61 results on '"Kubarych, Kevin J."'
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2. Nanoclustering in non-ideal ethanol/heptane solutions alters solvation dynamics.
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Crum VF and Kubarych KJ
- Abstract
Alcohol/alkane solutions widely used in chemical synthesis and as transportation fuels are highly non-ideal due to the nanoscale clustering of the amphiphilic alcohol molecules within the nonpolar alkanes. Besides impacting reactivity, such as combustion, non-ideal solutions are likely to exhibit unusual solvation dynamics on ultrafast time scales arising from the structurally heterogeneous nature of molecular-scale association. Using a convenient transition metal carbonyl vibrational probe [(C5H5)Mn(CO)3, CMT], linear absorption and nonlinear two-dimensional infrared (2D-IR) spectroscopy reveal composition-dependent solvation dynamics as reported by the frequency fluctuation correlation function in a series of ethanol/heptane solutions. Slow spectral diffusion with dilute ethanol indicates preferential solvation of the polar solute by the alcohol with a mechanism largely dominated by solvent exchange. Comparison with an ethanol/acetonitrile solution series yields no substantial preferential solvation or solvent exchange signatures in the linear or 2D-IR spectra. In ethanol/heptane solutions, increasing the ethanol concentration speeds up the solvation dynamics, which is largely consistent with a model that includes solvent exchange and single-solvent spectral diffusion. Detailed analysis of the deviation from the experimental time constants from the model's optimal parameters yields a remarkable resemblance of the concentration-weighted Kirkwood-Buff integrals for ethanol/heptane solutions. This trend indicates that solution non-ideality alters the spectral diffusion dynamics of the probe solute. Given that nanoscale clustering drives the non-ideality, these experiments reveal a dynamical consequence of nanoscale heterogeneity on the ultrafast dynamics of the solution. Refined understanding of the structural and dynamical aspects of mixed solvents will be necessary for predictive solution strategies in chemistry., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)
- Published
- 2024
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3. Special issue on time-resolved vibrational spectroscopy.
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Kubarych KJ, Thielges MC, Tahara T, and Elsaesser T
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- 2023
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4. Reply to "Comment on: 'Isolating Vibrational Polariton 2D-IR Transmission Spectra'".
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Duan R, Mastron JN, Song Y, and Kubarych KJ
- Abstract
In a Comment on our recent Letter, the authors take issue with our method of refining 2D-IR transmission spectra to remove a background contribution that arises from nonpolaritonic molecules in the cavity. In our response to their Comment, we describe how our approach was motivated by the previous work of the authors, and we present a spatially dependent molecule-cavity Tavis-Cummings model that can account for the significant response from localized molecules with nonzero oscillator strengths. The telltale signature of the localized molecule response is the spectral diffusion dynamics of the bare W(CO)
6 molecules in the polar butyl acetate solvent. Inhomogeneous broadening is absent from polaritonic states due to the extreme degree of exchange narrowing in coupling very large numbers of molecules to a cavity mode.- Published
- 2023
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5. Isolating Polaritonic 2D-IR Transmission Spectra.
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Duan R, Mastron JN, Song Y, and Kubarych KJ
- Abstract
Strong coupling between vibrational transitions in molecules within a resonant optical microcavity leads to the formation of collective, delocalized vibrational polaritons. There are many potential applications of "polaritonic chemistry", ranging from modified chemical reactivity to quantum information processing. One challenge in obtaining the polaritonic response is removing a background contribution due to the uncoupled molecules that generate an ordinary 2D-IR spectrum whose amplitude is filtered by the polariton transmission spectrum. We show that most features in 2D-IR spectra of vibrational polaritons can be explained by a linear superposition of this background signal and the true polariton response. Through a straightforward correction procedure, in which the filtered bare-molecule 2D-IR spectrum is subtracted from the measured cavity response, we recover the polaritonic spectrum.
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- 2021
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6. Correction to Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, and Zanni MT
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- 2021
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7. Ultrafast vibrational dynamics of a solute correlates with dynamics of the solvent.
- Author
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Crum VF, Kiefer LM, and Kubarych KJ
- Abstract
Two-dimensional infrared (2D-IR) spectroscopy is used to measure the spectral dynamics of the metal carbonyl complex cyclopentadienyl manganese tricarbonyl (CMT) in a series of linear alkyl nitriles. 2D-IR spectroscopy provides direct readout of solvation dynamics through spectral diffusion, probing the decay of frequency correlation induced by fluctuations of the solvent environment. 2D-IR simultaneously monitors intramolecular vibrational energy redistribution (IVR) among excited vibrations, which can also be influenced by the solvent through the spectral density rather than the dynamical friction underlying solvation. Here, we report that the CMT vibrational probe reveals solvent dependences in both the spectral diffusion and the IVR time scales, where each slows with increased alkyl chain length. In order to assess the degree to which solute-solvent interactions can be correlated with bulk solvent properties, we compared our results with low-frequency dynamics obtained from optical Kerr effect (OKE) spectroscopy-performed by others-on the same nitrile solvent series. We find excellent correlation between our spectral diffusion results and the orientational dynamics time scales from OKE. We also find a correlation between our IVR time scales and the amplitudes of the low-frequency spectral densities evaluated at the 90-cm
-1 energy difference, corresponding to the gap between the two strong vibrational modes of the carbonyl probe. 2D-IR and OKE provide complementary perspectives on condensed phase dynamics, and these findings provide experimental evidence that at least at the level of dynamical correlations, some aspects of a solute vibrational dynamics can be inferred from properties of the solvent.- Published
- 2021
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8. Direct comparison of amplitude and geometric measures of spectral inhomogeneity using phase-cycled 2D-IR spectroscopy.
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Duan R, Mastron JN, Song Y, and Kubarych KJ
- Abstract
Two-dimensional infrared (2D-IR) spectroscopy provides access to equilibrium dynamics with the extraction of the frequency-fluctuation correlation function (FFCF) from the measured spectra. Several different methods of obtaining the FFCF from experimental spectra, such as the center line slope (CLS), ellipticity, phase slope, and nodal line slope, all depend on the geometrical nature of the 2D line shape and necessarily require spectral extent in order to achieve a measure of the FFCF. Amplitude measures, on the other hand, such as the inhomogeneity index, rely only on signal amplitudes and can, in principle, be computed using just a single point in a 2D spectrum. With a pulse shaper-based 2D-IR spectrometer, in conjunction with phase cycling, we separate the rephasing and nonrephasing signals used to determine the inhomogeneity index. The same measured data provide the absorptive spectrum, needed for the CLS. Both methods are applied to two model molecular systems: tungsten hexacarbonyl (WCO
6 ) and methylcyclopentadienyl manganese tricarbonyl [Cp'Mn(CO)3 , MCMT]. The three degenerate IR modes of W(CO)6 lack coherent modulation or noticeable intramolecular vibrational redistribution (IVR) and are used to establish a baseline comparison. The two bands of the MCMT tripod complex include intraband coherences and IVR as well as likely internal torsional motion on a few-picosecond time scale. We find essentially identical spectral diffusion, but faster, non-equilibrium dynamics lead to differences in the FFCFs extracted with the two methods. The inhomogeneity index offers an advantage in cases where spectra are complex and energy transfer can mimic line shape changes due to frequency fluctuations.- Published
- 2021
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9. Transmission Mode 2D-IR Spectroelectrochemistry of In Situ Electrocatalytic Intermediates.
