• scott brewer
Associate Professor of Chemistry



Office: HAC403

Office: HAC 403
Lab: ​HAC 401B

Spring  2016 Office Hours:  Mondays 2 - 3 PM, & Fridays 3 - 4 PM


B.S. James Madison University, 1999
Ph.D. North Carolina State University, 2004 


My research focuses on the study of protein and nucleic acid structure with site-specificity utilizing a variety of spectroscopic methods including NMR and FTIR spectroscopy coupled with isotopic and/or chemical labels.

Grants & Awards


Brewer, S. H. Exploring Protein Structure and Hydration with Spectroscopic Reporter Unnatural Amino Acids and Modified Nucleosides. The Camille and Henry Dreyfus Teacher-Scholar Award (TH-15-009) $60,000.

Brewer, S. H.; Fenlon E. E. Investigating Protein Hydration and Structure with Azide Probes. National Institutes of Health. National Institute of General Medical Sciences: Academic Research Enhancement Award (2R15GM093330-02) $272,303 (9/30/14-8/31/17).

Brewer, S.H. Probing Protein Folding Using Site-Specifically Encoded Unnatural Amino Acids. National Science Foundation: CAREER (CHE-1053946). $403,115 (1/1/11-12/31/15).

Brewer, S.H.; Fenlon E.E. Development and Application of Multi-Spectroscopic, Site-Specific (MS3) Probes of Nucleic Acid Structure. National Institutes of Health. National Institute of General Medical Sciences: Academic Research Enhancement Award (1R15GM093330-01) $195,895 (6/1/10-5/31/14).

Brewer, S.H. Infrared Investigation of Short Helical Peptides with Residue Specificity. Research Corporation: Cottrell College Science Award $44,766 (1/1/08-1/1/10).

Brewer, S.H. Combined Experimental and Computational Vibrational Analysis of Short Helical Peptides with Residue Specificity. Pittsburgh Supercomputing Center 11,000 Service Units (8/14/07-8/15/08).


2000 - Present
(Undergraduate student coauthor are in bold.)

Rodgers, J. M.; Zhang, W.; Bazewicz, C. G.; Chen, J.; Brewer, S. H.; Gai, F. Kinetic Isotope Effect Provides Insight into the Vibrational Relaxation Mechanism of Aromatic Molecules: Application to Cyano-phenylalanine. Journal of Physical Chemistry Letters2016, 7, 1281-1287.

Levin, D. E.; Schmitz, A. J.; Hines, S. H.Hines, K. J.; Tucker, M. J.; Brewer, S. H.; Fenlon, E. E. Synthesis and Evaluation of the Sensitivity and Vibrational Lifetimes of Thiocyanate and Selenocyanate Infrared Reporters. RSC Advances 20166, 36231-36237

Dippel, A. B.; Olenginski, G. M.; Maurici, N.; Liskov, M. T.; Brewer, S. H.; Phillips-Piro, C. M. Probing the Effectiveness of Spectroscopic Reporter Unnatural Amino Acids: A Structural Study. Acta Crystallographica Section D2016, D72.

Tookmanian, E. M.; Phillips-Piro, C. M.; Fenlon, E. E.; Brewer, S. H. Azidoethoxyphenylalanine as a Vibrational Reporter and Click Chemistry Partner in Proteins. Chemistry – A European Journal2015, 21, 19096-19103.

Tookmanian, E. M.; Fenlon, E. E.; Brewer, S. H. Synthesis and protein incorporation of azido-modified unnatural amino acids. RSC Advances 20155, 1274-1281.

Bazewicz, C.G.; Liskov, M. T.; Hines, K. J.; Brewer, S. H. Sensitive, Site-Specific, and Stable Vibrational Probe of Local Protein Environments: 4-Azidomethyl-L-Phenylalanine. Journal of Physical Chemistry B 2013, 117, 8987-8993.

Vu, D. M.; Brewer, S.H.; Dyer, R.B. Early Turn Formation and Chain Collapse Drive Fast Folding of the Major Cold Shock Protein CspA of Escherichia coli. Biochemistry 2012, 51, 9104-9111.

