do we live in a quantum world? advances in multidimensional coherent spectroscopies refine our...

Do we live in a quantum world? Advances in multidimensionalcoherent spectroscopies refine our understanding of quantumcoherences and structural dynamics of biological systemsAndrea Nagy, Valentyn Prokhorenko and RJ Dwayne Miller

The issue of quantum effects in biological functions reduces to

determining the relevant length and/or time scales over which

phase relationships (coherence) in the wave properties of

matter are conserved and lead to observable interference

effects. Recent advances in femtosecond laser-based two-

dimensional spectroscopy and coherent control have made it

possible to directly determine the relevant timescales of

quantum coherence in biological systems and even manipulate

such effects, respectively, and also provide direct information

on the interactions between the different degrees of freedom

(electronic and nuclear) with sufficient time resolution to catch

the very chemical processes driving biological functions in

action. The picture that is emerging is that there are primary

events in biological processes that occur on timescales

commensurate with quantum coherence effects.

Addresses

Departments of Chemistry and Physics, and the Institute for Optical

Sciences, 80 St George Street, University of Toronto, Toronto,

Ontario, Canada

Corresponding author: Miller, RJ Dwayne

([email protected])

Current Opinion in Structural Biology 2006, 16:654–663

This review comes from a themed issue on

Biophysical methods

Edited by Arthur G Palmer III and Randy J Read

Available online 18th September 2006

0959-440X/$ – see front matter

# 2006 Elsevier Ltd. All rights reserved.

DOI 10.1016/j.sbi.2006.08.012

IntroductionThe question posed in the title of this review refers to the

relative importance of quantum mechanical effects with

respect to biological functions — processes that necessa-

rily occur on the mesoscale (dimensions of single proteins

as a lower limit), where quantum effects are expected to

converge to the classical limit. In this context, the relative

importance of quantum effects in biological systems has

been debated since the very birth of quantum mechanics

[1]. It has been well established since then that matter has

wave properties that require a quantum mechanical treat-

ment. However, it is equally well established that the

wave properties of matter only manifest their effect when

the phenomenon of interest involves motions on length


scales comparable to the de Broglie wavelength of the

constituent matter. An effective argument can be made

that any quantum effect would be negligible on the global

scale of the protein function. (The de Broglie wavelength

of a 30 kDa protein moving at thermal velocity is

�10�11 cm, which is negligible compared to typical pro-

tein motions involved in biological functions.) However,

the relevant motions involved in transition state processes

of the actual chemical processes driving the biological

response can typically be described by superposition of

more localized motions with smaller effective mass,

where the de Broglie wavelength is no longer negligible

and a quantum mechanical description is needed. (The

de Broglie wavelength of a carbon atom moving at the

speed of sound along the reaction coordinate is 0.03 nm,

which is greater than a typical displacement of heavy

atoms along reaction coordinates and large enough for

significant quantum effects.) In this regard, the single

most important distinguishing feature that separates

quantum mechanics from classical mechanics is the

underlying phase of the wave-function. It is not possible

to properly describe the constructive and destructive

interference effects of the wave properties of matter

without considering the relative phase relationships.

There can be a dramatic increase in transmission prob-

ability through barriers (e.g. transition states) for con-

structive interference effects relative to destructive

interference effects. In this regard, a central tenet of

biology is that Nature has evolved to optimize functions;

this tenet pertains to all length scales. At the molecular

level, the posed question can be rephrased to: do biolo-

gical systems exploit the phase of the wave properties of

matter to optimize their functionality?

To address this question, we need to consider the coher-

ence of the underlying wave functions. As with all wave

sources, interference effects only occur over length and

time scales for which the phase of the wave or coherence

is conserved. For example, the interference between two

monochromatic laser beams gives a light-dark fringe

pattern that can extend for meters, whereas the inter-

ference observed for an incandescent light bulb extends

only over a few microns. The importance of wave coher-

ence can be appreciated by considering the displacement

of a surfer to shore (as the target state) for well-formed

waves off Hawaii, as apposed to the motion of our intrepid

surfer in the chaotic seas off England. In the former case,

the motion is highly directed, whereas in the latter the

motion in which the wave coherence is quickly lost could

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http://dx.doi.org/10.1016/j.sbi.2006.08.012

Multidimensional coherent spectroscopy Nagy, Prokhorenko and Miller 655

be described as random diffusive motion. The efficiency

in realizing the target state is significantly higher for

conditions leading to constructive interference along

the target pathway. For quantum systems, the conserva-

tion of relative phase relationships is referred to as quan-

tum coherence [2]. The associated time and length scales

of coherence over which interference effects can be

observed are perhaps the most central part of this issue.

