“Femtosecond two-photon absorption spectra and permanent electric dipole moment change of tryptophan, 2-aminopurine and related intrinsic and synthetic fluorophores,” in the SPIE Digital Library as part of the proceedings of the Multiphoton Microscopy in the Biomedical Sciences XVII conference. March 14, 2017; http://dx.doi.org/10.1117/12.2249634.

Jianhua Xu, Binbin Chen, Patrik Callis, Pedro L. Muiño, Henriëtte Rozeboom, Jaap Broos, Dmitri Toptygin, Ludwig Brand, and Jay R. Knutson*, Picosecond Fluorescence Dynamics of Tryptophan and 5‑Fluorotryptophan in Monellin: Slow Water−Protein Relaxation Unmasked, J. Phys. Chem. B (2015) 119, 4230−4239

P.R. Callis, Simulating Electrostatic Effects on Electronic Transitions in Proteins. Molecular Simulation, (2015) 41, 190–204

P.R. Callis, Binding Phenomena and Fluorescence Quenching. I: Descriptive Quantum Principles of Fluorescence Quenching using a Supermolecule Approach, J. Mol. Struct. 1077 (2014) 14-21

P.R. Callis, Binding Phenomena and Fluorescence Quenching. II: Photophysics of Aromatic Residues and Dependence of Fluorescence Spectra on Protein Conformation, J. Mol. Struct. 1077 (2014) 22–29 

P.R. Callis, J.R. Tusell, MD + QM Correlations with Tryptophan Fluorescence Spectral Shifts and Lifetimes, Methods Mol. Biol. (Clifton NJ) 1076 (2014), p. 171-214. 

Drobizhev,M.; Scott,J.N.; Callis,P.R.; Rebane,A. All-Optical Sensing of the Components of the Internal Local Electric Field in ProteinsIeee Photonics Journal (2012), 4, 1996-2001. 

Drobizhev,M.; Hughes,T.E.; Stepanenko,Y.; Wnuk,P.; O'Donnell,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:, Scientific Reports (2012),2 Article Number: 688 DOI: 10.1038/srep00688 Published: SEP 24 2012 

Tusell,J.R.; Callis,P.R. Simulations of Tryptophan Fluorescence Dynamics during Folding of the Villin Headpiece, J. Phys. Chem. B (2012), 116, 2586-94. 

"Correlation of Tryptophan Fluorescence Spectral Shifts and Lifetimes Arising Directly from Heterogeneous Environment", C.-P. Pan, Pedro L. Muino, M.D. Barkley, and P.R. Callis, J. Phys. Chem. B (2011), 115, 3245-3253. 

"Predicting Fluorescence Lifetimes and Spectra of Biopolymers", P.R. Callis,Methods in Enzymology (2010), 487,1-38 .. 

"Exploring the Electrostatic Landscape of Proteins with Tryptophan Fluorescence", P. R. Callis, in Reviews in Fluorescence 2007 (2009), C. D. Geddes (ed.), Vol. 4, Springer, NY, pp 199-248.

"Femtosecond Fluorescence Spectra of Tryptophan in Human gamma-Crystallin Mutants: Site-Dependent Ultrafast Quenching", J. Xu, J. Chen, D. Toptygin, O. Tcherkasskaya, P.R. Callis, J. King, L. Brand and J.R. Knutson, J.Am.Chem.Soc.(2009), 131, 16751-16757.

"Mechanism of the Very Efficient Quenching of Tryptophan Fluorescence in Human .D- and .S-Crystallins: The gamma-Crystallin Fold May Have Evolved To Protect Tryptophan Residues from Ultraviolet Photodamage", J. Chen, P.R. Callis, and J. King, Biochemistry (2009), 48, 3708-3716.

"Solvent Effects on the Fluorescence Quenching of Tryptophan by Amides via Electron Transfer. Experimental and Computational Studies", P. R. Callis and P. L. Muino, J. Phys. Chem. B (2009), 113, 2572-2577.

"Molecular dynamics simulations of perylene and tetracene libratio\ ns: Comparison withfemtosecond upconversion data", Rosales T , Xu JH , Wu XW, Hodoseek M, Callis P, Brooks BR, Knutson JR, J. Phys. Chem. A (2008), 112, 5593-5597.

"Ab Initio Prediction of Tryptophan Fluorescence Quenching by Protein Electric Field Enabled Electron Transfer", Patrik R. Callis, Alexander Petrenko, Pedro L. Muino, and Jose R. Tusell. J. Phys. Chem. B (Letter); 2007;111(35) 10335-10339. DOI: 10.1021/jp0

Quantitative prediction of fluorescence quenching rates

"Mechanism of the Highly Efficient Quenching of Tryptophan Fluorescence in Human gammaD-Crystallin", Jiejin Chen, Shannon Flaugh, Patrik R. Callis*, and Jonathan King*, Biochemistry (2006), 45, 11552-11563.

"Short Range Photoinduced Electron Transfer in Proteins: QM-MM Simulations of Tryptophan and Flavin Fluorescence Quenching in Proteins", Patrik R. Callis and Tiqing Liu, Chem. Phys. (2006), 326, 230-239.

"Ultrafast Fluorescence Dynamics of Tryptophan in the Proteins Monellin and IIAGlc", Jianhua Xu, Dmitri Toptygin, Karen J. Graver, Rebecca A. Albertini, Regina S. Savtchenko, Norman D. Meadow, Saul Roseman, Patrik R. Callis, Ludwig Brand, and Jay R. Knutson*, J. Am. Chem. Soc. (2006), 128, 1214-1221.