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Kiefer LM, Michocki LB, and Kubarych KJ
- Abstract
Unraveling electrocatalytic mechanisms, as well as fundamental structural dynamics of intermediates, requires spectroscopy with high time and frequency resolution that can account for nonequilibrium in situ concentration changes inherent to electrochemistry. Two-dimensional infrared (2D-IR) spectroscopy is an ideal candidate, but several technical challenges have hindered development of this powerful tool for spectroelectrochemistry (SEC). We demonstrate a transmission-mode, optically transparent thin-layer electrochemical (OTTLE) cell adapted to 2D-IR-SEC to monitor the important Re(bpy)(CO)
3 Cl CO2 -reduction electrocatalyst. 2D-IR-SEC reveals pronounced differences in both spectral diffusion time scales and spectral inhomogeneity in the singly reduced catalyst, [Re(bpy)(CO)3 Cl]•- , relative to the starting Re(bpy)(CO)3 Cl. Cross-peaks between well-resolved symmetric vibrations and congested low-frequency bands enable direct assignment of all distinct species during the electrochemical reaction. With this information, 2D-IR-SEC provides new mechanistic insights regarding unproductive, catalyst-degrading dimerization. 2D-IR-SEC opens new experimental windows into the electrocatalysis foundation of future energy conversion and greenhouse gas reduction.- Published
- 2021
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10. Mechanistic Study of Charge Separation in a Nonfullerene Organic Donor-Acceptor Blend Using Multispectral Multidimensional Spectroscopy.
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Song Y, Liu X, Li Y, Nguyen HH, Duan R, Kubarych KJ, Forrest SR, and Ogilvie JP
- Abstract
Organic photovoltaics (OPVs) based on nonfullerene acceptors are now approaching commercially viable efficiencies. One key to their success is efficient charge separation with low potential loss at the donor-acceptor heterojunction. Due to the lack of spectroscopic probes, open questions remain about the mechanisms of charge separation. Here, we study charge separation of a model system composed of the donor, poly[(2,6-(4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)-benzo[1,2-b:4,5-b']dithiophene))- alt -(5,5-(1',3'-di-2-thienyl-5',7'-bis(2-ethylhexyl)benzo[1',2'-c:4',5'-c']dithiophene-4,8-dione) (PBDB-T), and the nonfullerene acceptor, 3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC), using multidimensional spectroscopy spanning the visible to the mid-infrared. We find that bound polaron pairs (BPPs) generated within ITIC domains play a dominant role in efficient hole transfer, transitioning to delocalized polarons within 100 fs. The weak electron-hole binding within the BPPs and the resulting polaron delocalization are key factors for efficient charge separation at nearly zero driving force. Our work provides useful insight into how to further improve the power conversion efficiency in OPVs.
- Published
- 2021
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11. The Photoactive Excited State of the B 12 -Based Photoreceptor CarH.
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Miller NA, Kaneshiro AK, Konar A, Alonso-Mori R, Britz A, Deb A, Glownia JM, Koralek JD, Mallik L, Meadows JH, Michocki LB, van Driel TB, Koutmos M, Padmanabhan S, Elías-Arnanz M, Kubarych KJ, Marsh ENG, Penner-Hahn JE, and Sension RJ
- Subjects
- Cobalt
- Abstract
We have used transient absorption spectroscopy in the UV-visible and X-ray regions to characterize the excited state of CarH, a protein photoreceptor that uses a form of B
12 , adenosylcobalamin (AdoCbl), to sense light. With visible excitation, a nanosecond-lifetime photoactive excited state is formed with unit quantum yield. The time-resolved X-ray absorption near edge structure difference spectrum of this state demonstrates that the excited state of AdoCbl in CarH undergoes only modest structural expansion around the central cobalt, a behavior similar to that observed for methylcobalamin rather than for AdoCbl free in solution. We propose a new mechanism for CarH photoreactivity involving formation of a triplet excited state. This allows the sensor to operate with high quantum efficiency and without formation of potentially dangerous side products. By stabilizing the excited electronic state, CarH controls reactivity of AdoCbl and enables slow reactions that yield nonreactive products and bypass bond homolysis and reactive radical species formation.- Published
- 2020
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12. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, and Zanni MT
- Subjects
- Humans, Spectrum Analysis, Raman, Static Electricity, Vibration, Models, Chemical, Proteins chemistry, Spectrum Analysis methods
- Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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- 2020
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13. Ultrafast XANES Monitors Femtosecond Sequential Structural Evolution in Photoexcited Coenzyme B 12 .
- Author
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Miller NA, Michocki LB, Konar A, Alonso-Mori R, Deb A, Glownia JM, Sofferman DL, Song S, Kozlowski PM, Kubarych KJ, Penner-Hahn JE, and Sension RJ
- Subjects
- Light, Molecular Conformation, Quantum Theory, Solvents chemistry, Ultraviolet Rays, Cobamides chemistry, X-Ray Absorption Spectroscopy
- Abstract
Polarized X-ray absorption near-edge structure (XANES) at the Co K-edge and broadband UV-vis transient absorption are used to monitor the sequential evolution of the excited-state structure of coenzyme B
12 (adenosylcobalamin) over the first picosecond following excitation. The initial state is characterized by sub-100 fs sequential changes around the central cobalt. These are polarized first in the y -direction orthogonal to the transition dipole and 50 fs later in the x -direction along the transition dipole. Expansion of the axial bonds follows on a ca. 200 fs time scale as the molecule moves out of the Franck-Condon active region of the potential energy surface. On the same 200 fs time scale there are electronic changes that result in the loss of stimulated emission and the appearance of a strong absorption at 340 nm. These measurements provide a cobalt-centered movie of the excited molecule as it evolves to the local excited-state minimum.- Published
- 2020
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14. Antivitamins B 12 in a Microdrop: The Excited-State Structure of a Precious Sample Using Transient Polarized X-ray Absorption Near-Edge Structure.
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Miller NA, Michocki LB, Alonso-Mori R, Britz A, Deb A, DePonte DP, Glownia JM, Kaneshiro AK, Kieninger C, Koralek J, Meadows JH, van Driel TB, Kräutler B, Kubarych KJ, Penner-Hahn JE, and Sension RJ
- Subjects
- Carbon chemistry, Cobalt chemistry, Kinetics, Molecular Conformation, Photochemical Processes, Quantum Theory, Thermodynamics, X-Rays, Coordination Complexes chemistry, Models, Molecular, Vitamin B 12 antagonists & inhibitors
- Abstract
Polarized transient X-ray absorption near-edge structure (XANES) was used to probe the excited-state structure of a photostable B
12 antivitamin (Coβ-2-(2,4-difluorophenyl)-ethynylcobalamin, F2 PhEtyCbl). A drop-on-demand delivery system synchronized to the LCLS X-ray free electron laser pulses was implemented and used to measure the XANES difference spectrum 12 ps following excitation, exposing only ∼45 μL of sample. Unlike cyanocobalamin (CNCbl), where the Co-C bond expands 15-20%, the excited state of F2 PhEtyCbl is characterized by little change in the Co-C bond, suggesting that the acetylide linkage raises the barrier for expansion of the Co-C bond. In contrast, the lower axial Co-NDMB bond is elongated in the excited state of F2 PhEtyCbl by ca. 10% or more, comparable to the 10% elongation observed for Co-NDMB in CNCbl.- Published
- 2019
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15. Probing the Excited State of Methylcobalamin Using Polarized Time-Resolved X-ray Absorption Spectroscopy.
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Michocki LB, Miller NA, Alonso-Mori R, Britz A, Deb A, Glownia JM, Kaneshiro AK, Konar A, Koralek J, Meadows JH, Sofferman DL, Song S, Toda MJ, van Driel TB, Kozlowski PM, Kubarych KJ, Penner-Hahn JE, and Sension RJ
- Abstract
We use picosecond time-resolved polarized X-ray absorption near-edge structure (XANES) measurements to probe the structure of the long-lived photoexcited state of methylcobalamin (MeCbl) and the cob(II)alamin photoproduct formed following photoexcitation of adenosylcobalamin (AdoCbl, coenzyme B
12 ). For MeCbl, we used 520 nm excitation and a time delay of 100 ps to avoid the formation of cob(II)alamin. We find only small spectral changes in the equatorial and axial directions, which we interpret as arising from small (<∼0.05 Å) changes in both the equatorial and axial distances. This confirms expectations based on prior UV-visible transient absorption measurements and theoretical simulations. We do not find evidence for the significant elongation of the Co-C bond reported by Subramanian [ J. Phys. Chem. Lett. 2018 , 9 , 1542 - 1546 ] following 400 nm excitation. For AdoCbl, we resolve the difference XANES contributions along three unique molecular axes by exciting with both 540 and 365 nm light, demonstrating that the spectral changes are predominantly polarized along the axial direction, consistent with the loss of axial ligation. These data suggest that the microsecond "recombination product" identified by Subramanian et al. is actually the cob(II)alamin photoproduct that is produced following bond homolysis of MeCbl with 400 nm excitation. Our results highlight the pronounced advantage of using polarization-selective transient X-ray absorption for isolating structural dynamics in systems undergoing atomic displacements that are strongly correlated to the exciting optical polarization.- Published
- 2019
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16. Multispectral multidimensional spectrometer spanning the ultraviolet to the mid-infrared.