If the process occurs over length or time scales that are

much longer than those over which the phase correlation

is conserved, both constructive and destructive interfer-

ence effects occur and quantum interference averages out

and vanishes. At this point, it needs to be recalled that

biological processes occur in the condensed phase, in

which random fluctuations of the environment lead to

dephasing (T2) and fast relaxation processes (T1) that

contribute to the net loss of coherence or phase relation-

ships. To address this issue, information is needed on the

loss in amplitude of the phase dependence or decoher-

ence times of the relevant degrees of freedom (electronic,

nuclear) in relation to the biological process of interest.

For instance, decoherence times for vibrational motions

are typically on the order of picoseconds, whereas elec-

tronic dephasing times are on the 10–100 fs timescale

[3,4]. These are phenomenally short timescales and

require femtosecond (10�15 s) laser pulses to probe the

relevant issues. There are, however, biological processes,

such as energy transfer and barrier crossing events, as

depicted in Figure 1, that occur on timescales that are

Figure 1

Representative examples of quantum effects in biological systems. (a) Excit

chromophores (monomers) in close proximity can have sufficient dipole–dip

effects in which the initial degenerate states are split into two new (exciton)

in the protein environment can modify the site energies and potentially spat

(b) Interfering wave functions at conical intersections. In nuclear configuratio

that create seams connecting the reactant surface to the product surface in

the wave function in the product channel. The schematic is specific for bR.

bond in concert with bond softening along this axis [43��]. The biological pr

non-radiative relaxation of the retinal chromophore, both processes occurrin

possible that the protein structure constrains thermal fluctuations to favor c

this point for optimal efficiency in the face of such competition.


comparable to the decoherence times. It is in these cases

that one can ask anew what the likelihood is that Nature

has even harnessed the purest form of quantum effects in

optimizing functions.

This question is intriguing, and technologically and the-

oretically challenging at the same time. It is only recently

that advances in spectroscopy have been made that

enable coherence effects in biological systems to be

appropriately addressed to probe this fundamental issue.

It needs to be emphasized that the general motivation for

the various spectroscopic advances has been unrelated to

the stated question. This issue of quantum effects is still

speculative and is discussed in the spirit of this type of

review, an ‘opinion’ on where we think some fundamen-

tal advances may be forthcoming beyond the immediate

goals of the current research.

Recent technological advances inmultidimensional coherent laserspectroscopyTwo general forms of multidimensional spectroscopy will

be discussed, namely non-linear four-wave mixing invol-

ving two time variables, in particular 2D spectroscopy, and

coherent control. Both methods are very analogous to

NMR. The major distinction is that these coherence

spectroscopies use laser pulses in the visible and IR region,

and thus address changes in electron distribution and

nuclear displacements, respectively, as opposed to probing

on formation and spatially directed excited state energy. Two

ole interaction to experience constructive and destructive interference

states (D is the interaction energy). Small changes in charge distribution

ially direct excited state energy in the process of light absorption.

n space, there are narrow regions in the potential energy surface

which only minute motions of the heavy atoms are enough to localize

The reaction involves small torsional motions along the C13–C14

ocess of photoisomerization is in strict competition with the very fast

g within electronic and vibrational decoherence timescales. It is

onstructive interference of the principle reactive modes through


656 Biophysical methods

and manipulating nuclear spins [5]. The important differ-

ence with respect to NMR is that the manipulation of

population and coherences in the electronic and vibra-

tional degrees of freedom can be directly related to reac-

tion dynamics on timescales well outside the range of

NMR. The current state of laser technology enables the

probing of the very fastest events in Nature with few

femtosecond time resolution. Figure 2 shows a typical

experimental setup for 2D spectroscopy and the associated

information content. In the case of coherent control, the

spectral amplitude and phase are manipulated to provide

multiple variables, but typically in a single beam approach

(Figure 3). The perturbations due to these shaped pulses

are deliberately targeted to affect or to control photoche-

mical and photobiological processes, resulting in active

intervention. Inverting the pulse shapes found with coher-

ent control protocols to molecular details [6] is not yet as

well defined as inverting measured maps in 2D experi-

ments, and one is still limited to asking fairly qualitative

questions for systems as complex as biological ones.