Web Release Date: March 1, 2005

"Ionization Potentials of Fluoroindoles and the Origin of Non-Exponential Tryptophan Fluorescence Decay in Proteins", Tiqing Liu, Patrik R. Callis, Ben H. Hesp, Mattijs de Groot, Wybren Jan Buma, and Jaap Broos, J. Am. Chem. Soc127, 4104-4113(2005).

"Photophysics of Tryptophan Fluorescence: Link with the Catalytic Strategy of the Citrate Synthase from Thermoplasma acidophilum", Linda C. Kurz, Brett Fite, John Jean, Jung Park, Tim Erpelding and Patrik Callis,  Biochemistry (2005), 44, 1394-1413.

"Quantitative predictions of fluorescence quantum yields for tryptophan in proteins", by Patrik R. Callis and Tiqing Liu. J. Phys. Chem. B 108, 4248-4259 (2004). 

"Experimental and theoretical investigations of environmentally sensitive single-molecule fluorophores", Katherine A. Willets, Patrik R. Callis, W.E. Moerner,  J. Phys. Chem. B (2004), 108, 10465-10473. 

Understanding the variable fluorescence quantum yield of tryptophan in proteins using QM-MM simulations. Quenching by charge transfer to the peptide backbone," P. R. Callis and J. T. Vivian. Chem. Phys. Lett. 369, 409-414 (2003). 

Quantitative prediction of fluorescence wavelengths

Biesso, J.H. Xu, P.L. Muiño, P.R. Callis, J.R. Knutson, Charge Invariant Protein-Water Relaxation in GB1 via Ultrafast Tryptophan Fluorescence, J. Am. Chem. Soc. 136 (2014), p. 2739-2747.

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

"Electrochromism and solvatochromism in fluorescence response of organic dyes. A nanoscopic view", P.R. Callis, in Advanced Fluorescence Reporters in Chemistry and Biology I (2010),A. Demchenko, Ed. , Springer-Verlag, Heidelberg, pp 309-330

"The Emitting State of Tryptophan in Proteins With Extremely Blue Fluorescence", Jaap Broos*, Karina Tveen-Jensen, Ellen de Waal, Ben H. Hesp, J. Baz Jackson*, Gerard W. Canters, and Patrik R. Callis,Angew. Chem. Int. Ed.(2007), 46, 5137"Dependence of Tryptophan Emission Wavelength on Conformation in Cyclic Hexapeptides", Chia-Pin Pan, Patrik R. Callis,*, and Mary D. Barkley*, 5139 J. Phys. Chem. B (2006), 110, 7009-7016.


"Mechanisms of tryptophan fluorescence shifts in proteins", J. T. Vivian and P. R. Callis, Biophys. J.80, 2093-2109 (2001).

"Tryptophan Fluorescence Shifts in Proteins From Hybrid Simulations: An Electrostatic Approach," Callis, P.R. and Burgess, B.K., J. Phys. Chem. B, 101, 9429-9432 (1997). 

Electronic structure of indoles and related systems 

"One- and two-photon spectra of jet-cooled 2,3-dimethylindole: 1 Lb and 1Laassignments," K. W. Short and P. R. Callis, Chemical Physics 283, 269-278 (2002).

"Electronic structure and hyperfine interactions in thioether-substituted tyrosyl radicals," A. M. Boulet, E. D. Walter, D. A. Schwartz, G. J. Gerfen, P. R. Callis, and D. J. Singel Chem. Phys. Lett.331, 108-114 (2000). 

"Evidence for 1La fluorescence from jet-cooled 3-methylindole-polar solvent complexes," K. W. Short and P. R. Callis, J. Chem. Phys.113, 5235-5244 (2000). 

"Fluorescence properties of benz[f]indole, a wavelength and quenching selective tryptophan analog," B. Liu, M. D. Barkley, G. A. Morales, M. L. McLaughlin, and P. R. Callis, J. Phys. Chem. B,104, 1837-1843 (2000). 

"Ground-State Proton-Transfer tautomer of the Salicylate Anion," D. M. Friedrich, Z. Wang, A. G. Joly, K. A. Peterson, and P. R. Callis, J. Phys. Chem.103, 9644-9653 (1999). 

"Vibrational Assignments for Indole with the Aid of Ultra-Sharp Phosphorescence Spectra," B. J. Fender, K. W. Short, D. K. Hahn and P .R. Callis, Int. J. Quantum Chem.72, 347-356 (1999). 

"Evidence of Pure 1Lb Fluorescence From Redshifted Indole-polar Solvent Complexes in a Supersonic Jet," Short, K.W. and Callis, P.R., J. Chem. Phys., 108, 10189-10196 (1998). 

"Two-photon Induced Fluorescence," Callis, P.R. Annual Reviews of Physical Chem.48, 271-297 (1997). 

"1La and 1Lb Transitions of Tryptophan: Applications of Theory and Experimental Observations to Fluorescence of Proteins," Callis, P.R., Methods in Enzymology,278, 113-151 (1997). 

"The Triplet State of Indole: An ab initio Study," Hahn, D.K. and Callis, P.R., J. Chem. Phys., 101, 2686-2691 (1997). 

"Ab initio Calculations of Vibronic Spectra for Indole," Callis, P.R., Vivian, J.T., and Slater, L.S., Chem. Phys. Letters, 244, 53-58 (1995). 

"Site Selective Photoselection Study of Indole in Argon Matrix: Location of the 1La Origin," Fender, B.J., Sammeth, D.M., and Callis, P.R., Chem. Phys. Letters,23931-37 (1995). 

"Fluorescence Anisotropy of Tyrosine Using one-and two-photon Excitation," Lakowicz, J.R., Kierdaszuk, B., Callis, P.R., Malak, H., and Grycznski, I., Biophysical Chemistry, 56, 263-271 (1995).