Chanelle Jumper | Princeton University (original) (raw)
Papers by Chanelle Jumper
Chemical Physics Letters, Apr 18, 2014
ABSTRACT Reports of long-lived exciton coherences have lead researchers to expect that model dime... more ABSTRACT Reports of long-lived exciton coherences have lead researchers to expect that model dimer systems inevitably generate exciton superposition states observable by two-dimensional electronic spectroscopy. Here we report a careful photophysical characterization of a model dimer system, a diacetylene-linked perylenediimide dimer to examine that issue. The absorption spectrum of the dimer shows molecular exciton splitting, indicating that excitation is delocalized. The assignment of exciton states was supported by other photophysical measurements as well as theoretical calculations. Ultrafast two-dimensional electronic spectroscopy was employed to identify and characterize excitonic and vibrational features, as they evolve over time. Population transfer between the two exciton states is found to happen in <50 fs, thus preventing the sustainment of exciton coherences. We show that such fast radiationless relaxation cannot be explained by coupling to a solvent spectral density and is therefore missed by standard approaches such as Redfield theory and the hierarchical equations of motion.
Solar light harvesting begins with electronic energy transfer in structurally complex light-harve... more Solar light harvesting begins with electronic energy transfer in structurally complex light-harvesting antennae such as the peridinin chlorophyll-a protein from dinoflagellate algae. Peridinin chlorophyll-a protein is composed of a unique combination of chlorophylls sensitized by carotenoids in a 4:1 ratio, and ultrafast spectroscopic methods have previously been utilized in elucidating their energy-transfer pathways and timescales. However, due to overlapping signals from various chromophores and competing pathways and timescales, a consistent model of intraprotein electronic energy transfer has been elusive. Here, we used a broad-band two-dimensional electronic spectroscopy, which alleviates the spectral congestion by dispersing excitation and detection wavelengths. Interchromophoric couplings appeared as cross peaks in two-dimensional electronic spectra, and these spectral features were observed between the peridinin S 2 states and chlorophyll-a Q x and Q y states. In addition, the inherently high time and frequency resolutions of two-dimensional electronic spectroscopy enabled accurate determination of the ultrafast energy-transfer dynamics. Kinetic analysis near the peridinin S 1 excited-state absorption, which forms in 24 fs after optical excitation, reveals an ultrafast energy-transfer pathway from the peridinin S 2 state to the chlorophyll-a Q x state, a hitherto unconfirmed pathway critical for fast interchromophoric transfer. We propose a model of ultrafast peridinin chlorophyll-a protein photophysics that includes (1) a conical intersection between peridinin S 2 and S 1 states to explain both the ultrafast peridinin S 1 formation and the residual peridinin S 2 population for energy transfer to chlorophyll-a, and (2) computationally and experimentally derived peridinin S 2 site energies that support the observed ultrafast peridinin S 2 to chlorophyll-a Q x energy transfer. ■ INTRODUCTION Almost all life on earth depends on photosynthesis, through which solar light energy is converted into chemical energy by algae, plants, and photosynthetic bacteria. Over billions of years of evolution, these photosynthetic organisms have evolved structurally complex machinery to make such a conversion of energy possible. 1 In the dinoflagellate Amphidinium carterae, the first step of photosynthesis involves highly efficient ultrafast downconversion of the solar photon energy in the photosynthetic light-harvesting pigment−protein complex (peridinin chlorophyll-a protein 2,3 (PCP)) into electronic excitation energy. 4,5 This is made possible by the unique chlorophyll sensitization by the carotenoid peridinin (PID) in PCP. While numerous experimental investigations 4,6−8 have been carried out to resolve the carotenoid− chlorophyll pathways, a consistent model is still lacking due to the difficulty in resolving competing pathways in multiple excited states by traditional time-resolved spectroscopic techniques. Here, we employed two-dimensional electronic spectroscopy (2DES) 9,10 to disentangle the competing contributions in the PCP light harvesting. PCP is utilized by the dinoflagellate algae A. carterae in harvesting blue-green light for photosynthesis. 2,11 This pig-ment−protein complex is composed of eight peridinin (PID) and two chlorophyll-a (CLA) molecules in close van der Waals contact and surrounded by a polypeptide chain (Figure 1A). 12 PID, upon absorption, is electronically excited from the ground state (S 0) to the second excited state (S 2); the first excited state (S 1) of PID is believed to be optically dark due to the C 2h symmetry of the polyene backbone. 13,14 The captured electronic excitation energy is subsequently funneled toward lower-energy CLA Q states, which yield absorptions in the 600−680 nm region. Current understanding of this excitation energy transfer (EET) involves one of the two following models: (1) internal conversion from PID S 2 to PID S 1 state and subsequent EET to CLA 15−17 or (2) ultrafast EET to CLA from the PID S 2 state, the latter of which accounts for the presence of residual PID S 2 electronic population, as relaxation through the conical intersection (CI) between the PID S 2 and
Photosynthetic organisms are a remarkable example of nanoscale engineering and have mastered the ... more Photosynthetic organisms are a remarkable example of nanoscale engineering and have mastered the process of solar energy harvesting over billions of years of evolution. Therefore, researchers seek insights from the light collection mechanisms of photosynthetic machinery. The initial energy transfer stage of photosynthesis, which begins with light absorption and leads to charge separation, is remarkably robust in conditions of strong energetic disorder, extreme physiological temperatures, and low light flux-very different from conventional solar conversion materials [1-3]. However, determining the key principles which are responsible for efficient conversion is a challenging task due to the complexity of the photosynthetic systems. The field encountered a fascinating lead in 2007 when oscillatory features were discovered in two-dimensional electronic spectroscopic data-the optical analogue of 2D NMR-and were assigned to quantum