Structural Evolution of Photoexcited Methylcobalamin toward a CarH-like Metastable State: Evidence from Time-Resolved X-ray Absorption and X-ray Emission

R.J. Sension T.P. McClain; L.B. Michocki, N.A. Miller, R. Alonso-Mori, F.A. Lima, F. Ardana-Lamas, M. Biednov, T. Chung, A. Deb, Y. Jiang, A.K. Kaneshiro, D. Khakhulin, K. J. Kubarych, R.M. Lamb, J.H. Meadows, F. Otte, D.L. Sofferman, S. Song, Y. Uemura, T.B. van Driel, J.E. Penner-Hahn, J. Phys. Chem. B 128 (2024) 8131–8144

CarH is a protein photoreceptor that uses a form of B₁₂, adenosylcobalamin (AdoCbl), to sense light via formation of a metastable excited state. Aside from AdoCbl bound to CarH, methylcobalamin (MeCbl) is the only other example─to date─of photoexcited cobalamins forming metastable excited states with lifetimes of nanoseconds or longer. The UV–visible spectra of the excited states of MeCbl and AdoCbl bound to CarH are similar. We have used transient Co K-edge X-ray absorption and X-ray emission spectroscopies in conjunction with transient absorption spectroscopy in the UV–visible region to characterize the excited states of MeCbl. These data show that the metastable excited state of MeCbl has a slightly expanded corrin ring and increased electron density on the cobalt, but only small changes in the axial bond lengths.

Nanoclustering in Non-ideal Ethanol/Heptane Solutions Alters Solvation Dynamics

Vivian F. Crum, Kevin J. Kubarych, J. Chem. Phys. 161 (2024) 044507

Alcohol/alkane solutions widely used in chemical synthesis and as transportation fuels are highly non-ideal due to nanoscale clustering of the amphiphilic alcohol molecules within the nonpolar alkanes. Be-sides 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 etha-nol/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 concen-tration 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 concentra-tion-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 structural and dynamical aspects of mixed solvents will be necessary for predictive solution strategies in chemistry.

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

Seth Wiley, Claire Griffith, Peter Eckert, Alexander P. Mueller, Robert Nogle, Séan D. Simpson, Michael Köpke, Mehmet Can, Ritimukta Sarangi, Kevin Kubarych, Stephen W. Ragsdale, J. Biol. Chem. (in press)

One of seven natural CO₂ fixation pathways, the anaerobic Wood-Ljungdahl Pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO₂ fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

Reply to "Comment on Isolating Polaritonic 2D-IR Transmission Spectra"

Rong Duan, Joseph N. Mastron, Yin Song, and Kevin J. Kubarych, J. Phys. Chem. Lett. 14 (2023) 1046

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.

Isolating Polaritonic 2D-IR Transmission Spectra

Rong Duan, Joseph N. Mastron, Yin Song, and Kevin J. Kubarych, J. Phys. Chem. Lett. 12 (2021) 11406

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.

Ultrafast vibrational dynamics of a solute correlates with dynamics of the solvent

Vivan F. Crum, Laura M. Kiefer, and Kevin J. Kubarych

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.

Direct comparison of amplitude and geometric measures of spectral inhomogeneity using phase-cycled 2D-IR spectroscopy

Rong Duan, Joseph N. Mastron, Yin Song, and Kevin J. Kubarych

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 (W(CO)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.

Transmission Mode 2D-IR Spectroelectrochemistry of In Situ Electrocatalytic Intermediates

Laura M. Kiefer, Lindsay B. Michocki, and Kevin J. Kubarych

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 situconcentration 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)₃Cl 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)₃Cl]^•–, relative to the starting Re(bpy)(CO)3Cl. 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.

Mechanistic Study of Charge Separation in a Nonfullerene Organic Donor–Acceptor Blend Using Multispectral Multidimensional Spectroscopy

Yin Song, Xiao Liu, Yongxi Li, Hoang Huy Nguyen, Rong Duan, Kevin J. Kubarych, Stephen R. Forrest, and Jennifer P. Ogilvie

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.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Carlos R. Baiz, Bartosz Błasiak, Jens Bredenbeck, Minhaeng Cho*, Jun-Ho Choi, Steven A. Corcelli, Arend G. Dijkstra, Chi-Jui Feng, Sean Garrett-Roe, Nien-Hui Ge, Magnus W. D. Hanson-Heine, Jonathan D. Hirst, Thomas L. C. Jansen, Kijeong Kwac, Kevin J. Kubarych, Casey H. Londergan, Hiroaki Maekawa, Mike Reppert, Shinji Saito, Santanu Roy, James L. Skinner, Gerhard Stock, John E. Straub, Megan C. Thielges, Keisuke Tominaga, Andrei Tokmakoff, Hajime Torii, Lu Wang, Lauren J. Webb, and Martin T. Zanni Chem. Rev. (2020) ASAP

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.