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Song Y, Konar A, Sechrist R, Roy VP, Duan R, Dziurgot J, Policht V, Matutes YA, Kubarych KJ, and Ogilvie JP
- Abstract
Multidimensional spectroscopy is the optical analog to nuclear magnetic resonance, probing dynamical processes with ultrafast time resolution. At optical frequencies, the technical challenges of multidimensional spectroscopy have hindered its progress until recently, where advances in laser sources and pulse-shaping have removed many obstacles to its implementation. Multidimensional spectroscopy in the visible and infrared (IR) regimes has already enabled respective advances in our understanding of photosynthesis and the structural rearrangements of liquid water. A frontier of ultrafast spectroscopy is to extend and combine multidimensional techniques and frequency ranges, which have been largely restricted to operating in the distinct visible or IR regimes. By employing two independent amplifiers seeded by a single oscillator, it is straightforward to span a wide range of time scales (femtoseconds to seconds), all of which are often relevant to the most important energy conversion and catalysis problems in chemistry, physics, and materials science. Complex condensed phase systems have optical transitions spanning the ultraviolet (UV) to the IR and exhibit dynamics relevant to function on time scales of femtoseconds to seconds and beyond. We describe the development of the Multispectral Multidimensional Nonlinear Spectrometer (MMDS) to enable studies of dynamical processes in atomic, molecular, and material systems spanning femtoseconds to seconds, from the UV to the IR regimes. The MMDS employs pulse-shaping methods to provide an easy-to-use instrument with an unprecedented spectral range that enables unique combination spectroscopies. We demonstrate the multispectral capabilities of the MMDS on several model systems.
- Published
- 2019
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17. Solvent Quality Controls Macromolecular Structural Dynamics of a Dendrimeric Hydrogenase Model.
- Author
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Eckert PA and Kubarych KJ
- Subjects
- Dendrimers chemistry, Diffusion, Hydrogenase chemistry, Iron Carbonyl Compounds chemistry, Macromolecular Substances chemistry, Models, Molecular, Molecular Conformation, Molecular Structure, Quality Control, Solvents chemistry, Spectroscopy, Fourier Transform Infrared, Sulfur chemistry, Sulfur metabolism, Vibration, Dendrimers metabolism, Hydrogenase metabolism, Iron Carbonyl Compounds metabolism, Macromolecular Substances metabolism
- Abstract
We report a spectroscopic investigation of the ultrafast dynamics of the second-generation poly(aryl ether) dendritic hydrogenase model using two-dimensional infrared (2D-IR) spectroscopy to probe the metal carbonyl vibrations of the dendrimer and a reference small molecule, [Fe(μ-S)(CO)
3 ]2 . We find that the structural dynamics of the dendrimer are reflected in a slow phase of the spectral diffusion, which is absent from [Fe(μ-S)(CO)3 ]2, and we relate the slow phase to the quality of the solvent for poly(aryl ether) dendrimers. We observe a solvent-dependent modulation of the initial phase of vibrational relaxation of the carbonyl groups, which we attribute to an inhibition of solvent assistance in the intramolecular vibrational redistribution process for the dendrimer. There is also a clear solvent dependence of the vibrational frequencies of both the dendrimer and [Fe(μ-S)(CO)3 ]2 . Our data represent the first 2D-IR study of a dendritic complex and provide insight into the solvent dependence of molecular conformation in solution and the ultrafast dynamics of moderately sized, conformationally mobile compounds.- Published
- 2018
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18. Ultrafast X-ray Absorption Near Edge Structure Reveals Ballistic Excited State Structural Dynamics.
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Miller NA, Deb A, Alonso-Mori R, Glownia JM, Kiefer LM, Konar A, Michocki LB, Sikorski M, Sofferman DL, Song S, Toda MJ, Wiley TE, Zhu D, Kozlowski PM, Kubarych KJ, Penner-Hahn JE, and Sension RJ
- Abstract
Polarized ultrafast time-resolved X-ray absorption near edge structure (XANES) allows characterization of excited state dynamics following excitation. Excitation of vitamin B
12 , cyanocobalamin (CNCbl), in the αβ-band at 550 nm and the γ-band at 365 nm was used to uniquely resolve axial and equatorial contributions to the excited state dynamics. The structural evolution of the excited molecule is best described by a coherent ballistic trajectory on the excited state potential energy surface. Prompt expansion of the Co cavity by ca. 0.03 Å is followed by significant elongation of the axial bonds (>0.25 Å) over the first 190 fs. Subsequent contraction of the Co cavity in both axial and equatorial directions results in the relaxed S1 excited state structure within 500 fs of excitation.- Published
- 2018
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19. Solvent exchange in preformed photocatalyst-donor precursor complexes determines efficiency.
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Kiefer LM and Kubarych KJ
- Abstract
In homogeneous photocatalytic reduction of CO
2 , it is widely assumed that the primary electron transfer from the sacrificial donor to the catalyst is diffusion controlled, thus little attention has been paid to optimizing this step. We present spectroscopic evidence that the precursor complex is preformed, driven by preferential solvation, and two-dimensional infrared spectroscopy reveals triethanolamine (donor)/tetrahydrofuran (solvent) exchange in the photocatalyst's solvation shell, reaching greatest magnitude at the known optimal concentration (∼20% v/v TEOA in THF) for catalytically reducing CO2 to CO. Transient infrared absorption shows the appearance of the singly reduced catalyst on an ultrafast (<70 ps) time scale, consistent with non-diffusion controlled electron transfer within the preformed precursor complex. Identification of preferential catalyst-cosolvent interactions suggests a revised paradigm for the primary electron transfer, while illuminating the pivotal importance of solvent exchange in determining the overall efficiency of the photocycle.- Published
- 2017
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20. An "Iceberg" Coating Preserves Bulk Hydration Dynamics in Aqueous PEG Solutions.
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Daley KR and Kubarych KJ
- Abstract
Ultrafast picosecond time scale two-dimensional infrared (2D-IR) spectroscopy of a new water-soluble transition metal complex acting as a vibrational probe shows that over a range of concentration and poly(ethylene glycol) (PEG) molecular mass (2000, 8000, and 20000 Da) the time scale of the sensed hydration dynamics differs negligibly from bulk water (D
2 O). PEG is well-known to establish a highly stable hydration shell because the spacing between adjacent ethereal oxygens nearly matches water's hydrogen-bonding network. Although these first-shell water molecules are likely significantly retarded, they present an interface to subsequent hydration shells and thus diminish the largely entropic perturbation to water's orientational dynamics. In addition to the longer PEGs, a series of concentration-dependent 2D-IR measurements using aqueous PEG-400 show a pronounced hydration slowdown in the vicinity of the critical overlap concentration (c*). Comparison between these dynamical results and previously reported steady-state infrared spectroscopy of aqueous PEG-1000 solutions reveals a strikingly identical dependence on number of water molecules per ethylene oxide monomer, scaled according to the critical overlap concentration.- Published
- 2017
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21. Interfacial Hydration Dynamics in Cationic Micelles Using 2D-IR and NMR.
