Publications of Richard A. Mathies - The Journal of Physical Chemistry

Special Issue Preface pubs.acs.org/JPCB

Publications of Richard A. Mathies 15. Braiman, M. and Mathies, R. Resonance Raman Evidence for an All-trans to 13-cis Isomerization in the ProtonPumping Cycle of Bacteriorhodopsin. Biochemistry 19, 5421−5428 (1980). 16. Eyring, G., Curry, B., Mathies, R., Broek, A. and Lugtenburg, J. Assignment of the Anomalous Resonance Raman Vibrations of Bathorhodopsin. J. Am. Chem. Soc., 102, 5390−5392 (1980). 17. Mathies, R., Eyring, G., Curry, B., Broek, A., Palings, I., Fransen, R. and Lugtenburg, J. Interpretation of the Resonance Raman Spectrum of Bathorhodopsin, In Proceedings of the VIIth International Conference on Raman Spectroscopy (Murphy, W. F., Ed.), North-Holland, pp 546−547 (1980). 18. Mathies, R. Resonance Raman Spectroscopy of Rhodopsin and Bacteriorhodopsin Isotopic Analogs. Meth. Enzymol. 88, 633−643 (1982). 19. Eyring, G., Curry, B., Broek, A., Lugtenburg, J. and Mathies, R. Assignment and Interpretation of Hydrogen Out-of-Plane Vibrations in the Resonance Raman Spectra of Rhodopsin and Bathorhodopsin. Biochemistry 21, 384− 393 (1982). 20. Braiman, M. and Mathies, R. Resonance Raman Spectra of Bacteriorhodopsin’s Primary Photoproduct: Evidence for a Distorted 13-cis Retinal Chromophore. Proc. Natl. Acad. Sci. U.S.A. 79, 403−407 (1982). 21. Braiman, M. and Mathies, R. Spinning Sample Raman Spectroscopy at 77° K: Bacteriorhodopsin’s Primary Photoproduct. Meth. Enzymol. 88, 648−659 (1982). 22. Barry, B. and Mathies, R. Resonance Raman Microscopy of Rod and Cone Photoreceptors. J. Cell Biol. 94, 479−482 (1982). 23. Curry, B., Broek, A., Lugtenburg, J. and Mathies, R. Vibrational Analysis of All-trans Retinal. J. Am. Chem. Soc. 104, 5274−5286 (1982). 24. Myers, A. B., Mathies, R. A., Tannor, D. J. and Heller, E. J. Excited State Geometry Changes from Preresonance Raman Intensities: Isoprene and Hexatriene. J. Chem. Phys. 77, 3857−3866 (1982). 25. Mathies, R. Resonance Raman Investigations of the Primary Photochemistry in Visual Pigments and Bacteriorhodopsin, In Frontiers in Biochemical and Biophysical Studies of Proteins and Membranes (Liu, T.-Y., Sakakibara, S., Schechter, A. N., Yagi, K., Yagima, H. and Yasunobu, K. T., Eds.), Elsevier, pp 367−386 (1983). 26. Smith, S. O., Braiman, M. and Mathies, R. Time-Resolved Resonance Raman Spectroscopy of the K610 and O640 Photointermediates of Bacteriorhodopsin, In TimeResolved Vibrational Spectroscopy (Atkinson, G., Ed.), Academic Press, pp 219−230 (1983). 27. Harris, R. A., Mathies, R. and Myers, A. A Simple Sum Rule in Raman Theory. Chem. Phys. Lett. 94, 327−330 (1983).

