Baiz Group Publications

 

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*undergraduate authors are underlined

  1. Joseph C. Shirley and Carlos R. Baiz, “Local Crowds, Local Probes: Strengths and Drawbacks of Azides as a Site-Specific Crowding Probes“, Submitted (2024).
  2. Carlos Baiz, Jens Bredenbeck, Minhaeng Cho, Thomas Jansen, Amber Krummel,
    Sean Roberts, “Celebrating 25 years of 2D IR spectroscopy“, Journal of Chemical Physics (2024), [PDF]
  3. Eman A. Alasadi1, Wonseok Choi, Xiaobing Chen, Joseph A. Cotruvo, Jr., and Carlos R. Baiz “Lanmodulin’s EF 2-3 Domain: Insights from Infrared Spectroscopy and Simulations“, ACS Chemical Biology, In Press (2024)
  4. Joseph A. Shirley, Carlos R. Baiz “Experimental Two Dimensional Infrared Spectra of Methyl Thiocyanate in Water and Organic Solvents“, Journal of Chemical Physics, In Press (2024)
  5. Eman A. Alasadi , Carlos R. Baiz “Bloom’s Vision Reimagined: AI’s Role in Closing the Two Sigma Educational Gap”, Submitted (2023)
  6. Carlos R. Baiz, Robert F. Berger, Kelling J. Donald, Julio C. de Paula, Stephen D. Fried, Brenda Rubenstein, Grace Y. Stokes, Kana Takematsu, Casey Londergan, “Lowering Activation Barriers to Success in Physical Chemistry (LABSIP): A Community Project“, Journal of Physical Chemistry A (2024) [PDF]
  7. Ziareena A. Al-Mualem,† , Keegan A. Lorenz-Ochoa,†, Lei Pan, Hang Ren, Carlos R. Baiz, “DMSO Cosolvent Mixtures Modulate Hydrogen Bonding at a Gold Electrode Interface“, Submitted (2023)
    †equal contribution
  8. Ziareena A. Al-Mualem, Xiaobing Chen, Azam Shafieenezhad, Eric N. Senning, Carlos R. Baiz,”Binding-Induced Lipid Domains: Peptide-Membrane Interactions with PIP2 and PS“, Biophysical Journal (2023) [PDF]
  9. Cong Xu, and Carlos. R. Baiz, “Cutting Through the Noise: Extracting Dynamics from Ultrafast Spectra using Dynamic Mode Decomposition“, Journal of Physical Chemistry A (2023)[PDF] [ChemRXiv]
  10. Paul Garrett and Carlos R. Baiz, “Hidden Beneath the Layers: Extending the Core/Shell Model of Reverse Micelles“, Journal of Physical Chemistry B (2023) [PDF]
  11. Xiaobing Chen, Ziareena A. Al-Mualem, Carlos R. Baiz, “Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity“, Annual Reviews of Physical Chemistry (2023). [ChemRXiv]
  12. Keegan A. Lorenz-Ochoa and Carlos R. Baiz, “Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates”, Journal of the American Chemical Society (2023) [PDF] [ChemRXiv]
  13. Raiza N. A. Maia, Sunayana Mitra, and Carlos R. Baiz, “Extracting accurate infrared lineshapes from weak vibrational probes at low concentrations”, MethodsX (2023) [PDF]
  14. Xiaobing Chen, Steven Roeters, Francis Cavanna, José Alvarado, and Carlos R. Baiz, “Crowding alters F-actin secondary structure and hydration”, Communications Biology (2023) [PDF][ChemRXiv]
  15. Eman A Alasadi, and Carlos R. Baiz, “Generative AI in Education and Research: Opportunities, Concerns, and Solutions“, Journal of Chemical Education (2023) [PDF]
  16. Carlos R Baiz, “Editorial: Authorship Best Practices in Biophysics, Biophysical Journal, (2023), [PDF]
  17. Paul Garrett, Joseph Shirley, and Carlos R. Baiz, “Forced Interactions: Ionic Polymers at Charged Surfactant Interfaces”, Journal of Physical Chemistry A (2023) [PDF]