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Roy VP and Kubarych KJ
- Abstract
Using the thiocyanate anion as a vibrational probe chromophore in conjunction with infrared and NMR spectroscopy, we find that SCN
- strongly associates with the cationic head group of dodecyltrimethylammonium bromide (DTAB) micelles, both in normal-phase and reverse micelles. In competition with chloride and iodide ions, we find no evidence for displacement of thiocyanate, in accord with the chaotropicity of the Hofmeister ordering, while lending support to a direct interaction picture of its origin. Ultrafast 2D-IR spectroscopy of the SCN- probe in a range of DTAB micelle sizes (w0 = 4 to w0 = 12) shows little if any size dependence on the time scale for spectral diffusion, which is found to be ∼3.5 times slower than in bulk water (both D2 O and H2 O). Normal-phase micelles studied with 2D-IR exhibit essentially the same spectral dynamics as do reverse micelles, indicating a lack of sensitivity to interfacial curvature. Combined with1 H NMR chemical shift perturbations, we conclude that the SCN- ions tightly associate with the head groups and are partially buried. The 3-4-fold slowdown in spectral diffusion is consistent with the excluded volume model for interfacial perturbation to hydrogen bond reorientation dynamics. On the basis of these observations and comparisons to previous studies of zwitterionic interfaces probed with phosphate transitions, we conclude that the SCN- spectral dynamics in both reverse- and normal-phase micelles is largely dominated by hydration contributions, and offers a promising probe of interfacial hydration at cationic interfaces. Addition of competitive anions alters neither the IR spectra nor the ultrafast dynamics, indicating that SCN- is robustly associated with the head groups.- Published
- 2017
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22. Oxidation-State-Dependent Vibrational Dynamics Probed with 2D-IR.
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Eckert PA and Kubarych KJ
- Abstract
In an effort to examine the role of electronic structure and oxidation states in potentially modifying intramolecular vibrational dynamics and intermolecular solvation, we have used 2D-IR to study two distinct oxidation states of an organometallic complex. The complex, [1,1'-bis(diphenylphosphino)ferrocene]tetracarbonyl chromium (DPPFCr), consists of a catalytic diphenylphosphino ferrocene redox-active component as well as a Cr that can be switched from a Cr(0) to a Cr(I) oxidation state using a chemical oxidant in dichloromethane (DCM) solution. The DPPFCr(I) radical cation is sufficiently stable to investigate with 2D-IR spectroscopy, which provides dynamical information such as vibrational relaxation, intramolecular vibrational redistribution, as well as solvation dynamics manifested as spectral diffusion. Our measurements show that the primarily intramolecular dynamical processes-vibrational relaxation and redistribution-differ significantly between the two oxidation states, with faster relaxation in the oxidized DPPFCr(I) radical cation. The primarily intermolecular spectral diffusion dynamics, however, exhibit insignificant oxidation state dependence. We speculate that the low nucleophilicity (i.e., donicity) of the DCM solvent, which is chosen to facilitate the chemical oxidation, masks any potential changes in solvation dynamics accompanying the substantial decrease in the 2.5 D molecular dipole moment of DPPFCr(I) relative to DPPFCr(0) (7.5 D).
- Published
- 2017
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23. Polarized XANES Monitors Femtosecond Structural Evolution of Photoexcited Vitamin B 12 .
- Author
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Miller NA, Deb A, Alonso-Mori R, Garabato BD, Glownia JM, Kiefer LM, Koralek J, Sikorski M, Spears KG, Wiley TE, Zhu D, Kozlowski PM, Kubarych KJ, Penner-Hahn JE, and Sension RJ
- Subjects
- Molecular Structure, Photochemical Processes, Time Factors, X-Ray Absorption Spectroscopy, X-Rays, Vitamin B 12 chemistry
- Abstract
Ultrafast, polarization-selective time-resolved X-ray absorption near-edge structure (XANES) was used to characterize the photochemistry of vitamin B
12 , cyanocobalamin (CNCbl), in solution. Cobalamins are important biological cofactors involved in methyl transfer, radical rearrangement, and light-activated gene regulation, while also holding promise as light-activated agents for spatiotemporal controlled delivery of therapeutics. We introduce polarized femtosecond XANES, combined with UV-visible spectroscopy, to reveal sequential structural evolution of CNCbl in the excited electronic state. Femtosecond polarized XANES provides the crucial structural dynamics link between computed potential energy surfaces and optical transient absorption spectroscopy. Polarization selectivity can be used to uniquely identify electronic contributions and structural changes, even in isotropic samples when well-defined electronic transitions are excited. Our XANES measurements reveal that the structural changes upon photoexcitation occur mainly in the axial direction, where elongation of the axial Co-CN bond and Co-NIm bond on a 110 fs time scale is followed by corrin ring relaxation on a 260 fs time scale. These observations expose features of the potential energy surfaces controlling cobalamin reactivity and deactivation.- Published
- 2017
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24. Dynamic Flexibility of Hydrogenase Active Site Models Studied with 2D-IR Spectroscopy.
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Eckert PA and Kubarych KJ
- Abstract
Hydrogenase enzymes enable organisms to use H
2 as an energy source, having evolved extremely efficient biological catalysts for the reversible oxidation of molecular hydrogen. Small-molecule mimics of these enzymes provide both simplified models of the catalysis reactions and potential artificial catalysts that might be used to facilitate a hydrogen economy. We have studied two diiron hydrogenase mimics, μ-pdt-[Fe(CO)3 ]2 and μ-edt-[Fe(CO)3 ]2 (pdt = propanedithiolate, edt = ethanedithiolate), in a series of alkane solvents and have observed significant ultrafast spectral dynamics using two-dimensional infrared (2D-IR) spectroscopy. Since solvent fluctuations in nonpolar alkanes do not lead to substantial electrostatic modulations in a solute's vibrational mode frequencies, we attribute the spectral diffusion dynamics to intramolecular flexibility. The intramolecular origin is supported by the absence of any measurable solvent viscosity dependence, indicating that the frequency fluctuations are not coupled to the solvent motional dynamics. Quantum chemical calculations reveal a pronounced coupling between the low-frequency torsional rotation of the carbonyl ligands and the terminal CO stretching vibrations. The flexibility of the CO ligands has been proposed to play a central role in the catalytic reaction mechanism, and our results highlight that the CO ligands are highly flexible on a picosecond time scale.- Published
- 2017
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25. NOESY-Like 2D-IR Spectroscopy Reveals Non-Gaussian Dynamics.
- Author
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Kiefer LM and Kubarych KJ
- Abstract
We have identified an unexpected signature of non-Gaussian dynamics in a conventional 2D IR measurement on a system with rapid intermolecular vibrational energy transfer. In a ternary mixture of the CO
2 reduction photocatalyst, ReCl(bpy)(CO)3 , NaSCN, and THF solvent, preferential association between the metal carbonyl catalyst and the NaSCN ion pairs facilitates intermolecular energy transfer on a few picoseconds time scale. Monitoring the cross peak between the highest frequency metal carbonyl band and the CN bands of NaSCN contact ion pairs, we find a striking time evolution of the cross-peak position on the detection axis. This frequency shift, which is due to spectral diffusion following intermolecular energy transfer, occurs with a time scale that is distinct from either the donor or acceptor spectral diffusion measured simultaneously. We argue that the energy transfer, a second-order Förster process, effectively increases the dimensionality of the 2D-IR spectroscopy and thus enables sensitivity to non-Gaussian dynamics.- Published
- 2016
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26. Histidine Orientation Modulates the Structure and Dynamics of a de Novo Metalloenzyme Active Site.
