Jones Clock Tower

Clear Research Group

Bioorganic and Supramolecular Chemistry

Recent Group News

July 2019: Dr. Clear starts a new position as Assistant Professor of Chemistry at Indiana University South Bend in the Department of Chemistry & Biochemistry
May 2019: Gena and Natalie graduate and move on to bigger and better things!
April 2019: Natalie Jarret presents her research during Scholars Week and defends her thesis
February 2019: Gena Wilson presents her research at SURC 2019
November 2019: Dr. Clear presents his research at the Univeristy of Notre Dame
May 2018: Shelby and Hannah graduate and move on to bigger and better things!
March 2018: Dr. Clear and students Hannah Adamson and Shelby Wakefield present research at the Spring 2018 ACS National Meeting in New Orleans, LA
September 2017: The Clear group is awarded startup funding from the KY NSF EPSCoR
May 2017: The Clear group receives an MSU CISR grant
February 2017: The Clear group receives the 2017 Marshall and Annette Gordon chemistry research grant

Research in the Clear Group

Research in the Clear Lab integrates themes from organic, physical, and analytical chemistry to address questions regarding recognition of biologically important anions. The emphasis of projects currently underway in the group is on the development of synthetic receptors for solution and membrane recognition of inositol phosphates and phosphatidylinositide lipids, a class of molecues that are important for cell communication. The results of this research will contribute to the scientific knowledge that will be both directly and indirectly beneficial to biological or biochemical separations, understanding of signaling pathways and lipid dynamics, molecular imaging, and therapeutic applications. Importantly, students participating in research will be exposed to a range of techniques, from traditional organic synthesis to binding studies requiring repetitive measurement and extensive data analysis. As a result, this research experience will help train students for graduate and professional studies as well as careers in industry.

1. Solution Anion Recognition

2. Membrane Anion Recognition

3. Assays for Lipid Receptor Affinity & Selectivity

1. Solution recognition of the inositol phosphates using zinc(II) coordination complexes.
The underlying hypothesis is that synthetic receptors with multiple anion recognition units and appropriate scaffolds will exhibit high affinity and selectivity for particular isomers of the inositol phosphates. To test this, a series of bivalent synthetic receptors containing zinc(II)-cyclen and zinc(II)-dipcolylamine anion recognition units presented on a chiral scaffold will be synthesized and the binding toward a series of inositol triphosphate isoforms will be evaluated using isothermal titration calorimetry (ITC). ITC is a technique which measures the heat generated upon association of the two molecules and gives detailed information on the thermodymaics of the binding event.

2. Membrane recognition of the phosphitidylinositol phosphate lipids using zinc(II)-cyclen complexes
The membrane is known to play an important role in molecular recognition mechanisms. The project will use methods like ITC to compare the binding thermodynamics of a bivalent zinc(II)-cyclen receptor with phosphatidylinositol(4,5)bisphosphate (PI(4,5)P2) to association of the same receptor with a soluble analog of PI(4,5)P2, inositol(1,4,5)triphosphate.

3. Assay for evaluating the lipid affinity and selectivity of biological and synthetic receptors.
A new fluorescent indicator displacement assay (IDA) will be developed to facilitate fast and accurate evaluation of the affinity of unlabeled receptors for lipid-bound inositol phosphates while consuming fewer resources than techniques such as ITC. The assay is expected to be useful for studying the lipid selectivity of both synthetic and biological (protein) receptors for various phosphatidylinositides. This project uses instrumentation for fluorescence measurements in both cuvettes and microplates.