Bazewicz, C. G.; Lipkin, J. S.; Smith, E. E.; Liskov, M. T.; Brewer, S. H. Expanding the Utility of 4-Cyano-L-Phenylalanine as a Vibrational Reporter of Protein Environments. Journal of Physical Chemistry B 2012, 116, 10824-10831.

Brewer, S. H.; Tang, Y.; Vu, D. M.; Gnanakaran, S.; Raleigh, D. P.; Dyer, R. B. Temperature Dependence of Water Interactions with the Amide Carbonyls of alpha-Helices. Biochemistry 2012, 51, 5293-5299.

Bazewicz, C.G.; Lipkin, J.S.; Lozinak, K.A.; Watson, M.D.; Brewer, S. H. Synthesis of Isotopomers of N-(tert-Butoxycarbonyl)-4-Cyano-L-Phenylalanine Methyl Ester: Choice of Cyanation Solvent. Tetrahedron Letters 2011, 52, 6865-6868.

Lipkin, J.S.; Song, R.; Fenlon, E.E.; Brewer, S.H. Modulating Accidental Fermi Resonance: What a Difference a Neutron Makes. Journal of Physical Chemistry Letters 2011, 2, 1672-1676.

Gai, X.S.; Coutifaris, B.A.; Brewer, S.H.; Fenlon, E.E. A Direct Comparison of Azide and Nitrile Vibrational Probes. Physical Chemistry Chemical Physics 2011, 13, 5926-5930.

Smith, E.E.; Linderman, B.Y.; Luskin, A.C.; Brewer. S.H. Probing Local Environments with the Infrared Probe: L-4-Nitrophenylalanine. Journal of Physical Chemistry B 2011, 115, 2380-2385. 

Tucker, M.J.; Gai, X.S.; Fenlon, E.E.; Brewer, S.H.; Hochstrasser, R.M. 2D IR Photon Echo of Azido-Probes for Biomolecular Dynamics. Physical Chemistry Chemical Physics 2011, 13, 2237-2241.

Gillies, A.T.; Gai, X.S.; Buckwalter, B.L.; Fenlon, E.E.; Brewer, S.H. 15N NMR Studies of a Nitrile-Modified Nucleoside. Journal of Physical Chemistry B 2010, 114, 17136-17141.

Gai, X.S.; Fenlon, E.E.; Brewer, S.H. A Sensitive Multispectroscopic Probe for Nucleic Acids. Journal of Physical Chemistry B 2010, 114, 7958-7966.

Taskent-Sezgin, H.; Chung, J.; Patsalo, V.; Miyake-Stoner, S.J.; Miller, A.M.; Brewer, S.H.; Mehl, R.A.; Green, D. F.; Raleigh, D. P.; Carrico, I. Interpretation of p-Cyanophenylalanine Fluorescence in Proteins in Terms of Solvent Exposure and Contribution of Side-chain Quenchers: A Combined Fluorescence, IR and Molecular Dynamics Study. Biochemistry 2009, 48, 9040-9046.

Miyake-Stoner, S.J.; Miller, A.M.; Hammill, J.T.; Peeler, J.C.; Hess, K.R.; Mehl, R.A.; Brewer, S.H. Probing Protein Unfolding Using Site-Specifically Encoded Unnatural Amino Acids as FRET Donors with Tryptophan. Biochemistry 2009, 48, 5953-5962.

Deng, D.; Brewer, S.H.; Vu, D.M.; Clinch, K.; Callender, R.; Dyer, R.B. On the Pathway to Forming Enzymatically Productive Ligand-Protein Complexes in Lactate Dehydrogenase. Biophysical Journal 2008, 95, 804-813.

Watson, M.D.; Gai, X.S.; Gillies, A.T.; Brewer, S.H.; Fenlon, E.E. A Vibrational Probe for Local Nucleic Acid Environments: 5’-Cyano-2’-deoxyuridine. Journal of Physical Chemistry B 2008, 112, 13188-13192.

Rhodes, C. L.; Brewer, S. H.; Folmer, J.; Franzen, S. Investigation of Hexadecanethiol Self-Assembled Monolayers on Cadmium Tin Oxide Thin Films.  Thin Solid Films 2008, 516, 1838-1842.