1. Gouterman, M., Mathies, R. A., Smith, B. E. and Caughey, W. S. Porphyrins XIX: Tripdoublet and Quartet Luminescence in Cu and VO Complexes. J. Chem. Phys. 52, 3795−3802 (1970). 2. Mathies, R. and Albrecht, A. C. Electric Field Perturbation of the 1A1g→1B2u Transition in Benzene. Chem. Phys. Lett. 16, 231−234 (1972). 3. Mathies, R. and Albrecht, A. C. Electric Field Broadening of the 1A1(2) Transition in Azulene. J. Chem. Phys. 60, 1420−1423 (1974). 4. Mathies, R. and Albrecht, A. C. Experimental and Theoretical Studies on the Excited State Polarizabilities of Benzene, Naphthalene and Anthracene. J. Chem. Phys. 60, 2500−2508 (1974). 5. Friedrich, D. M., Mathies, R. and Albrecht, A. C. Studies of Excited Electronic States of Anthracene and Some of its Derivatives by Photoselection and PPP-SCF Calculations. J. Mol. Spectrosc. 51, 166−188 (1974). 6. Veatch, W. R., Mathies, R., Eisenberg, M. and Stryer, L. Simultaneous Fluorescence and Conductance Studies of Planar Bilayer Membranes Containing a Highly Active and Fluorescent Analog of Gramicidin A. J. Mol. Biol. 99, 75− 92 (1975). 7. Mathies, R., Oseroff, A. R. and Stryer, L. Rapid-Flow Resonance Raman Spectroscopy of Photolabile Molecules: Rhodopsin and Isorhodopsin. Proc. Natl. Acad. Sci. U.S.A. 73, 1−5 (1976). 8. Mathies, R. and Stryer, L. Retinal Has a Highly Dipolar Vertically Excited Singlet State: Implications for Vision. Proc. Natl. Acad. Sci. U.S.A. 73, 2169−2173 (1976). 9. Mathies, R., Oseroff, A. R., Freedman, T. B. and Stryer, L. Resonance Raman Spectroscopy: Application of Tunable Lasers to the Study of the Molecular Mechanisms and Dynamics of Visual Excitation, In Tunable Lasers and Applications (Mooradian, A., Jaeger, T. and Stokseth, P., Eds.), Springer-Verlag, pp 294−302 (1976). 10. Mathies, R., Freedman, T. B. and Stryer, L. Resonance Raman Studies of the Conformation of Retinal in Rhodopsin and Isorhodopsin. J. Mol. Biol. 109, 367−372 (1977). 11. Mathies, R. and Yu, N.-T. Raman Spectroscopy with Intensified Vidicon Detectors: A Study of Intact Bovine Lens Proteins. J. Raman Spectrosc. 7, 349−352 (1978). 12. Eyring, G. and Mathies, R. Resonance Raman Studies of Bathorhodopsin: Evidence for a Protonated Schiff Base Linkage. Proc. Natl. Acad. Sci. U.S.A. 76, 33−37 (1979). 13. Mathies, R. Biological Applications of Resonance Raman Spectroscopy in the Visible and Ultraviolet: Visual Pigments, Purple Membrane, and Nucleic Acids, In Chemical and Biochemical Applications of Lasers, Vol. 4 (Moore, C. B., Ed.), Academic Press, pp 55−99 (1979). 14. Eyring, G., Curry, B., Mathies, R., Fransen, R., Palings, I. and Lugtenburg, J. Interpretation of the Resonance Raman Spectrum of Bathorhodopsin Based on Visual Pigment Analogues. Biochemistry 19, 2410−2418 (1980). © 2012 American Chemical Society

Special Issue: Richard A. Mathies Festschrift Published: September 6, 2012 10414

dx.doi.org/10.1021/jp3066713 | J. Phys. Chem. B 2012, 116, 10414−10429

The Journal of Physical Chemistry B

Special Issue Preface

44. Myers, A. B., Trulson, M. O. and Mathies, R. A. Quantitation of Homogeneous and Inhomogeneous Broadening Mechanisms in Trans-stilbene Using Absolute Resonance Raman Intensities. J. Chem. Phys., 83, 5000− 5006 (1985). 45. Stern, D. and Mathies, R. Picosecond and Nanosecond Resonance Raman Evidence for Structural Relaxation in Bacteriorhodopsin’s Primary Photoproduct, In TimeResolved Vibrational Spectroscopy, (M. Stockburger and A. Laubereau, Eds.) Proceedings in Physics, Vol. 4, Springer-Verlag, pp 250−254 (1985). 46. Myers, A. B., Trulson, M. O., Pardoen, J. A., Heeremans, C., Lugtenburg, J. and Mathies, R. A. Absolute Resonance Raman Intensities Demonstrate That the Spectral Broadening Induced by the β-ionone Ring in Retinal is Homogeneous, J. Chem. Phys., 84, 633−640 (1986). 47. Trulson, M. O. and Mathies, R. A. Raman Cross Section Measurements in the Visible and Ultraviolet Using an Integrating Cavity: Application to Benzene, Cyclohexane and Cacodylate. J. Chem. Phys., 84, 2068−2074 (1986). 48. Mathies, R. A. and Stryer, L. Single-Molecule Fluorescence Detection: A Feasibility Study Using Phycoerythrin, In Fluorescence in the Biological Sciences (D. L. Taylor, A.S. Waggoner, F. Lanni, R. F. Murphy and R. Birge, Eds.) Alan R. Liss, pp 129−140 (1986). 49. Smith, S. O., Hornung, I., van der Steen, R., Pardoen, J. A., Braiman, M. S., Lugtenburg, J. and Mathies, R. A. Are C14− C15 Single Bond Isomerizations of the Retinal Chromophore Involved in the Proton-Pumping Mechanism of Bacteriorhodopsin? Proc. Natl. Acad. Sci. U.S.A. 83, 967− 971 (1986). 50. Lugtenburg, J., Muradin-Szweykowska, M., Harbison, G. S., Smith, S. O., Heeremans, C., Pardoen, J. A., Herzfeld, J., Griffin, R. G. and Mathies, R. A. Mechanism for the Opsin Shift of Retinal’s Absorption in Bacteriorhodopsin. J. Am. Chem. Soc., 108, 3104−3105 (1986). 51. Cruz, P., Hall, K., Puglisi, J., Davis, P., Hardin, C.C., Trulson, M. O., Mathies, R. A., Tinoco, I., Jr., Johnson, W.C., Jr. and Neilson, T. The Left-Handed Z-form of Double-Stranded RNA, In Biomolecular Stereodynamics IV (R. H. Sarma and M. H. Sarma, Eds.), Adenine Press, IV, pp 179−200 (1986). 52. Harris, R. A., Mathies, R. A. and Pollard, W. T. Simple Interpretation of Dephasing in Absorption and Resonance Raman Theory. J. Chem. Phys. 85, 3744−3748 (1986). 53. van der Steen, R., Biesheuvel, P. L., Mathies, R. A. and Lugtenburg, J. Retinal Analogues with Locked 6−7 Conformations Show That Bacteriorhodopsin Requires the 6-s-trans Conformation of the Chromophore. J. Am. Chem. Soc., 108, 6410−6411 (1986). 54. Myers, A. B. and Mathies, R. A. Resonance Raman Intensities: A Probe of Excited State Structure and Dynamics, In Biological Applications of Raman Spectroscopy: Vol. Two - Resonance Raman Spectra of Polyenes and Aromatics (T. G. Spiro, Ed.), John Wiley & Sons, Inc., pp 1−58 (1987). 55. Mathies, R. A., Smith, S. O. and Palings, I. Determination of Retinal Chromophore Structure in Rhodopsins, In Biological Applications of Raman Spectroscopy: Vol. Two Resonance Raman Spectra of Polyenes and Aromatics (T. G. Spiro, Ed.), John Wiley & Sons, Inc., pp 59−108 (1987). 56. Mathies, R. A. and Myers, A. B. Femtosecond Excited State Dynamics from Resonance Raman Intensities. In Time-