A simple lattice Monte Carlo simulation to model interfacial and crowded water rearrangements

Ved Prakash Roy, and Kevin J. Kubarych Chem. Phys. (2020) 531, 110653

A finite, two-dimensional lattice model of liquid water captures the essential nearly four-coordinate hydrogen bonding network, while permitting a simple Metropolis Monte Carlo simulation in conditions ranging from crowded to dilute. This model examines excluded volume perturbations of hydrogen bond switching, avoiding complex topological and chemical heterogeneity of realistic interfaces. Retardation factors (relative to bulk) for switching agree with previous statistical models and atomistic molecular dynamics simulations of hydrated proteins. The model enables straightforward spatial mapping of retardation factors that are difficult to measure in atomistic simulations. The spatially-dependent retardation factors decrease exponentially from the interface. Simulating varying degrees of crowding, we do not find any cooperative, collective contributions anticipated from some recent spectroscopic observations suggesting correlated hydrogen bonding rearrangements of confined water. Longer-range cooperative interfacial influences may arise from complex chemical patterning of the surface, or to non-entropic influences such as multi-body interactions or altered hydrogen bond strengths.

Ultrafast XANES Monitors Femtosecond Sequential Structural Evolution in Photoexcited Coenzyme B12

Nicholas A. Miller, Lindsay B. Michocki, Arkaprabha Konar, Roberto Alonso-Mori, Aniruddha Deb, James M. Glownia, Danielle L. Sofferman, Sanghoon Song, Pawel M. Kozlowski, Kevin J. Kubarych, James E. Penner-Hahn, and Roseanne J. Sension J. Phys. Chem. B (2020) 124, 199-209

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 B12 (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.

Antivitamins B12 in a Microdrop: The Excited-State Structure of a Precious Sample Using Transient Polarized X-ray Absorption Near-Edge Structure

Nicholas A. Miller, Lindsay B. Michocki, Roberto Alonso-Mori, Alexander Britz, Aniruddha Deb, Daniel P. DePonte, James M. Glownia, April K. Kaneshiro, Christoph Kieninger, Jake Koralek, Joseph H. Meadows, Tim B. van Driel, Bernhard Kräutler, Kevin J. Kubarych, James E. Penner-Hahn, and Roseanne J. Sension J. Phys. Chem. Lett. (2019) 10, 5484-5489

Polarized transient X-ray absorption near-edge structure (XANES) was used to probe the excited-state structure of a photostable B₁₂ antivitamin (Coβ-2-(2,4-difluorophenyl)-ethynylcobalamin, F₂PhEtyCbl). 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 F₂PhEtyCbl 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 F₂PhEtyCbl by ca. 10% or more, comparable to the 10% elongation observed for Co–NDMB in CNCbl.

Vibrational coherence transfer illuminates dark modes in models of the FeFe hydrogenase active site

Peter A. Eckert, Kevin J. Kubarych J. Chem. Phys. (2019) 151, 054307

Within the conceptual framework of Redfield theory, the optical response function arises from the dynamical evolution of the system’s density operator, where nonunitary relaxation is encoded in the Redfield relaxation superoperator. In the conventional approach, the so-called secular approximation neglects terms that induce transitions between distinct coherences and among coherences and populations. The rationale is that these nonsecular terms are small in comparison to the far more dominant population relaxation and coherence dephasing contributions. Since two-dimensional infrared (2D-IR) spectroscopy has significant contributions arising from population relaxation and transfer pathways, it can be challenging to isolate signatures of the nonsecular relaxation. We report here that in three diiron dithiolate hexacarbonyl complexes that serve as small-molecule models of the [FeFe] hydrogenase H-cluster subsite, a fortuitous vibrational energy structure enables direct and clear signatures of vibrational coherence transfer in alkane solution. This finding holds promise towards developing a molecularly detailed understanding of the mechanism of vibrational coherence transfer processes, thanks to the ease of synthesizing derivatives based on the chemical modularity of these well studied diiron compounds. In addition to the fundamental need to characterize coherence transfer in molecular spectroscopy, we find in this set of molecules a practical utility for the nonsecular dynamics: the ability to determine the frequency of an IR-inactive mode. A coherence generated during the waiting time of the 2D-IR measurement transfers to a coherence involving the single dark CO stretching mode, which modulates some peak amplitudes in the 2D spectrum, revealing its transient excitation.