coherence between donor and acceptor electronic states [4 ]. In this review, we describe the evolution in our understanding of quantum effects in photosynthetic energy transfer. A vibronic model is described to demonstrate the current opinion on how quantum effects can optimize energy transfer. The energy transfer mechanism in photosynthesis has often been described by semiclassical models that invoke hopping of energy among discrete energy levels [1-3]. While quantum effects during energy transfer had been predicted long ago-as manifested in oscillatory population dynamics-they were not expected to have a functional role in robust transfer owing to their fleeting presence [4 ,5,6,7]. From an experimental perspective, measuring quantum effects (coherences in particular) was a difficult challenge because standard ultrafast spectro-scopic experiments tend to measure only probabilities (i. e. rate constants), but hide coherences. The advent of two-dimensional spectroscopy in early 2000s made the detection of coherences within reach [8]. Being able to detect electronic coherences enabled researchers to address the long-standing goal of working out the possible functional role of coherences. 2DES generates and probes a coherent superposition of spectroscopic states by employing a specific sequence of ultrashort excitation and detection pulses [8,9]. This results in an excitation-detection correlation map whereby energy levels and their couplings are revealed by the patterns of peaks along the diagonal and cross positions (Figure 1). A cross peak in particular reveals coupled excited and detected transitions, and amplitude modulations as a function of delay time indicates coherence between those transitions (Figure 1). Coherence involving only electronic states is referred to as excitonic or electronic coherence (Figure 2a top). In addition to generating electronic coherences, short laser pulses create vibrational coherences. Electronic and vibrational coher-ences produce oscillations at different sets of coordinates in 2DES maps. Analysis of 'beat maps', that display the coherence frequencies and their coordinates helps us to discriminate the origins of coherences because electronic and vibrational coherences exhibit unique patterns (Figure 2a top versus middle). 2DES measurements reported by Fleming and coworkers revealed the first observation of the long-lived amplitude oscillations (ca. 660-fs time-constant) assigned to electronic coherence. This work investigated the Fenna-Mathews-Olson (FMO) photosynthetic complex at cryo-genic temperatures [4 ]. These oscillations were proposed to originate from excitonic coherence based on the cross peak position, which is present at the energy intersection between the exciton states in the system. Vibra-tional coherences were not suspected because it was thought they should have insignificant amplitude owing to a small displacement of the vibrational mode in the excited state of isolated chromophores. The finding was remarkable because it led researchers to speculate about wave-like transport through quantum coherence. It was imagined that coherent energy migration would sample a vast phase space to carve the most efficient pathway.
Determining the key features of high-efficiency photosynthetic energy transfer remains an ongoing... more Determining the key features of high-efficiency photosynthetic energy transfer remains an ongoing task. Recently, there has been evidence for the role of vibronic coherence in linking donor and acceptor states to redistribute oscillator strength for enhanced energy transfer. To gain further insights into the interplay between vibronic wave-packets and energy-transfer dynamics, we systematically compare four structurally related phycobiliproteins from cryptophyte algae by broad-band pump−probe spectroscopy and extend a parametric model based on global analysis to include vibrational wavepacket characterization. The four phycobiliproteins isolated from cryptophyte algae are two "open" structures and two "closed" structures. The closed structures exhibit strong exciton coupling in the central dimer. The dominant energy-transfer pathway occurs on the subpicosecond timescale across the largest energy gap in each of the proteins, from central to peripheral chromophores. All proteins exhibit a strong 1585 cm −1 coherent oscillation whose relative amplitude, a measure of vibronic intensity borrowing from resonance between donor and acceptor states, scales with both energy-transfer rates and damping rates. Central exciton splitting may aid in bringing the vibronically linked donor and acceptor states into better resonance resulting in the observed doubled rate in the closed structures. Several excited-state vibrational wavepackets persist on timescales relevant to energy transfer, highlighting the importance of further investigation of the interplay between electronic coupling and nuclear degrees of freedom in studies on high-efficiency photosynthesis.
The Journal of Chemical Physics, 2016
When exciting a complex molecular system with a short optical pulse, all chromophores present in ... more When exciting a complex molecular system with a short optical pulse, all chromophores present in the system can be excited. The resulting superposition of electronically and vibrationally excited states evolves in time, which is monitored with transient absorption spectroscopy. We present a methodology to resolve simultaneously the contributions of the different electronically and vibrationally excited states from the complete data. The evolution of the excited states is described with a superposition of damped oscillations. The amplitude of a damped oscillation cos(ωnt)exp(-γnt) as a function of the detection wavelength constitutes a damped oscillation associated spectrum DOASn(λ) with an accompanying phase characteristic φn(λ). In a case study, the cryptophyte photosynthetic antenna complex PC612 which contains eight bilin chromophores was excited by a broadband optical pulse. Difference absorption spectra from 525 to 715 nm were measured until 1 ns. The population dynamics is described by four lifetimes, with interchromophore equilibration in 0.8 and 7.5 ps. We have resolved 24 DOAS with frequencies between 130 and 1649 cm(-1) and with damping rates between 0.9 and 12 ps(-1). In addition, 11 more DOAS with faster damping rates were necessary to describe the &amp;quot;coherent artefact.&amp;quot; The DOAS contains both ground and excited state features. Their interpretation is aided by DOAS analysis of simulated transient absorption signals resulting from stimulated emission and ground state bleach.
