70. Jeffries, W. R.; Sandeno, S. F.; Cossairt, B. M.; Khalil, M. Surface Carboxylate Sensitivity to Electron and Hole Relaxation in Photoexcited Cadmium Sulfide Nanocrystals. The Journal of Physical Chemistry Letters 2025, 16 (19), 4690-4697.
69. Nimmrich, A.; Govind, N.; Khalil, M. Capturing Coupled Structural and Electronic Motions During Excited-State Intramolecular Proton Transfer via Computational Multiedge Resonant Inelastic X-ray Scattering. J. Phys. Chem. Lett. 2024, 12652-12662
68. Loe, C. M.; Chatterjee, S.; Weakly, R. B.; Khalil, M. Observing vibronic coupling in a strongly hydrogen bonded system with coherent multidimensional vibrational–electronic spectroscopy. J. Chem. Phys. 2024, 161 (17), 174203.
67. Prampolini, G.; Andersen, A.; Poulter, B. I.; Khalil, M.; Govind, N.; Biasin, E.; Pastore, M. Integrated Quantum-Classical Protocol for the Realistic Description of Solvated Multinuclear Mixed-Valence Transition-Metal Complexes and Their Solvatochromic Properties. J. Chem. Theory Comput. 2024, 20 (3), 1306-1323.
66. Klein, M. D.; Bisted, C. H.; Dou, F. Y.; Sandwisch, J. W.; Cossairt, B. M.; Khalil, M. Measuring Relative Energies of Ligand Binding Conformations on Nanocluster Surfaces with Temperature-Dependent FTIR Spectroscopy. The Journal of Physical Chemistry C 2023, 127 (34), 16970-16978.
65. Poulter, B. I.; Biasin, E.; Nowak, S. H.; Kroll, T.; Alonso-Mori, R.; Schoenlein, R. W.; Govind, N.; Sokaras, D.; Khalil, M. Uncovering the 3d and 4d Electronic Interactions in Solvated Ru Complexes with 2p3d Resonant Inelastic X-ray Scattering. Inorganic Chemistry 2023, 62 (25), 9904-9911.
64. Weakly, R. B.; Liekhus-Schmaltz, C. E.; Poulter, B. I.; Biasin, E.; Alonso-Mori, R.; Aquila, A.; Boutet, S.; Fuller, F. D.; Ho, P. J.; Kroll, T.; Loe, C. M.; Lutman, A.; Zhu, D.; Bergmann, U.; Schoenlein, R. W.; Govind, N.; Khalil, M. Revealing core-valence interactions in solution with femtosecond X-ray pump X-ray probe spectroscopy. Nat. Commun. 2023, 14 (1), 3384.
63. Liekhus-Schmaltz, C.; Fox, Z. W.; Andersen, A.; Kjaer, K. S.; Alonso-Mori, R.; Biasin, E.; Carlstad, J.; Chollet, M.; Gaynor, J. D.; Glownia, J. M.; Hong, K.; Kroll, T.; Lee, J. H.; Poulter, B. I.; Reinhard, M.; Sokaras, D.; Zhang, Y.; Doumy, G.; March, A. M.; Southworth, S. H.; Mukamel, S.; Cordones, A. A.; Schoenlein, R. W.; Govind, N.; Khalil, M., Femtosecond X-ray Spectroscopy Directly Quantifies Transient Excited-State Mixed Valency. J. Phys. Chem. Lett. 2022, 378-386.
62. Loe, C. M.; Liekhus-Schmaltz, C.; Govind, N.; Khalil, M. Spectral Signatures of Ultrafast Excited-State Intramolecular Proton Transfer from Computational Multi-edge Transient X-ray Absorption Spectroscopy. J. Phys. Chem. Lett. 2021, 9840-9847.
61. Nascimento, D. R.; Biasin, E.; Poulter, B. I.; Khalil, M.; Sokaras, D.; Govind, N. Resonant Inelastic X-ray Scattering Calculations of Transition Metal Complexes Within a Simplified Time-Dependent Density Functional Theory Framework. J. Chem. Theory Comput. 2021, 17 (5), 3031-3038.
60. Gu, B.; Cavaletto, S. M.; Nascimento, D. R.; Khalil, M.; Govind, N.; Mukamel, S. Manipulating valence and core electronic excitations of a transition-metal complex using UV/Vis and X-ray cavities. Chemical Science 2021, 12 (23), 8088-8095.
59. Liekhus-Schmaltz, C. E.; Ho, P. J.; Weakly, R. B.; Aquila, A.; Schoenlein, R. W.; Khalil, M.; Govind, N. Ultrafast x-ray pump x-ray probe transient absorption spectroscopy: A computational study and proposed experiment probing core-valence electronic correlations in solvated complexes. J. Chem. Phys. 2021, 154 (21), 214107.
