{113, 2012.

17. D. B. Shenoy, A. A. Antipov, G. B. Sukhorukov, and H. Mohwald. \Layer-by-layer engineering of
biocompatible, decomposable core-shell structures." Biomacromol., 4(2):265{72, 2003.

18. M. E. Leunissen, C. G. Christova, A.-P. Hynninen, et al. \Ionic colloidal crystals of oppositely charged
particles." Nature, 437(7056):235{40, 2005.

19. G. A. Chapela, F. del Ro, and J. Alejandre. \Liquid-vapor phase diagram and surface properties in
oppositely charged colloids represented by a mixture of attractive and repulsive Yukawa potentials." J.
Chem. Phys., 138(5):054507, 2013.

20. K. Iwata, H. Okajima, S. Saha, and H.-o. Hamaguchi. \Local structure formation in alkyl-imidazoliumbased
ionic liquids as revealed by linear and nonlinear Raman spectroscopy." Acc. Chem. Res., 40:1174{1181, 2007.

21. H.Weingartner. \Understanding ionic liquids at the molecular level: Facts, problems, and controversies."
Angew. Chem. Int. Ed., 47:654{670, 2008.

22. J. Qin, D. Priftis, R. Farina, et al. \Interfacial tension of polyelectrolyte complex coacervate phases."
ACS Macro Letters, 3(6):565{568, 2014.

23. S. L. Perry and C. E. Sing. \Prism-based theory of complex coacervation: Excluded volume versus chain
correlation." Macromolecules, 2015.

24. Z. Ou and M. Muthukumar. \Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics
simulations." J. Chem. Phys., 124(15):154902, 2006.

25. S. Plimpton. \Fast parallel algorithms for short-range molecular dynamics." J. Comp. Phys., 117(1):1{19, 1995.

Contact: Associate Professor Jonathan Whitmer, 122A Cushing, 574 631-1417, (jwhitme1@nd.edu)
Department of Chemical and Biomolecular Engineering

Performance of Functional Metal–Organic Frameworks

Research description:
The beautiful and intricate geometries of metal{organic frameworks (MOFs),1 together with their impressive
capacities for energy storage, 2-5 carbon sequestration6,7 and catalysis8,9 inspire their study in equal amounts.
This array of applications is facilitated by the open structure of the MOF and the myriad choices of linking
molecules. In this project, we will examine the properties of some recently synthesized open structures,
including the ZnO2/pyridine carboxylate structures studied in the lab of Jason Hicks at Notre Dame.10
Of particular interest are the adsorption free energies and diusion constants for compounds within these
lattices, as they will influence operating conditions and capabilities of the MOF structure.

Student Involvement:
During the REU, the student will build molecular simulation models and learn techniques for statistically
characterizing the properties of crystal lattices, in addition to thermodynamic integration and manifold
reduction methods. The student will be expected to have some familiarity with writing computer codes,
preferably in C++. Beyond this, only general knowledge of physics and chemistry is required.

References:
1. O'Keee, Michael and Yaghi, Omar M., \Deconstructing the Crystal Structures of Metal-Organic Frame-
works and Related Materials into Their Underlying Nets." Chemical Reviews, 112, 675{702 (2012),
doi:10.1021/cr200205j.

2. Yue, Hongyun, Shi, Zhenpu, Wang, Qiuxian, Cao, Zhaoxia, Dong, Hongyu, Qiao, Yun, Yin, Yan-
hong, and Yang, Shuting, \MOF-Derived Cobalt-Doped ZnO@C Composites as a High-Performance
Anode Material for Lithium-Ion Batteries." ACS Applied Materials & Interfaces, 6, 17067{17074 (2014),
doi:10.1021/am5046873.

3. Zhang, Guanhua, Hou, Sucheng, Zhang, Hang, Zeng, Wei, Yan, Feilong, Li, Cheng Chao, and Duan,
Huigao, \High-Performance and Ultra-Stable Lithium-Ion Batteries Based on MOF-Derived ZnO@ZnO
Quantum Dots/C CoreShell Nanorod Arrays on a Carbon Cloth Anode." Advanced Materials, 27, 2400{
2405 (2015), doi:10.1002/adma.201405222.

4. Li, Shun-Li and Xu, Qiang, \Metal-organic frameworks as platforms for clean energy." Energy Environ.
Sci., 6, 1656{1683 (2013), doi:10.1039/C3EE40507A.

5. Getman, Rachel B., Miller, Jacob H., Wang, Kenneth, and Snurr, Randall Q., \Metal Alkoxide Function-
alization in Metal-Organic Frameworks for Enhanced Ambient-Temperature Hydrogen Storage." Journal
of Physical Chemistry C, 115, 2066{2075 (2011), doi:10.1021/jp1094068.

6. Millward, Andrew R. and Yaghi, Omar M., \Metal{Organic Frameworks with Exceptionally High Ca-
pacity for Storage of Carbon Dioxide at Room Temperature." Journal of the American Chemical Society,
127, 17998{17999 (2005), doi:10.1021/ja0570032.

7. Wilmer, Christopher E., Farha, Omar K., Bae, Youn-Sang, Hupp, Joseph T., and Snurr, Randall Q.,
\Structure-property relationships of porous materials for carbon dioxide separation and capture." Energy
Environ. Sci., 5, 9849{9856 (2012), doi:10.1039/C2EE23201D.

