Examples of hula-twist in photochemical cis- trans isomerization

Investigation of Ultrafast Configurational Photoisomerization of Bilirubin Using Femtosecond Stimulated Raman Spectroscopy

Phototherapy is an efficient and safe way to reduce high levels of free 4Z,15Z-bilirubin (ZZ-BR) in the serum of newborns. The success of BR phototherapy lies in photoinduced configurational and structural isomerization processes that form excretable isomers. However, the physical picture of photoinduced photoisomerization of ZZ-BR is still unclear. Here, we strategically implement tunable femtosecond stimulated Raman spectroscopy and several time-resolved electronic spectroscopies, assisted by quantum chemical calculations, to dissect the detailed primary configurational isomerization dynamics of free ZZ-BR in organic solvents. The results of this study demonstrate that upon photoexcitation, ultrafast configurational isomerization proceeds by a volume-conserving "hula twist", followed by intramolecular hydrogen-bond distortion and large-scale rotation of the two dipyrrinone halves of the ZZ-BR isomer in a few picoseconds. After that, most of the population recovers back to ZZ-BR, and a very small amount is converted into stable BR isomers via structural isomerization.

Structure, Spectra and Photochemistry of 2-Amino-4-Methylthiazole: FTIR Matrix Isolation and Theoretical Studies

The structure, tautomerization pathways, vibrational spectra, and photochemistry of 2-amino-4-methylthiazole (AMT) molecule were studied by matrix isolation FTIR spectroscopy and DFT calculations undertaken at the B3LYP/6-311++G(3df,3pd) level of theory. The most stable tautomer with the five-membered ring stabilized by two double C=C and C=N bonds, was detected in argon matrices after deposition. When the AMT/Ar matrices were exposed to 265 nm selective irradiation, three main photoproducts, N-(1-sulfanylprop-1-en-2-yl)carbodiimide (fp1), N-(1-thioxopropan-2-yl)carbodiimide (fp2) and N-(2-methylthiiran-2-yl)carbodiimide (fp3), were photoproduced by a cleavage of the CS–CN bond together with hydrogen atom migration. The minor photoreaction caused by the cleavage of the CS–CC bond and followed by hydrogen migration formed 2-methyl-1H-azirene-1-carbimidothioic acid (fp15). We have also found that cleavage of the CS–CN bond followed by disruption of the N–C bond produced cyanamide (fp11) and the C(CH3)=CH–S biradical that transformed into 2-methylthiirene (fp12) and further photoreactions produced 1-propyne-1-thiole (fp13) or methylthioketene (fp14). Cleavage of the CS–CC bond followed by disruption of the N–C bond produced propyne (fp22) and the S–C(NH₂)=N biradical that transformed into 3-aminethiazirene (fp23); further photoreactions produced N-sulfanylcarbodiimide (fp25). As a result of these transformations, several molecular complexes were identified as photoproducts besides new molecules in the AMT photolysis process.

Dynamics of Excitons in Conjugated Molecules and Organic Semiconductor Systems

The exciton, an excited electron-hole pair bound by Coulomb attraction, plays a key role in photophysics of organic molecules and drives practically important phenomena such as photoinduced mechanical motions of a molecule, photochemical conversions, energy transfer, generation of free charge carriers, etc. Its behavior in extended π-conjugated molecules and disordered organic films is very different and very rich compared with exciton behavior in inorganic semiconductor crystals. Due to the high degree of variability of organic systems themselves, the exciton not only exerts changes on molecules that carry it but undergoes its own changes during all phases of its lifetime, that is, birth, conversion and transport, and decay. The goal of this review is to give a systematic and comprehensive view on exciton behavior in π-conjugated molecules and molecular assemblies at all phases of exciton evolution with emphasis on rates typical for this dynamic picture and various consequences of the above dynamics. To uncover the rich variety of exciton behavior, details of exciton formation, exciton transport, exciton energy conversion, direct and reverse intersystem crossing, and radiative and nonradiative decay are considered in different systems, where these processes lead to or are influenced by static and dynamic disorder, charge distribution symmetry breaking, photoinduced reactions, electron and proton transfer, structural rearrangements, exciton coupling with vibrations and intermediate particles, and exciton dissociation and annihilation as well.