58. Weakly, R. B.; Gaynor, J. D.; Khalil, M. Multimode two-dimensional vibronic spectroscopy. II. Simulating and extracting vibronic coupling parameters from polarization-selective spectra. J. Chem. Phys. 2021, 154 (18), 184202.
57. Gaynor, J. D.; Weakly, R. B.; Khalil, M. Multimode two-dimensional vibronic spectroscopy. I. Orientational response and polarization-selectivity. J. Chem. Phys. 2021, 154 (18), 184201.
56. Biasin, E.; Fox, Z.; Andersen, A.; Ledbetter, K.; Kjær, K. S.; Alonso-Mori, R.; Carlstad, J.; Chollet, D. M.; Gaynor, J.; Glownia, J.; Hong, K.; Kroll, T.; Lee, J. H.; Liekhus-Schmaltz, C.; Reinhard, M.; Sokaras, D.; Zhang, Y.; Doumy, G.; March, A. M.; Southworth, S.; Mukamel, S.; Gaffney, K.; Schoenlein, R.; Govind, N.; Cordones, A.; Khalil, M., Direct observation of coherent femtosecond solvent reorganization coupled to intramolecular electron transfer. Nature Chemistry 2021, 13, 343–349.
55. Biasin, E.; Nascimento, D. R.; Poulter, B. I.; Abraham, B.; Kunnus, K.; Garcia-Esparza, A. T.; Nowak, S. H.; Kroll, T.; Schoenlein, R. W.; Alonso-Mori, R.; Khalil, M.; Govind, N.; Sokaras, D. Revealing the bonding of solvated Ru complexes with valence-to-core resonant inelastic X-ray scattering. Chemical Science 2021, 12 (10), 3713-3725.
54. Khalil, M.; Mukamel, S. Ultrafast spectroscopy and diffraction from XUV to x-ray. J. Chem. Phys. 2020, 153 (10), 100401.
53. Fox, Z. W.; Blair, T. J.; Khalil, M. Determining the Orientation and Vibronic Couplings between Electronic and Vibrational Coordinates with Polarization-Selective Two-Dimensional Vibrational-Electronic Spectroscopy. J. Phys. Chem. Lett. 2020, 11 (4), 1558-1563.
52. Gaynor, J. D.; Sandwisch, J.; Khalil, M. Vibronic coherence evolution in multidimensional ultrafast photochemical processes. Nat. Commun. 2019, 10 (1), 5621.
51. Zhang, Y.; Bergmann, U.; Schoenlein, R.; Khalil, M.; Govind, N. Double core hole valence-to-core x-ray emission spectroscopy: A theoretical exploration using time-dependent density functional theory. J. Chem. Phys. 2019, 151 (14), 144114.
50. Leger, J. D.; Friedfeld, M. R.; Beck, R. A.; Gaynor, J. D.; Petrone, A.; Li, X.; Cossairt, B. M.; Khalil, M., Carboxylate Anchors Act as Exciton Reporters in 1.3 nm Indium Phosphide Nanoclusters. J. Phys. Chem. Lett. 2019, 10 (8), 1833-1839.
49. Shafranek, R. T.; Leger, J. D.; Zhang, S.; Khalil, M.; Gu, X.; Nelson, A., Sticky ends in a self-assembling ABA triblock copolymer: the role of ureas in stimuli-responsive hydrogels. Molecular Systems Design & Engineering 2019.
48. Balasubramanian, M.; Reynolds, A.; Blair, T. J.; Khalil, M., Probing ultrafast vibrational dynamics of intramolecular hydrogen bonds with broadband infrared pump-probe spectroscopy. Chem. Phys. 2019, 519, 38-44.
47. Fox, Z. W.; Blair, T. J.; Weakly, R. B.; Courtney, T. L.; Khalil, M., Implementation of continuous fast scanning detection in femtosecond Fourier-transform two-dimensional vibrational-electronic spectroscopy to decrease data acquisition time. Rev. Sci. Instr. 2018, 89 (11), 113104.
46. Gaynor, J. D.; Petrone, A.; Li, X.; Khalil, M., Mapping Vibronic Couplings in a Solar Cell Dye with Polarization-Selective Two-Dimensional Electronic–Vibrational Spectroscopy. J. Phys. Chem. Lett. 2018, 9 (21), 6289-6295.