8. Lee, JeongYong, Farha, Omar K., Roberts, John, Scheidt, Karl a, Nguyen, SonBinh T., and Hupp,
Joseph T., \Metal-organic framework materials as catalysts." Chemical Society Reviews, 38, 1450{1459
(2009), doi:10.1039/b807080f.

9. Yoon, Minyoung, Srirambalaji, Renganathan, and Kim, Kimoon, \Homochiral metal{organic
frameworks for asymmetric heterogeneous catalysis." Chemical Reviews, 112, 1196{1231 (2012),
doi:10.1021/cr2003147.

10. Kim, Jongsik, Oliver, Allen G., Neumann, Gregory T., and Hicks, Jason C., \Zn-MOFs Containing
Pyridine and Bipyridine Carboxylate Organic Linkers and Open Zn2+ Sites." European Journal of
Inorganic Chemistry, 2015, 3011{3018 (2015), doi:10.1002/ejic.201500245.

Contact: Associate Professor Jonathan Whitmer, 122A Cushing, 574 631-1417, (jwhitme1@nd.edu)
Department of Chemical and Biomolecular Engineering

Predicting Material Elastic Responses from Molecular Simulations

Research description:
Elastic materials exhibit a restoring force which opposes applied stress, resulting from a perturbation away
from thermodynamic equilibrium. Materials may exhibit dierent types of elasticity depending on their
character.1 Each opposed deformation denes an elastic modulus; liquid crystals may have three or more
elastic moduli characterizing their response to curvature deformations in their ordering eld;2 solids, both
crystalline and amorphous, also have several elastic moduli, such as the bulk modulus, shear modulus and
Young's modulus. Each of these moduli may be related to derivatives of the system's free energy relative
to a variable characterizing the extent of deformation. The Whitmer group has three potential projects
related to measurements of elastic properties in silico, which build on recent formalisms3-5 utilizing free
energy perturbation simulations to extract the elastic coecients of liquid crystals into the domain of two
dimensional membranes and three dimensional solids. We aim to characterize the typical elastic properties
of each phase, and validate our data against previous simulations and theoretical models.
In particular, the three projects are:

  • Application of free-energy perturbations to atomistic models of liquid crystals to predict elastic constants
    in silico
    , and contribute to development of a high throughput workflow for elastic property screening.
  • The utilization of recently developed coarse-grained models of biological membranes to understand the enthalpic interactions and entropic packing alter the elastic behavior of a membrane. This project also seeks to demonstrate the eectiveness of flat-histogram" methods6 relative to fluctuation methods in determining surface tension and elasticity of membranes.
  • Ionic liquid crystals, salt species which self-assemble into phases with charged and uncharged domains, have recently been of interest as novel battery electrolytes. Here we will examine the response behavior of self-assembled phases in the ionic liquid crystal [C16mim][PF6], to obtain structure-property relationships which will be useful in processing these materials.

During the summer REU, the student will work intensively on molecular simulation models and learn techniques of advanced sampling, in particular flat-histogram methods7 used for the measurement of free energies. The student will be expected to have some familiarity with writing computer codes, preferably in
C++. Beyond this, only general knowledge of physics and chemistry is required.

Preferred discipline(s), expertise, lab skills, etc.: Basic graphics and/or visualization knowledge, familiar
with programming in C/C++, OpenGL/GLSL/WebGL, or D3.js.

Contact: Associate Professor Jonathan Whitmer, 122A Cushing, 574 631-1417, (jwhitme1@nd.edu)
Department of Chemical and Biomolecular Engineering

The Limits of Stability in Frank-Oseen Representations of Liquid Crystal Elasticity

Research description:
Liquid crystalline (LC) materials, which produce phases intermediate to the standard vapor, liquid, and solid, have a large array of possible applications in biology and technology. Importantly, the self-organization and assembly which leads to the formation of these phases facilitates molecular transport and nanostructure formation. Traditionally, LC materials have been successful in applications which utilize their anisotropic optical properties---fast-switching, low power displays whose pixels are controlled by external fields interacting with molecular orientations, and chemical sensors which amplify nanoscale disturbances in orientation due to an analyte to optical length scales. Key to these applications is the presence of an ordering elasticity which is experimentally characterized by the Frank-Oseen elastic moduli. In this project, we will examine how novel molecular interactions in atomistic and coarse-grained molecular systems results in large elastic anisotropies and "negative" elasticity. These results will be utilized to tune the behavior and response of novel molecules and mixtures.

Preferred discipline(s), expertise, lab skills, etc.: Linux skills are helpful, previous experience with molecular simulations (LAMMPS or GROMACS) a plus, but not required.

Contact: Associate Professor Jonathan Whitmer, 122A Cushing, 574 631-1417, (jwhitme1@nd.edu)
Department of Chemical and Biomolecular Engineering

Surface Adsorption Properties of Molecular Dipolar Ions

Research description:
Many ionic solutions exhibit species-dependent properties, including surface tension and the salting out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. Here, our interest is to understand molecular effects which can influence Hofmeister-like behavior. Students working on this project will examine a coarse-grained model of fluid and ionic inclusions within the software packages LAMMPS and SSAGES to understand the influence of dipole moments and ionic polarizability on Hofmeister behavior.

Preferred discipline(s), expertise, lab skills, etc.: Linux skills are helpful, previous experience with molecular simulations (LAMMPS or GROMACS) a plus, but not required.

Contact: Associate Professor Jonathan Whitmer, 122A Cushing, 574 631-1417, (jwhitme1@nd.edu)
Department of Chemical and Biomolecular Engineering