Marecek, J.; Song, B.; Brewer, S.; Belyea, J.; Dyer, R. B.; Raleigh, D. P.  A Simple and Economical Method for the Production of 13C,18O-Labeled Fmoc-Amino Acids with High Levels of Enrichment: Applications to Isotope-Edited IR Studies of Proteins. Organic Letters 2007, 9, 4935-4937.

Moses, S.; Brewer, S. H.; Kraemer, S.; Fuierer, R. R.; Lowe, L. B.; Agbasi, C.; Sauthier, M; Franzen, S. Detection of DNA Hybridization on Indium Tin Oxide Surfaces. Sensors and Actuators B: Chemical 2007, 125, 574-580.

Religa, T.L.; Johnson, C. M.; Vu, D. M.; Brewer, S. H.; Dyer, R. B.; Fersht, A. R. The Helix-Turn-Helix Motif as an Ultra-Fast Independently Folding Domain: The Pathway of Folding of Engrailed Homeodomain. Proceedings of the National Academy of Sciences of the United States of America 2007, 104, 9272-9277.

Brewer, S. H.; Song, B.; Raleigh, D. P.; Dyer, R. B. Residue Specific Resolution of Protein Folding Dynamics Using Isotope-Edited Infrared Temperature Jump Spectroscopy. Biochemistry 2007, 46, 3279-3285.

Toepke, M. W.; Brewer, S. H.; Vu, D. M.; Rector, K. D.; Morgan, J. E.; Gennis, R. B.; Kenis, P. J. A.; Dyer, R. B. Microfluidic Flow-Flash: A New Method for Investigating Protein Dynamics. Analytical Chemistry 2007, 79(1), 122-128.

Franzen, S.; Jasaitis, A.; Belyea, J.; Brewer, S. H.; Casey, R.; MacFarlane, A. W.; Stanley, R. J.; Vos, M. H.; Martin, J. L. Hydrophobic Distal Pocket Affects NO-Heme Geminate Recombination Dynamics in Dehaloperoxidase and H64V Myoglobin. Journal of Physical Chemistry B 2006, 110(29), 14483-14493.

Bin-Salamon, S.; Brewer, S. H.; Depperman, E. C.; Franzen, S.; Kampf, J. W.; Kirk, M. L.; Kumar, R. K.; Lappi, S.; Peariso, K.; Preuss, K. E.; Shultz, D. A. Testing Bridge-Mediated Differences in Dinuclear Valence Tautomeric Behavior. Inorganic Chemistry 2006, 45(11), 4461-4467.

Barry, B. A.; Cooper, I. B.; De Riso, A.; Brewer, S. H.; Vu, D. M.; Dyer, R. B. Time-Resolved Vibrational Spectroscopy Detects Protein-Based Intermediates in the Photosynthetic Oxygen-Evolving Cycle. Proceedings of the National Academy of Sciences of the United States of America 2005, 103(19), 7288-7291.

Brewer, S. H.; Vu, D. M.; Tang, Y.; Li, L.; Franzen, S.; Raleigh, D. P.; Dyer, R. B. Effect of Modulating Unfolded State Structure on the Folding Kinetics of the Villin Headpiece Subdomain. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(46), 16662-16667.

Bin-Salamon, S; Brewer, S. H.; Franzen, S.; Feldheim, D. L.; Lappi, S.; Shultz, D. A. Supramolecular Control of Valence-Tautomeric Equilibrium on Nanometer-Scale Gold Clusters. Journal of the American Chemical Society Communication 2005, 127(15), 5328-5329.

Brewer, S. H.; Glomm, W. R.; Johnson, M. C.; Knag, M. K.; Franzen, S. Probing BSA Binding to Citrate-Coated Gold Nanoparticles and Surfaces. Langmuir 2005, 21(20), 9303-9307.

Brewer, S.H.; Wicaksana, D.; Maria, J.; Kingon, A. I.; Franzen, S. Investigation of the Electrical and Optical Properties of Iridium Oxide by Reflectance FTIR Spectroscopy and Density Functional Theory Calculations. Chemical Physics 2005, 313(1-3), 25-31.