Figure 2

2D spectroscopy. (a) Experimental setup. Schematic showing a femtosecon

specifically generate the beams in the correct spatial relationship for phase

a local oscillator for phase-sensitive detection. The DO approach [44–46,47

either correlating the noise in a symmetric arrangement or anti-correlating th

sequence is shown at the bottom. The delay between the initial excitation a

excitation wavelength (n1) and the signal field radiating from the sample is d

dimension (n3) in a 2D plot. This information is collected as a function of pro

function of time. (b) Information content in 2D spectroscopy. The signal alo

spectrum (shown at bottom). The signal along the anti-diagonal is the homo

off-diagonal peaks directly give the coupling between states/modes (D from

excited state features off-diagonal that can be readily assigned as they are

different colors and signs) and red shifted relative to the fundamental due to

if the plot is elongated along the diagonal, the absorption spectrum is inhom

(homogeneous) gives direct information on the coupling of the energy levels


2D spectroscopy of biological systems2D IR spectroscopy of protein dynamics

Recent work has focused on exploiting the information on

dynamics and structure that is simultaneously accessible

with 2D IR. This connection is essential to understanding

the structure-function relationships of biological mole-

cules. The key terms for the intramolecular and inter-

molecular interactions are the anharmonic components in

the potential energy surface, which rapidly fluctuates in

time. This information is contained in the off-diagonal

features in the 2D spectrum (Figure 2b) and in the time-

dependent evolution of the frequency–frequency corre-

lations, as evident from the changing shapes in the 2D

spectra. Considerable effort is being directed towards the

study of various conformational states of model polypep-

tides [7–9,10�], polynucleotides [11�,12], photo-induced

unfolding processes [13,14] and coupling between vibra-

tions [15,16]. There are now double-resonance methods

[17�,18], akin to NMR, and even 3D methods on the

horizon [19].

d laser beam coming into a diffractive optic (DO) that is designed to

-matched four-wave mixing, along with a reference beam to serve as�] solved the phase stability problem for heterodyne detection by

e noise in an optical system with inversion symmetry. The pulse

nd rephasing pulse (t1) is Fourier transformed to provide the

etected in a spectrometer to provide the second frequency

be delay (T) to map out the frequency–frequency correlation as a

ng the diagonal is identical to a 1D frequency domain absorption

geneous linewidth, isolated from the signal rephasing. The

Figure 1a) and information on spectral diffusion. There are also

opposite in sign (increased absorption with excitation denoted by

the anharmonic progression in excited state levels. From inspection,

ogeneously broadened. The time it takes to become symmetric

to the surroundings.



Figure 3

Coherent control experimental setup. Schematic showing a closed-loop experiment [48] in which the signal monitoring the amount of a target

state is used as feedback to a pulse-shaping system. The feedback typically employs a genetic search algorithm for solving multivariable

problems to either increase or decrease the amount of target state. The pulse shaper can be either a programmable acoustic filter (as shown)

or a spatial light modulator based on liquid-crystal displays. It is now possible to modulate both the spectral amplitude and phase to create

nearly any desired pulse shape. By modulating the phase, it is possible to have different colors arrive at different times and imprint phase

information on the molecular system through the excitation of a superposition state. The phase dependence gives direct information on the

importance of quantum coherence effects in the system response.

A new probe of protein dynamics is now available that

provides information on both structure and dynamics.

One can foresee rapid advances in this area, whereby

several different combinations of isotopic labeling and

double-resonance 2D IR methods are used to map out

key elements in the early phases of protein folding and

other structurally relevant protein motions.

Direct probes of the hydrogen-bond network in

liquid water

To understand protein structure and dynamics, one

should start with the host medium. In this regard, one

of the most important recent advances in 2D IR spectro-

scopy has been the study of the hydrogen-bond network

in liquid water. By tuning to the OH stretch frequency of

liquid water, around 3400 cm�1, it is possible to directly

access information about the hydrogen-bond network, the

very forces that give rise to water’s special properties. The

anomalously broad spectrum of the OH stretch [20–22] is

a direct consequence of the structural heterogeneity of

the dynamic structure of liquid water. The stronger the

hydrogen bond between waters, the more red shifted is

the OH stretch frequency, as electron withdrawal in

forming the hydrogen bond weakens the OH bond.