  18. Alessandro Fracassi, Kira A. Podolsky, Sudip Pandey, Cong Xu, Josh Hutchings, Soenke Seifert, Carlos R. Baiz, Sunil K. Sinha, and Neal K. Devaraj, “Characterization of lipid monoolein derivative mesophases”, Journal of Physical Chemistry B (2023) [PDF]
  19. Cong Xu, Alessandro Fracassi, Christopher P. Baryiames, Ahanjit Bhattacharya, Neal K. Devaraj and Carlos R. Baiz, “Mechanism of sponge-phase droplet formation: an ultrafast study of interfacial environments in synthetic organelles”, ChemPhysChem (2023) [PDF]
  20. Ziareena A. Al-Mualem, Xiaobing Chen, Joseph C. Shirley, Cong Xu, Carlos R. Baiz “BoxCARS 2D IR Spectroscopy with Pulse Shaping“, Optics Express (2023) [PDF]
  21. Xiao You, and Carlos R. Baiz “Importance of Hydrogen-bonding in Crowded Environments: A Physical Chemistry Perspective“, Journal of Physical Chemistry A (2022) [PDF]
  22. Euihyun Lee, and Carlos R. Baiz, “How cryoprotectants work: hydrogen-bonding in low-temperature vitrified solutions“, Chemical Science (2022) [PDF]
  23. Moshe Giladi, Sunayana Mitra, Luba Simhaev, Reuben Hiller, Bosmat Refaeli, Tali Strauss, Carlos R. Baiz,and Daniel Khananshvili “Exploring the Li+ transporting mutant of NCX_Mj for assigning ion binding sites of mitochondrial NCLX“, Cell Calcium (2022) [PDF]
  24. Xiao You, Naveen Thakur, Arka Prabha Ray, Matthew T. Eddy, Carlos R. Baiz “A Comparative Study of Interfacial Environments in Lipid Nanodiscs and Vesicles“, Biophysical Reports (2022) [PDF]
  25. Ziareena A. Al-Mualem, and Carlos R. Baiz, “Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra“, Journal of Physical Chemistry A (2022) [PDF]
  26. Judith Flores, Roberto J. Brea, Alejandro Lamas, Marta Salvador-Castell, Cong Xu, Carlos R. Baiz, Sunil K. Sinha, and Neal K. Devaraj, “Rapid and Sequential Dual Oxime Ligation Enables De Novo Formation of Functional Synthetic Membranes from Water-soluble Precursors“, Angewandte Chemie (2022) [PDF]
  27. Ruoqi Zhao, Joseph C. Shirley, Euihyun Lee, Adam Grofe, Hui Li, Carlos R. Baiz, and Jiali Gao, “Origin of Thiocyanate Spectral Shifts of in Water and Organic Solvents“, Journal of Chemical Physics (2022) [PDF]
  28. Euihyun Lee, Xiao You, and Carlos R. Baiz, “Interfacial Dynamics in Inverted-Headgroup Lipid Membranes“, Journal of Chemical Physics (2022) [PDF]
  29. Paul Garrett, and Carlos R. Baiz, “Dynamic effect of polymers at the surfactant–water interface: an ultrafast study“, Soft Matter (2022) [PDF]
  30. Xiao You, Euihyun Lee, Cong Xu, Carlos R. Baiz, “Molecular Mechanism of Cell Membrane Protection by Sugars: A Study of Interfacial H-bond Networks“, Journal of Physical Chemistry Letters (2021) [PDF]
  31. Mason L. Valentine, Ziareena A. Al-Mualem, Carlos R. Baiz, “Pump Slice Amplitudes: A Simple and Robust Method for Connecting 2D IR and FTIR Spectra” Journal of Physical Chemistry A (2021) [PDF]
  32. Stephanie Liu, Emily R. Featherston, Joseph A. Cotruvo, Jr., and Carlos R. Baiz, “Lanthanide-dependent coordination interactions in lanmodulin: a 2D IR and molecular dynamics simulations study“, Physical Chemistry Chemical Physics,  (2021) [PDF]
  33. Bosmat Refaeli, Stephanie Liu, Reuben Hiller, Carlos R. Baiz and Daniel Khananshvili, “Proton-modulated interactions of ions with transport sites of prokaryotic and eukaryotic NCX prototypes  ”, Cell Calcium  (2021) [PDF]
  34. Christopher P Baryiames, Paul Garrett, and Carlos R. Baiz, “Bursting the bubble: a molecular understanding of surfactant-water interfaces“, Journal of Chemical Physics (2021) [PDF]