Optimizing Photochirogenic Performance by Solvent-Driven Conformational Fixation in Enantiodifferentiating Photoisomerization of (Z)-Cyclooctene Mediated by Sensitizing β-Cyclodextrin Hosts

Catalytic enantiodifferentiating photoisomerization of cyclooctene (1Z) included and sensitized by regioisomeric 6-O-(o-, m-, and p-methoxybenzoyl)-β-cyclodextrins (CDs) was performed under a variety of solvent conditions for higher enantioselectivities. The enantiomeric excess (ee) of chiral (E)-isomer (1E) produced was a critical function of all the internal and external factors examined, in particular, the sensitizer structure and the solvent conditions, to afford (R)-1E in record-high ee's of up to 67% upon sensitization with the meta-substituted β-CD host in water and salt solutions but neither in 50% aqueous ethanol nor with the ortho- and para-substituted hosts. The mechanistic origin of the sudden ee enhancement achieved under the specific conditions is discussed on the basis of the circular dichroism spectral behaviors upon substrate inclusion and the compensatory enthalpy-entropy relationship of the activation parameters for the enantiodifferentiating photoisomerization.

Theoretical Study of the Photoisomerization Mechanism of All-Trans-Retinyl Acetate

The compound 9-cis-retinyl acetate (9-cis-RAc) is a precursor to 9-cis-retinal, which has potential application in the treatment of some hereditary diseases of the retina. An attractive synthetic route to 9-cis-RAc is based on the photoisomerization reaction of the readily available all-trans-RAc. In the present study, we examine the mechanism of the photoisomerization reaction with the use of state-of-the-art electronic structure calculations for two polyenic model compounds: tEtEt-octatetraene and tEtEtEc-2,6-dimethyl-1,3,5,7,9-decapentaene. The occurrence of photoisomerization is attributed to a chain-kinking mechanism, whereby a series of S₁/S₀ conical intersections associated with kinking deformations at different positions along the polyenic chain mediate internal conversion to the S₀ state, and subsequent isomerization around one of the double bonds. Two other possible photoisomerization mechanisms are taken into account, but they are rejected as incompatible with simulation results and/or the available spectroscopic data.

Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water

The chromophore of the green fluorescent protein (GFP) is critical for probing environmental influences on fluorescent protein behavior. Using the aqueous system as a bridge between the unconfined vacuum system and a constricting protein scaffold, we investigate the steric and electronic effects of the environment on the photodynamical behavior of the chromophore. Specifically, we apply ab initio multiple spawning to simulate five picoseconds of nonadiabatic dynamics after photoexcitation, resolving the excited-state pathways responsible for internal conversion in the aqueous chromophore. We identify an ultrafast pathway that proceeds through a short-lived (sub-picosecond) imidazolinone-twisted (I-twisted) species and a slower (several picoseconds) channel that proceeds through a long-lived phenolate-twisted (P-twisted) intermediate. The molecule navigates the non-equilibrium energy landscape via an aborted hula-twist-like motion toward the one-bond-flip dominated conical intersection seams, as opposed to following the pure one-bond-flip paths proposed by the excited-state equilibrium picture. We interpret our simulations in the context of time-resolved fluorescence experiments, which use short- and long-time components to describe the fluorescence decay of the aqueous GFP chromophore. Our results suggest that the longer time component is caused by an energetically uphill approach to the P-twisted intersection seam rather than an excited-state barrier to reach the twisted intramolecular charge-transfer species. Irrespective of the location of the nonadiabatic population events, the twisted intersection seams are inefficient at facilitating isomerization in aqueous solution. The disordered and homogeneous nature of the aqueous solvent environment facilitates non-selective stabilization with respect to I- and P-twisted species, offering an important foundation for understanding the consequences of selective stabilization in heterogeneous and rigid protein environments.

Advances in the E → Z Isomerization of Alkenes Using Small Molecule Photocatalysts