28. Myers, A. B., Harris, R. A. and Mathies, R. A. Resonance Raman Excitation Profiles of Bacteriorhodopsin. J. Chem. Phys. 79, 603−613 (1983). 29. Ponder, M. and Mathies, R. Excited-State Polarizabilities and Dipole Moments of Diphenylpolyenes and Retinal. J. Phys. Chem. 87, 5090−5098 (1983). 30. Smith, S. O., Pardoen, J. A., Mulder, P. P. J., Curry, B., Lugtenburg, J. and Mathies, R. Chromophore Structure in Bacteriorhodopsin’s O640 Photointermediate. Biochemistry 22, 6141−6148 (1983). 31. Curry, B., Palings, I., Broek, A., Pardoen, J. A., Mulder, P. P. J., Lugtenburg, J. and Mathies, R. Vibrational Analysis of 13-cis Retinal. J. Phys. Chem. 88, 688−702 (1984). 32. Mathies, R. A. Resonance Raman Determination of Retinal Chromophore Structure in Bacteriorhodopsin, In Spectroscopy of Biological Molecules, NATO ASI Series C, Vol. 139, pp 303−328 (1984). 33. Harbison, G. S., Smith, S. O., Pardoen, J. A., Mulder, P. P. J., Lugtenburg, J., Herzfeld, J., Mathies, R. and Griffin, R. G. Solid-State 13C NMR Studies of Retinal in Bacteriorhodopsin. Biochemistry 23, 2662−2667 (1984). 34. Smith, S. O., Myers, A. B., Pardoen, J. A., Winkel, C., Mulder, P. P. J., Lugtenburg, J. and Mathies, R. Determination of Retinal Schiff Base Configuration in Bacteriorhodopsin. Proc. Natl. Acad. Sci. U.S.A. 81, 2055− 2059 (1984). 35. Harbison, G. S., Smith, S. O., Pardoen, J. A., Winkel, C., Lugtenburg, J., Herzfeld, J., Mathies, R. and Griffin, R. G. Dark-Adapted Bacteriorhodopsin Contains 13-cis,15-syn and All-trans,15-anti Retinal Schiff Bases. Proc. Natl. Acad. Sci. U.S.A. 81, 1706−1709 (1984). 36. Myers, A. B. and Mathies, R. A. Excited-State Torsional Dynamics of Cis-stilbene from Resonance Raman Intensities. J. Chem. Phys. 81, 1552−1558 (1984). 37. Rothschild, K. J., Marrero, H., Braiman, M. and Mathies, R. Primary Photochemistry of Bacteriorhodopsin: Comparison of Fourier Transform Infrared Difference Spectra with Resonance Raman Spectra. Photochem. Photobiol. 40, 675−679 (1984). 38. Smith, S. O., Marvin, M. J., Bogomolni, R. A. and Mathies, R. A. Structure of the Retinal Chromophore in the hR578 Form of Halorhodopsin. J. Biol. Chem. 259, 12326−12329 (1984). 39. Curry, B., Palings, I., Broek, A. D., Pardoen, J. A., Lugtenburg, J. and Mathies, R. Vibrational Analysis of the Retinal Isomers. Adv. Inf rared Raman Spectrosc. 12, 115−178 (1985). 40. Smith, S. O., Myers, A. B., Mathies, R. A., Pardoen, J. A., Winkel, C., van den Berg, E. M. M. and Lugtenburg, J. Vibrational Analysis of the All-trans Retinal Protonated Schiff Base. Biophys. J. 47, 653−664 (1985). 41. Smith, S. O. and Mathies, R. A. Resonance Raman Spectra of the Acidified and Deionized Forms of Bacteriorhodopsin. Biophys. J., 47, 251−254 (1985). 42. Smith, S. O., Lugtenburg, J. and Mathies, R. A. Determination of Retinal Chromophore Structure in Bacteriorhodopsin with Resonance Raman Spectroscopy. J. Membr. Biol. 85, 95−109 (1985). 43. Harbison, G. S., Smith, S. O., Pardoen, J. A., Courtin, J. M. L., Lugtenburg, J., Herzfeld, J., Mathies, R. A. and Griffin, R. G. Solid-State 13C NMR Detection of a Perturbed 6-strans Chromophore in Bacteriorhodopsin. Biochemistry, 24, 6955−6962 (1985). 10415