- Author
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Ross MR, White AM, Yu F, King JT, Pecoraro VL, and Kubarych KJ
- Subjects
- Carbon chemistry, Carbon Monoxide chemistry, Catalytic Domain, Enzymes chemistry, Enzymes metabolism, Metalloproteins chemistry, Metalloproteins metabolism, Models, Chemical, Nitrite Reductases metabolism, Oxygen chemistry, Peptides chemistry, Spectrophotometry, Infrared methods, Static Electricity, Copper chemistry, Histidine chemistry, Nitrite Reductases chemistry
- Abstract
The ultrafast dynamics of a de novo metalloenzyme active site is monitored using two-dimensional infrared spectroscopy. The homotrimer of parallel, coiled coil α-helices contains a His3-Cu(I) metal site where CO is bound and serves as a vibrational probe of the hydrophobic interior of the self-assembled complex. The ultrafast spectral dynamics of Cu-CO reveals unprecedented ultrafast (2 ps) nonequilibrium structural rearrangements launched by vibrational excitation of CO. This initial rapid phase is followed by much slower ∼40 ps vibrational relaxation typical of metal-CO vibrations in natural proteins. To identify the hidden coupled coordinate, small molecule analogues and the full peptide were studied by QM and QM/MM calculations, respectively. The calculations show that variation of the histidines' dihedral angles in coordinating Cu controls the coupling between the CO stretch and the Cu-C-O bending coordinates. Analysis of different optimized structures with significantly different electrostatic field magnitudes at the CO ligand site indicates that the origin of the stretch-bend coupling is not directly due to through-space electrostatics. Instead, the large, ∼3.6 D dipole moments of the histidine side chains effectively transduce the electrostatic environment to the local metal coordination orientation. The sensitivity of the first coordination sphere to the protein electrostatics and its role in altering the potential energy surface of the bound ligands suggests that long-range electrostatics can be leveraged to fine-tune function through enzyme design., Competing Interests: Notes The authors declare no competing financial interest.
- Published
- 2015
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27. Ultrafast 2D-IR and simulation investigations of preferential solvation and cosolvent exchange dynamics.
- Author
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Dunbar JA, Arthur EJ, White AM, and Kubarych KJ
- Subjects
- Solvents chemistry, Water chemistry, Biotin analogs & derivatives, Dimethylformamide chemistry, Molecular Dynamics Simulation, Spectroscopy, Fourier Transform Infrared methods
- Abstract
Using a derivative of the vitamin biotin labeled with a transition-metal carbonyl vibrational probe in a series of aqueous N,N-dimethylformamide (DMF) solutions, we observe a striking slowdown in spectral diffusion dynamics with decreased DMF concentration. Equilibrium solvation dynamics, measured with the rapidly acquired spectral diffusion (RASD) technique, a variant of heterodyne-detected photon-echo peak shift experiments, range from 1 ps in neat DMF to ∼3 ps in 0.07 mole fraction DMF/water solution. Molecular dynamics simulations of the biotin-metal carbonyl solute in explicit aqueous DMF solutions show marked preferential solvation by DMF, which becomes more pronounced at lower DMF concentrations. The simulations and the experimental data are consistent with an interpretation where the slowdown in spectral diffusion is due to solvent exchange involving distinct cosolvent species. A simple two-component model reproduces the observed spectral dynamics as well as the DMF concentration dependence, enabling the extraction of the solvent exchange time scale of 8 ps. This time scale corresponds to the diffusive motion of a few Å, consistent with a solvent-exchange mechanism. Unlike most previous studies of solvation dynamics in binary mixtures of polar solvents, our work highlights the ability of vibrational probes to sense solvent exchange as a new, slow component in the spectral diffusion dynamics.
- Published
- 2015
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28. Dynamics of rhenium photocatalysts revealed through ultrafast multidimensional spectroscopy.
- Author
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Kiefer LM, King JT, and Kubarych KJ
- Abstract
Rhenium catalysts have shown promise to promote carbon neutrality by reducing a prominent greenhouse gas, CO2, to CO and other starting materials. Much research has focused on identifying intermediates in the photocatalysis mechanism as well as time scales of relevant ultrafast processes. Recent studies have implemented multidimensional spectroscopies to characterize the catalyst's ultrafast dynamics as it undergoes the many steps of its photocycle. Two-dimensional infrared (2D-IR) spectroscopy is a powerful method to obtain molecular structure information while extracting time scales of dynamical processes with ultrafast resolution. Many observables result from 2D-IR experiments including vibrational lifetimes, intramolecular redistribution time scales, and, unique to 2D-IR, spectral diffusion, which is highly sensitive to solute-solvent interactions and motional dynamics. Spectral diffusion, a measure of how long a vibrational mode takes to sample its frequency space due to multiple solvent configurations, has various contributing factors. Properties of the solvent, the solute's structural flexibility, and electronic properties, as well as interactions between the solvent and solute, complicate identifying the origin of the spectral diffusion. With carefully chosen experiments, however, the source of the spectral diffusion can be unveiled. Within the context of a considerable body of previous work, here we discuss the spectral diffusion of several rhenium catalysts at multiple stages in the catalysis. These studies were performed in multiple polar liquids to aid in discovering the contributions of the solvent. We also performed electronic ground state 2D-IR and electronic excited state transient-2D-IR experiments to observe how spectral diffusion changes upon electronic excitation. Our results indicate that with the original Lehn catalyst in THF, relative to the ground state, the spectral diffusion slows by a factor of 3 in the equilibrated triplet metal-to-ligand charge transfer state. We attribute this slowdown to a decrease in dielectric friction as well as an increase in molecular flexibility. It is possible to partially simulate the charge transfer by altering the electron density moderately by adding electron donating or withdrawing substituents symmetrically to the bipyridine ligand. We find that unlike the significant electronic structure change induced by MLCT, such small substituent effects do not influence the spectral diffusion. A solvent study in THF, DMSO, and CH3CN found there to be an explicit solvent dependence that we can correlate to the solvent donicity, which is a measure of its nucleophilicity. Future studies focused on the solvent effects on spectral diffusion in the crucial photoinitiated state can illuminate the role the solvent plays in the catalysis.
- Published
- 2015
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29. Solvent-dependent dynamics of a series of rhenium photoactivated catalysts measured with ultrafast 2DIR.
- Author
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Kiefer LM and Kubarych KJ
- Abstract
The spectral dynamics of a series of rhenium photocatalysts, fac-Re(4,4'-R2-bpy)(CO)3Cl, where R = H, methyl, t-butyl, and carboxylic acid, as well as Re(1,10-phenanthroline)(CO)3Cl were observed in multiple aprotic solvents using two-dimensional infrared spectroscopy (2DIR). The carbonyl vibrational stretching frequencies showed slight variations due to the electron-donating or -withdrawing nature of the substituents on the bipyridine. The different substituents had minimal to no influence on the spectral diffusion time scales of the compounds within a particular solvent, but among the three different solvents investigated (DMSO, THF, and CH3CN), we find the spectral diffusion times to correlate with the solvent's donor number (DN). Because the donicity is a measure the Lewis basicity of the solvent, these findings may help establish a more complete dynamical picture of the photocatalysis, where the first chemical step following optical excitation is electron transfer from a sacrificial donor to the rhenium complex.
- Published
- 2015
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30. Equilibrium excited state dynamics of a photoactivated catalyst measured with ultrafast transient 2DIR.
- Author
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Kiefer LM, King JT, and Kubarych KJ
- Abstract
A detailed understanding of photocatalyzed reaction dynamics requires a sensitive means of investigating the transient catalytically active species. Ideally, the method should be able to compare the electronically excited photocatalyst directly to the ground state species. We use equilibrium and transient two-dimensional infrared (2DIR and t-2DIR) spectroscopy to study the ground and excited state spectral dynamics of [Re(CO)3(bpy)Cl] in tetrahydrofuran (THF). We leverage the long-lived triplet excited state of the molecule to re-establish an equilibrated state relative to intersystem crossing dynamics and external solvent fluctuations, allowing access to the dynamics experienced by the excited state photocatalyst. The decay of frequency correlations within the excited triplet state species differs significantly from the ground state (slower by a factor of 3), indicating that the electronic excitation and subsequent metal-to-ligand charge transfer and associated structural changes are sufficient to perturb the spectral dynamics as sensed by the carbonyl ligands. In addition, we observe a 2-fold slowdown in ground state spectral dynamics around the in-phase symmetric vibrational mode compared to the two lower frequency, out-of-phase symmetric and asymmetric modes. Following electronic absorption and metal-to-ligand charge transfer the symmetry of the vibrational modes are disrupted, and all vibrational modes experience inhomogeneous broadening and spectral diffusion. The qualitative change in broadening mechanisms arises from the charge redistribution, indicating that direct comparisons of vibrational spectral dynamics on different electronic states-reported here for the first time-can be highly sensitive indicators of changes in electronic structure and in the concomitant solvation dynamics that underlie the microscopic details of charge transfer reactions.
