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Author: Kayla Benson

Campagna Group Published in Environmental Microbiology

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The Campagna Group has published a collaborative piece titled “Nitrogen flux into metabolites and microcystins changes in response to different nitrogen sources in Microcystis aeruginosa NIES-843” in Environmental Biology. 

The over-enrichment of nitrogen (N) in the environment has contributed to severe and recurring harmful cyanobacterial blooms, especially by the non-N2 -fixing Microcystis spp. N chemical speciation influences cyanobacterial growth, persistence and the production of the hepatotoxin microcystin, but the physiological mechanisms to explain these observations remain unresolved.

Stable-labelled isotopes and metabolomics were employed to address the influence of nitrate, ammonium, and urea on cellular physiology and production of microcystins in Microcystis aeruginosa NIES-843. Global metabolic changes were driven by both N speciation and diel cycling. Tracing 15 N-labelled nitrate, ammonium, and urea through the metabolome revealed N uptake, regardless of species, was linked to C assimilation.

The production of amino acids, like arginine, and other N-rich compounds corresponded with greater turnover of microcystins in cells grown on urea compared to nitrate and ammonium. However, 15 N was incorporated into microcystins from all N sources. The differences in N flux were attributed to the energetic efficiency of growth on each N source.

While N in general plays an important role in sustaining biomass, these data show that N-speciation induces physiological changes that culminate in differences in global metabolism, cellular microcystin quotas and congener composition.

 

Honors Day 2020

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Department of Chemistry recognized the achievements among students, faculty and staff members of the department. Below, you will find a complete list of recipients for the Honors Day 2020.

UNDERGRADUATE AWARDS

ACS-Hach Land Grant Scholarship Natalie Parsons
CRC Press General Chemistry Award Kara Holt
C.W. Keenan Outstanding General Chemistry Student Award Marissa Knofczynski
Department of Chemistry Scholarships Maggie Eslinger, Elizabeth Lander and Sean Weiland
Dr. Lucy E. Scroggie Scholarship Ghaeath Abbas
Halbert and Anne Carmichael Scholarship Elijah Hix and Thaddeus Puzdrakiewicz
C.A. Buehler Chemistry Scholarship Nicholas Legaux and Kristopher Reynolds
Melaven-Rhenium Scholarships Catherine Armstrong, Nicholas Legaux and Clayton West

GRADUATE AWARDS

Keenan Teaching Award Amber Gray
Outstanding Teaching Award Alexandria Bone
Second Year Candidacy Award Alexandria Bone
Gleb Mamantov Graduate Chemistry Scholar Jacob Townsend
Jerome Eastham Fellowship in Organic Chemistry Jinchao Lou
Eugene John Barber Fellowship in Physical Chemistry Kevin Smith
Burchfield Burridge Warner Fellowship in Polymer Chemistry Bishnu Prasad Thapaliya

STUDENT RECOGNITIONS

Goldwater Scholarship Kristopher Reynolds
Winners of the Board of Visitor’s Poster Competition Jinchao Lou and Brandon Colon

STAFF AWARDS

Outstanding Service Award Pam Roach and Linda Sherman
Carol Moulton ACGS Service Award Linda C. Sherman
James F. Green ACGS Service Award Noah Hathcock

FACULTY AWARDS

Ziegler Professorship David Jenkins
T. Ffrancon Williams Professorship Konstantinos Vogiatzis
Gleb Mamantov Professorship in Chemistry Brian Long
2020 Max Bredig Award Sheng Dai

FACULTY RECOGNITION

New Faculty Fred Heberle
Retiring Charles Feigerle

Vogiatzis Lab Published in Nature Communications

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Machine learning applications for chemical problems have been rapidly increasing. Their popularity is justified since they have led to the discovery of new molecules and materials with enhanced properties, new reactions, or have contributed to the reduction of computational effort needed of complex calculations and simulations.

The Vogiatzis Lab seeks to address how a computational algorithm can efficiently “read” and “learn” patterns from molecular structures in their research “Representation of molecular structures with persistent homology for machine learning applications in chemistry” recently published in Nature Communications.

In this collaborative work between Jacob Townsend, John Hymel and Konstantinos Vogiatzis (Chemistry, University of Tennessee) and Cassie Micucci and Vasileios Maroulas (Mathematics, University of Tennessee), the group is presenting a novel molecular representation method based on persistent homology, an applied branch of topology, which encodes the atomistic structure of molecules.

A molecule is mapped into a persistence diagram, a two-dimensional point summary, which demystifies the connected components and the empty space that exist in a molecule based on the atom types and the distances among them. A persistence diagram is further vectorized to a persistence image (PI), a weighted representation of the diagram, which captures the chemically driven uncertainty. The PI in that sense is a “molecular fingerprint”, and when used with machine learning, offers an efficient and reliable approach to screen large molecular databases when compared to other popular molecular representation schemes.