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Resolved Vibrational Spectroscopy (Atkinson, G. H., Ed.), Gordon and Breach, pp 41−54 (1987). Smith, S. O., Braiman, M. S., Myers, A. B., Pardoen, J. A., Courtin, J. M. L., Winkel, C., Lugtenburg, J. and Mathies, R. A. Vibrational Analysis of the All-trans Retinal Chromophore in Light-Adapted Bacteriorhodopsin. J. Am. Chem. Soc., 109, 3108−3125 (1987). Smith, S. O., Pardoen, J. A., Lugtenburg, J. and Mathies, R. A. Vibrational Analysis of the 13-cis Retinal Chromophore in Dark-Adapted Bacteriorhodopsin. J. Phys. Chem., 91, 804−819 (1987). Smith, S. O., Palings, I., Copié, V., Raleigh, D. P., Courtin, J., Pardoen, J. A., Lugtenburg, J., Mathies, R. A. and Griffin, R. G. Low-Temperature Solid-State 13C NMR Studies of the Retinal Chromophore in Rhodopsin. Biochemistry, 26, 1606−1611 (1987). Smith, S. O., Copie, V., Raleigh, D. P., Griffin, R. G., Palings, I., Mathies, R. A., Courtin, J., Winkel, C. and Lugtenburg, J. NMR Studies of Isotopically Labeled Rhodopsins, In Biophysical Studies of Retinal Proteins (T. G. Ebrey, H. Frauenfelder, B. Honig and K. Nakanishi, Eds.), University of Illinois Press, pp 226−232 (1987). Mathies, R. A., Smith, S. O. and Lugtenburg, J. Determination of Retinal Chromophore Structure and Photochemistry in Bacteriorhodopsin with Resonance Raman Spectroscopy, In Biophysical Studies of Retinal Proteins (T. G. Ebrey, H. Frauenfelder, B. Honig and K. Nakanishi, Eds.) University of Illinois Press, pp 126−132 (1987). Mathies, R. A., Smith, S. O., Harbison, G. S., Herzfeld, J., Griffin, R. G. and Lugtenburg, J. Determination of Chromophore Structure and Photochemistry in Bacteriorhodopsin with Resonance Raman, NMR, and Chemical Analogues, In Primary Processes in Photobiology (T. Kobayashi, Ed.), Springer-Verlag Proceedings in Physics, Vol. 20, pp 136−143 (1987). Barry, B. and Mathies, R. A. Raman Microscope Studies of the Primary Photochemistry of Vertebrate Visual Pigments with Absorption Maxima from 430 to 502 nm. Biochemistry, 26, 59−64 (1987). Mathies, R. A., Smith, S. O., Harbison, G. S., Courtin, J. M. L., Herzfeld, J., Griffin, R. G. and Lugtenburg, J. Determination of Retinal Chromophore Structure and Photochemistry in Rhodopsins with Resonance Raman, NMR and Chemical Analogues, In Retinal Proteins (U. Ovchinnikov, Ed.), VNU Press, Utrecht, The Netherlands, pp 231−240 (1987). Palings, I., Pardoen, J. A., van den Berg, E., Winkel, C., Lugtenburg, J. and Mathies, R. A. Assignment of Fingerprint Vibrations in the Resonance Raman Spectra of Rhodopsin, Isorhodopsin and Bathorhodopsin: Implications for Chromophore Structure and Environment. Biochemistry, 26, 2544−2556 (1987). Trulson, M. O., Dollinger, G. D. and Mathies, R. A. Femtosecond Photochemical Excited State Ring-Opening Dynamics of 1,3-Cyclohexadiene from Resonance Raman Intensities. J. Am. Chem. Soc., 109, 586−587 (1987). Barry, B., Mathies, R. A., Pardoen, J. A. and Lugtenburg, J. Raman Microscope and Quantum Yield Studies on the Primary Photochemistry of A2-Visual Pigments. Biophys. J., 52, 603−610 (1987). Fodor, S. P. A., Bogomolni, R. A. and Mathies, R. A. Structure of the Retinal Chromophore in the hR L

