Organic-Inorganic-Materials Chemistry Seminar Series
Department of Chemistry and Biochemistry

Professor David A. Leigh, University of Manchester, UK
April 26, 2024
3:00 pm, 110 Willamette Hall
Hosted by Mike Haley and Darren Johnson

Much Ado About Knotting

Knots are important structural features in DNA and some proteins, and play a significant role in the physical properties of both natural and synthetic polymers.¹ Although billions of prime knots are known to mathematics, few have been realized through chemical synthesis.² Here we will discuss the latest progress from our laboratory, including the synthesis of some of the most complex molecular knots and links (catenanes) to date^3-9 and the introduction of 2D molecular weaving.¹⁰

References
[1] “Molecular knots”, Angew. Chem. Int. Ed. 56, 11166 (2017).
[2] “Knotting matters: orderly molecular entanglements”, Chem. Soc. Rev. 51, 7779 (2022).
[3] “A synthetic molecular pentafoil knot”, Nat. Chem. 4, 15 (2012).
[4] “A Star of David catenane”, Nat. Chem. 6, 978 (2014).
[5] “Allosteric initiation and regulation of catalysis with a molecular knot”, Science 352, 1555 (2016).
[6] “Braiding a molecular knot with eight crossings”, Science 355, 159 (2017).
[7] “Stereoselective synthesis of a composite knot with nine crossings”, Nat. Chem. 10, 1083 (2018).
[8] “A molecular endless (74) knot”, Nat. Chem. 13, 117 (2021).
[9] “Vernier template synthesis of molecular knots”, Science 375, 1035 (2022). [10] “Self-assembly of a layered two-dimensional molecularly woven fabric”, Nature 588, 429 (2020).

Organic-Inorganic-Materials Chemistry Seminar Series
Department of Chemistry and Biochemistry

Professor David A. Leigh, University of Manchester, UK
April 24, 2024
4:00 pm, 182 Lillis Hall
Hosted by Mike Haley and Darren Johnson

Giving Chemistry Direction

In recent years examples of synthetic molecular machines and motors¹ have been developed,² all be they primitive by biological standards. Such molecules are best designed to work through statistical mechanisms. In a manner reminiscent of Maxwell’s Demon,³ random thermal motion is rectified through ratchet mechanisms,^3-8 giving chemistry direction.

It is increasingly being recognised that similar concepts can be applied to other chemical exchange processes⁹. Ratchet mechanisms—effectively chemical engines¹⁰ in which atalysis^4,6,7 of ‘fuel’ to ‘waste’ is used to drive another chemical process—can cause directional impetus in what are otherwise stochastic systems, including reversible chemical reactions. This is ushering in a new era of non-equilibrium chemistry, providing fundamental advances in functional molecule design and the first examples of molecular robotics,^11,12 overturning existing dogma and offering fresh insights into biology and molecular nanotechnology.

For a musical introduction, see ‘Nanobot’

[1] The Nobel Prize in Chemistry 2016–Advanced Information. Nobelprize.org. Nobel Media AB 2014. Web. 6 Oct, 2016, http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2016/advanced.html.
[2] “Rise of the molecular machines”, Angew. Chem. Int. Ed. 54, 10080 (2015).
[3] “A molecular information ratchet”, Nature 445, 523 (2007).
[4] “An autonomous chemically fuelled small molecule motor”, Nature 534, 235 (2016).
[5] “Rotary and linear molecular motors driven by pulses of a chemical fuel”, Science 358, 340 (2017).
[6] “A catalysis-driven artificial molecular pump”, Nature 594, 529 (2021).
[7] “Autonomous fuelled directional rotation about a covalent single bond”, Nature 604, 80 (2022). [8] “A tape-reading molecular ratchet”, Nature 612, 78 (2022).
[9] “Design, synthesis and operation of small molecules that walk along tracks”, J. Am. Chem. Soc. 132, 16134 (2010).
[10] “Chemical engines: Driving systems away from equilibrium through catalyst reaction cycles”, Nat. Nanotechnol. 16, 1057 (2021).
[11] “Sequence-specific peptide synthesis by an artificial small-molecule machine”, Science 339, 189 (2013).
[12] “Stereodivergent synthesis with a programmable molecular machine”, Nature 549, 374 (2017).

Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series

Professor Anatoly Kolomeisky, Rice University
April 22, 2024—2:00pm
Tykeson 140
Hosted by: Marina Guenza

How To Find Targets That Are Always Hidden:
The Story of Nucleosome-Covered DNA and Pioneer Transcription Factors

All major biological processes start after transcription factors detect specific regulatory sequences on DNA and initiate genetic expression by associating to them. But in eukaryotic cells, much of the DNA is covered by nucleosomes, preventing the transcription factors from binding to their targets. At the same time, experiments show that there are several classes of proteins, called “pioneer transcription factors”, that can penetrate chromatin structures. However, the underlying microscopic mechanisms remain not well understood. We propose a new theoretical approach that might explain these observations. It is argued that due to structural similarity with linker histones, pioneer transcription factors might weaken the interactions between the DNA and the nucleosome by substituting them with similar interactions between pioneer transcription factors and DNA. Using this idea, we develop a discrete-state stochastic framework that allows for explicit calculations of target search dynamics on nucleosomal DNA. It is found that finding specific sequences on nucleosomal DNA for pioneer transcription factors might be significantly accelerated while the search is slower on naked DNA segments in comparison with normal transcription factors. In addition, it is shown that nucleosome breathing makes the target search by pioneer transcription factors even faster, and theoretical arguments to explain these observations are presented. Our theoretical predictions are supported by Monte Carlo computer simulations, and they also agree with available experimental observations, providing new microscopic insights on complex nature of protein-DNA interactions.