45. Ross, M.; Andersen, A.; Fox, Z. W.; Zhang, Y.; Hong, K.; Lee, J. H.; Cordones, A.; March, A. M.; Doumy, G.; Southworth, S. H.; Marcus, M. A.; Schoenlein, R. W.; Mukamel, S.; Govind, N.; Khalil, M., Comprehensive Experimental and Computational Spectroscopic Study of Hexacyanoferrate Complexes in Water: From Infrared to X-ray Wavelengths. J. Phys. Chem. B 2018, 122 (19), 5075-5086.
44. Gaynor, J. D.; Khalil, M. Signatures of Vibronic Coupling in Two-Dimensional Electronic-Vibrational and Vibrational-Electronic Spectroscopies. J. Chem. Phys. 2017, 147 (9), 094202 (21 pp.).
43. Van Kuiken, B. E.; Ross, M. R.; Strader, M. L.; Cordones, A. A.; Cho, H.; Lee, J. H.; Schoenlein, R. W.; Khalil, M. Picosecond sulfur K-edge X-ray absorption spectroscopy with applications to excited state proton transfer. Structural Dynamics 2017, 4 (4), 044021 (10 pp.).
42. Eckert, S.; Norell, J.; Miedema, P. S.; Beye, M.; Fondell, M.; Quevedo, W.; Kennedy, B.; Hantschmann, M.; Pietzsch, A.; Van Kuiken, B. E.; Ross, M.; Minitti, M. P.; Moeller, S. P.; Schlotter, W. F.; Khalil, M.; Odelius, M.; Föhlisch, A. Ultrafast Independent N–H and N–C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering. Angew. Chem., Int. Ed. 2017, 56 (22), 6088–6092.
41. Balasubramanian, M.; Courtney, T. L.; Gaynor, J. D.; Khalil, M. Compression of tunable broadband mid-IR pulses with a deformable mirror pulse shaper. J. Opt. Soc. Am. B 2016, 33 (10), 2033–2037.
40. Gaynor, J. D.; Courtney, T. L.; Balasubramanian, M.; Khalil, M. Fourier transform two-dimensional electronic-vibrational spectroscopy using an octave-spanning mid-IR probe. Opt. Lett. 2016, 41 (12), 2895–2898.
39. Van Kuiken, B. E.; Cho, H.; Hong, K.; Khalil, M.; Schoenlein, R. W.; Kim, T. K.; Huse, N. Time-Resolved X-ray Spectroscopy in the Water Window: Elucidating Transient Valence Charge Distributions in an Aqueous Fe(II) Complex. J. Phys. Chem. Lett. 2016, 7 (3), 465–470.
38. Slenkamp, K. M.; Lynch, M. S.; Brookes, J. F.; Bannan, C. C.; Daifuku, S. L.; Khalil, M. Investigating vibrational relaxation in cyanide-bridged transition metal mixed-valence complexes using two-dimensional infrared and infrared pump-probe spectroscopies. Structural Dynamics 2016, 3, 023609 (16 pp.).
37. Zhang, Y.; Mukamel, S.; Khalil, M.; Govind, N. Simulating Valence-to-Core X-ray Emission Spectroscopy of Transition Metal Complexes with Time-Dependent Density Functional Theory. J. Chem. Theory Comput. 2015, 11 (12), 5804–5809.
36. Courtney, T. L.; Fox, Z. W.; Slenkamp, K. M.; Khalil, M. Two-dimensional vibrational-electronic spectroscopy. J. Chem. Phys. 2015, 143 (15), 154201 (15 pp.).
35. Eckert, S.; Beye, M.; Pietzsch, A.; Quevedo, W.; Hantschmann, M.; Ochmann, M.; Ross, M.; Minitti, M. P.; Turner, J. J.; Moeller, S. P.; Schlotter, W. F.; Dakovski, G. L.; Khalil, M.; Huse, N.; Föhlisch, A. Principles of femtosecond X-ray/optical cross-correlation with X-ray induced transient optical reflectivity in solids. Appl. Phys. Lett. 2015, 106 (6), 061104 (4 pp.).
34. Courtney, T. L.; Fox, Z. W.; Estergreen, L.; Khalil, M. Measuring Coherently Coupled Intramolecular Vibrational and Charge-Transfer Dynamics with Two-Dimensional Vibrational–Electronic Spectroscopy. J. Phys. Chem. Lett. 2015, 6 (7), 1286–1292.
33. Slenkamp, K. M.; Lynch, M. S.; Van Kuiken, B. E.; Brookes, J. F.; Bannan, C. C.; Daifuku, S. L.; Khalil, M. Investigating vibrational anharmonic couplings in cyanide-bridged transition metal mixed-valence complexes dissolved in polar solvents using two-dimensional infrared spectroscopy. J. Chem. Phys. 2014, 140 (8), 084505 (10 pp.).