The Journal of Physical Chemistry Letters, 2016
In this work, we demonstrate the use of broad-band pump-probe spectroscopy to measure femtosecond... more In this work, we demonstrate the use of broad-band pump-probe spectroscopy to measure femtosecond solvation dynamics. We report studies of a rhodamine dye in methanol and cryptophyte algae light-harvesting proteins in aqueous suspension. Broad-band impulsive excitation generates a vibrational wavepacket that oscillates on the excited-state potential energy surface, destructively interfering with itself at the minimum of the surface. This destructive interference gives rise to a node at a certain probe wavelength that varies with time. This reveals the Gibbs free-energy changes of the excited-state potential energy surface, which equates to the solvation time correlation function. This method captures the inertial solvent response of water (∼40 fs) and the bimodal inertial response of methanol (∼40 and ∼150 fs) and reveals how protein-buried chromophores are sensitive to the solvent dynamics inside and outside of the protein environment.
The Journal of Chemical Physics, 2016
We rebuild the theory of ultrafast transient-absorption/transmission spectroscopy starting from t... more We rebuild the theory of ultrafast transient-absorption/transmission spectroscopy starting from the optical response of an individual molecule to incident femtosecond pump and probe pulses. The resulting description makes use of pulse propagators and free molecular evolution operators to arrive at compact expressions for the several contributions to a transient-absorption signal. In this alternative description, which is physically equivalent to the conventional response-function formalism, these signal contributions are conveniently expressed as quantum mechanical overlaps between nuclear wave packets that have undergone different sequences of pulse-driven optical transitions and time-evolution on different electronic potential-energy surfaces. Using this setup in application to a simple, multimode model of the light-harvesting chromophores of PC577, we develop wave-packet pictures of certain generic features of ultrafast transient-absorption signals related to the probed-frequency dependence of vibrational quantum beats. These include a Stokes-shifting node at the time-evolving peak emission frequency, antiphasing between vibrational oscillations on opposite sides (i.e., to the red or blue) of this node, and spectral fingering due to vibrational overtones and combinations. Our calculations make a vibrationally abrupt approximation for the incident pump and probe pulses, but properly account for temporal pulse overlap and signal turn-on, rather than neglecting pulse overlap or assuming delta-function excitations, as are sometimes done.
Analytical Chemistry, Apr 5, 2012
Carbene chemistry has been used recently in structural mass spectrometry as a labeling method for... more Carbene chemistry has been used recently in structural mass spectrometry as a labeling method for mapping protein surfaces. The current study presents a method for quantitating label distribution at the amino acid level and explores the nature and basis for an earlier observation of labeling bias. With the use of a method based on liquid chromatography−tandem mass spectrometry (LC−MS/MS) applied to digests of holo-calmodulin, we developed a quantitation strategy to map site-specific incorporation of carbene, generated from photolysis of ionic label precursors 2amino-4,4-azipentanoic acid and 4,4-azipentanoic acid. The approach provides reliable incorporation data for fragments generated by electron-transfer dissociation, whereas highenergy collisional dissociation leads to energy and sequence-dependent loss of the label as a neutral. However, both can produce data suitable for mapping residues in the interaction of holo-calmodulin with M13 peptide ligand. Site-specific labeling was monitored as a function of reagent, ionic strength, and temperature, demonstrating that electrostatic interactions at the protein surface can "steer" the distribution of label precursors to sites of surface charge and favor label insertion into residues in the vicinity of the surface charge. A further preference for insertion into carboxylates was observed, based on chemical reactivity. We suggest that decoupling surface partitioning from the chemistry of insertion offers a flexible, tunable labeling strategy for structural mass spectrometry that can be applied to a broad range of protein surface compositions and promotes the design of reagents to simplify the workflow.
The Journal of Physical Chemistry A, 2015
Broadband transient absorption and two-dimensional electronic spectroscopy (2DES) studies of meth... more Broadband transient absorption and two-dimensional electronic spectroscopy (2DES) studies of methylene blue in aqueous solution are reported. By isolating the coherent oscillations of the nonlinear signal amplitude and Fourier transforming with respect to the population time, we analyzed a significant number of coherences in the frequency domain and compared them with predictions of the vibronic spectrum from density function theory (DFT) calculations. We show here that such a comparison enables reliable assignments of vibrational coherences to particular vibrational modes, with their constituent combination bands and overtones also being identified via Franck-Condon analysis aided by DFT. Evaluation of the Fourier transform (FT) spectrum of transient absorption recorded to picosecond population times, in coincidence with 2D oscillation maps that disperse the FT spectrum into the additional excitation axis, is shown to be a complementary approach toward detailed coherence determination. Using the Franck-Condon overlap integrals determined from DFT calculations, we modeled 2D oscillation maps up to two vibrational quanta in the ground and excited state (six-level model), showing agreement with experiment. This semiquantitative analysis is used to interpret the geometry change upon photoexcitation as an expansion of the central sulfur/nitrogen containing ring due to the increased antibonding character in the excited state.
The journal of physical chemistry. B, Jan 18, 2015
The first step of photosynthesis is the absorption of light by antenna complexes. Recent studies ... more The first step of photosynthesis is the absorption of light by antenna complexes. Recent studies of light harvesting complexes using two-dimensional electronic spectroscopy have revealed interesting coherent oscillations. Some contributions to those coherences are assigned to electronic coherence and therefore have implications for theories of energy transfer. To assign these femtosecond data and gain insight into the interplay among electronic and vibrational resonances, we need detailed information on vibrations and coherences in the excited electronic state compared to the ground electronic state. Here we used broad band transient absorption and femtosecond stimulated Raman spectroscopies to record ground and excited state coherences in four related photosynthetic proteins: PC577 from Hemiselmis pacifica CCMP706, PC612 from Hemiselmis virescens CCAC 1635 B, PC630 from Chroomonas CCAC 1627 B (marine), and PC645 from Chroomonas mesostigmatica CCMP269. Two of those proteins (PC630 a...
