Faculty and Staff

at Saint Francis University

Apply Now

<< Go Back

Dr. J. Nathan Scott

James Nathan Scott

Title: Assistant Professor
School: Sciences
Academic Department: Chemistry
Phone: 814-472-3995
E-mail: jscott@francis.edu
Office Location: Science Center 214


  • B.S., Louisiana Tech University ( Physics, summa cum laude)
  • Ph.D., University of Pennsylvania (Biochemistry and Biophysics)


Dr. Scott comes to Saint Francis from Montana State University in Bozeman, MT where he researched the photophysical properties of fluorescent proteins as a postdoctoral fellow. He conducted extensive undergraduate research in physics at Louisiana Tech University in areas as diverse as gravity wave physics, seismic analysis, solid state/materials physics, and high energy particle physics. Dr. Scott's graduate research at the University of Pennsylvania focused on experimental and theoretical investigations of the structure of water in biologically important contexts, as well as the nature of the hydrogen bond itself. As a graduate student he also worked as a teaching assistant in graduate level chemistry and biochemistry classes.

Dr. Scott has published in a number of peer-reviewed chemistry journals, and he has presented at seminars and conferences in Pennsylvania, California, Montana, Alabama, Louisiana, Massachusetts, and Belgium. He is a member of the Biophysical Society, the American Chemical Society, and the American Physical Society.


8. Scott, J.N.; Callis, P.R. "Insensitivity of Tryptophan Fluorescence to Local Charge Mutations" J. Phys. Chem. B 2013, 117 (33), 9598-9605.

7. Drobizhev, M.; Hughes, T.E.; Stepanenko, Y.; Wnuk, P.; O’Donell, K.; Scott, J.N.; Callis, P.R.; Mikhaylov, A.; Dokken, L.; Rebane, A. “Primary Role of the Chromophore Bond Length Alternation in Reversible Photoconversion of Red Fluorescence Proteins” Sci. Rep. 2012, 2.

6. Scott, J.N.; Vanderkooi, J.M. “Evidence of a Structural Defect in Ice VII and the Side Chain Dependent Response of Small Model Peptides to Increased Pressure Appl. Spectrosc. 2011, 65(7), 756-764.

5. Scott, J.N.; Vanderkooi, J.M. “A New Hydrogen Bond Angle/Distance Potential Energy Surface of the Quantum Water Dimer” WATER: A Multidisciplinary Online Journal 2010, Volume 2.

4. Vorobyev, D.Y.; Kuo, C.-H.; Kuroda, D.G.; Scott, J.N.; Vanderkooi, J.M.; Hochstrasser, R.M. “Water Induced Relaxation of a Degenerate Vibration of Guanidinium Using 2D IR Echo Spectroscopy” J. Phys. Chem. B 2010, 114(8), 2944-2953.

3. Vorobyev, D.Y.; Kuo, C.-H.; Chen, J.-X.; Kuroda, D.G.; Scott, J.N.; Vanderkooi, J.M.; Hochstrasser, R.M. “Ultrafast Vibrational Spectroscopy of a Degenerate Mode of Guanidinium Chloride” J. Phys. Chem. B 2009,113(46),15382-15391.

2. Scott, J.N.; Nucci, N.V.; Vanderkooi, J.M. “Changes in Water Structure Induced by the Guanidinium Cation and Implications for Protein Denaturation” J. Phys. Chem. A 2008, 112(43), 10939-10948.

1. Nucci, N.V.; Scott, J.N.; Vanderkooi, J.M. “Coupling of Complex Aromatic Ring Vibrations to Solvent Through Hydrogen Bonds: Effect of Varied On-Ring and Off-Ring Hydrogen-Bonding Substitutions” J. Phys. Chem. B 2008, 112(13), 4022-4035.



  • SCI 101: Science for Active Citizenship
  • CHEM 103: Human Chemistry I
  • CHEM 104L: Human Chemistry II Lab
  • CHEM 102L General Chemistry II Lab
  • CORE 113: The Future
  • CHEM 301L/PHYS 301L: Physical Chemistry I Lab
  • CHEM 251: Quantitative Chemical Analysis

Summer Workshops

  • 2013 Green Chemistry, Biodiesel Production and Testing
  • 2014 Investigations into Protein Chemistry
Research Interests

Dr. Scott's research interests are as varied as his background is diverse. He is currently investigating the optical properties of a class of proteins known as red fluorescent proteins. These proteins are ubiquitous in modern biochemistry, used world wide for a huge variety of purposes, but the physical and dynamic properties that differentiate them are very poorly understood. Dr. Scott employs modern dynamic simulation techniques and quantum chemical methods to elucidate the optical and physical properties of these proteins using the NSF-sponsored XSEDE system of computational resources.

Dr. Scott also maintains an interest in water structure, particularly water structure in unusual or extreme contexts, such as at extremely high pressures or temperatures. His interest in this area is motivated by the goal of understanding the physical limits to life as we know it with respect to intensive quantities such as pressure and temperature. Dr. Scott has used a Diamond Anvil Cell (DAC) to investigate condensed phase systems at pressures of over 70,000 atmospheres and biological systems across a wide range of temperatures and pressures using spectroscopic techniques.

Schedule a Visit