The proper interpretation of this line-shape with respect

to the degree of hydrogen bonding and the making and

breaking of hydrogen bonds is one of the longest standing

problems in spectroscopy. This is because the


information content of 1D spectra (absorption) cannot

distinguish between such classic issues as homogeneous

or inhomogeneous broadening. Resolution of this issue

requires a second time variable to spread out the frequen-

cies in time and to directly observe the effect of the

fluctuations of the surrounding waters on the frequency

spectrum.

The first work to address this problem used three-pulse

photon echo approaches to study HOD in D2O as a model

system for H2O [23,24�]. The first frequency-resolved 2D

IR spectrum of water exploited the longer lived nature of

the OD vibration in the HOD/H2O model system [25��].The OD stretch is spectrally well isolated from other

resonances in the spectrum of water, and serves as a

reference in which there are no resonant interactions

between the OD stretch and the surrounding waters with

respect to effects on the frequency correlations. Consis-

tent with the previous three-pulse photon echo studies,

this work found that the spectrum of HOD/H2O is

inhomogeneously broadened out to �1 ps. The 2D spec-

trum beautifully depicted the frequency correlations and

persistent memory in the liquid. The results for this

reference system (no resonant interactions) need to be

compared to results for pure H2O, in which the coupling

coefficients/frequency modulation of the OH stretch to

the various degrees of freedom could be enhanced under

the fully resonant conditions of the hydrogen-bond



Figure 4

2D IR spectroscopy of water. (a) HOD/H2O. Schematic 2D plot showing the observations of Asbury et al. [25��]. (Note that the figure is rotated

908 from Figure 2b.) The OD stretch at 2500 cm�1 is markedly inhomogeneously broadened (elongated along the diagonal), with loss of frequency

correlations extending beyond 1 ps. The signal showed frequency-dependent broadening on early timescales and spectral diffusion on the

same timescale as hydrogen-bond formation and breaking. Reprinted with permission from [25��]. (b) H2O. 2D IR spectrum of pure H2O [26��].

Note the more than order of magnitude faster memory loss in the bath correlations (signal becomes symmetric along the diagonal in <100 fs)

and energy relaxation pathways in relation to isotopic water studies. This difference was attributed to enhancement of the resonant coupling

mediated through hindered rotations or librations between neighboring waters. Adapted from [26��]. (c) Loss of memory and energy relaxation

pathways of liquid H2O. Each higher frequency mode is a harmonic of a lower frequency mode. All relaxation pathways in pure H2O can relax

into lower energy modes with conservation of energy in a nearly perfectly matched resonant network on a 100–200 fs timescale, consistent

Current Opinion in Structural Biology 2006, 16:654–663 www.sciencedirect.com


network. The challenge has been that the concentration

of pure H2O is 55 M and one needs path lengths on the

order of 400 nm to avoid high optical density effects from

distorting the pulses as they propagate through the med-

ium. The last remaining barriers to studying pure liquid

H2O were overcome in a recent study employing a unique

combination of nanofluidics and diffractive optics [26��].The H2O spectrum was determined to be inhomogen-

eously broadened and this long-standing problem was

finally resolved. Interestingly, the frequency correlations

for H2O were predominately lost within 50 fs, in stark

contrast to the much longer lived correlations for isotopic

water (Figure 4).

We now have a fairly complete map of the energy

relaxation pathways in liquid water (Figure 4). Energy

relaxation and exchange pathways occur at the maximum

rate — that of mixing through the highest frequency

intermolecular type of motion (librations). There is also

evidence that small perturbations, such as lowering the

temperature by only 108, have a profound effect on the

frequency correlations, so much so that decoherence

effects slow down for sufficiently long enough to engage

quantum-type effects, such as the formation of excitonic

coupling among water molecules [27]. Liquid H2O is

truly a marvel.