32. Cheng, M.; Brookes, J. F.; Montfort, W. R.; Khalil, M. pH-Dependent Picosecond Structural Dynamics in the Distal Pocket of Nitrophorin 4 Investigated by 2D IR Spectroscopy. J. Phys. Chem. B 2013, 117 (49), 15804–15811.
31. Brookes, J. F.; Slenkamp, K. M.; Lynch, M. S.; Khalil, M. Effect of Solvent Polarity on the Vibrational Dephasing Dynamics of the Nitrosyl Stretch in an FeII Complex Revealed by 2D IR Spectroscopy. J. Phys. Chem. A 2013, 117 (29), 6234–6243.
30. Van Kuiken, B. E.; Valiev, M.; Daifuku, S. L.☼; Bannan, C. C.; Strader, M. L.; Cho, H.; Huse, N.; Schoenlein, R. W.; Govind, N.; Khalil, M. Simulating Ru L3-Edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers. J. Phys. Chem. A 2013, 117 (21), 4444–4454.
29. Lopata, K.^; Van Kuiken, B. E.; Khalil, M.; Govind, N. Linear-Response and Real-Time Time-Dependent Density Functional Theory Studies of Core-Level Near-Edge X-Ray Absorption. J. Chem. Theory Comput. 2012, 8 (9), 3284–3292.
28. Van Kuiken, B. E.; Huse, N.; Cho, H.; Strader, M. L.; Lynch, M. S.; Schoenlein, R. W.; Khalil, M. Probing the Electronic Structure of a Photoexcited Solar Cell Dye with Transient X-ray Absorption Spectroscopy. J. Phys. Chem. Lett. 2012, 3 (12), 1695–1700.
27. Lynch, M. S.; Slenkamp, K.; Khalil, M. Probing non-equilibrium vibrational relaxation pathways of highly excited C≡N stretching modes following ultrafast back-electron transfer. J. Chem. Phys. 2012, 136 (24), 241101 (4 pp.).
26. Lynch, M. S.; Slenkamp, K.; Cheng, M.; Khalil, M. Coherent Fifth-Order Visible–Infrared Spectroscopies: Ultrafast Nonequilibrium Vibrational Dynamics in Solution. J. Phys. Chem. A 2012, 116 (26), 7023–7032.
25. Cheng, M.; Reynolds, A.; Widgren, H.; Khalil, M. Generation of tunable octave-spanning mid-infrared pulses by filamentation in gas media. Opt. Lett. 2012, 37 (11), 1787–1789.
24. Van Kuiken, B. E.; Khalil, M. Simulating Picosecond Iron K-Edge X-ray Absorption Spectra by Ab Initio Methods to Study Photoinduced Changes in the Electronic Structure of Fe(II) Spin Crossover Complexes. J. Phys. Chem. A 2011, 115 (39), 10749–10761.
23. Lynch, M. S.; Van Kuiken, B. E.; Daifuku, S. L.; Khalil, M. On the Role of High-Frequency Intramolecular Vibrations in Ultrafast Back-Electron Transfer Reactions. J. Phys. Chem. Lett. 2011, 2 (17), 2252–2257.
22. Lynch, M. S.; Cheng, M.; Van Kuiken, B. E.; Khalil, M. Probing the Photoinduced Metal–Nitrosyl Linkage Isomerism of Sodium Nitroprusside in Solution Using Transient Infrared Spectroscopy. J. Am. Chem. Soc. 2011, 133 (14), 5255–5262.
21. Loh, Z.-H.; Khalil, M.; Correa, R. E.; Leone, S. R. “A tabletop femtosecond time-resolved soft x-ray transient absorption spectrometer.” Rev. Sci. Instr. 2008, 79 (7), 073101 (13 pp.).
20. Loh, Z.-H.; Khalil, M.; Correa, R. E.; Santra, R.; Buth, C.; Leone, S. R. “Quantum State-Resolved Probing of Strong-Field-Ionized Xenon Atoms Using Femtosecond High-Order Harmonic Transient Absorption Spectroscopy.” Phys. Rev. Lett. 2007, 98 (14), 143601 (4 pp.).
19. Chung, H. S.; Khalil, M.; Smith, A. W.; Tokmakoff, A. “Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics.” Rev. Sci. Instr. 2007, 78 (6), 063101 (10 pp.).
