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A New Understanding of Ionic Interactions with Graphene and Water

Findings could inform design of environmental technologies behind water purification processes and electric energy storage

November 17, 2020 // Alex Gerage News Link

A research team led by Northwestern engineers and Argonne National Laboratory researchers have uncovered new findings into the role of ionic interaction within graphene and water. The insights could inform the design of new energy-efficient electrodes for batteries or provide the backbone ionic materials for neuromorphic computing applications.

Known for possessing extraordinary properties, from mechanical strength to electronic conductivity to wetting transparency, graphene plays an important role in many environmental and energy applications, such as water desalination, electrochemical energy storage, and energy harvesting. Water-mediated electrostatic interactions drive the chemical processes behind these technologies, making the ability to quantify the interactions between graphene, ions, and charged molecules vitally important in order to design more efficient and effective iterations.

Monica Olvera de la Cruz
Monica Olvera de la Cruz

“Every time you have interactions with ions in matter, the medium is very important. Water plays a vital role in mediating interactions between ions, molecules, and interfaces, which lead to a variety of natural and technological processes,” said Monica Olvera de La Cruz, Lawyer Taylor Professor of Materials Science and Engineering, who led the research. “Yet, there is much we don’t understand about how water-mediated interactions are influenced by nanoconfinement at the nanoscale.”

Using computer model simulations at Northwestern Engineering and x-ray reflectivity experiments at Argonne, the research team investigated the interaction between two oppositely charged ions in different positions in water confined between two graphene surfaces. They found that the strength of the interaction was not equivalent when the ions’ positions were interchanged. This break of symmetry, which the researchers’ dubbed non-reciprocal interactions, is a phenomenon not previously predicted by electrostatic theory.

The researchers also found that the interaction between oppositely charged ions became repulsive when one ion was inserted into the graphene layers, and the other was absorbed at the interface.

“From our work, one can conclude that the water structure alone near interfaces cannot determine the effective electrostatic interactions between ions,” said Felipe Jimenez-Angeles, senior research associate in Northwestern Engineering’s Center for Computation and Theory of Soft Materials and a lead author on the study. “The non-reciprocity we observed implies that ion-ion interactions at the interface do not obey the isotropic and translational symmetries of Coulomb's law and can be present in both polarizable and non-polarizable models. This non-symmetrical water polarization affects our understanding of ion-differentiation mechanisms such as ion selectivity and ion specificity.”

“These results reveal another layer to the complexity of how ions interact with interfaces,” said Paul Fenter, a senior scientist and group leader in the Chemical Sciences and Engineering Division at Argonne, who led the study’s x-ray measurements using Argonne’s Advanced Photon Source. “Significantly, these insights derive from simulations that are validated against experimental observations for the same system.”

Illustration showing the interaction between ions at graphene-water interface.
Illustration showing the interaction between ions at graphene-water interface.

These results could influence the future design of membranes for selective ion adsorption used in environmental technologies, like water purification processes, batteries and capacitors for electric energy storage, and the characterization of biomolecules, like proteins and DNA.

Understanding ion interaction could also impact advances in neuromorphic computing — where computers function like human brains to perform complex tasks much more efficiently than current computers. Lithium ion can achieve plasticity, for example, by being inserted in or removing from graphene layers in neuromorphic devices.

“Graphene is an ideal material for devices that transmit signals via ionic transport in electrolytes for neuromorphic applications,” said Olvera de la Cruz. “Our study demonstrated that the interactions between intercalated ions in the graphene and physically adsorbed ions in the electrolyte is repulsive, affecting the mechanics of such devices.”

The study provides researchers with a fundamental understanding of the electrostatic interactions in aqueous media near interfaces that go beyond water’s relationship with graphene, which is crucial for studying other processes in the physical and sciences.

“Graphene is a regular surface, but these findings can help explain electrostatic interactions in more complex molecules, like proteins,” said Jimenez-Angeles. “We know that what’s inside the protein and the electrostatic charges outside of it matters. This work gives us a new opportunity to explore and look at these important interactions.”

A paper describing the work, titled “Non-Reciprocal Interactions Induced by Water in Confinement,” was published November 17 in the journal Physical Review Research.


‘Like a fishing net,’ nanonet collapses to trap drug molecules

Novel method presents possibilities for rapidly making and testing vaccine formulations

Northwestern University researchers are casting a net for nanoparticles.