  35. Sean C. Edington, Stephanie Liu, and Carlos R. Baiz, “Infrared spectroscopy probes ion binding geometries”, Methods in Enzymology, Volume 651 Pages 157-191, (2021)
  36. Xiao You, Joseph C. Shirley, Euihyun Lee, Carlos R. Baiz, “Short- and long-range crowding effects on water’s hydrogen bond networks“, Cell Reports Physical Science (2021) [PDF]
  37. Christopher P. Baryiames, Emily Ma, and Carlos R. Baiz, “Ions slow water dynamics at non-ionic surfactant interfaces“, Journal of Physical Chemistry A (2020) [PDF]
  38. Mason L. Valentine, Maya K Waterland, Arman Fatizadeh, Ron Elber, and Carlos R. Baiz, “Interfacial Dynamics in Lipid Membranes: the Effects of Headgroup Structure“, Journal of Physical Chemistry A (2020) [PDF]
  39. Jennifer C. Flanagan, Mason L. Valentine, Carlos R. Baiz, “Ultrafast dynamics at lipid-water interfaces“, Accounts of Chemical Research  (2020) [PDF]
  40. Arman Fathizadeh, Mason Valentine, Carlos R. Baiz, Ron Elber, “Phase Transition in a Heterogeneous Membrane: Atomically Detailed Picture“, Journal of Physical Chemistry Letters  (2020)[PDF]
  41. Carlos R. Baiz, Bartosz Blasiak, Jens Bredenbeck, Minhaeng Cho* (corresponding author), Jun-Ho Choi, Steven A. Corcelli, Arend G. Dijkstra, Chi-Jui Feng, Sean Garrett-Roe, Nien-Hui Ge, Magnus W. Hanson-Heine, Jonathan D. Hirst, Thomas la Cour Jansen, Kijeong Kwac, Kevin J. Kubarych, Casey H. Londergan, Hiroaki Maekawa, Mike Reppert, Shinji Saito, Santunu Roy, James L. Skinner, Gerhard Stock, John E. Straub, Megan C. Thielges, Keisuke Tominaga, Andrei Tokmakoff, Hajime Torii, Lu Wang, Lauren J. Webb, and Martin T. Zanni,  Vibrational Frequency Map, Vibrational Spectroscopy, and Intermolecular Interaction, Chemical Reviews (2020) [PDF]
  42. Ravi K. Venkatraman, and Carlos R. Baiz, “Ultrafast dynamics at the lipid-water interface: DMSO modulates H-bond lifetimes“, Langmuir (2020) [PDF]
  43. Kwang-Im Oh, and Carlos R. Baiz, “Perspective: Molecular Heterogeneity in Aqueous Cosolvent Systems”, Journal of Chemical Physics (2020)[PDF]
  44. Jennifer C. Flanagan, Alfredo E. Cardenas, Carlos R. Baiz, “Ultrafast spectroscopy of lipid-water interfaces: transmembrane crowding drives H-bond dynamics”, Journal of Physical Chemistry Letters (2020) [PDF]
  45. Ji Yeon Kim, Philip Liu, Michael J. Maher, Devon Callan, Christopher M. Bates, Matthew C. Carlson, Yusuke Asano, Gregory Blachut, Charles T. Rettner, Joy Y. Cheng, Daniel F. Sunday, R. Joseph Kline, Daniel P. Sanders, Nathaniel A. Lynd, Christopher J. Ellison, C. Grant Willson, and Carlos R. Baiz, “Spatial Control of Self-Assembled Block Copolymer Domain Orientation and Alignment on Photo-Patterned Surfaces“, ACS Applied Materials and Interfaces (2020)[PDF]
  46. Christopher P. Baryiames, and Carlos R. Baiz, “Slow oil, slow water: long-range dynamic coupling across a liquid-liquid interface“, Journal of the American Chemical Society (2020)[PDF]
  47. Kwang-Im Oh, Xiao You, Jennifer C. Flanagan, and Carlos R. Baiz, “Liquid–Liquid Phase Separation Produces Fast H-Bond Dynamics in DMSO–Water Mixtures“, Journal of Physical Chemistry Letters,  11, 5, 1903-1908, (2020) [PDF]
  48. Mason L. Valentine, Alfredo Cardenas, Ron Elber, and Carlos R. Baiz, “Calcium-Lipid Interactions Observed with Isotope-Edited Infrared Spectroscopy“, Biophysical Journal, In Press (2020).