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Intermediate of Halorhodopsin from Resonance Raman Spectroscopy. Biochemistry, 26, 6775−6778 (1987). Trulson, M. O., Cruz, P., Puglisi, J. D., Tinoco, I., Jr. and Mathies, R. A. Raman Spectroscopic Study of Left-Handed Z-RNA. Biochemistry, 26, 8624−8630 (1987). Loppnow, G. R. and Mathies R. A. Excited-State Structure and Isomerization Dynamics of the Retinal Chromophore in Rhodopsin from Resonance Raman Intensities. Biophys. J., 54, 35−43 (1988). Mathies, R. A., Fodor, S. P. A., Smith, S. O., van den Berg, E. M. M., Gebhard, R. and Lugtenburg, J. Determination of Retinal Chromophore Structure in Rhodopsins with Resonance Raman Spectroscopy, In Spectroscopy of Biological Molecules - New Advances (E. D. Schmid, F. W. Schneider and F. Siebert, Eds.), John Wiley & Sons, Inc., England, pp 215−223 (1988). Fodor, S. P. A., Pollard, W. T., Gebhard, R., van den Berg, E. M. M., Lugtenburg, J. and Mathies, R. A. Bacteriorhodopsin’s L550 Intermediate Contains a C14−C15 strans Retinal Chromophore. Proc. Natl. Acad. Sci. U.S.A., 85, 2156−2160 (1988). Mathies, R. A., Brito Cruz, C. H., Pollard, W. T. and Shank, C. V. Direct Observation of the Femtosecond ExcitedState cis-trans Isomerization in Bacteriorhodopsin. Science 240, 777−779 (1988). Lugtenburg, J., Mathies, R. A., Griffin, R. G. and Herzfeld, J. Structure and Function of Rhodopsins from Solid-State NMR and Resonance Raman Spectroscopy of Isotopic Retinal Derivatives. Trends Biochem. Sci., 13, 388−393 (1988). Fodor, S. P. A., Ames, J. B., Gebhard, R., van den Berg, E. M. M., Stoeckenius, W., Lugtenburg, J. and Mathies, R. A., Chromophore Structure in Bacteriorhodopsin’s N Intermediate: Implications for the Proton-Pumping Mechanism. Biochemistry 27, 7097−7101 (1988). Fodor, S. P. A., Lagarias, J. C. and Mathies, R. A., Resonance Raman Spectra of the Pr-Form of Phytochrome. Photochem. Photobiol. 48, 129−136 (1988). Mathies, R. A., Pollard, W. T., Brito Cruz, C. H. and Shank, C. V. Direct Observation of the Femtosecond ExcitedState Cis−Trans Isomerization in Bacteriorhodopsin, In Ultrafast Phenomena VI Springer Series in Chemical Physics (Yajima, T., Yoshihara, K., Harris, C.B. and Shionoya, S., Eds.), Springer-Verlag, Berlin Heidelberg, Vol. 48, pp 584−589 (1988). Lee, S.-Y. and Mathies, R. A. Polarizability Theory and Sum Rules. Chem. Phys. Lett. 151, 9−15 (1988). Baselt, D. R., Fodor, S. P. A., van der Steen, R., Lugtenburg, J., Bogomolni, R. A. and Mathies, R. A. Halorhodopsin and Sensory Rhodopsin Contain a C6−C7 s-trans Retinal Chromophore. Biophys. J. 55, 193−196 (1989). Palings, I., van den Berg, E. M. M., Lugtenburg, J. and Mathies, R. A. Complete Assignment of the Hydrogen Out-of-Plane Wagging Vibrations of Bathorhodpsin: Chromophore Structure and Energy Storage in the Primary Photoproduct of Vision. Biochemistry 28, 1498− 1507 (1989). van der Steen, R., Biesheuvel, P. L., Erkelens, C., Mathies, R. A., and Lugtenburg, J. 8,16- and 8,18-Methanobacteriorhodopsin. Synthesis and Spectroscopy of 8,16- and 8,18-Methanoretinal and Their Interaction with Bacteriorhodopsin. Recl. Trav. Chim. Pays-Bas, 108, 83−93 (1989). dx.doi.org/10.1021/jp3066713 | J. Phys. Chem. B 2012, 116, 10414−10429



82. Pollard, W. T., Brito Cruz, C. H., Shank, C. V. and Mathies, R. A. Direct Observation of the Femtosecond ExcitedState Cis-trans Photoisomerization of Bacteriorhodopsin: Multilevel Line Shape Theory for Femtosecond Dynamic Hole Burning and its Application. J. Chem. Phys. 90, 199− 208 (1989). 83. Loppnow, G. R., Barry, B. A. and Mathies, R. A. Why Are Blue Visual Pigments Blue? A Resonance Raman Microprobe Study. Proc. Natl. Acad. Sci. U.S.A. 86, 1515−1518 (1989). 84. Ames, J. B., Fodor, S. P. A., Gebhard, R., Raap, J., van den Berg, E. M. M., Lugtenburg, J. and Mathies, R. A. Bacteriorhodopsin’s M412 Intermediate Contains a 13-cis, 14-s-trans, 15-anti-Retinal Schiff Base Chromophore. Biochemistry 28, 3681−3687 (1989). 85. Trulson, M. O., Dollinger, G. D. and Mathies, R. A. Excited-State Structure and Femtosecond Ring-Opening Dynamics of 1,3-Cyclohexadiene from Absolute Resonance Raman Intensities. J. Chem. Phys. 90, 4274−4281 (1989). 86. Reid, P. J., Doig, S. J. and Mathies, R. A. Direct Measurement of the Photochemical Ring-Opening in 1,3-Cyclohexadiene by Picosecond Time-Resolved UV Resonance Raman. Chem. Phys. Lett. 156, 163−168 (1989). 87. Mathies, R. A., Lugtenburg, J. and Shank C. V. From Femtoseconds to Biology: Mechanism of the Light-Driven Proton Pump in Bacteriorhodopsin. Proceedings of the International Society for Optical Engineering - SPIE, “Biomolecular Spectroscopy”, Volume 1057, pp 138−145 (1989). 88. Lee, S.-Y., Pollard, W. T. and Mathies, R. A. Classical Theory for Real-Time Femtosecond Probing of the NaI* Photodissociation. J. Chem. Phys. 90, 6146−6150 (1989). 89. Loppnow, G. R. and Mathies, R. A. A 77-K Cold Stage for Raman Microprobes and Optical Microscopy. Rev. Sci. Instrum. 60, 2628−2630 (1989). 90. Peck, K., Stryer, L., Glazer, A. N. and Mathies, R. A. SingleMolecule Fluorescence Detection: Autocorrelation Criterion and Experimental Realization with Phycoerythrin. Proc. Natl. Acad. Sci. U.S.A. 86, 4087−4091 (1989). 91. Lin, S. W. and Mathies, R. A. Orientation of the Protonated Retinal Schiff Base Group in Bacteriorhodopsin from Absorption Linear Dichroism. Biophys. J. 56, 653−660 (1989). 92. Lee, S.-Y., Pollard, W. T. and Mathies, R. A. QuasiClassical Models of Transition State Absorption or Emission. Chem. Phys. Lett. 163, 11−18 (1989). 93. Lee, S.-Y., Pollard, W. T. and Mathies, R. A. Quantum Theory for Transition State Absorption. Chem. Phys. Lett. 160, 531−537 (1989). 94. Fodor, S. P. A., Gebhard, R., Lugtenburg, J., Bogomolni, R. A. and Mathies, R. A. Structure of the Retinal Chromophore in Sensory Rhodopsin I from Resonance Raman Spectroscopy. J. Biol. Chem. 264, 18280−18283 (1989). 95. Mathies, R. A., Peck, K. and Stryer, L. High-Sensitivity Single-Molecule Fluorescence Detection in Theory and Practice. Proceedings of the Sixth Annual BIOTECH U.S.A. Conference, San Francisco, CA, Oct. 2−4, pp 205−213 (1989). 96. Pollard, W. T., Lee, S.-Y. and Mathies, R. A. Wave Packet Theory of Dynamic Absorption Spectra in Femtosecond