Geometrical E → Z alkene isomerization is intimately entwined in the historical fabric of organic photochemistry and is enjoying a renaissance (Roth et al. Angew. Chem., Int. Ed. Engl. 1989 28, 1193-1207). This is a consequence of the fundamental stereochemical importance of Z-alkenes, juxtaposed with frustrations in thermal reactivity that are rooted in microscopic reversibility. Accessing excited state reactivity paradigms allow this latter obstacle to be circumnavigated by exploiting subtle differences in the photophysical behavior of the substrate and product chromophores: this provides a molecular basis for directionality. While direct irradiation is operationally simple, photosensitization via selective energy transfer enables augmentation of the alkene repertoire to include substrates that are not directly excited by photons. Through sustained innovation, an impressive portfolio of tailored small molecule catalysts with a range of triplet energies are now widely available to facilitate contra-thermodynamic and thermo-neutral isomerization reactions to generate Z-alkene fragments. This review is intended to serve as a practical guide covering the geometric isomerization of alkenes enabled by energy transfer catalysis from 2000 to 2020, and as a logical sequel to the excellent treatment by Dugave and Demange (Chem. Rev. 2003 103, 2475-2532). The mechanistic foundations underpinning isomerization selectivity are discussed together with induction models and rationales to explain the counterintuitive directionality of these processes in which very small energy differences distinguish substrate from product. Implications for subsequent stereospecific transformations, application in total synthesis, regioselective polyene isomerization, and spatiotemporal control of pre-existing alkene configuration in a broader sense are discussed.

Approximating Periodic Potential Energy Surfaces with Sparse Trigonometric Interpolation

The potential energy surface (PES) describes the energy of a chemical system as a function of its geometry and is a fundamental concept in computational chemistry. A PES provides much useful information about the system, including the structures and energies of various stationary points, such as local minima, maxima, and transition states. Construction of full-dimensional PESs for molecules with more than 10 atoms is computationally expensive and often not feasible. Previous work in our group used sparse interpolation with polynomial basis functions to construct a surrogate reduced-dimensional PESs along chemically significant reaction coordinates, such as bond lengths, bond angles, and torsion angles. However, polynomial interpolation does not preserve the periodicity of the PES gradient with respect to angular components of geometry, such as torsion angles, which can lead to nonphysical phenomena. In this work, we construct a surrogate PES using trigonometric basis functions, for a system where the selected reaction coordinates all correspond to the torsion angles, resulting in a periodically repeating PES. We find that a trigonometric interpolation basis not only guarantees periodicity of the gradient but also results in slightly lower approximation error than polynomial interpolation.

Previtamin D: Z-E photoisomerization via a Hula-twist conical intersection

On photoisomerization of previtamin D - a steroid Z-triene - produced in situ by ring opening of 7-dehydrocholesterol in a cold matrix, it was found in A. M. Müller et al. [Angew. Chem., Int. Ed., 1998, 37, 505-507] that the product (tachysterol) had rotated not only its central double bond but also an adjacent single bond. This is called a Hula twist (HT) due to the alternative description, in which it is just one central CH group that rotates. It was pointed out that the results directly support the calculated molecular structure at a conical intersection, which mediates the Z-E isomerization of polyenes. With a more sophisticated technique, Saltiel et al. (J. Phys. Chem. Lett., 2013, 4, 716-721) confirmed this tachysterol rotamer as the main product but found two additional conformers. They believed to have seen also three previtamin D conformers, suggested to be a result of hot-ground-state reactions from the primary rotamer, and interpreted all tachysterol products to be a result of a double-bond twist (DBT), not a HT. On the basis of published circular dichroism data and consideration of other reactions, it is here shown that under these conditions hot-ground-state reactions are unimportant or even negligible and that there is practically only a single conformer of previtamin D after ring opening. All products can be easily understood on the basis of an HT-type conical intersection, which is thus further supported. Invoking a published pretwist model even rationalizes product ratios. The two twists in HT are concerted. Furthermore HT is fully consistent with the NEER principle (nonequilibration of excited rotamers) and even offers additional possibilities for conformer control.

Direct evidence for hula twist and single-bond rotation photoproducts

Photoisomerization reactions are quintessential processes driving molecular machines and motors, govern smart materials, catalytic processes, and photopharmacology, and lie at the heart of vision, phototaxis, or vitamin production. Despite this plethora of applications fundamental photoisomerization mechanisms are not well understood at present. The famous hula-twist motion—a coupled single and double-bond rotation—was proposed to explain proficient photoswitching in restricted environments but fast thermal follow-up reactions hamper identification of primary photo products. Herein we describe an asymmetric chromophore possessing four geometrically distinct diastereomeric states that do not interconvert thermally and can be crystallized separately. Employing this molecular setup direct and unequivocal evidence for the hula-twist photoreaction and for photoinduced single-bond rotation is obtained. The influences of the surrounding medium and temperature are quantified and used to favor unusual photoreactions. Based on our findings molecular engineers will be able to implement photo control of complex molecular motions more consciously.

Photoisomerization mechanisms govern important (bio)catalytic reactions and lie at the core of many functional materials. Here, the authors report a molecular setup that allows for the direct and separate observation of three fundamental photoreactions, namely the hula twist, single-bond rotation, as well as double-bond isomerization.