2D electronic spectroscopy — direct probes of energy

transfer in photosynthesis

Significant progress in understanding light-driven primary

events during photosynthesis has been made over the past

approximately 20 years. From the simple picture of For-

ster-like energy transfer (incoherent or random jumping of

excitation between chromophores), the paradigm has

changed to include the exciton concept [28], whereby

energy migration is essentially delocalized among strongly

coupled chromophores faster than bath randomization of

the phase of the excited state wave function [29]. To

visualize and spatially resolve the energy transfer process,

the first 2D electronic (2D-E) experiment on the Fenna-

Matthews-Olson (FMO) complex, the photosynthetic

light-harvesting complex from green sulfur bacteria, was

conducted [30��,31��]. This antenna complex is composed

of three identical proteins arranged in a trimeric unit, with

each unit containing seven bacteriochlorophylls in a spe-

cific structural arrangement. The absorption spectrum has

been assigned to a linear combination of seven exciton

states that form as a result of the electronic interaction

between primarily nearest neighbors [32]. The question

that naturally arises is whether or not there are specific

pathways for energy transfer in this spatial arrangement of

chromophores. 2D-E provides a complete map in the

(Figure 4 Legend Continued) with the largest effective couplings to interm

depicted in stop frame fashion (�10 fs time steps) for two central waters to

frequency modulation. This motion also enables relaxation pathways betwe

Despite this fast relaxation and frequency modulation, energy transfer is fou

correlation, suggesting that even the primary excitations of liquid H2O can t


spectral domain of energy transfer and relaxation processes

in a single measurement.

This study found that excitation transfer did not follow a

simple funnel-like energy cascade from higher lying

energy states to lower energy states in which all possible

pathways were involved. Rather, there were specific path-

ways through which the energy flowed and some possible

pathways appeared to be decoupled (Figure 5). This

finding is significant as it indicates a spatial correlation

to the energy flow. The implications are that there are

constructive and destructive quantum interference

effects occurring that lead to specific pathways that more

strongly focus the excitation to the trap pigment (bacter-

iochlorophyll number 3). This prospect requires that the

electronic coherence time be sufficiently long to support

such interference effects. These experiments were con-

ducted at 77 K, at which the electronic coherence time

(100–300 fs) is comparable to the spatial migration of the

excitation energy [33]. It would be very interesting to see

if these coherence effects survive at room temperature to

play a role in the light-harvesting process. At the very

least, this work brings to our attention that light-harvest-

ing systems are working close to the quantum coherence

limits for exploiting quantum interference effects for

optimizing energy transfer efficiency.

Coherent control studies of biologicalsystemsThere is a long history of using coherent control as an

elegant demonstration of the fundamental differences

between classical and quantum mechanics, that is to

say, the transfer of coherence from laser excitation to

quantum states of matter has been used to create con-

structive and destructive pathways and thereby control

the flow of matter waves [34]. It is only recently that

coherent control protocols have been exploited to probe

underlying issues of quantum coherence in biological

systems, and whether or not such complex systems could

be manipulated [35].

Control of energy transfer in light-harvesting systems

The first coherent control study of a biological process

was the work by Herek et al. [35,36��]. This group

focused on controlling the energy transfer pathways of

the antennae complex from the bacterial light-harvesting

(LH2) system. They used the change in the energy

transfer efficiency from the initially excited donors (car-

otenoids) to surrounding bacteriochlorophylls as feed-

back in a closed-loop pulse-shaping system. The

results were especially interesting in that, even for a

system as large as LH2, they were able to demonstrate

olecular librations. The effect of correlated librations (long arrows) is

show the effect of this motion on the hydrogen bond and associated

en intramolecular stretch and bend modes (shown as short arrows).

nd to occur on timescales comparable to the loss of frequency

ake on delocalized excitonic character.



Figure 5

2D-E of energy transfer in FMO. (a) Structure of the FMO complex, with light numbers giving the physical structure of the bacteriochlorophylls.

The color scheme indicates the assigned excitons numbered from 1–7, with 1 being the lowest energy exciton [30��]. With the previous assignment

of the spatial arrangement of the excitons [32], the 2D information gives a femtosecond time-resolved picture of energy transfer with nanometer

spatial resolution. It appears there are interference effects that spatially direct the energy transfer pathways so that no more than two or three

steps are involved in transmitting the absorbed energy to the energy trap (bacteriochlorophyll number 3). (b) 2D spectrum from which the

physical picture shown in (a) was derived. The 1D spectrum is shown at top and color coded to match the spatial assignment of the excitons

shown in (a) and shows the spreading out in frequency space of the different interactions in the 2D spectrum. The off-diagonal features evolve

in time to map out the energy transfer pathways [30��]. A detailed comparison to theoretical treatments of the electronic couplings between

bacteriochlorophylls and quantum interference effects is given in [31��]. Reproduced with permission from [31��].

some degree of control over the flow of excitation energy.