- Published
- 2014
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31. Monitoring equilibrium reaction dynamics of a nearly barrierless molecular rotor using ultrafast vibrational echoes.
- Author
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Nilsen IA, Osborne DG, White AM, Anna JM, and Kubarych KJ
- Abstract
Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ∼3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C6H6Cr(CO)3, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of kBT. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 kBT above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy.
- Published
- 2014
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32. Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes.
- Author
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Arthur EJ, King JT, Kubarych KJ, and Brooks CL 3rd
- Subjects
- Hydrophobic and Hydrophilic Interactions, Molecular Dynamics Simulation, Solubility, Solvents chemistry, Muramidase chemistry, Trifluoroethanol chemistry, Water chemistry
- Abstract
Cytoplasmic osmolytes can significantly alter the thermodynamic and kinetic properties of proteins relative to those under dilute solution conditions. Spectroscopic experiments of lysozymes in cosolvents indicate that such changes may arise from the heterogeneous, site-specific hydrophobic interactions between protein surface residues and individual solvent molecules. In pursuit of an accurate and predictive model for explaining biomolecular interactions, we study the averaged structural characteristics of mixed solvents with homologous lysozyme solutes using all-atom molecular dynamics. By observing the time-averaged densities of different aqueous solutions of trifluoroethanol, we deduce trends in the heterogeneous solvent interactions over each protein's surface, and investigate how the homology of protein structure does not necessarily translate to similarities in solvent structure and composition-even when observing identical side chains.
- Published
- 2014
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33. Crowding induced collective hydration of biological macromolecules over extended distances.
- Author
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King JT, Arthur EJ, Brooks CL 3rd, and Kubarych KJ
- Subjects
- Crystallography, X-Ray, Infrared Rays, Models, Molecular, Egg Proteins chemistry, Molecular Dynamics Simulation, Proteins chemistry, Water chemistry
- Abstract
Ultrafast two-dimensional infrared (2D-IR) spectroscopy reveals picosecond protein and hydration dynamics of crowded hen egg white lysozyme (HEWL) labeled with a metal-carbonyl vibrational probe covalently attached to a solvent accessible His residue. HEWL is systematically crowded alternatively with polyethylene glycol (PEG) or excess lysozyme in order to distinguish the chemically inert polymer from the complex electrostatic profile of the protein crowder. The results are threefold: (1) A sharp dynamical jamming-like transition is observed in the picosecond protein and hydration dynamics that is attributed to an independent-to-collective hydration transition induced by macromolecular crowding that slows the hydration dynamics up to an order of magnitude relative to bulk water. (2) The interprotein distance at which the transition occurs suggests collective hydration of proteins over distances of 30-40 Å. (3) Comparing the crowding effects of PEG400 to our previously reported experiments using glycerol exposes fundamental differences between small and macromolecular crowding agents.
- Published
- 2014
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34. Site-specific measurements of lipid membrane interfacial water dynamics with multidimensional infrared spectroscopy.
- Author
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Osborne DG, Dunbar JA, Lapping JG, White AM, and Kubarych KJ
- Subjects
- Cholesterol chemistry, Diffusion, Hydrogen Bonding, Lipid Bilayers chemistry, Membrane Lipids metabolism, Membrane Lipids chemistry, Spectrophotometry, Infrared, Water chemistry
- Abstract
One route to accessing site-specific dynamical information available with ultrafast multidimensional infrared spectroscopy is the development of robust and versatile vibrational probes. Here we synthesize and characterize a vibrationally labeled cholesterol derivative, (cholesteryl benzoate) chromium tricarbonyl, to probe model lipid membranes, focusing specifically on the membrane-water interface. Utilizing FTIR and polarized-ATR spectroscopies, we determine the location of the chromium tricarbonyl motif to be situated at the water-membrane interface with an orientation of 46 ± 2° relative to the vector normal to the membrane surface. We test the dynamical sensitivity of the (cholesteryl benzoate) chromium tricarbonyl label with two different nonlinear infrared spectroscopy methods, both of which show that the probe is well-suited to the study of membrane dynamics as well as the dynamics of water at the membrane interface. The metal carbonyl vibrational probe located at the surface of a bicelle exhibits spectral diffusion dynamics induced by membrane hydration water that is roughly three times slower than observed using a nearly identical vibrational probe in bulk water.
- Published
- 2013
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35. Rapid and accurate measurement of the frequency-frequency correlation function.
- Author
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Osborne DG and Kubarych KJ
- Abstract
Using an implementation of heterodyne-detected vibrational echo spectroscopy, we show that equilibrium spectral diffusion caused by solvation dynamics can be measured in a fraction of the time required using traditional two-dimensional infrared spectroscopy. Spectrally resolved, heterodyne-detected rephasing and nonrephasing signals, recorded at a single delay between the first two pulses in a photon echo sequence, can be used to measure the full waiting time dependent spectral dynamics that are typically extracted from a series of 2D-IR spectra. Hence, data acquisition is accelerated by more than 1 order of magnitude, while permitting extremely fine sampling of the spectral dynamics during the waiting time between the second and third pulses. Using cymantrene (cyclopentadienyl manganese tricarbonyl, CpMn(CO)3) in alcohol solutions, we compare this novel approach--denoted rapidly acquired spectral diffusion (RASD)--with a traditional method using full 2D-IR spectra, finding excellent agreement. Though this approach is largely limited to isolated vibrational bands, we also show how to remove interference from cross-peaks that can produce characteristic modulations of the spectral dynamics through vibrational quantum beats.
- Published
- 2013
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36. Ultrafast 2DIR probe of a host-guest inclusion complex: structural and dynamical constraints of nanoconfinement.
- Author
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Osborne DG, King JT, Dunbar JA, White AM, and Kubarych KJ
- Abstract
Two-dimensional infrared (2DIR) spectroscopy is used to study the influence of nanoconfinement on the spectral diffusion dynamics of cyclopentadienyl manganese tricarbonyl (CpMn(CO)3, CMT) free in solution and confined in the cavity of β-cyclodextrin. Contrary to the reorientation correlation function of the solvent molecules, determined through molecular dynamics simulations, measurements in three different solvents indicate that CMT confined in β-cyclodextrin undergoes spectral diffusion that is faster than free CMT. To account for this discrepancy, we propose that spectral diffusion time scales contain a dynamical contribution that is dependent on the effective size of the conformational space presented by the solvation environment. This solvation state space size is related to the number of participating solvent molecules, which in turn is proportional to the solvent accessible surface area (SASA). We test the role of the number of participating solvent molecules using a simple Gaussian-Markov simulation and find that an increase in the number of participating solvent molecules indeed slows the time required to search the available conformational space. Finally, we test this dependence by comparing the spectral diffusion of a previously studied manganese carbonyl, dimanganese decacarbonyl (Mn2(CO)10, DMDC), to CMT and find that DMDC, which has a larger SASA, exhibits slower spectral diffusion. The experimental observations and the supporting simplistic solvation model suggest that vibrational probe molecules, such as CMT, might be able to function as sensors of conformational entropy.
- Published
- 2013
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37. Site-specific coupling of hydration water and protein flexibility studied in solution with ultrafast 2D-IR spectroscopy.
- Author
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King JT and Kubarych KJ
- Subjects
- Glycerol chemistry, Models, Molecular, Molecular Dynamics Simulation, Muramidase metabolism, Solutions, Spectrophotometry, Infrared, Deuterium chemistry, Deuterium Oxide chemistry, Muramidase chemistry
- Abstract
There is considerable evidence for the slaving of biomolecular dynamics to the motions of the surrounding solvent environment, but to date there have been few direct experimental measurements capable of site-selectively probing both the dynamics of the water and the protein with ultrafast time resolution. Here, two-dimensional infrared spectroscopy (2D-IR) is used to study the ultrafast hydration and protein dynamics sensed by a metal carbonyl vibrational probe covalently attached to the surface of hen egg white lysozyme dissolved in D(2)O/glycerol solutions. Surface labeling provides direct access to the dynamics at the protein-water interface, where both the hydration and the protein dynamics can be observed simultaneously through the vibrational probe's frequency-frequency correlation function. In pure D(2)O, the correlation function shows a fast initial 3 ps decay corresponding to fluctuations of the hydration water, followed by a significant static offset attributed to fluctuations of the protein that are not sampled within the <20 ps experimental window. Adding glycerol increases the bulk solvent viscosity while leaving the protein structurally intact and hydrated. The hydration dynamics exhibit a greater than 3-fold slowdown between 0 and 80% glycerol (v/v), and the contribution from the protein's dynamics is found to slow in a nearly identical fashion. In addition, the magnitude of the dynamic slowdown associated with hydrophobic hydration is directly measured and shows quantitative agreement with predictions from molecular dynamics simulations.