RSC Energy and Environment Series, 2013
ABSTRACT
Science, 2013
Although the energy transfer processes in natural light-harvesting systems have been intensively ... more Although the energy transfer processes in natural light-harvesting systems have been intensively studied for the past 60 years, certain details of the underlying mechanisms remain controversial. We performed broadband two-dimensional (2D) electronic spectroscopy measurements on light-harvesting proteins from purple bacteria and isolated carotenoids in order to characterize in more detail the excited-state manifold of carotenoids, which channel energy to bacteriochlorophyll molecules. The data revealed a well-resolved signal consistent with a previously postulated carotenoid dark state, the presence of which was confirmed by global kinetic analysis. The results point to this state&amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s role in mediating energy flow from carotenoid to bacteriochlorophyll.
Physics of Life Reviews, 2014
One of the most far-reaching questions in the science of living systems is that of the nature of ... more One of the most far-reaching questions in the science of living systems is that of the nature of consciousness. While the field of biology has made enormous progress through the application of Newtonian physical principles, significant unanswered questions abound in many facets of biological function, ranging from the inception of life all the way to free will, and potentially further into the metaphysical realm of human capabilities. It is not clear that we presently have the right tools and foundation to address such ethereal concepts. The mystery of life is readily highlighted, in many cases, when one attempts to apply known physical laws, established for non-living matter, to biological systems.
Chemical Physics Letters, 2014
Reports of long-lived exciton coherences have lead researchers to expect that model dimer systems... more Reports of long-lived exciton coherences have lead researchers to expect that model dimer systems inevitably generate exciton superposition states observable by two-dimensional electronic spectroscopy. Here we report a careful photophysical characterization of a model dimer system, a diacetylene-linked perylenediimide dimer to examine that issue. The absorption spectrum of the dimer shows molecular exciton splitting, indicating that excitation is delocalized. The assignment of exciton states was supported by other photophysical measurements as well as theoretical calculations. Ultrafast two-dimensional electronic spectroscopy was employed to identify and characterize excitonic and vibrational features, as they evolve over time. Population transfer between the two exciton states is found to happen in <50 fs, thus preventing the sustainment of exciton coherences. We show that such fast radiationless relaxation cannot be explained by coupling to a solvent spectral density and is therefore missed by standard approaches such as Redfield theory and the hierarchical equations of motion.
Analytical Chemistry, 2012
Carbene chemistry has been used recently in structural mass spectrometry as a labeling method for... more Carbene chemistry has been used recently in structural mass spectrometry as a labeling method for mapping protein surfaces. The current study presents a method for quantitating label distribution at the amino acid level and explores the nature and basis for an earlier observation of labeling bias. With the use of a method based on liquid chromatography−tandem mass spectrometry (LC−MS/MS) applied to digests of holo-calmodulin, we developed a quantitation strategy to map site-specific incorporation of carbene, generated from photolysis of ionic label precursors 2amino-4,4-azipentanoic acid and 4,4-azipentanoic acid. The approach provides reliable incorporation data for fragments generated by electron-transfer dissociation, whereas highenergy collisional dissociation leads to energy and sequence-dependent loss of the label as a neutral. However, both can produce data suitable for mapping residues in the interaction of holo-calmodulin with M13 peptide ligand. Site-specific labeling was monitored as a function of reagent, ionic strength, and temperature, demonstrating that electrostatic interactions at the protein surface can "steer" the distribution of label precursors to sites of surface charge and favor label insertion into residues in the vicinity of the surface charge. A further preference for insertion into carboxylates was observed, based on chemical reactivity. We suggest that decoupling surface partitioning from the chemistry of insertion offers a flexible, tunable labeling strategy for structural mass spectrometry that can be applied to a broad range of protein surface compositions and promotes the design of reagents to simplify the workflow.
Analytical Chemistry, 2011
T he close relationship between protein structure and function fuels ongoing research in method d... more T he close relationship between protein structure and function fuels ongoing research in method development for structural characterization of proteins and their interactions. X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are well-established tools for such applications but present fundamental limitations related to crystallization, molecular weight, solubility, and concentration. Methods in structural mass spectrometry (MS) provide a useful supplement by providing topographical data that can be mined for structure-building and characterizing protein conformational change, particularly for systems involving large protein complexes and their interactions. 2 Such data can be obtained from differential chemical labeling experiments. 3 Altered rates of labeling can reflect changes in the exposure of the protein, depending on the mechanism of the labeling chemistry. Changes in surface exposure can be probed by examining the permanent or temporary bonds formed from reactions of the protein with chemical reagents. The location of the modifications can be mapped down to the peptide level by proteolytic digestion prior to analysis. Mass spectrometry is wellsuited for detecting and quantifying modified proteins and peptides, since the modifications result in a mass shift that can be accurately detected with high sensitivity and speed, while tandem MS offers possibilities for residue-level resolution. For example, hydrogen/deuterium exchange (H/DX)ÀMS has been used extensively for probing protein structure and dynamics. 4À7 With the exception of amide bonds N-terminal to proline residues, exchange is not limited to specific backbone amides and therefore offers a relatively unbiased view of protein topography. The spatial resolution may be limited to the peptide level by H/D for most practical applications, as a result of hydrogen scrambling in the gas phase upon collisionally induced dissociation. However, recent efforts using electron-transfer or electron-capture dissociation on "cool" ions show some promise in locating amide hydrogens, particularly for small intact proteins. 8À11 Nevertheless, the temporal constraints imposed by amide hydrogen backexchange limit H/DX-MS to protein systems of modest complexity.