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400. Jensen, E. C., Bhat, B. P. and Mathies, R. A. A Digital Microfluidic Platform for the Automation of Quantitative Biomolecular Assays. Lab Chip, 10, 685−691 (2010). 401. Benhabib, M., Chiesl, T. N., Stockton, A. M., Scherer, J. R. and Mathies, R. A. Multichannel Capillary Electrophoresis Microdevice and Instrumentation for In Situ Planetary Analysis of Organic Molecules and Biomarkers. Anal. Chem., 82, 2372−2379 (2010). 402. Zeng, Y., Novak, R., Shuga, J., Smith, M. T. and Mathies, R. A. High-Performance Single Cell Genetic Analysis Using Microfluidic Emulsion Generator Arrays. Anal. Chem., 82, 3183−3190 (2010). 403. Yeo, B. S., Klaus, S. L., Ross, P. N., Mathies, R. A. and Bell, A. T. Identification of Hydroperoxy Species as Reaction Intermediates in the Electrochemical Evolution of Oxygen. ChemPhysChem, 11, 1854−1857 (2010). 404. Stockton, A. M., Tjin, C. C., Huang, G. L., Benhabib, M., Chiesl, T. N. and Mathies, R. A. Analysis of Carbonaceous Biomarkers with the Mars Organic Analyzer Microchip Capillary Electrophoresis System: Aldehydes and Ketones. Electrophoresis, 31, 3642−3649 (2010). 405. Jensen, E. C., Zeng, Y., Kim, J. and Mathies, R. A. Microvalve Enabled Digital Microfluidic Systems for High-Performance Biochemical and Genetic Analysis. JALA, 15, 455−463 (2010). 406. Shuga, J., Zeng, Y., Novak, R., Mathies, R. A., Hainaut, P. and Smith, M. T., Selected Technologies for Measuring Acquired Genetic Damage in Humans, Environmental and Molecular Mutagenesis, 51, 851−870 (2010). 407. Novak, R., Zeng, Y., Shuga, J., Venugopalan, G., Fletcher, D., Zhang, L., Smith, M. T. and Mathies, R. A., Microdroplet Emulsion Generator Arrays for HighThroughput Single Cell Genetic Variation Analysis, In MicroTAS 2010 Proceedings (S. Verpoorte, H. AnderssonSvahn, J. Emnéus, and N. Pamme, Eds.), pp 1649−1651, 2010. 408. Thaitrong, N., Liu, P., Briese, T., Lipkin, W. I., Chiesl, T. N., Higa, Y. and Mathies, R. A. Integrated Capillary Electrophoresis Microsystem for Multiplex Analysis of Human Respiratory Viruses. Anal. Chem., 82, 10102− 10109 (2010). 409. Scherer, J. R., Liu, P. and Mathies, R. A. Design and Operation of a Portable Scanner for High Performance Microchip Capillary Array Electrophoresis. Rev. Sci. Instrum., 81, 113105−1−7 (2010). 410. Liu, P., Scherer, J. R., Greenspoon, S. A., Chiesl, T. N. and Mathies, R. A. Integrated Sample Cleanup and Capillary Electrophoresis Microchip for Forensic Short Tandem Repeat Analysis. Forensic Sci. Int.: Genet., 5, 484−492 (2011). 411. Frontiera, R. R. and Mathies, R. A. Femtosecond Stimulated Raman Spectroscopy. Laser Photonics Rev., 5, 102−113 (2011). 412. Novak, R., Zeng, Y., Shuga, J., Venugopalan, G., Fletcher, D. A., Smith, M. T. and Mathies, R. A. Single Cell Multiplex Gene Detection and Sequencing Using Microfluidically-Generated Agarose Emulsions. Angew. Chem., Int. Ed., 50, 390−395 (2011). 413. Liu, P., Li, X., Greenspoon, S. A., Scherer, J. R. and Mathies, R. A., Integrated DNA Purification, PCR, Sample Cleanup, and Capillary Electrophoresis Microchip for Forensic Human Identification, Lab Chip, 11, 1041−1048 (2011).