- Published
- 2012
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38. Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents.
- Author
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King JT, Arthur EJ, Brooks CL 3rd, and Kubarych KJ
- Subjects
- Animals, Chickens, Deuterium Oxide chemistry, Egg Proteins chemistry, Humans, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Molecular Structure, Organometallic Compounds chemistry, Spectrophotometry, Infrared, Spectroscopy, Fourier Transform Infrared, Surface Properties, Thermodynamics, Trifluoroethanol chemistry, Vibration, Muramidase chemistry, Solvents chemistry, Water chemistry
- Abstract
The thermodynamic driving forces for protein folding, association, and function are often determined by protein-water interactions. With a novel covalently bound labeling approach, we have used sensitive vibrational probes, site-selectively conjugated to two lysozyme variants-in conjunction with ultrafast two-dimensional infrared (2D-IR) spectroscopy-to investigate directly the protein-water interface. By probing alternatively a topologically flat, rigid domain and a flexible domain, we find direct experimental evidence for spatially heterogeneous hydration dynamics. The hydration environment around globular proteins can vary from exhibiting bulk-like hydration dynamics to dynamically constrained water, which results from stifled hydrogen bond switching dynamics near extended hydrophobic surfaces. Furthermore, we leverage preferential solvation exchange to demonstrate that the liberation of dynamically constrained water is a sufficient driving force for protein-surface association reactions. These results provide an intuitive picture of the dynamic aspects of hydrophobic hydration of proteins, illustrating an essential function of water in biological processes.
- Published
- 2012
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39. Ultrafast α-like relaxation of a fragile glass-forming liquid measured using two-dimensional infrared spectroscopy.
- Author
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King JT, Ross MR, and Kubarych KJ
- Abstract
Ultrafast two-dimensional infrared (2D-IR) spectroscopy is used to study the picosecond dynamics of a vibrational probe molecule dissolved in a fragile glass former. The spectral dynamics are observed as the system is cooled to within a few degrees of the glass transition temperature (T(g)). We observe nonexponential relaxation of the frequency-frequency correlation function, similar to what has been reported for other dynamical correlation functions. In addition, we see evidence for α-like relaxation, typically associated with long-time, cooperative molecular motion, on the ultrafast time scale. The data suggests that the spectral dynamics are sensitive to cooperative motion occurring on time scales that are necessarily longer than the observation time.
- Published
- 2012
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40. Water-assisted vibrational relaxation of a metal carbonyl complex studied with ultrafast 2D-IR.
- Author
-
King JT, Ross MR, and Kubarych KJ
- Abstract
Water is capable of assisting exceptionally rapid vibrational relaxation within dissolved solute species. Although ultrafast dynamics of metal carbonyl complexes have long served as models for vibrational relaxation, all reports to-date have investigated nonaqueous solutions due to the insolubility of the vast majority of metal carbonyl complexes in water. Using the water-soluble complex [RuCl(2)(CO)(3)](2), which belongs to a class known as "carbon monoxide (CO) releasing molecules" (CORM), we report the first ultrafast vibrational relaxation measurements of a metal carbonyl complex in water and compare this relaxation with polar organic solvents, namely, methanol. The vibrational relaxation, measured by two-dimensional IR (2D-IR) spectroscopy, is an order of magnitude faster in H(2)O (3.12 ± 0.29 ps) than in methanol (42.25 ± 3 ps). The accelerated relaxation times of the coupled CO units in H(2)O and D(2)O is interpreted as resulting from the enhancement of intramolecular relaxation pathways through additional coupling induced by the solvent. In addition, the vibrational lifetime shows a significant isotope dependence: in D(2)O the relaxation time is 4.27 ± 0.27 ps, a difference of roughly 30%. We interpret these measurements in terms of a nonresonant channel primarily arising from water's reorientational dynamics, which occur primarily through large angular jumps, as well as a resonant transfer of vibrational energy from the carbonyl bands to the libration-bend combination band. These measurements indicate that metal carbonyls, which are among the strongest IR transitions, are exquisitely sensitive to the presence of water and hold promise as IR analogs of EPR spin labels.
- Published
- 2012
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41. Multiple structures and dynamics of [CpRu(CO)2]2 and [CpFe(CO)2]2 in solution revealed with two-dimensional infrared spectroscopy.
- Author
-
Anna JM, King JT, and Kubarych KJ
- Abstract
Two-dimensional infrared (2DIR) spectroscopy is applied to both (Cp)(2)Fe(2)(CO)(4) and its ruthenium analog (Cp)(2)Ru(2)(CO)(4) in order to study the vibrational dynamics of these two systems. Combining the results of 2DIR spectroscopy and DFT calculations, the different structural forms of both the iron and the ruthenium complexes were characterized, furthering the previous assignment of the linear IR spectrum by determining the transition frequencies associated with the different isomeric forms. Monitoring the time-dependent amplitudes of the cross peaks enabled the observation of equilibrium energy transfer dynamics between different vibrational modes of the cis-B (Cp)(2)Fe(2)(CO)(4) and the gauche-NB (Cp)(2)Ru(2)(CO)(4) complexes. Treating the energy transfer as an equilibrium process, we extracted the rate constants associated with both the uphill and the downhill transfer of vibrational energy, finding that the difference in the rate constants of the two metal complexes maps to the difference in the energy gap between the two modes involved.
- Published
- 2011
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42. Local-mode approach to modeling multidimensional infrared spectra of metal carbonyls.
- Author
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Baiz CR, Kubarych KJ, Geva E, and Sibert EL 3rd
- Abstract
We present a general approach for modeling multidimensional infrared spectra based on a combination of phenomenological fitting and ab initio electronic structure calculations. The vibrational Hamiltonian is written in terms of bilinearly coupled Morse oscillators that represent local carbonyl stretches. This should be contrasted with the previous approach, where the anharmonic Hamiltonian was given in terms of normal-mode coordinates ( Baiz et al. J. Phys. Chem. A 2009 , 113 , 9617 ). The bilinearly coupled Morse oscillator Hamiltonian is parametrized such that the frequencies and couplings are consistent with experiment, and the anharmonicities are computed by density functional theory. The advantages of the local-mode versus normal-mode approaches are discussed, as well as the ability of different density functionals to provide accurate estimates of the model parameters. The applicability and usefulness of the new approach are demonstrated in the context of the recently measured multidimensional infrared spectra of dimanganese decacarbonyl. The shifts in local site frequencies, couplings, and anharmonicities due to hydrogen bonding to the individual carbonyls are explored. It is found that, even though the effect of hydrogen bonding is nonlocal, it is additive., (© 2011 American Chemical Society)
- Published
- 2011
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43. Molecular theory and simulation of coherence transfer in metal carbonyls and its signature on multidimensional infrared spectra.
- Author
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Baiz CR, Kubarych KJ, and Geva E
- Abstract
We present a general and comprehensive theoretical and computational framework for modeling ultrafast multidimensional infrared spectra of a vibrational excitonic system in liquid solution. Within this framework, we describe the dynamics of the system in terms of a quantum master equation that can account for population relaxation, dephasing, coherence-to-coherence transfer, and coherence-to-population transfer. A unique feature of our approach is that, in principle, it does not rely on any adjustable fitting parameters. More specifically, the anharmonic vibrational Hamiltonian is derived from ab initio electronic structure theory, and the system-bath coupling is expressed explicitly in terms of liquid degrees of freedom whose dynamics can be obtained via molecular dynamics simulations. The applicability of the new approach is demonstrated by employing it to model the recently observed signatures of coherence transfer in the two-dimensional spectra of dimanganese decacarbonyl in liquid cyclohexane. The results agree well with experiment and shed new light on the nature of the molecular interactions and dynamics underlying the spectra and the interplay between dark and bright states, their level of degeneracy, and the nature of their interactions with the solvent.