Probing the Excited State of Methylcobalamin Using Polarized Time-Resolved X-ray Absorption Spectroscopy

Lindsay B. Michocki, Nicholas A. Miller, Roberto Alonso-Mori, Alexander Britz, Aniruddha Deb, James M. Glownia, April K. Kaneshiro, Arkaprabha Konar, Jake Koralek, Joseph H. Meadows, Danielle L. Sofferman, Sanghoon Song, Megan J. Toda, Tim B. van Driel, Pawel M. Kozlowski, Kevin J. Kubarych, James E. Penner-Hahn, Roseanne J. Sension J. Phys. Chem. B (2019) 123, 6042-6048

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 B₁₂). 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 data-preserve-html-node="true" 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.

Multispectral multidimensional spectrometer spanning the ultraviolet to the mid-infrared

Yin Song, Arkaprabha Konar, Riley Sechrist, Ved Prakash Roy, Rong Duan, Jared Dziurgot, Veronica Policht, Yassel Acosta Matutes, Kevin J. Kubarych, Jennifer P. Ogilvie Rev. Sci. Instr. (2019) 90, 013108

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.

Solvent Quality Controls Macromolecular Structural Dynamics of a Dendrimeric Hydrogenase Model

Peter A. Eckert, Kevin J. Kubarych J. Phys. Chem. B (2018) 122, 12154–12163

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.

Interfacial Water Dynamics

Kevin J. Kubarych, Ved Prakash Roy, Kimberly R. Daley, Encyclopedia of Interfacial Chemistry (2018) 1, 443-461

Intense experimental, theoretical, and computational effort has been dedicated to characterizing the dynamics of water at interfaces. Experimental approaches employ variations of surface specificity through even-order nonlinear spectroscopy, or in isotopic samples using intrinsic or extrinsic probes coupled with ultrafast transient absorption, time-resolved fluorescence, multidimensional infrared, as well as nuclear magnetic resonance spectroscopy. Theoretical developments have focused on linking the interface-induced perturbations with the resulting motion of the hydrating water molecules, with a principal focus on changes in the free energy surface. Both theory and simulation have been instrumental in modeling the microscopic molecular dynamics as well as in computing experimental observables arising from the dynamics. This article provides an overview of experimental techniques that have been applied to study interfacial water dynamics, highlighting the numerous successes, as well as pointing out future directions. Since theoretical work is so central to the understanding of water, this article also outlines the extensive progress made using models and computational simulation.

Two-dimensional infrared spectroscopy of coordination complexes: From solvent dynamics to photocatalysis

Laura M. Kiefer, Kevin J. Kubarych, Coord. Chem. Rev. (2018) 372, 153-176

Two-dimensional infrared (2D-IR) spectroscopy is a powerful technique capable of accessing structure and dynamics with ultrafast time resolution in a wide range of chemical contexts. Since the early development of 2D-IR and related nonlinear IR spectroscopy methods, coordination complexes have been used primarily due to their well-defined structures and large transition intensities. As research interests have broadened to include catalysis and photocatalysis, however, 2D-IR spectroscopy has found great success in characterizing structural dynamics in a wide range of coordination complexes.

Ultrafast X-ray Absorption Near Edge Structure Reveals Ballistic Excited State Structural Dynamics

Nicholas A. Miller, Aniruddha Deb, Roberto Alonso-Mori, James M. Glownia, Laura M. Kiefer, Arkaprabha Konar, Lindsay B. Michocki, Marcin Sikorski, Danielle L. Sofferman, Sanghoon Song, Megan J. Toda, Theodore E. Wiley, Diling Zhu, Pawel M. Kozlowski, Kevin J. Kubarych, James E. Penner-Hahn, and Roseanne J. Sension J. J. Phys. Chem. A (2018) 122, 4963-4971

Polarized ultrafast time-resolved X-ray absorption near edge structure (XANES) allows characterization of excited state dynamics following excitation. Excitation of vitamin B₁₂, 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.