Organic Analyzer Microchip Capillary Electrophoresis System. Anal. Chem., 81, 2537−2544 (2009). Shim, S., Dasgupta, J. and Mathies, R. A., Femtosecond Time-Resolved Stimulated Raman Reveals the Birth of Bacteriorhodopsin’s J and K Intermediates. J. Am. Chem. Soc., 131, 7592−7597 (2009). Douglas, E. S., Hsiao, S. C., Onoe, H., Bertozzi, C. R., Francis, M. B. and Mathies, R. A. DNA-Barcode Directed Capture and Electrochemical Metabolic Analysis of Single Mammalian Cells on a Microelectrode Array. Lab Chip, 9, 2010−2015 (2009). Beyor, N., Yi, L., Seo, T. S. and Mathies, R. A. Integrated Capture, Concentration, PCR and Electrophoretic Analysis of Pathogens on a Chip. Anal. Chem., 81, 3523−3528 (2009). Fang, C., Frontiera, R. R., Tran, R. and Mathies, R. A. Mapping GFP Structure Evolution During Proton Transfer with Femtosecond Raman Spectroscopy. Nature, 462, 200−205 (2009). Stockton, A. M., Chiesl, T. N., Lowenstein, T. K., Amashukeli, X., Grunthaner, F. G. and Mathies, R. A. Analysis of Organic Biomolecules in Challenging Samples by Microchip Capillary Electrophoresis Using the Mars Organic Analyzer. Astrobiology, 9, 823−830 (2009). Hsiao, S. C., Shum, B. J., Onoe, H., Douglas, E. S., Gartner, Z. J., Mathies, R. A., Bertozzi, C. R. and Francis, M. B. Direct Cell Surface Modification with DNA for the Capture of Primary Cells and the Investigation of Myotube Formation on Defined Patterns. Langmuir, 25, 6985−6991 (2009). Tran, R., Boon, E. M., Marletta, M. A. and Mathies, R. A. Resonance Raman Spectra of an O2-Binding H-NOX Domain Reveal Heme Relaxation upon Mutation. Biochemistry, 48, 8568−8577 (2009). Liu, P. and Mathies, R. A. Integrated Microfluidic Systems for High-performance Genetic Analysis. Trends Biotechnol., 27, 572−581 (2009). Polli, D., Altoe, P., Weingart, O., Spillane, K. M., Manzoni, C., Brida, D., Tomasello, G., Orlandi, G., Kukura, P., Mathies, R. A., Garavelli, M. and Cerullo, G. Conical Intersection Dynamics of the Primary Photoisomerization Event in Vision. Nature, 467, 440−443 (2010). Zhang, W., Lin, S., Wang, C., Hu, J., Li, C., Zhuang, Z., Zhou, Y., Mathies, R. A. and Yang, C. Y. PMMA/PDMS Valves and Pumps for Disposable Microfluidics. Lab Chip, 9, 3088−3094 (2009). Wu, A., Wang, L., Jensen, E., Mathies, R. A. and Boser, B. Modular Integration of Electronics and Microfluidic Systems Using Flexible Printed Circuit Boards. Lab Chip, 10, 519−521 (2010). Frontiera, R. R., Dasgupta, J. and Mathies, R. A. Probing Interfacial Electron Transfer in Coumarin 343 Sensitized TiO 2 Nanoparticles with Femtosecond Stimulated Raman. J. Am. Chem. Soc., 131, 15630−15632 (2009). Bovee-Geurts, P. H. M., Fernandez, I. F., Liu, R. S. H., Mathies, R. A., Lugtenburg, J. and DeGrip, W. J. FluoroDerivatives of Retinal Illuminate the Decisive Role of the C12−H Element in Photoisomerization and Rhodopsin Activation. J. Am. Chem. Soc., 131, 17933−17942 (2009). Spillane, K. M., Dasgupta, J., Lagarias, J. C. and Mathies, R. A. Homogeneity of Phytochrome Cph1 Vibronic Absorption Revealed by Resonance Raman Intensity Analysis. J. Am. Chem. Soc., 131, 13946−13948 (2009). 10428