The team has discovered a new, rapid method for fabricating nanoparticles from a simple, self-assembling polymer. The novel method presents new possibilities for diverse applications, including water purification, diagnostics and rapidly generating vaccine formulations, which typically require many different types of molecules to be either captured or delivered at the same time.

Using a polymer net that collapses into nanoscale hydrogels (or nanogels), the method efficiently captures over 95% of proteins, DNA or small molecule drugs — alone or in combinations. By comparison, loading efficiency is typically between 5% and 20% for other nanoparticle delivery systems.

“We use a polymer that forms a wide net throughout an aqueous solution,” said Northwestern’s Evan A. Scott, who led the study. “Then we induce the net to collapse. It collects anything within the solution, trapping therapeutics inside of nanogel delivery vehicles with very high efficiency.”

“It works like a fishing net, which first spreads out due to electrostatic repulsion and then shrinks upon hydration to trap ‘fish,’” added Fanfan Du, a postdoctoral fellow in Scott’s laboratory.

The paper was published last week (Sept. 29) in the journal Nature Communications. 

Scott is the Kay Davis Professor of Biomedical Engineering at Northwestern’s McCormick School of Engineering. Northwestern professors Monica Olvera de la Cruz and Vinayak Dravid coauthored the paper. 

Molecules found in nature, such as DNA and peptides, can rapidly self-assemble and organize into diverse structures. Mimicking this process using human-made polymer systems, however, has remained limited. Previously developed processes for self-assembling drug delivery systems are time consuming, labor intensive and difficult to scale. The processes also tend to be woefully inefficient, culminating in a small fraction of the drug actually making it inside the delivery system.

“Clinical application of self-assembled nanoparticles has been limited by difficulties with scalability and with loading large or multiple therapeutics, especially proteins,” Scott said. “We present a highly scalable mechanism that can stably load nearly any therapeutic molecule with high efficiency.”

Scott’s team found success by using a polypropylene sulfone (PPSU) homopolymer, which is highly soluble in dimethylsulfoxide (DMSO) solution, but forms electrostatic and hydrophilic aggregates in water. The aggregates are amphiphilic, which causes them to assemble into networks and eventually collapse into gels.

“Adding more water induces the network to collapse, leading to the formation of nanogels,” Du said. “The manner in which water is added affects the PPSU chain formation, which changes the nanogels’ size and structure.”

Atomistic simulations — performed by Baofu Qiao in the Olvera de la Cruz group — confirmed that the nanostructures were stabilized by weak sulfone-sulfone bonding. Using coarse-grained simulations performed by Northwestern postdoctoral fellow Trung Dac Nguyen, the researchers observed the nanonet structures. This opens a new avenue for soft materials assembly by means of sulfone-sulfone bonding.

In addition to drug delivery applications, the researchers also believe the novel method could be used for water purification. The network could collapse to collect contaminants in water, leaving pure water behind.

Scott is a member of Northwestern’s Simpson Querrey Institute, Chemistry of Life Processes Institute, Interdisciplinary Biological Sciences Program and Northwestern University Robert H. Lurie Comprehensive Cancer Center. He has a secondary appointment in the department of microbiology-immunology at the Feinberg School of Medicine.

The paper, “Homopolymer self-assembly of poly(propylene sulfone) hydrogels via dynamic noncovalent sulfone-sulfone bonding,” was supported by the Department of Energy (award number DE-FG02-08ER46539), the National Institutes of Health (grant number 1DP2HL132390-01), the National Institute of Allergy and Infectious Diseases (grant number 5R21AI137932-02), the National Science Foundation CAREER Award (grant number 1453576), the Louis A. Simpson and Kimberly K. Querrey Center for Regenerative Nanomedicine Catalyst Award and the Sherman Fairchild Foundation.

Research exposes new vulnerability in SARS-CoV-2

Electrostatic interactions enhance the spike protein’s bond to host cells

August 11, 2020 | By Amanda Morris

Northwestern University researchers have uncovered a new vulnerability in the novel coronavirus’ infamous spike protein — illuminating a relatively simple, potential treatment pathway.