They were able to quench energy transfer by a factor of

30% and demonstrated that the degree of quenching

depended on the phase profile of the pulse. The opti-

mized pulse shape was found to be composed of a ‘comb’

of separated pulses; this comb structure appears to be a

general feature of controlling complex molecules [37�].The period between subpulses was in resonance with the

160 cm�1 mode of the carotenoids, which corresponds to

the torsional bending of the C–C backbone; this mode is

believed to facilitate the internal conversion from the S2

and S1 electronic surfaces [36��]. The energy transfer

step to the bacteriochlorophylls occurs almost exclusively

from the excited S2 state of the carotenoid. It was argued

that displacing this 160 cm�1 mode increased the rate of

non-radiative relaxation and thereby increased the

quenching of energy transfer. They were not able to

show increased energy transfer or constructive interfer-

ence effects.

These experiments were done at relatively high pulse

energies, where singlet–singlet annihilation effects can

contribute and even access intermediate states that could

potentially lead to complex kinetics [38�]. The phase-

dependent component observed in these experiments is

considered to be the coherent control contribution to the

optimal pulse shape. By examining b-carotene as a model


system for the LH2 carotenoids and phase-only control in

an open-loop experiment, Hauer et al. [39�] demonstrated

that, under electronically resonant conditions, it is possi-

ble to enhance the excitation of certain Raman active

modes over others. This very recent finding is all the more

significant as the electronic dephasing time of the elec-

tronic resonance enhancement is expected to be on the

order of 100 fs or less, which is shorter than the time

between subpulses in the crafted pulses; presumably

pathways for the laser field interaction that couples upper

excited states account for the additional enhancement.

So far, only quenching of energy transfer in LH2 has been

observed. If the above mechanism is correct, then it

should be possible to couple to modes that avoid relaxa-

tion paths, so that both constructive and destructive

interference pathways are demonstrated. By selectively

exciting the higher frequency skeletal modes around

1500 cm�1, rather than the low-frequency modes, it

should be possible to avoid the conical intersection in

the excited states of carotenoids that leads to non-radia-

tive relaxation and increase the net quantum yield for

energy transfer [36��]. This new insight is intriguing and

offers great potential for learning details of biological

systems that would be impossible without the advent

of the optical control knobs provided by coherent control

protocols to turn on and off different processes.



Figure 6

Coherent control of retinal isomerization in bR. (a) Optimization process

using a genetic search algorithm to shape the laser pulse for increasing

the effective quantum yield for photoisomerization of retinal in bR. The

baseline (thick black line) for no control is given by the amount of cis-

photoproduct observed for unstructured transform-limited pulses. Blue

circles are the best results in a ‘population’ of trial pulses within the

genetic algorithm rule set and the green squares are the average values

for the whole population. (b) Wigner transform of the optimal pulse. The

complex regular feature in the electric field amplitude (forcing function)

contains frequency components corresponding to the low-frequency

torsional mode involved in the isomerization process and its harmonics

(�200 cm�1). This pulse shape was found to be sensitive to the specific

phase of the different frequency components, indicating the

isomerization step conserves coherence through a critical seam in

nuclear configuration space, as schematically represented in Figure 1b,

to the point that the reaction yield can be optically manipulated through

phase control. Figure adapted from [43��].

Coherent control of biological function:

photoisomerization of retinal — the primary step

of the proton pump

The photoisomerization of retinal provides a nearly ideal

system to probe whether there are conserved phase rela-

tionships in barrier crossing events of biological systems.