427. Onoe, H., Hsiao, S. C., Douglas, E. S., Gartner, Z. J., Bertozzi, C. R., Francis, M. B. and Mathies, R. A. Cellular Microfabrication: Observing Intercellular Interactions Using Lithographically Defined DNA Capture Sequences. Langmuir, 28, 8120−8126 (2012). 428. Fujisawa, T., Creelman, M. and Mathies, R. A. Structural Dynamics of a Noncovalent Charge Transfer Complex from Femtosecond Stimulated Raman Spectroscopy. J. Phys. Chem., 2012 Apr 11. [Epub ahead of print]. 429. Dasgupta, J., Frontiera, R. R., Fang, C. and Mathies, R. A. Decoding Chemical Reactivity by Femtosecond-Stimulated Raman Spectroscopy, In Encyclopedia of Biophysics (G. C. K. Roberts, Ed.), Springer-Verlag, Berlin Heidelberg, in press (2012). 430. Kaiser, R. I., Stockton, A. M., Kim, Y. S., Jensen, E. and Mathies, R. A. Synthesis of Dipeptides in Interstellar Model Ices by Ionizing Radiation, submitted. 431. Duberow, D. P., Brait, M., Dasgupta, S., Hoque, M. O., Theodorescu, D., Sidransky, D. and Mathies, R. A. HighPerformance Detection of Somatic Bladder Cancer Mutations in the Mitochondrial Genome by Polymorphism Ratio Sequencing, submitted. 432. Jensen, E. C., Stockton, A. M., Chiesl, T. N., Kim, J., Bera, A. and Mathies, R. A. Digital Microfluidic Automaton for Multiscale Combinatorial Mixing and Sample Processing, submitted.

414. Stockton, A. M., Tjin, C. C., Chiesl, T. N. and Mathies, R. A. Analysis of Carbonaceous Biomarkers with the Mars Organic Analyzer Microchip Capillary Electrophoresis System: Carboxylic Acids. Astrobiology, 11, 519−528 (2011). 415. Kim, J., Jensen, E. C., Megens, M., Boser, B. and Mathies, R. A. Integrated Microfluidic Bioprocessor for Solid Phase Capture Immunoassays. Lab Chip, 11, 3106−3112 (2011). 416. Tran, R., Weinert, E. E., Boon, E. M., Mathies, R. A. and Marletta, M. A. Determinants of the Heme-CO Vibrational Modes in the H-NOX Family. Biochemistry, 50, 6519−6530 (2011). 417. Weinert, E. E., Phillips-Piro, C. M., Tran, R., Mathies, R. A. and Marletta, M. A. Controlling Conformational Flexibility of an O2−Binding H-NOX Domain. Biochemistry, 50, 6832−6840 (2011). 418. Bromberg, A., Jensen, E. C., Kim, J., Jung, Y. K. and Mathies, R. A. Microfabricated Linear Hydrogel Microarray for Single-Nucleotide Polymorphism Detection. Anal. Chem., 84, 963−970 (2011). 419. Hoffman, D. P. and Mathies, R. A. Photoexcited Structural Dynamics of a Stilbene Analog, 4-Nitro-4′-Dimethylamino-Azobenzene, from Femtosecond Stimulated Raman. Phys. Chem. Chem. Phys., 14, 6298−6306 (2012). 420. Dasgupta, S., Shao, C., Keane, T. E., Duberow, D. P., Mathies, R. A., Fisher, P. B., Kiemeney, L. A. and Sidransky, D. Detection of Mitochondrial DNA Alterations in Urine from Urothelial Cell Carcinoma Patients. Int. J. Cancer, 131, 158−164 (2012). 421. Spillane, K. M., Dasgupta, J. and Mathies, R. A. Conformational Homogeneity and Excited-State Isomerization Dynamics of the Bilin Chromophore in Phytochrome Cph1 from Resonance Raman Intensities. Biophys. J., 102, 709−717 (2012). 422. Carlson, H. K., Iavarone, A. T., Gorur, A., Yeo, B. S., Tran, R., Melnyk, R. A., Mathies, R. A., Auer, M. and Coates, J. D. Surface Multiheme c-Type Cytochromes from Thermincola potens: Implications for Dissimilatory Metal Reduction by Gram-Positive Bacteria. Proc. Natl. Acad. Sci. U.S.A., 109, 1702−1707 (2012). 423. Frontiera, R. R., Fang, C., Dasgupta, J. and Mathies, R. A. Probing Structural Evolution Along Multidimensional Reaction Coordinates with Femtosecond Stimulated Raman Spectroscopy. Phys. Chem. Chem. Phys. 14, 405− 414 (2012). 424. Liedert, R., Amundsen, L. K., Hokkanen, A., Mäki, M., Aittakorpi, A., Pakanen, M., Scherer, J. R., Mathies, R. A., Kurkinen, M., Uusitalo, S., Hakalahti, L., Nevanen, T. K., Siitari, H. and Söderlund, H. Disposable Roll-to-Roll Hot Embossed Electrophoresis Chip for Detection of Antibiotic Resistance Gene mecA in Bacteria. Lab Chip, 12, 333−339 (2012). 425. Twite, A. A., Hsiao, S. C., Onoe, H., Mathies, R. A. and Francis, M. B. Direct Attachment of Microbial Organisms to Material Surfaces Through Sequence Specific DNA Hybridization Control. Adv. Mater., 24, 2380−2385 (2012). 426. Kim, J., Kang, M., Jensen, E. C. and Mathies, R. A. Lifting Gate Polydimethylsiloxane Microvalves and Pumps for Microfluidic Control. Anal. Chem., 84, 2067−2071 (2012). 10429


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