Organic-Inorganic-Materials Chemistry Seminar Series
Department of Chemistry and Biochemistry

Professor Kayode D. Oshin, Creighton University
April 19, 2024
3:00pm in Willamette Hall, Room 110
Hosted by Darren Johnson

Catalyst Development & Kinetic Investigation of ATRA Reactions: Integrating Undergraduate Research and Chemical Education

Atom Transfer Radical Addition (ATRA) of haloalkanes and halocarbonyls to α-olefins is one of the most atom economical methods to simultaneously form C–C and C–X bonds, providing synthetic access to functionalized monoadducts. Studies that attempt to improve this reaction model are important as developing efficient methods to convert olefins into monoadducts for use in subsequent transformation reactions (reductions, displacements, making Grignards) are highly desirable. This presentation will highlight; (i) our research work designing copper and iron complexes for use as catalysts in ATRA, (ii) development of an experimental technique to measure kinetic parameters (activation rate constant values) for ideal ATRA reactions, and (iii) transformation of our results into effective laboratory modules, guided by important academic learning objectives and assessments, so they can be incorporated in the chemistry curriculum. This effort provides faculty at other academic institutions with current and effective modules that can be used in their courses and contributes to the important field of chemical education.

Organic-Inorganic-Materials Chemistry Seminar Series
Department of Chemistry and Biochemistry

Maxwell J. Robb, California Institute of Technology
April 12, 2024
3:00pm in Willamette Hall, Room 110
Hosted by Ramesh Jasti

MOLECULAR DESIGN STRATEGIES FOR MECHANOCHEMICALLY ACTIVE POLYMERS

The use of mechanical force to selectively activate covalent bond transformations presents unique opportunities for the design of stimuli-responsive polymers for applications ranging from sensing to drug delivery. By incorporating stress-sensitive molecules called mechanophores into polymer chains, force is transduced selectively to weak bonds in the mechanophore to elicit a productive chemical reaction. Mechanochromic mechanophores that produce a change in color are particularly useful and have been widely developed as molecular force probes, empowering the visualization of critical stress and/or strain in materials. These same attributes also make force-induced color changes in polymeric materials appealing for patterning and encryption. The mechanically triggered release of small molecules is also a powerful approach for sensing and delivery. This presentation will highlight some of our recent research on the development of molecular design strategies and structure–activity relationships for several different mechanophore platforms enabling visual stress reporting and mechanically triggered molecular release as well as some unusual reactivity.

Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series

Ken Halvorsen, University at Albany
April 1, 2024
2:00pm in Tykeson 140
Hosted by: Julia Widom

“Pulling On Individual Biomolecules with Centrifugal Force”

Probing individual biomolecules such as proteins and nucleic acids with force continues to shape our understanding of how biological molecules stretch, deform, move, reconfigure, and interact with each other. However, such experiments can be technically challenging, tedious, and costly. Here, I will discuss the conception, design, and continued development of the centrifuge force microscope (CFM), an instrument designed to increase the throughput and the accessibility of single-molecule experiments. I will then dive into applications and uses of the CFM, focusing on a recent study in my lab measuring individual stacking energies between bases in DNA and RNA.

Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series

Professor Niya Sa, University of Massachusetts
February 29th ~ 3:00 pm, 125 McKenzie Hall
Hosted by Paul Kempler

Probe the Dynamic Interfaces of Beyond Lithium-ion Energy Storage Systems

Rapid growth of technology in the past few decades has spurred a demand for advanced energy storage devices. The invention of a more advanced battery system with higher levels of performance will be a groundbreaking discovery in the rechargeable battery field. Multivalent chemistry offers promising benefits in the development of beyond lithium-ion technologies. The direct usage of the multivalent metal anode is essential to enhance the energy density of the multivalent ion battery. For instance, Magnesium, Calcium and Zinc offer an immense alternative to the existing Li-ion batteries due to their multivalent nature and vast abundance in the Earth’s crust. However, possible film formation at the solid/liquid interface complicates the electrochemical properties of such systems. The least understood solid electrolyte interphase (SEI), its formation and dynamic evolution has not been extensively explored for multivalent battery systems with many unknowns remain to be answered. We aim to use electroanalytical tools to probe the dynamic evolution of the solid electrolyte interface in-situ for multivalent systems and investigate its correlation with the electrochemical processes. This presentation focuses on some very recent research findings from our team for understanding the interfacial chemistry, evolution, and stability for different multivalent battery systems.