The spike protein contains the virus’ binding site, which adheres to host cells and enables the virus to enter and infect the body. Using nanometer-level simulations, the researchers discovered a positively charged site (known as the polybasic cleavage site) located 10 nanometers from the actual binding site on the spike protein. The positively charged site allows strong bonding between the virus protein and the negatively charged human-cell receptors.

Leveraging this discovery, the researchers designed a negatively charged molecule to bind to the positively charged cleavage site. Blocking this site inhibits the virus from bonding to the host cell.

“Our work indicates that blocking this cleavage site may act as a viable prophylactic treatment that decreases the virus’ ability to infect humans,” said Northwestern’s Monica Olvera de la Cruz, who led the work. “Our results explain experimental studies showing that mutations of the SARS-CoV-2 spike protein affected the virus transmissibility.”

The research was published online last week in the journal ACS Nano.

Olvera de la Cruz is the Lawyer Taylor Professor of Materials Science and Engineering in Northwestern’s McCormick School of Engineering. Baofu Qiao, a research assistant professor in Olvera de la Cruz’s research group, is the paper’s first author.

Made up of amino acids, SARS-CoV-2’s polybasic cleavage sites have remained elusive since the COVID-19 outbreak began. But previous research indicates that these mysterious sites are essential for virulence and transmission. Olvera de la Cruz and Qiao discovered that polybasic cleavage site is located 10 nanometers from human cell receptors — a finding that provided unexpected insight.

 cleavage site spike protein“We didn’t expect to see electrostatic interactions at 10 nanometers,” Qiao said. “In physiological conditions, all electrostatic interactions no longer occur at distances longer than 1 nanometer.”

“The function of the polybasic cleavage site has remained elusive,” Olvera de la Cruz said. “However, it appears to be cleaved by an enzyme (furin) that is abundant in lungs, which suggests the cleavage site is crucial for virus entry into human cells.”

With this new information, Olvera de la Cruz and Qiao next plan to work with Northwestern chemists and pharmacologists to design a new drug that could bind to the spike protein.

Olvera de la Cruz is a member of Northwestern's Chemistry of Life Processes Institute.

The research, “Enhanced binding of SARS-CoV-2 spike protein to receptor by distal polybasic cleavage sites,” was supported by the U.S. Department of Energy (award number DE-FG02-08ER46539), the Sherman Fairchild Foundation and the Center for Computation and Theory of Soft Materials at Northwestern University.

Researchers Find Enzymes Naturally Select their Own Polymer Sequences

Findings could impact fields like pharmaceutical development and industrial waste processing

Jun 11, 2018 //Danny Smith   News Link

As free-flowing enzymes travel amid a sea of polymers, a Northwestern Engineering team has found those enzymes prefer to join certain polymer sequences over others, a discovery that could lead to applications in a diverse array of fields ranging from nuclear waste processing to drug delivery.

“From all these batches of randomness, we discovered each particular enzyme selects a sequence it likes best,” said Monica Olvera de la Cruz, the Lawyer Taylor Professor of Materials Science and Engineering at Northwestern’s McCormick School of Engineering and Applied Science, who led the study. “That’s important because it sheds light on how we might design the composition of a batch of polymers, so they will disperse enzymes actively in non-biological environments.” 

Authored by Olvera de la Cruz and two colleagues in McCormick’s Department of Materials Science and Engineering — senior research associate Trung Dac Nguyen and research assistant professor Baofu Qiao — the study, titled “Efficient encapsulation of proteins with random copolymers,” published today, June 11, in the Proceedings of the National Academy of Sciences.

Enzymes play a vital role in a range of chemical and biological processes by facilitating and directing biochemical reactions. Due to the limited solubility of some substrates in water, preserving and/or enhancing the catalytic capability of some enzymes in non-aqueous solutions is of increasing demand. However, most enzymes rapidly lose their chemical activity when exposed to non-biological environments, including organic solvents like toluene and tetrahydrofuran. While numerous enzyme stabilization strategies have been employed such as reverse engineering enzyme sequences, decorating enzymes with surfactants, or modifying the solvents, most of them are either limited to specific enzymes and solvents or cost ineffective.

Performing computer simulations at Quest, Northwestern’s high-powered computational facility, the researchers examined: the key factors that determined the coverage of the random copolymers with different types of enzymes in a given solvent; how the enzymes selected the random copolymers to protect themselves from unfavorable solvents; and the relationship between the enzyme surface characteristics and the polymer features.