18. Khalil, M.; Marcus, M. A.; Smeigh, A. L.; McCusker, J. K.; Chong, H. H. W.; Schoenlein, R. W. “Picosecond X-ray Absorption Spectroscopy of a Photoinduced Iron(II) Spin Crossover Reaction in Solution.” J. Phys. Chem. A 2006, 110 (1), 38–44.
17. Chung, H. S.; Khalil, M.; Smith, A. W.; Ganim, Z.; Tokmakoff, A. “Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin.” Proc. Nat. Acad. Sci. 2005, 102 (3), 612–617.
16. Khalil, M.; Demirdöven, N.; Tokmakoff, A. “Vibrational coherence transfer characterized with Fourier-transform 2D IR spectroscopy.” J. Chem. Phys. 2004, 121 (1), 362–373.
15. Demirdöven, N.; Cheatum, C. M.; Chung, H. S.; Khalil, M.; Knoester, J.; Tokmakoff, A. “Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure.” J. Am. Chem. Soc. 2004, 126 (25), 7981–7990.
14. Chung, H. S.; Khalil, M.; Tokmakoff, A. “Nonlinear infrared spectroscopy of protein conformational change during thermal unfolding.” J. Phys. Chem. B 2004, 108 (39), 15332–15342.
13. Khalil, M.; Demirdöven, N.; Tokmakoff, A. “Obtaining absorptive line shapes in two-dimensional infrared vibrational correlation spectra.” Phys. Rev. Lett. 2003, 90, 47401 (4 pp.).
12. Khalil, M.; Demirdöven, N.; Tokmakoff, A. “Coherent 2D IR spectroscopy: Molecular structure and dynamics in solution.” J. Phys. Chem. A 2003, 107 (27), 5258–5279.
11. Demirdöven, N.; Khalil, M.; Tokmakoff, A. “Correlated vibrational dynamics revealed by two-dimensional infrared spectroscopy.” Phys. Rev. Lett. 2002, 89, 237401/1–237401/4.
10. Demirdöven, N.; Khalil, M.; Golonzka, O.; Tokmakoff, A. “Dispersion compensation with optical materials for compression of intense sub-100-fs mid-infrared pulses.” Opt. Lett. 2002, 27 (6), 433–435.
9. Khalil, M. and Tokmakoff, A. “Signatures of vibrational interactions in coherent two-dimensional infrared spectroscopy.” Chem. Phys. 2001, 266 (2/3), 213–230.
8. Golonzka, O.; Khalil, M.; Demirdöven, N.; Tokmakoff, A. “Vibrational anharmonicities revealed by coherent two-dimensional infrared spectroscopy.” Phys. Rev. Lett. 2001, 86 (10), 2154–2157.
7. Golonzka, O.; Khalil, M.; Demirdöven, N.; Tokmakoff, A. “Coupling and orientation between anharmonic vibrations characterized with two-dimensional infrared vibrational echo spectroscopy.” J. Chem. Phys. 2001, 115 (23), 10814–10828.
6. Demirdöven, N.; Khalil, M.; Golonzka, O.; Tokmakoff, A. “Correlation effects in the two-dimensional vibrational spectroscopy of coupled vibrations.” J. Phys. Chem. A 2001, 105 (34), 8025–8030.
5. Khalil, M.; Golonzka, O.; Demirdöven, N.; Fecko, C. J.; Tokmakoff, A. “Polarization-selective femtosecond Raman spectroscopy of isotropic and anisotropic vibrational dynamics in liquids.” Chem. Phys. Lett. 2000, 321 (3/4), 231–237.
4. Khalil, M.; Demirdöven, N.; Golonzka, O.; Fecko, C. J.; Tokmakoff, A. “A phase-sensitive detection method using diffractive optics for polarization-selective femtosecond Raman spectroscopy.” J. Phys. Chem. A 2000, 104 (24), 5711–5715.
3. Golonzka, O.; Demirdöven, N.; Khalil, M.; Tokmakoff, A. “Separation of cascaded and direct fifth-order Raman signals using phase-sensitive intrinsic heterodyne detection.” J. Chem. Phys. 2000, 113 (22), 9893–9896.
2. Khalil, M.; Shen, Q. “Molecular Structure and Conformational Composition of 3,4-Epoxy-1-butene As Determined by Ab Initio Molecular Orbital Calculations, Microwave Spectroscopy, and Gas-Phase Electron Diffraction.” J. Phys. Chem. A 1999, 103 (28), 5585–5589.
Uberna, R.; Khalil, M.; Williams, R. M.; Papanikolas, J. M.; Leone, S. R. “Phase and amplitude control in the formation and detection of rotational wave packets in the E1Σg+ state of Li2.” J. Chem. Phys. 1998, 108 (22), 9259–9274.