The efficiency arises from the low computation effort needed to compare a large number of fingerprints, and the similar-size representations that are generated, independently of the molecular sizes.

The group demonstrates the applicability of the PI method by screening a large molecular database (GDB-9) with 133,885 organic molecules. Their target was to identify novel molecular units that selectively interact with CO2 and can be used as building blocks of materials, such as polymeric membranes.

They began their study by computing with density functional theory (DFT) the CO2 interaction energies of 100 organic molecules. “Since the initial, limited 100 data points were not capturing the diversity of the GDB-9 database, we applied a technique called active learning in order to incrementally obtain data which helped us efficiently screen the 133,885 molecules,” Vogiatzis said. “We found out that the combination of PIs with active learning performed well with data (interaction energies) from only 220 molecules in order to identify new molecules with stronger CO2 binding.”

Their data-driven methodology was able to identify molecular patterns previously unknown to us that increase the CO2 affinity of organic molecules.

 

Two Journal Covers from the Sokolov Group

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The Sokolov Group’s primary focus of research on dynamics of soft materials, including dynamics of biological macromolecules, and nano-composite materials.

Their recent publication “Correlation between the temperature evolution of the interfacial region and the growing dynamic cooperativity length scale” was featured on cover of The Journal of Chemical Physics. They presented an analyses that revealed a clear correlation between the temperature dependence of the characteristic relaxation time, ln(τα(T)/τ0), and the interfacial layer thickness, Lint(T), in nanocomposite materials.

The group also published their work “Perspectives for Polymer Electrolytes: A View from Fundamentals of Ionic Conductivity” which was on the cover of Macromolecules. This research analyzes fundamental mechanisms controlling ionic conductivity and suggests design of novel polymer electrolytes with enhanced conductivity.

Zhao Group Published in Nature Communications

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The Zhao Group is a polymer chemistry research group, focusing on responsive, functional soft and hybrid materials.

The group recently published their work “Breaking translational symmetry via polymer chain overcrowding in molecular bottlebrush crystallization” in Nature Communication.

The research focuses on  the fundamental laws in crystallization is translational symmetry. This piece reports on the spontaneous formation of spherical hollow crystals with broken translational symmetry in crystalline molecular bottlebrush (mBB) polymers. This study unravels a new principle of spontaneous translational symmetry breaking, providing a general route towards designing versatile nanostructures.

First Publication from Bailey Lab

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The Bailey Lab just published their first review article “Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases” in Synthetic and Systems Biotechnology. 

This article is an overview on a way to target genetic changes to change as little as one amino acid to change the function of polyketide synthases.  

“Polyketides have a correspondence between their sequence and the structure of the small molecules they create, which are often important pharmaceuticals,” said Assistant Professor Constance Bailey. “Finding ways to subtly alter the structure of the metabolite that forms is a way to enable the discovery of new important drugs.”

The group reviews examples of targeted point mutagenesis to one or a few residues harbored within the PKS that alter domain specificity or selectivity, affect protein stability and interdomain communication, and promote more complex catalytic reactivity.

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Calhoun Lab Publishes Online Detection Method for Microfluidics

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The Calhoun Lab published their article “Total Internal Reflection Transient Absorption Microscopy: An Online Detection Method for Microfluidics” in The Journal of Physical Chemistry A. Brandon Colon, a graduate student in the Calhoun Lab, is the primary author of this work.

Microreactors have garnered widespread attention for their tunability and precise control of synthetic parameters to efficiently produce target species. Despite associated advances, a lack of on-line detection and optimization methods has stalled the progression of microfluidic reactors.

“Here we employ and characterize a total internal reflection transient absorption microscopy (TIRTAM) instrument to image excited state dynamics on a continuous flow device,” Colon said. “The experiments presented demonstrate the capability to discriminate between different chromophores as well as in differentiating the effects of local chemical environments that a chromophore experiences.”

This work presents the first such on-line transient absorption measurements and provides a new direction for the advancement and optimization of chemical reactions in microfluidic devices. 

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Do Lab Published in Physical Chemistry Chemical Physics

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The Do Group’s research combines ion-mobility mass spectrometry (IM-MS), mass spectrometry imaging (MSI), and computational modeling to bring a chemical physics outlook to problems of broad chemical interest. 

The group recently published their work “Selective host–guest chemistry, self-assembly and conformational preferences of m-xylene macrocycles probed by ion-mobility spectrometry mass spectrometry” in the journal Physical Chemistry Chemical Physics.

 The group demonstrates ion-mobility spectrometry mass spectrometry (IMS-MS) as a powerful tool for interrogating and preserving selective chemistry including non-covalent and host–guest complexes of m-xylene macrocycles formed in solution. 

Their experiments collectively unravel multiple facets of macrocycle chemistry including conformational flexibility, self-assembly and ligand binding; all in one analysis. Their findings illustrate an inexpensive and widely applicable approach to investigate weak but important interactions that define the shape and binding of macrocycles.