Group Members

Dr. Kasey J. Clear
  1. Dr. Clear is a native of Niles, Michigan and was awarded his B.S. in Chemistry from Indiana University South Bend in 2011. He completed his Ph.D. in 2016 at the University of Notre Dame under the supervision of Professor Bradley D. Smith, where he studied anion and biomembrane molecular recognition using synthetic receptors and fluorescent dyes. As a graduate student, Dr. Clear co-authored six peer-reviewed articles and one book chapter. He began his independent career in academia at Murray State University in fall of 2016, and moved back to IU South Bend in Summer 2019, this time as a faculty member. His research interests include the design and study of synthetic receptors for biologically important anions that will have application in separations, imaging, and chemical biology. Dr. Clear primarily teaches organic chemistry at both the undergraduate and graduate level. He is currently teaching or has taught the following courses at Murray State or IU South Bend:
    -Introductory Chemistry
    -General Chemistry I discussion
    -Brief Organic Chemistry Lecture & Laboratory
    -Organic Chemistry I Lecture & Laboratory
    -Organic Chemisty II Lecture & Laboratory
    -Advanced Organic Chemistry
    -In addition, Dr. Clear was the seminar coordinator for the chemistry department at Murray State and serves as the Department library liason at IU South Bend.
    To contact:
    Department of Chemistry & Biochemistry
    Indiana University South Bend
    051 Northside Hall
    Office phone: (574) 520-4223

Curent Members:

Past Members:
Ryan Garcia (Chemistry, Murray State)
Josh Batson (Chemistry, Murray State)
Erin Calvert (Chemistry, Murray State)
Natalie Jarrett (BS Chemistry, Muray State)
Gena Wilson (BS Chemistry, Murray State); Current Position: Biochemistry Ph.D. program at Univeristy of Notre Dame
Bailey Morales (BS Chemistry, Murray State)
Hannah Adamson (BSA Vet Tech); Current position: DVM program at Ross University School of Veterinary Medicine
Shelby Wakefield (BS Chemistry); Current position: Chemistry Ph.D program at University of Wyoming
Dmitriy Bachynsky, graduate student
Jacob Meadows, B.S. Chemistry

Prospective Students:
Motivated undergraduate students who are interested in doing research are welcome to join. If you are interested, contact Dr. Clear by e-mail ( or just stop by his office (NS 051).


Graduate Publications:
7. Harmatys, K. M., Musso, A. J., Clear, K. J., Smith, B. D. (2016) Small molecule additive enhances cell uptake of 5-aminolevulinic acid and conversion to protoporphyrin IX. Photochem. Photobiol. Sci. Advance Article, DOI: 10.1039/C6PP00151C Link
6. Rice, D. R., Clear, K. J., Smith, B. D. (2016) Imaging and therapeutic applications of zinc(ii)-dipicolylamine molecular probes for anionic biomembranes. Chem. Commun. 52, 8787-8801 Link
5. Clear, K. J., Virga, K., Gray, L., and Smith, B. D. (2016) Using membrane composition to fine-tune the pKa of an optical liposome pH sensor. J. Mater. Chem. C 4, 2925-2930 Link
4. Clear, K. J., Harmatys, K. M., Rice, D. R., Wolter, W. R., Suckow, M. A., Wang, Y., Rusckowski, M., and Smith, B. D. (2016) Phenoxide-bridged zinc(II)-bis(dipicolylamine) probes for molecular imaging of cell death. Bioconjugate Chem. 27, 363-375 Link
3. Clear, K. J. and Smith, B. D. (2015) Synthetic Receptors for Polar Lipids. Synthetic Receptors for Biomolecules, Monographs in Supramolecular Chemistry, Royal Society of Chemistry: pp 405-436 Link
2. Plaunt, A. J., Clear, K. J., and Smith, B. D. (2014) 19F NMR indicator displacement assay using a synthetic receptor with appended paramagnetic relaxation agent. Chem. Commun. 50, 10499-10501 Link
1. Clear, K. J., Stroud, S., and Smith, B. D. (2013) Dual colorimetric and luminescent assay for dipicolinate, a biomarker of bacterial spores. Analyst 138, 7079-7082 Link

Group Photos

April 2018: Chemistry Night at Murray Elementary School (featuring Gena Wilson and other chem students)
Murray Elementart School visit

March 2018: Dr. Clear with Hannah Adamson and Shelby Wakefield by their poster at the Spring 2018 ACS National Meeting