Chemical Physics Letters, Apr 18, 2014
ABSTRACT Reports of long-lived exciton coherences have lead researchers to expect that model dime... more ABSTRACT Reports of long-lived exciton coherences have lead researchers to expect that model dimer systems inevitably generate exciton superposition states observable by two-dimensional electronic spectroscopy. Here we report a careful photophysical characterization of a model dimer system, a diacetylene-linked perylenediimide dimer to examine that issue. The absorption spectrum of the dimer shows molecular exciton splitting, indicating that excitation is delocalized. The assignment of exciton states was supported by other photophysical measurements as well as theoretical calculations. Ultrafast two-dimensional electronic spectroscopy was employed to identify and characterize excitonic and vibrational features, as they evolve over time. Population transfer between the two exciton states is found to happen in <50 fs, thus preventing the sustainment of exciton coherences. We show that such fast radiationless relaxation cannot be explained by coupling to a solvent spectral density and is therefore missed by standard approaches such as Redfield theory and the hierarchical equations of motion.
Solar light harvesting begins with electronic energy transfer in structurally complex light-harve... more Solar light harvesting begins with electronic energy transfer in structurally complex light-harvesting antennae such as the peridinin chlorophyll-a protein from dinoflagellate algae. Peridinin chlorophyll-a protein is composed of a unique combination of chlorophylls sensitized by carotenoids in a 4:1 ratio, and ultrafast spectroscopic methods have previously been utilized in elucidating their energy-transfer pathways and timescales. However, due to overlapping signals from various chromophores and competing pathways and timescales, a consistent model of intraprotein electronic energy transfer has been elusive. Here, we used a broad-band two-dimensional electronic spectroscopy, which alleviates the spectral congestion by dispersing excitation and detection wavelengths. Interchromophoric couplings appeared as cross peaks in two-dimensional electronic spectra, and these spectral features were observed between the peridinin S 2 states and chlorophyll-a Q x and Q y states. In addition, the inherently high time and frequency resolutions of two-dimensional electronic spectroscopy enabled accurate determination of the ultrafast energy-transfer dynamics. Kinetic analysis near the peridinin S 1 excited-state absorption, which forms in 24 fs after optical excitation, reveals an ultrafast energy-transfer pathway from the peridinin S 2 state to the chlorophyll-a Q x state, a hitherto unconfirmed pathway critical for fast interchromophoric transfer. We propose a model of ultrafast peridinin chlorophyll-a protein photophysics that includes (1) a conical intersection between peridinin S 2 and S 1 states to explain both the ultrafast peridinin S 1 formation and the residual peridinin S 2 population for energy transfer to chlorophyll-a, and (2) computationally and experimentally derived peridinin S 2 site energies that support the observed ultrafast peridinin S 2 to chlorophyll-a Q x energy transfer. ■ INTRODUCTION Almost all life on earth depends on photosynthesis, through which solar light energy is converted into chemical energy by algae, plants, and photosynthetic bacteria. Over billions of years of evolution, these photosynthetic organisms have evolved structurally complex machinery to make such a conversion of energy possible. 1 In the dinoflagellate Amphidinium carterae, the first step of photosynthesis involves highly efficient ultrafast downconversion of the solar photon energy in the photosynthetic light-harvesting pigment−protein complex (peridinin chlorophyll-a protein 2,3 (PCP)) into electronic excitation energy. 4,5 This is made possible by the unique chlorophyll sensitization by the carotenoid peridinin (PID) in PCP. While numerous experimental investigations 4,6−8 have been carried out to resolve the carotenoid− chlorophyll pathways, a consistent model is still lacking due to the difficulty in resolving competing pathways in multiple excited states by traditional time-resolved spectroscopic techniques. Here, we employed two-dimensional electronic spectroscopy (2DES) 9,10 to disentangle the competing contributions in the PCP light harvesting. PCP is utilized by the dinoflagellate algae A. carterae in harvesting blue-green light for photosynthesis. 2,11 This pig-ment−protein complex is composed of eight peridinin (PID) and two chlorophyll-a (CLA) molecules in close van der Waals contact and surrounded by a polypeptide chain (Figure 1A). 12 PID, upon absorption, is electronically excited from the ground state (S 0) to the second excited state (S 2); the first excited state (S 1) of PID is believed to be optically dark due to the C 2h symmetry of the polyene backbone. 13,14 The captured electronic excitation energy is subsequently funneled toward lower-energy CLA Q states, which yield absorptions in the 600−680 nm region. Current understanding of this excitation energy transfer (EET) involves one of the two following models: (1) internal conversion from PID S 2 to PID S 1 state and subsequent EET to CLA 15−17 or (2) ultrafast EET to CLA from the PID S 2 state, the latter of which accounts for the presence of residual PID S 2 electronic population, as relaxation through the conical intersection (CI) between the PID S 2 and
Photosynthetic organisms are a remarkable example of nanoscale engineering and have mastered the ... more Photosynthetic organisms are a remarkable example of nanoscale engineering and have mastered the process of solar energy harvesting over billions of years of evolution. Therefore, researchers seek insights from the light collection mechanisms of photosynthetic machinery. The initial energy transfer stage of photosynthesis, which begins with light absorption and leads to charge separation, is remarkably robust in conditions of strong energetic disorder, extreme physiological temperatures, and low light flux-very different from conventional solar conversion materials [1-3]. However, determining the key principles which are responsible for efficient conversion is a challenging task due to the complexity of the photosynthetic systems. The field encountered a fascinating lead in 2007 when oscillatory features were discovered in two-dimensional electronic spectroscopic data-the optical analogue of 2D NMR-and were assigned to quantum coherence between donor and acceptor