“We found that the enzymes indeed select certain polymer sequences that best cover their surface out of the pool of the polymers,” Trung said. “The random copolymers provide the composition and sequence diversity similar to that in disordered enzymes, which explains why they can efficiently cover numerous enzymes in different size, shape, and surface patterns.”

The study, fueled by a grant from the US Department of Energy and support from the Sherman Fairchild Foundation that enabled the computational work, highlights that this special family of copolymers is an excellent candidate material for synthesizing membraneless organelles — the micron-sized liquid droplets inside cells of living organisms — as well as for stabilizing and delivering enzymes across multiple non-biological media.

“Right now, for instance, researchers in the pharmaceutical industry are trying to match sequences perfectly,” Olvera de la Cruz said. “Our discovery provides guidelines to make the dispersion of enzymes much more cost-effective and efficient.”

Olvera de la Cruz and her colleagues now plan to investigate how the membraneless organelles might spontaneously form with these copolymers-enzymes, how to control their sizes, and how the structural properties of the enzymes might be affected inside the organelles.

“The next step will be exploring the possibilities of concentrating different enzymes together, which is highly promising in advancing their catalytic ability, in creating new chemicals, as well as in processing industrial waste, in an efficient fashion,” Olvera de la Cruz said.

Posted: Feb 02, 2018 Publication Link

Kirigami Nanofluidic Devices

(Nanowerk Spotlight) Recent research in nanofluidics has adopted reconstructed layered two-dimensional (2D) sheets (such as graphene oxide or clay) as a promising material platform for nanofluidics. These membranes contain a high volume fraction of interconnected 2D nanochannels.

This nanochannel fabrication method is straightforward and scalable, and does not rely on lithography or etching.

"Compared to other scalable nanofluidic materials such as anodized aluminum oxide membrane, block copolymer membrane and nanofluidic crystals, a unique feature of such layered membranes is that the channels are horizontally aligned and the channel height (i.e., interlayer spacing), which is responsible for confinement of the electrolyte, remains uniform throughout the entire thin film," Jiaxing Huang, a Professor of Materials Science and Engineering at Northwestern University, tells Nanowerk. "Therefore, nanofluidic ionic transport properties are maintained regardless of the lateral dimensions or shape of the 2D nanochannel network."

The researchers termed this process, which opens up a range of new opportunities for manipulating ionic transport by tailoring the shape of the films, kirigami nanofluidics. They reported their findings in Materials Chemistry Frontiers ("Kirigami nanofluidics").

The work shows that these 2D membranes behave like 'ionic wafers', which can be patterned by kirigami to realize device functions such as diodes.

"Although these ionic functions are still quite simple, compared to electronic devices, they did show that ionic transport through a layered membrane, which is a nanoscale phenomenon, could be tuned by tailor cutting the macroscopic shape of the film," notes Jun Gao, the paper's first author. "We hope the mechanistic understanding and the demonstrations in this work can help people better understand ionic transport through these 2D films, which is useful for designing large scale nanofluidic channels arrays for separation purposes."

Compared to the classical ionic diodes, which typically are made of channels with asymmetric ends such as a conical nanopore (Figure 1a), the 2D nanochannels have uniform channel size (i.e. interlayer spacing) throughout the entire volume of the film (Figure 1b). This simplifies the factors affecting ionic transport, making it possible to control the overall ionic conductance by tailoring the ionic resistance at the channel-reservoir interfaces. 

For example, a graphene oxide film with asymmetric ends, such as a T-shape, exhibits ionic rectification (Figure 2d). While shapes with symmetric ends, such as a diode-sign, exhibits no rectification (Figure 2c).

Kirigami nanofluidics allows the fabrication of nanofluidic devices and the control of their performance in a very straightforward way. For example, the ionic current rectification ratio can be adjusted by 'tailor cutting' the geometry of the film, which has been quite difficult in previous works.

Nanofluidic devices are ionic analogs to semiconductor devices. Kirigami-made resistors and diodes can be connected to realize some simple logic functions such as the AND gate and OR gate.