  49. Carlos R. Baiz, “Interactive Tools for Teaching Fourier Transforms“, The Biophysicist, 1,1, (2020). [Inaugural Issue] [PDF] [MATLAB Software]
  50. Kwang-Im Oh, and Carlos R. Baiz, “Empirical S=O stretch vibrational frequency map“, Journal of Chemical Physics, 151,234107, (2019) [PDF]
  51. Jennifer C. Flanagan, and Carlos R. Baiz, “Ultrafast pH-jump 2D IR spectroscopy“, Optics Letters, 44.20, 4937-4940, (2019).[PDF]
  52. Christopher P. Baryiames, Morgan Teel, and Carlos R. Baiz, “Interfacial H-bond dynamics in reverse micelles: the role of surfactant heterogeneity“, Langmuir, 35, 11463-11470 (2019) [PDF].
  53. Sean C. Edington, D. Brent Halling, Suzanna Bennett, Thomas R. Middendorf, Richard W. Aldrich and Carlos R. Baiz, “Non-additive Effects of Binding Site Mutations in Calmodulin“, Biochemistry, 58, 24, 2730-2739, (2019) [PDF]
  54. Jennifer C. Flanagan, and Carlos R. Baiz, “Site-specific peptide probes detect buried water in a lipid membrane“, Biophysical Journal, 116, 9, 1692-1700 (2019).[PDF]
  55. Sean C. Edington, and Carlos R. Baiz, “Vibrational Relaxation in EDTA is Ion Dependent“, Journal of Physical Chemistry A, 122, 32, 6585–6592 (2018). [PDF]
  56. Mason L. Valentine, Alfredo E. Cardenas, Ron Elber, and Carlos R. Baiz “Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface“, Biophysical Journal, 115, 8, 1541-1551 (2018)[PDF]
  57. Kwang-Im Oh, and Carlos R. Baiz “Crowding Stabilizes DMSO – Water Hydrogen-bonding Interactions“, Journal of Physical Chemistry B, 122 (22), pp 5984–5990 (2018) [PDF]
  58. Sean C. Edington, Andrea Gonzalez, Thomas R. Middendorf, D. Brent Halling, Richard W. Aldrich, and Carlos R. Baiz, “Coordination to lanthanide ions distorts binding site conformation in calmodulin“, Proceedings of the National Academies of Science, 115 (14) E3126-E3134, (2018) [DOI: 10.1073/pnas.1722042115]
  59. Kwang-Im Oh, Kavya Rajesh, John F. Stanton, and Carlos R. Baiz, “Quantifying Hydrogen-Bond Populations in Dimethyl Sulfoxide/Water Mixtures“, Angewandte Chemie International Edition, 56, 11375 (2017) [DOI: 10.1002/ange.201704162]
  60. Sean Coleman Edington, Jennifer C. Flanagan, and Carlos R. Baiz, “An Empirical IR Frequency Map for Ester C=O Stretching Vibrations“, Journal of Physical Chemistry A, 120, 3888 (2016) [PDF]
  61. Xin-Xing Zhang, Kevin C. Jones, Ann Fitzpatrick, Chunte Sam Peng, Chi-Jui Feng, Carlos R. Baiz, and Andrei Tokmakoff, “Studying Protein-Protein Binding Through T-Jump Induced Dissociation: Transient 2D IR Spectroscopy of Insulin Dimer“, J. Phys. Chem. B, ASAP (2016) [PDF]Insulin_Paper_Abstract
  62. Paul Stevenson, Christoph Götz, Carlos R. Baiz, Jasper Akerboomf, Andrei Tokmakoff and Alipasha Vaziri, “Visualizing KcsA conformational changes upon ion binding by atomistic modeling of infrared spectroscopy” J. Phys. Chem. B, 118, 5824 (2015) [PDF]Stevenson_JPCA_2015