electronic states [4 ]. In this review, we describe the evolution in our understanding of quantum effects in photosynthetic energy transfer. A vibronic model is described to demonstrate the current opinion on how quantum effects can optimize energy transfer. The energy transfer mechanism in photosynthesis has often been described by semiclassical models that invoke hopping of energy among discrete energy levels [1-3]. While quantum effects during energy transfer had been predicted long ago-as manifested in oscillatory population dynamics-they were not expected to have a functional role in robust transfer owing to their fleeting presence [4 ,5,6,7]. From an experimental perspective, measuring quantum effects (coherences in particular) was a difficult challenge because standard ultrafast spectro-scopic experiments tend to measure only probabilities (i. e. rate constants), but hide coherences. The advent of two-dimensional spectroscopy in early 2000s made the detection of coherences within reach [8]. Being able to detect electronic coherences enabled researchers to address the long-standing goal of working out the possible functional role of coherences. 2DES generates and probes a coherent superposition of spectroscopic states by employing a specific sequence of ultrashort excitation and detection pulses [8,9]. This results in an excitation-detection correlation map whereby energy levels and their couplings are revealed by the patterns of peaks along the diagonal and cross positions (Figure 1). A cross peak in particular reveals coupled excited and detected transitions, and amplitude modulations as a function of delay time indicates coherence between those transitions (Figure 1). Coherence involving only electronic states is referred to as excitonic or electronic coherence (Figure 2a top). In addition to generating electronic coherences, short laser pulses create vibrational coherences. Electronic and vibrational coher-ences produce oscillations at different sets of coordinates in 2DES maps. Analysis of 'beat maps', that display the coherence frequencies and their coordinates helps us to discriminate the origins of coherences because electronic and vibrational coherences exhibit unique patterns (Figure 2a top versus middle). 2DES measurements reported by Fleming and coworkers revealed the first observation of the long-lived amplitude oscillations (ca. 660-fs time-constant) assigned to electronic coherence. This work investigated the Fenna-Mathews-Olson (FMO) photosynthetic complex at cryo-genic temperatures [4 ]. These oscillations were proposed to originate from excitonic coherence based on the cross peak position, which is present at the energy intersection between the exciton states in the system. Vibra-tional coherences were not suspected because it was thought they should have insignificant amplitude owing to a small displacement of the vibrational mode in the excited state of isolated chromophores. The finding was remarkable because it led researchers to speculate about wave-like transport through quantum coherence. It was imagined that coherent energy migration would sample a vast phase space to carve the most efficient pathway.
Determining the key features of high-efficiency photosynthetic energy transfer remains an ongoing... more Determining the key features of high-efficiency photosynthetic energy transfer remains an ongoing task. Recently, there has been evidence for the role of vibronic coherence in linking donor and acceptor states to redistribute oscillator strength for enhanced energy transfer. To gain further insights into the interplay between vibronic wave-packets and energy-transfer dynamics, we systematically compare four structurally related phycobiliproteins from cryptophyte algae by broad-band pump−probe spectroscopy and extend a parametric model based on global analysis to include vibrational wavepacket characterization. The four phycobiliproteins isolated from cryptophyte algae are two "open" structures and two "closed" structures. The closed structures exhibit strong exciton coupling in the central dimer. The dominant energy-transfer pathway occurs on the subpicosecond timescale across the largest energy gap in each of the proteins, from central to peripheral chromophores. All proteins exhibit a strong 1585 cm −1 coherent oscillation whose relative amplitude, a measure of vibronic intensity borrowing from resonance between donor and acceptor states, scales with both energy-transfer rates and damping rates. Central exciton splitting may aid in bringing the vibronically linked donor and acceptor states into better resonance resulting in the observed doubled rate in the closed structures. Several excited-state vibrational wavepackets persist on timescales relevant to energy transfer, highlighting the importance of further investigation of the interplay between electronic coupling and nuclear degrees of freedom in studies on high-efficiency photosynthesis.
The Journal of Chemical Physics, 2016
When exciting a complex molecular system with a short optical pulse, all chromophores present in ... more When exciting a complex molecular system with a short optical pulse, all chromophores present in the system can be excited. The resulting superposition of electronically and vibrationally excited states evolves in time, which is monitored with transient absorption spectroscopy. We present a methodology to resolve simultaneously the contributions of the different electronically and vibrationally excited states from the complete data. The evolution of the excited states is described with a superposition of damped oscillations. The amplitude of a damped oscillation cos(ωnt)exp(-γnt) as a function of the detection wavelength constitutes a damped oscillation associated spectrum DOASn(λ) with an accompanying phase characteristic φn(λ). In a case study, the cryptophyte photosynthetic antenna complex PC612 which contains eight bilin chromophores was excited by a broadband optical pulse. Difference absorption spectra from 525 to 715 nm were measured until 1 ns. The population dynamics is described by four lifetimes, with interchromophore equilibration in 0.8 and 7.5 ps. We have resolved 24 DOAS with frequencies between 130 and 1649 cm(-1) and with damping rates between 0.9 and 12 ps(-1). In addition, 11 more DOAS with faster damping rates were necessary to describe the &amp;quot;coherent artefact.&amp;quot; The DOAS contains both ground and excited state features. Their interpretation is aided by DOAS analysis of simulated transient absorption signals resulting from stimulated emission and ground state bleach.