- Published
- 2011
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44. Solvent-hindered intramolecular vibrational redistribution.
- Author
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King JT, Anna JM, and Kubarych KJ
- Abstract
Ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations of Mn(2)(CO)(10) in a series of linear alcohols reveal that the rate of intramolecular vibrational redistribution among the terminal carbonyl stretches is dictated by the average number of hydrogen bonds formed between the solute and solvent. The presence of hydrogen bonds was found to hinder vibrational redistribution between eigenstates, while leaving the overall T(1) relaxation rate unchanged.
- Published
- 2011
- Full Text
- View/download PDF
45. Ultrabroadband detection of a mid-IR continuum by chirped-pulse upconversion.
- Author
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Baiz CR and Kubarych KJ
- Subjects
- Absorption, Carbon Dioxide chemistry, Spectrophotometry, Infrared methods
- Abstract
Ultrabroadband mid-IR continuum pulses can be detected on a single-shot basis using chirped-pulse upconversion. Converting the mid-IR pulse to the visible reduces the fractional bandwidth and enables use of a silicon CCD camera. Removing the cross-phase modulation of the chirped pulse results in 1 cm(-1) resolution over a 600 cm(-1) detected bandwidth.
- Published
- 2011
- Full Text
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46. Watching solvent friction impede ultrafast barrier crossings: a direct test of Kramers theory.
- Author
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Anna JM and Kubarych KJ
- Abstract
A systematic investigation of the solvent's dynamic influence on activated barrier crossings on an electronic ground state is performed using ultrafast two-dimensional infrared chemical exchange spectroscopy. These measurements facilitate a direct comparison with the widely adopted Kramers theory of condensed phase reaction kinetics, and for the first time avoid the significant complication of electronic excitation to probe directly in the time domain a ground electronic state reaction with a well-defined transition state. The picosecond timescale interconversion between two stable isomers of the metal carbonyl complex Co(2)(CO)(8) in a series of linear alkane solvents shows negligible energetic variation with solvent carbon chain length, providing an exclusive probe of the effects of solvent friction. Relative to the linear alkane series, cyclohexane does alter the potential energy surface by preferentially stabilizing one of the isomers. Despite this pronounced modification of the reaction barrier energetics, combination of experiment and computation enables the removal of the nondynamical barrier contribution to the rate constant, isolating the dynamical influence of solvent friction. The experimental data, supported with quantum and classical computations, show agreement with a simple Markovian Kramers theory for the isomerization rate constant's dependence on solvent viscosity.
- Published
- 2010
- Full Text
- View/download PDF
47. Solvent-dependent spectral diffusion in a hydrogen bonded "vibrational aggregate".
- Author
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King JT, Baiz CR, and Kubarych KJ
- Subjects
- Diffusion, Hydrogen Bonding, Manganese Compounds chemistry, Solvents chemistry, Spectrophotometry, Infrared, Vibration, Viscosity, Alcohols chemistry
- Abstract
Two-dimensional infrared spectroscopy (2DIR) is used to measure the viscosity-dependent spectral diffusion of a model vibrational probe, Mn(2)(CO)(10) (dimanganese decacarbonyl, DMDC), in a series of alcohols with time scales ranging from 2.67 ps in methanol to 5.33 ps in 1-hexanol. Alcohol-alkane solvent mixtures were found to produce indistinguishable linear IR spectra, while still demonstrating viscosity-dependent spectral diffusion. Using a vibrational exciton model to characterize the inhomogeneous energy landscape, several analogies emerge with multichromophoric electronic systems, such as J-aggregates and light-harvesting protein complexes. An excitonic, local vibrational mode Hamiltonian parametrized to reproduce the vibrational structure of DMDC serves as a starting point from which site energies (i.e., local carbonyl frequencies) are given Gaussian distributed disorder. The model gives excellent agreement with both the linear IR spectrum and the inhomogeneous widths extracted from 2DIR, indicating the system can be considered to be a "vibrational aggregate." This model naturally leads to exchange narrowing due to disorder-induced exciton localization, producing line widths consistent with our 1D and 2D measurements. Further, the diagonal disorder alone effectively reduces the molecular symmetry, leading to the appearance of Raman bands in the IR spectrum in accord with the measurements. Here, we show that the static inhomogeneity of the excitonic model with disorder successfully captures the essential details of the 1D spectrum while predicting the degree of IR activity of forbidden modes as well as the inhomogeneous widths and relative magnitudes of the transition moments.
- Published
- 2010
- Full Text
- View/download PDF
48. Ultrafast vibrational Stark-effect spectroscopy: exploring charge-transfer reactions by directly monitoring the solvation shell response.
- Author
-
Baiz CR and Kubarych KJ
- Subjects
- Betaine chemistry, Electron Transport, Models, Molecular, Molecular Conformation, Photochemical Processes, Time Factors, Solvents chemistry, Spectrum Analysis, Vibration
- Abstract
We present the first implementation of transient vibrational Stark-effect spectroscopy as an ultrafast probe of solvation dynamics. The method is applied to the phototriggered intramolecular charge-transfer reaction of Betaine-30, where the vibrational Stark shifts of the nearby solvent molecules--arising from the change in the electrostatic environment--are measured using a three-pulse photon echo probe. This new experiment provides a direct subpicosecond measure of the chromophore's excited-state dynamics and back electron transfer as viewed from the solvent's perspective. We develop a simple ab initio model that offers semiquantitative prediction of the experimental Stark shifts.
- Published
- 2010
- Full Text
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49. Transient vibrational echo versus transient absorption spectroscopy: a direct experimental and theoretical comparison.
- Author
-
Baiz CR, McCanne R, and Kubarych KJ
- Subjects
- Absorption, Nonlinear Dynamics, Vibration, Algorithms, Models, Theoretical, Spectrophotometry, Infrared methods
- Abstract
Transient dispersed vibrational echo (DVE) spectroscopy is a practical alternative to transient-absorption spectroscopy because it affords increased sensitivity as well as greater signal-to-noise ratio without the need to detect a reference spectrum. However, as a third-order nonlinear probe, the extraction of kinetic information from transient-DVE is somewhat cumbersome compared to transient absorption. This article provides a direct experimental and theoretical comparison between transient-absorption and transient-DVE measurements and presents a framework for analyzing kinetic measurements while exploring the implications of making some simplifying assumptions in the data analysis. The equations for computing the signal-to-noise ratios under different experimental conditions are derived and used in the analysis of the experimental data. The results, obtained under the same experimental conditions, show that for a relatively strong terminal carbonyl stretching mode, signal-to-noise ratios in transient-DVE spectroscopy are approximately 2.5 times greater than transient absorption. The experimental results along with the theoretical models indicate that transient-DVE could become an attractive alternative to transient-absorption spectroscopy for measuring the kinetics of light-induced processes.
- Published
- 2010
- Full Text
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50. Structurally selective geminate rebinding dynamics of solvent-caged radicals studied with nonequilibrium infrared echo spectroscopy.
- Author
-
Baiz CR, McCanne R, and Kubarych KJ
- Abstract
Cyclopentadienylmolybdenum(II) tricarbonyl dimer exists in two different equilibrium conformations: trans and gauche. Ultrafast photoexcitation in the ultraviolet cleaves the Mo-Mo bond, permitting observation of the subsequent geminate rebinding reaction (t(rebinding) = 31.6 ps) by monitoring infrared bleach recoveries at frequencies corresponding to the CO stretches of the trans and gauche isomers, the time-resolved measurements revealed that the monomers rebind in the trans configuration only. Further insight into the rebinding reaction was obtained by mapping the full potential energy surface along the reaction coordinate using electronic-structure methods.
- Published
- 2009
- Full Text
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