Moses, S.; Brewer, S. H.; Lowe, L. B.; Lappi, S. E.; Gilvey, L. B. G.; Tenent, R. C.; Feldheim, D. L.; Franzen, S. Characterization of Single and Double Stranded DNA on Gold Surfaces. Langmuir 2004, 20(25), 11134-11140.

Brewer, S. H.; Allen, A. M.; Lappi, S. E.; Chasse, T. L.; Briggman, K. A.; Gorman, C. B.; Franzen, S. Infrared Detection of a Phenylboronic Acid Terminated Alkane Thiol Monolayer on Gold Surfaces. Langmuir 2004, 20(13), 5512-5520.

Brewer, S. H.; Franzen, S. Calculation of the Electronic and Optical Properties of Indium Tin Oxide by Density Functional Theory. Chemical Physics 2004, 300, 285-293.

Smith, B. M.; Lappi, S. E.; Brewer, S. H.; Dembowy, S.; Belyea, J.; Franzen, S. Covalent Attachment of a Nickel Nitrilotriacetic Acid Group to a Germanium Attenuated Total Reflectance Element. Langmuir 2004, 20(4), 1184-1188.

Lowe, L. B.; Brewer, S. H.; Kramer, S.; Fuierer, R. R.; Qian, G.; Agbasi-Porter, C. O.; Moses, S.; Franzen, S.; Feldheim, D. L. Laser-Induced Temperature Jump Electrochemistry on Gold Nanoparticle-Coated Electrodes. Journal of the American Chemical Society Communication 2003, 125(47), 14258-14259.

Brewer, S. H.; Franzen, S. A Quantitative Theory and Computational Approach for the Vibrational Stark Effect. Journal of Chemical Physics 2003, 119(2), 851-858.

Franzen, S.; Fritsch, K.; Brewer, S. H. Experimental Observation of Anharmonic Coupling of the Heme-Doming and Iron-Ligand Out-of-Plane Vibrational Modes Confirmed by Density Functional Theory. Journal of Physical Chemistry B 2002, 106, 11641-11646.

Brewer, S. H.; Franzen, S. Indium Tin Oxide Plasma Frequency Dependence on Sheet Resistance and Surface Adlayers Determined by Reflectance FTIR Spectroscopy. Journal of Physical Chemistry B 2002, 106, 12986-12992.

Brewer, S. H.; Brown, D. A.; Franzen, S. Formation of Thiolate and Phophonate Adlayers on Indium Tin Oxide: Optical and Electronic Characterization of the Bonding. Langmuir 2002, 18(18), 6857-6865.

Brewer, S. H.; Franzen, S. Optical Properties of Indium Tin Oxide and Fluorine-Doped Tin Oxide Surfaces: Correlation of Reflectivity, Skin Depth, and Plasmon Frequency with Conductivity. Journal of Alloys and Compounds 2002, 338, 73-79.

Brewer, S. H.; Anthireya, S. J.; Lappi, S. E.; Drapcho, D. L.; Franzen, S. Detection of DNA Hybridization on Gold Surfaces by Polarization Modulation Infrared Reflection Absorption Spectroscopy. Langmuir 2002, 18(11), 4460-4464.

Brewer, S. H.; Cresawn, S. G.; Nguyen, D. T.; MacDonald, G.  Difference FT-IR Studies of Nucleotide Binding to the Recombination Protein RecA.  Journal of Physical Chemistry B 2000, 104, 6950-6954.






Course Information

Dr. Brewer teaches the following courses:
    CHM 111 - General Chemistry I
    CHM 112 - General Chemistry II
    CHM 321 - Thermodynamics & Kinetics
    CHM 322 - Structure and Bonding

In the News

Story 8/25/2015

Chemistry Professor Earns National Award for Scholarship,...

Franklin & Marshall College Associate Professor of Chemistry Scott H. Brewer has been named a Henry Dreyfus Teacher-Scholar.

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Story 10/15/2014

Science Faculty Secure Vital Funding in Competitive Grant...

At a time when federal grants are becoming increasingly scarce, four Franklin & Marshall science professors each have been awarded funding from the National Institutes of Health (NIH) for...

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