The Journal of Physical Chemistry Letters, 2016
In this work, we demonstrate the use of broad-band pump-probe spectroscopy to measure femtosecond... more In this work, we demonstrate the use of broad-band pump-probe spectroscopy to measure femtosecond solvation dynamics. We report studies of a rhodamine dye in methanol and cryptophyte algae light-harvesting proteins in aqueous suspension. Broad-band impulsive excitation generates a vibrational wavepacket that oscillates on the excited-state potential energy surface, destructively interfering with itself at the minimum of the surface. This destructive interference gives rise to a node at a certain probe wavelength that varies with time. This reveals the Gibbs free-energy changes of the excited-state potential energy surface, which equates to the solvation time correlation function. This method captures the inertial solvent response of water (∼40 fs) and the bimodal inertial response of methanol (∼40 and ∼150 fs) and reveals how protein-buried chromophores are sensitive to the solvent dynamics inside and outside of the protein environment.
The Journal of Chemical Physics, 2016
We rebuild the theory of ultrafast transient-absorption/transmission spectroscopy starting from t... more We rebuild the theory of ultrafast transient-absorption/transmission spectroscopy starting from the optical response of an individual molecule to incident femtosecond pump and probe pulses. The resulting description makes use of pulse propagators and free molecular evolution operators to arrive at compact expressions for the several contributions to a transient-absorption signal. In this alternative description, which is physically equivalent to the conventional response-function formalism, these signal contributions are conveniently expressed as quantum mechanical overlaps between nuclear wave packets that have undergone different sequences of pulse-driven optical transitions and time-evolution on different electronic potential-energy surfaces. Using this setup in application to a simple, multimode model of the light-harvesting chromophores of PC577, we develop wave-packet pictures of certain generic features of ultrafast transient-absorption signals related to the probed-frequency dependence of vibrational quantum beats. These include a Stokes-shifting node at the time-evolving peak emission frequency, antiphasing between vibrational oscillations on opposite sides (i.e., to the red or blue) of this node, and spectral fingering due to vibrational overtones and combinations. Our calculations make a vibrationally abrupt approximation for the incident pump and probe pulses, but properly account for temporal pulse overlap and signal turn-on, rather than neglecting pulse overlap or assuming delta-function excitations, as are sometimes done.
Analytical Chemistry, Apr 5, 2012
Carbene chemistry has been used recently in structural mass spectrometry as a labeling method for... more Carbene chemistry has been used recently in structural mass spectrometry as a labeling method for mapping protein surfaces. The current study presents a method for quantitating label distribution at the amino acid level and explores the nature and basis for an earlier observation of labeling bias. With the use of a method based on liquid chromatography−tandem mass spectrometry (LC−MS/MS) applied to digests of holo-calmodulin, we developed a quantitation strategy to map site-specific incorporation of carbene, generated from photolysis of ionic label precursors 2amino-4,4-azipentanoic acid and 4,4-azipentanoic acid. The approach provides reliable incorporation data for fragments generated by electron-transfer dissociation, whereas highenergy collisional dissociation leads to energy and sequence-dependent loss of the label as a neutral. However, both can produce data suitable for mapping residues in the interaction of holo-calmodulin with M13 peptide ligand. Site-specific labeling was monitored as a function of reagent, ionic strength, and temperature, demonstrating that electrostatic interactions at the protein surface can "steer" the distribution of label precursors to sites of surface charge and favor label insertion into residues in the vicinity of the surface charge. A further preference for insertion into carboxylates was observed, based on chemical reactivity. We suggest that decoupling surface partitioning from the chemistry of insertion offers a flexible, tunable labeling strategy for structural mass spectrometry that can be applied to a broad range of protein surface compositions and promotes the design of reagents to simplify the workflow.
The Journal of Physical Chemistry A, 2015
Broadband transient absorption and two-dimensional electronic spectroscopy (2DES) studies of meth... more Broadband transient absorption and two-dimensional electronic spectroscopy (2DES) studies of methylene blue in aqueous solution are reported. By isolating the coherent oscillations of the nonlinear signal amplitude and Fourier transforming with respect to the population time, we analyzed a significant number of coherences in the frequency domain and compared them with predictions of the vibronic spectrum from density function theory (DFT) calculations. We show here that such a comparison enables reliable assignments of vibrational coherences to particular vibrational modes, with their constituent combination bands and overtones also being identified via Franck-Condon analysis aided by DFT. Evaluation of the Fourier transform (FT) spectrum of transient absorption recorded to picosecond population times, in coincidence with 2D oscillation maps that disperse the FT spectrum into the additional excitation axis, is shown to be a complementary approach toward detailed coherence determination. Using the Franck-Condon overlap integrals determined from DFT calculations, we modeled 2D oscillation maps up to two vibrational quanta in the ground and excited state (six-level model), showing agreement with experiment. This semiquantitative analysis is used to interpret the geometry change upon photoexcitation as an expansion of the central sulfur/nitrogen containing ring due to the increased antibonding character in the excited state.
The journal of physical chemistry. B, Jan 18, 2015
The first step of photosynthesis is the absorption of light by antenna complexes. Recent studies ... more The first step of photosynthesis is the absorption of light by antenna complexes. Recent studies of light harvesting complexes using two-dimensional electronic spectroscopy have revealed interesting coherent oscillations. Some contributions to those coherences are assigned to electronic coherence and therefore have implications for theories of energy transfer. To assign these femtosecond data and gain insight into the interplay among electronic and vibrational resonances, we need detailed information on vibrations and coherences in the excited electronic state compared to the ground electronic state. Here we used broad band transient absorption and femtosecond stimulated Raman spectroscopies to record ground and excited state coherences in four related photosynthetic proteins: PC577 from Hemiselmis pacifica CCMP706, PC612 from Hemiselmis virescens CCAC 1635 B, PC630 from Chroomonas CCAC 1627 B (marine), and PC645 from Chroomonas mesostigmatica CCMP269. Two of those proteins (PC630 a...