  63. Carlos R. Baiz, and Andrei Tokmakoff “Structural Disorder of Folded Proteins: Isotope-Edited 2D IR Spectroscopy and Markov State Modeling” Biophys J. 108, 7, 1747 (2015) [PDF]Baiz_Biophys_J_2015
  64. Carlos R. Baiz, Denise Schach, and Andrei Tokmakoff, “Ultrafast 2D IR microscopy” Optics Express, 22, 18724 (2014) [PDF]Baiz_OptExp_2014
  65. Carlos R. Baiz, Yu-Shan Lin, Chunte Sam Peng, Kyle A. Beauchamp, Vincent A. Voelz, Vijay S. Pande, and Andrei Tokmakoff “A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models“, Biophysical Journal, 106, 1359 (2014) [PDF]Baiz_Biophys_J_2014
  66. Chunte Sam Peng, Carlos R. Baiz, Andrei Tokmakoff, “Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy”, Proc. Nat. Acad. Sci. 110, 9243-9248 (2013) [PDF]Peng_PNAS_2013
  67. Bowu Luan, Bing Shan, Carlos R. Baiz, Andrei Tokmakoff, and Daniel P. Raleigh, “Cooperative Cold Denaturation: The Case of the C-Terminal Domain of Ribosomal Protein L9”, Biochem. 52, 2402-2409 (2013) [PDF]Luan_Biochem_2013
  68. Carlos R. Baiz, Mike Reppert, and Andrei Tokmakoff, “Amide I Two-Dimensional Infrared Spectroscopy: Methods for Visualizing the Vibrational Structure of Large Proteins”, J. Phys. Chem. A.  117, 5955-5961 (2013) [PDF]Baiz_JPCA_2013
  69. Jessica M. Anna, Carlos R. Baiz, Matthew R. Ross, Robert McCanne, and Kevin J. Kubarych,  Ultrafast equilibrium and non-equilibrium chemical reaction dynamics probed with multidimensional infrared spectroscopy, Int. Rev. Phys. Chem. 3, 367 (2012) [PDF]Anna_IntRevPhysChem_2012
  70. Carlos R. Baiz, Chunte S. Peng, Michael E. Reppert, Kevin C. Jones, and Andrei Tokmakoff, “Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution”, Analyst, 137, 1793-1799 (2012) [PDF]Baiz_Analyst_2012
  71. Carlos R. Baiz, Kevin J. Kubarych, Eitan Geva and Edwin L. Sibert III, “Local-mode approach to modeling multidimensional infrared spectra of metal carbonyls”,  J. Phys. Chem. A. 115 (21), 5354 ,(2011) [PDF]Baiz_JPCA_2011
  72. Carlos R. Baiz, Kevin J. Kubarych, and Eitan Geva, “Molecular Theory and Simulation of Coherence Transfer in Metal Carbonyls and Its Signature on Multidimensional Infrared Spectra” J. Phys. Chem. B, 115, (18) , 5322, (2011) [PDF]Baiz_JPCA_2010
  73. Carlos R. Baiz, and Kevin J. Kubarych and Eitan Geva, “Ultrabroadband Detection of an Infrared Continuum by Chirped-Pulse Upconversion” Optics Letters, 36 (2) 187, (2011) [PDF]Baiz_OptLett_2011
  74. John T. King, Carlos R. Baiz and Kevin J. Kubarych. “Solvent-Dependent Spectral Diffusion in a Hydrogen Bonded “Vibrational Aggregate”” J. Phys. Chem. A. 114 (39) 10590 (2010) [PDF]King_JPCA_2010
  75. Carlos R. Baiz and Kevin J. Kubarych, “Ultrafast Transient Vibrational Stark Spectroscopy: Exploring Excited-State Charge-Transfer by Measuring the Solvent Response”,  J. Amer. Chem. Soc (Comm), 132 (37), 12784-12785 (2010) [PDF]Baiz_JACS_2010