This process occurs in competition with the extremely fast

non-radiative relaxation of the retinal excited state. In

solution phase, the photoisomerization of retinal results

in many different photoisomers with quantum yields typi-

cally on the order of a few percent. In a protein environ-

ment, the photoisomerization of retinal in, for example,

bacteriorhodopsin (bR) exhibits only one photoproduct,

which involves isomerization along the C13–C14 bond

with a quantum yield of 65% [40]. It is clear that the

protein structure is imposing constraints on the fluctua-

tions along this reaction coordinate. Equally important is

the speed of this biological process. This reaction occurs

within 200 and 500 fs for the primary event behind vision

and proton translocation in bR, respectively [41,42]. These

timescales are close to the expected decoherence time-

scales of the optically excited vibrational wave packets and

enable the imprinting of phase information in the excited

state using trial pulses to test for coherence effects.

The first experiment to demonstrate control over a bio-

logical function is the very recent work of Prokhorenko

et al. on bR [43��]. These experiments introduced the

constraint of constant actinic energy during pulse shaping

and optimization, and the use of weak excitation condi-

tions relevant to biological processes. Weak field control

was used to eliminate possible multiphoton processes and

to ensure that the electronic levels probed are the same as

those in the actual biological process. It was found that

the absolute quantum yield for photoisomerization of bR

could be enhanced from 65% to 85% or suppressed to

45%, giving an overall range of manipulation of the

reaction coordinate of more than 40%. The optimized

pulse shapes were quite interesting. Using a Wigner

transform, the electric field amplitude of the measured

shaped pulse could be projected as a function of time and

frequency to get a direct feeling for the forces the mole-

cule was experiencing through the applied field. The

optimal pulses showed a highly periodic shape, with

features that closely match the low-frequency torsional

mode of retinal that is involved in the isomerization step.

The anti-optimal pulse that suppresses the isomerization

was also interesting in that the frequency modulation of

the electric field corresponds to a different frequency that

is aperiodic. The frequency in the anti-optimal pulse

would be akin to pushing a child on a swing out of phase

to dampen the amplitude of the swing motion. The basic

findings are summarized in Figure 6 (and a physical

picture of the photo-induced steering of the reaction is

shown in Figure 1b). In relation to the question posed in

this review, this work provides evidence that quantum

coherence effects not only persist along reaction


coordinates in biological systems but also can be signifi-

cantly manipulated. The degree to which protein struc-

ture imposes correlations to favor quantum interference

effects awaits further exploration of model systems.

Concluding remarksMultidimensional coherent spectroscopies (2D and

coherent control) are beginning to address key issues

with respect to connecting our understanding of the

quantum world to the biological world in which we live



— how Nature has exploited the correspondence princi-

ple that connects quantum mechanics to continuum

mechanics to harness chemical and solar energy to per-

form functions. The current picture is that there are

correlations imposed on biologically relevant systems,

whether they be frequency correlations in the dynamic

structure of liquid H2O, energy transfer in light-harvest-

ing complexes or the actual motions of heavy atoms in a

biological process (bR), that operate on timescales com-

parable to decoherence timescales and thus involve con-

served phase relationships or quantum coherence effects

to a certain extent. The degree to which the structural

correlations in biological systems have been optimized to

take advantage of constructive and destructive interfer-

ence effects is still an open question; however, the issue

of whether or not quantum interference effects can man-

ifest themselves in biological functions has been

answered. Purely quantum effects can play a role in

optimizing function. It is highly probable that such effects

have been explicitly exploited for the execution of bio-

logically important functions whereby the particular path-

way is in strong competition with very fast dissipation

processes that are unavoidable in large molecules with a

myriad of anharmonically coupled degrees of freedom.

For example, key primary energy transfer and photoi-

somerization steps, which serve as the powerhouse for

life, are in competition with the very fast relaxation of

carotenoid excited states and occur right at the coherence

limit; constructively interfering correlations (structurally

imposed) could make a significant difference to the over-

all efficiency, as demonstrated by the coherent control

studies of bR (>20%). Enhancements of this magnitude

would provide strong filter functions for structural opti-

mization. The challenge will be to extend coherent multi-

dimensional spectroscopies in which 2D methods are

combined with pulse-shaping protocols of coherent con-

trol to extract information on mode-specific couplings and

conserved phase relationships in biological response func-

tions. It is exactly this kind of information that we need to

understand the structure-function relationships of biolo-

gical systems and how the wave properties of matter play

a role.

AcknowledgementsRJDM would like to thank the Natural Sciences and Engineering ResearchCouncil of Canada and the Canada Research Chair program for support.The authors thank A Paarmann for help with the figures.

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