RSC Energy and Environment Series, 2013
ABSTRACT
Science, 2013
Although the energy transfer processes in natural light-harvesting systems have been intensively ... more Although the energy transfer processes in natural light-harvesting systems have been intensively studied for the past 60 years, certain details of the underlying mechanisms remain controversial. We performed broadband two-dimensional (2D) electronic spectroscopy measurements on light-harvesting proteins from purple bacteria and isolated carotenoids in order to characterize in more detail the excited-state manifold of carotenoids, which channel energy to bacteriochlorophyll molecules. The data revealed a well-resolved signal consistent with a previously postulated carotenoid dark state, the presence of which was confirmed by global kinetic analysis. The results point to this state&amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s role in mediating energy flow from carotenoid to bacteriochlorophyll.
Physics of Life Reviews, 2014
One of the most far-reaching questions in the science of living systems is that of the nature of ... more One of the most far-reaching questions in the science of living systems is that of the nature of consciousness. While the field of biology has made enormous progress through the application of Newtonian physical principles, significant unanswered questions abound in many facets of biological function, ranging from the inception of life all the way to free will, and potentially further into the metaphysical realm of human capabilities. It is not clear that we presently have the right tools and foundation to address such ethereal concepts. The mystery of life is readily highlighted, in many cases, when one attempts to apply known physical laws, established for non-living matter, to biological systems.
Chemical Physics Letters, 2014
Reports of long-lived exciton coherences have lead researchers to expect that model dimer systems... more Reports of long-lived exciton coherences have lead researchers to expect that model dimer systems inevitably generate exciton superposition states observable by two-dimensional electronic spectroscopy. Here we report a careful photophysical characterization of a model dimer system, a diacetylene-linked perylenediimide dimer to examine that issue. The absorption spectrum of the dimer shows molecular exciton splitting, indicating that excitation is delocalized. The assignment of exciton states was supported by other photophysical measurements as well as theoretical calculations. Ultrafast two-dimensional electronic spectroscopy was employed to identify and characterize excitonic and vibrational features, as they evolve over time. Population transfer between the two exciton states is found to happen in <50 fs, thus preventing the sustainment of exciton coherences. We show that such fast radiationless relaxation cannot be explained by coupling to a solvent spectral density and is therefore missed by standard approaches such as Redfield theory and the hierarchical equations of motion.
Analytical Chemistry, 2012
Carbene chemistry has been used recently in structural mass spectrometry as a labeling method for... more Carbene chemistry has been used recently in structural mass spectrometry as a labeling method for mapping protein surfaces. The current study presents a method for quantitating label distribution at the amino acid level and explores the nature and basis for an earlier observation of labeling bias. With the use of a method based on liquid chromatography−tandem mass spectrometry (LC−MS/MS) applied to digests of holo-calmodulin, we developed a quantitation strategy to map site-specific incorporation of carbene, generated from photolysis of ionic label precursors 2amino-4,4-azipentanoic acid and 4,4-azipentanoic acid. The approach provides reliable incorporation data for fragments generated by electron-transfer dissociation, whereas highenergy collisional dissociation leads to energy and sequence-dependent loss of the label as a neutral. However, both can produce data suitable for mapping residues in the interaction of holo-calmodulin with M13 peptide ligand. Site-specific labeling was monitored as a function of reagent, ionic strength, and temperature, demonstrating that electrostatic interactions at the protein surface can "steer" the distribution of label precursors to sites of surface charge and favor label insertion into residues in the vicinity of the surface charge. A further preference for insertion into carboxylates was observed, based on chemical reactivity. We suggest that decoupling surface partitioning from the chemistry of insertion offers a flexible, tunable labeling strategy for structural mass spectrometry that can be applied to a broad range of protein surface compositions and promotes the design of reagents to simplify the workflow.
Analytical Chemistry, 2011
T he close relationship between protein structure and function fuels ongoing research in method d... more T he close relationship between protein structure and function fuels ongoing research in method development for structural characterization of proteins and their interactions. X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are well-established tools for such applications but present fundamental limitations related to crystallization, molecular weight, solubility, and concentration. Methods in structural mass spectrometry (MS) provide a useful supplement by providing topographical data that can be mined for structure-building and characterizing protein conformational change, particularly for systems involving large protein complexes and their interactions. 2 Such data can be obtained from differential chemical labeling experiments. 3 Altered rates of labeling can reflect changes in the exposure of the protein, depending on the mechanism of the labeling chemistry. Changes in surface exposure can be probed by examining the permanent or temporary bonds formed from reactions of the protein with chemical reagents. The location of the modifications can be mapped down to the peptide level by proteolytic digestion prior to analysis. Mass spectrometry is wellsuited for detecting and quantifying modified proteins and peptides, since the modifications result in a mass shift that can be accurately detected with high sensitivity and speed, while tandem MS offers possibilities for residue-level resolution. For example, hydrogen/deuterium exchange (H/DX)ÀMS has been used extensively for probing protein structure and dynamics. 4À7 With the exception of amide bonds N-terminal to proline residues, exchange is not limited to specific backbone amides and therefore offers a relatively unbiased view of protein topography. The spatial resolution may be limited to the peptide level by H/D for most practical applications, as a result of hydrogen scrambling in the gas phase upon collisionally induced dissociation. However, recent efforts using electron-transfer or electron-capture dissociation on "cool" ions show some promise in locating amide hydrogens, particularly for small intact proteins. 8À11 Nevertheless, the temporal constraints imposed by amide hydrogen backexchange limit H/DX-MS to protein systems of modest complexity.