"An electrolyte confined in nanochannels exhibits unusual behaviors owing to strong influences from the channel walls," explains Erik Luijten, a Professor of Materials Science and Engineering at Northwestern University. "When the size of a charged channel is comparable to the Debye length of the electrolyte, co-ions are effectively repelled from the channel and counterions are concentrated, leading to the so called unipolar ionic transport properties with the counterions as the majority charge carrier."

The team first hypothesized that such nanochannels can be readily formed by stacking up 2D sheets, such as graphene oxide. Indeed, they had previously demonstrated that films of graphene oxide or clay sheets contain massive arrays of parallel 2D nanofluidic channels.

In this regard, films of 2D sheets are conceptually analogous to extrinsically doped semiconductors, a material foundation that has enabled the realization of numerous electronic devices and integrated circuits.
In the current work, Huang's team showed that like semiconductor wafers, papers of graphene oxide can also be 'patterned' to realize some analogous functions such as ionic diodes or logic circuits. The patterning is done by cutting the film into various shapes.

In one demonstration, Huang's team showed that programmable rectification ratio can be realized in multi-armed films, by varying the numbers of arms for the source and drain, respectively.

Going forward, the scientists are interested in creating nanofluidic devices with active gating function, which would allow us to manipulate nanofluidic transport with more freedom.

Monica Olvera de la Cruz, a co-author of the paper and a Professor of Materials Science and Engineering at Northwestern University, concludes that "It will be very exciting to realize some form of gating mechanism to make ionic transistors, and to integrate all of these device elements to achieve a bit more complex logic or even computing functions."

By Michael Berger – Michael is author of two books by the Royal Society of Chemistry: Nano-Society: Pushing the Boundaries of Technology and Nanotechnology: The Future is Tiny. Copyright © Nanowerk

Honors and Awards

Monica Olvera de la Cruz and Chad Mirkin are recognized by Sherman Fairchild Foundation

Northwestern University’s Monica Olvera de la Cruz and Chad A. Mirkin have received significant five-year grants from the Sherman Fairchild Foundation in support of their innovative materials science research.

Olvera de la Cruz, the Lawyer Taylor Professor of Materials Science and Engineering in the McCormick
School of Engineering, will receive $4.5 million to accelerate the discovery of new functions and application of synthetic structures, including hybrid biological and synthetic assemblies. She will focus on structures that mimic and enhance the action of protein membranes and cells to better understand biological functions, with applications in environmental remediation and health care. The project promises to push forward the field of biomimicry, which seeks to solve pressing problems by emulating nature.

Olvera de la Cruz is recognized internationally for her contributions to analyzing, modeling and designing new materials that mimic effective biological processes. She also is a professor of chemical and biological engineering, chemistry, and physics and astronomy and director of the Center for Computation and Theory of Soft Materials.

Mirkin, the George B. Rathmann Professor of Chemistry at the Weinberg College
of Arts and Scienc es, will receive $5 million to develop a novel design method called “nanocombinatorics.” The chemistry-based approach would systematically and comprehensively screen innumerable nanomaterial combinations and identify the most promising for a given area of study or application. The resulting encyclopedic resource of high-performance nanomaterials could be used in energy production, environmental remediation, health care, computing technology and homeland security.

Mirkin is world-renowned for his nanoscience expertise and invention of spherical nucleic acids and the development of biological and chemical diagnostic and therapeutic systems based upon them. He also is director of Northwestern’s International Institute for Nanotechnology and a professor of medicine, chemical and biological engineering, biomedical engineering, and materials science and engineering.

The funds raised through We Will. The Campaign for Northwestern are helping realize the transformational vision set forth in Northwestern’s strategic plan and solidify the University’s position among the world’s leading research universities.

Breaking the Protein-DNA Bond

Study finds that free-floating proteins break up protein-DNA bonds at the single-binding site

Apr 4, 2017 // Amanda Morris

The verdict is in: too many single, flirty proteins can break up a strong relationship.

A new interdisciplinary Northwestern University study reports that the important protein-DNA bond can be broken by unbound proteins floating around in the cell. This discovery sheds light on how molecules self-organize and how gene expression is dynamically controlled.

“The way proteins interact with DNA determines the biological activity of all living organisms,” said John F. Marko, professor of molecular biosciences, physics, and astronomy in Northwestern’s Weinberg College of Arts and Sciences. “Inevitably, any malfunction in this interaction network can lead to malevolent conditions. It is paramount to precisely understand the interaction mechanisms underlying protein-DNA associations.”