  76. Carlos R. Baiz, Robert McCanne, and Kevin J. Kubarych, “Transient vibrational echo versus transient absorption spectroscopy: A direct experimental and theoretical comparison”, Applied Spectroscopy, 64 (9) 1037-1044 (2010) [PDF]Baiz_ApplSpec_2010
  77. Jessica. M. Anna, Matthew. J. Nee, Carlos. R. Baiz, Robert. McCanne, Kevin. J. Kubarych, “Measuring Absorptive Two-Dimensional Infrared Spectra Using Chirped-Pulse Upconversion Detection”,  J. Opt. Soc. Am. B, 27, 382-393 (2010) [PDF]Anna_JOSAB_2010
  78. Carlos R. Baiz, Robert McCanne, and Kevin J. Kubarych, “Structurally Selective Geminate Rebinding Dynamics of Solvent-Caged Radicals Studied with Nonequilibrium Infrared Echo Spectroscopy”, J. Amer. Chem. Soc, 131 (38), 13590, (2009) [PDF]Baiz_JACS_2009
  79. Carlos R. Baiz, Porscha L. McRobbie, Nicholas K. Preketes, Kevin J. Kubarych, and Eitan Geva, “Two-Dimensional Infrared Spectroscopy of Dimanganese Decacarbonyl and Its Photoproducts: An Ab Initio Study”, J. Phys. Chem. A, 113, (35), 9617, (2009) [PDF]Baiz_JPCA_2009_3
  80. Carlos R. Baiz, Robert McCanne, Matthew J. Nee, and Kevin J. Kubarych, “Orientational dynamics of transient molecules measured by non-equilibrium two-dimensional infrared spectroscopy”,  J. Phys. Chem A, 113 (31), 8907, (2009) [PDF]Baiz_JPCA_2009_2
  81. Carlos R. Baiz, Porscha L. McRobbie, Jessica M. Anna, Eitan Geva, and Kevin J. Kubarych, “Two-dimensional Spectroscopy of Metal Carbonyls”,  Accounts of Chemical Research, 42, (9), 1395, (2009) [PDF]Baiz_AccChemRes_2009
  82. Carlos R. Baiz, Sarah J. Ledford, Kevin J Kubarych, and Barry D. Dunietz, “Beyond 7-Azaindole:  Conjugation Effects on Intermolecular Double Hydrogen-atom Transfer Reactions”, J. Phys. Chem A., 113 (17), 4862, (2009) [PDF]Baiz_JPCA_2009
  83. Carlos R. Baiz, Matthew J. Nee, Robert McCanne, and Kevin J. Kubarych, “Ultrafast non-equilibrium Fourier-transform two-dimensional infrared spectroscopy”, Optics Letters, 33, 2533, (2008) [PDF]
    Baiz_OptLett_2008
  84. Matthew J. Nee, Carlos R. Baiz, Jessica M. Anna, Robert McCanne, and Kevin J. Kubarych, “Multilevel vibrational coherence transfer and wavepacket dynamics probed with multidimensional IR spectroscopy”, J. Chem. Phys. 129, 084503. (2008) [PDF]Nee_JCP_2008
  85. Carlos R. Baiz and Barry D. Dunietz, “Theoretical Studies of Conjugation Effects on Excited State Intramolecular Hydrogen-Atom Transfer Reactions in Model Systems”, J. Phys. Chem. A, 111 (40), 10139, (2007) [PDF]Baiz_JPCA_2007

Book Chapter

  1. Carlos R. Baiz, Mike E. Reppert, and Andrei Tokmakoff, “An Introduction to Protein 2D IR Spectroscopy“, Ultrafast Infrared Vibrational Spectroscopy, Edited by Michael D. Fayer CRC Press, ISBN: 1466510137, (2013) [PDF]Baiz_BookChapter_2013