To understand this vital relationship, Marko led a study examining the sites where a single protein binds to DNA. Strands of DNA have specific sites on which other molecules can bind and become a part of the DNA’s genetic code. One type of DNA-binding proteins, called transcription factors (TF), are key players in the transcription of genetic information from DNA to messenger RNA (mRNA) to produce new proteins or other types of RNA. TF proteins control the biological processes in living cells by binding and unbinding to DNA. In the experiment, Marko and his team developed a concentration of TF proteins bound to DNA mixed with unbound TF proteins, which competed with the bound proteins for their binding sites. They observed that unbound proteins caused the bound proteins to dissociate from the DNA. The unbound proteins then stole the newly available single-binding sites.

“Our experiments show that dissociation happens on the level of a single protein-DNA interaction,” Marko said. “This is new information for the field.”

Supported by the National Institutes of Health and National Science Foundation, the research was published online this week in the journal Proceedings of the National Academy of Sciences. Ramsey Kamara, a former postdoctoral researcher in Marko’s laboratory, served as the paper’s first author. Northwestern Engineering’s Monica Olvera de la Cruz, the Lawyer Taylor Professor of Materials Science and Engineering, coauthored the paper.

Olvera de la Cruz led the development of a theoretical model and performed molecular dynamics simulations to show the prevalence of the protein-DNA break up at the single-binding site due to the competitor proteins. This disproves former beliefs that protein-DNA bonds were unaffected by unbound proteins and instead resulted from more “cooperative” interactions among many molecules, large protein clusters, or long DNA segments.

“Our results suggest that protein-DNA dissociation could have a profound effect on the dynamics of biological processes that depend on protein binding in vivo,” Olvera de la Cruz said. “This may be an important factor to take into account when modeling gene expression in living cells.”

Olvera de la Cruz to Receive 2017 APS Polymer Physics Prize

The prestigious award honors her contributions to the theoretical understanding of polymers

Oct 17, 2016 // Amanda Morris

Northwestern Engineering’s Monica Olvera de la Cruz to receive the 2017 Polymer Physics Prize from the American Physical Society (APS).

Olvera de la Cruz was selected for her “outstanding contributions to the theoretical understanding of polymers and the effects of electrostatic interactions on their structure and properties.” She will officially accept the award at the APS March Meeting next year.

“I am honored to receive the 2017 APS Polymer Physics Prize,” said Olvera de la Cruz, the Lawyer Taylor Professor of Materials Science and Engineering in Northwestern’s McCormick School of Engineering. “It is given to highly distinguished scientists, including three Nobel Prize winners — Pierre Gilles de Gennes, Peter J.W. Debye, and Paul Flory — and my PhD adviser Sir Sam Edwards.”

Olvera de la Cruz’s research focuses on the development of models to describe the self-assembly of heterogeneous molecules, including amphiphiles, copolymers, and synthetic and biological polyelectrolytes. She also studies the segregation and interface adsorption in multicomponent complex fluids. Her group’s work has resulted in a revised model of ionic-driven assembly, and its investigations into soft and condensed matter physics have advanced scientific knowledge and opened new research fields of technological importance.

“Polymers have fascinating physical properties,” Olvera de la Cruz said. “They have attracted studies by scientists and mathematicians for decades, given that they are one-dimensional molecules with nanoscale dimensions that are capable of taking multiple conformations.”

A member of the National Academy of Sciences, Olvera de la Cruz has received several other honors and awards, including the Engineering and Applied Sciences Cozzarelli Prize from the National Academies, a National Security Science and Engineering Faculty Fellowship, an Alfred P. Sloan Fellowship, and the NSF Presidential Young Investigator Award and the David and Lucile Packard Fellowship in Science and Engineering. She is also a fellow of the American Academy of Arts and Sciences and the American Physical Society.

Honors and Awards

Chad Mirkin Honored at Awards Ceremony in Israel

News Link

Northwestern’s Chad Mirkin (center) accepts the 2016 Dan David Prize in the Future Time Dimension from Joseph Klafter (left), president of Tel Aviv University and chairman of the Dan David Prize Board of Directors. Northwestern President Morton Schapiro (right), along with other Northwestern officials, also attended the May 22 awards ceremony. Photo by Hadari Photography