Impact of kilobar pressures on ultrafast triazene and thiacyanine photodynamics

Application of high hydrostatic pressure leads to changes in (sub)picosecond emission dynamics, depending on the mechanism at work for the photoreaction.

Joint spectroscopic and theoretical investigation of cationic cyanine dye Astrazon Orange-R: solvent viscosity controlled relaxation of excited states

In this paper, the first study of cationic cyanine dye Astrazon Orange-R by combined spectroscopic and theoretical investigation is presented.

Photophysical and dynamical properties of doubly linked Cy3-DNA constructs

Photophysical measurements are reported for Cy3-DNA constructs in which both Cy3 nitrogen atoms are attached to the DNA backbone by short linkers. While this linking was thought to rigidify the orientation of the dye and hinder cis-isomerization, the relatively low fluorescence quantum yield and the presence of a short component in the time-resolved fluorescence decay of the dye indicated that cis-isomerization remained possible. Fluorescence correlation spectroscopy and transient absorption experiments showed that photoisomerization occurred with high efficiency. Molecular dynamics simulations of the trans dye system indicated the presence of stacked and unstacked states, and free energy simulations showed that the barriers for stacking/unstacking were low. In addition, simulations showed that the ground cis state was feasible without DNA distortions. Based on these observations, a model is put forward in which the doubly linked dye can photoisomerize in the unstacked state.

Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment

The nonadiabatic photodynamics of the all-trans-2,4-pentadiene-iminium cation (protonated Schiff base 3, PSB3) and the all-trans-3-methyl-2,4-pentadiene-iminium cation (MePSB3) were investigated in the gas phase and in polar (aqueous) and nonpolar (n-hexane) solutions by means of surface hopping using a multireference configuration-interaction (MRCI) quantum mechanical/molecular mechanics (QM/MM) level. Spectra, lifetimes for radiationless deactivation to the ground state, and structural and electronic parameters are compared. A strong influence of the polar solvent on the location of the crossing seam, in particular in the bond length alternation (BLA) coordinate, is found. Additionally, inclusion of the polar solvent changes the orientation of the intersection cone from sloped in the gas phase to peaked, thus enhancing considerably its efficiency for deactivation of the molecular system to the ground state. These factors cause, especially for MePSB3, a substantial decrease in the lifetime of the excited state despite the steric inhibition by the solvent.

The effect of protein environment on photoexcitation properties of retinal

Retinal is the photon absorbing chromophore of rhodopsin and other visual pigments, enabling the vertebrate vision process. The effects of the protein environment on the primary photoexcitation process of retinal were studied by time-dependent density functional theory (TDDFT) and the algebraic diagrammatic construction through second order (ADC(2)) combined with our recently introduced reduction of virtual space (RVS) approximation method. The calculations were performed on large full quantum chemical cluster models of the bluecone (BC) and rhodopsin (Rh) pigments with 165-171 atoms. Absorption wavelengths of 441 and 491 nm were obtained at the B3LYP level of theory for the respective models, which agree well with the experimental values of 414 and 498 nm. Electrostatic rather than structural strain effects were shown to dominate the spectral tuning properties of the surrounding protein. The Schiff base retinal and a neighboring Glu-113 residue were found to have comparable proton affinities in the ground state of the BC model, whereas in the excited state, the proton affinity of the Schiff base is 5.9 kcal/mol (0.26 eV) higher. For the ground and excited states of the Rh model, the proton affinity of the Schiff base is 3.2 kcal/mol (0.14 eV) and 7.9 kcal/mol (0.34 eV) higher than for Glu-113, respectively. The protein environment was found to enhance the bond length alternation (BLA) of the retinyl chain and blueshift the first absorption maxima of the protonated Schiff base in the BC and Rh models relative to the chromophore in the gas phase. The protein environment was also found to decrease the intensity of the second excited state, thus improving the quantum yield of the photoexcitation process. Relaxation of the BC model on the excited state potential energy surface led to a vanishing BLA around the isomerization center of the conjugated retinyl chain, rendering the retinal accessible for cis-trans isomerization. The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process.

Chemically modulating the photophysics of the GFP chromophore

There is growing interest in engineering the properties of fluorescent proteins through modifications to the chromophore structure utilizing mutagenesis with either natural or unnatural amino acids. This entails an understanding of the photophysical and photochemical properties of the modified chromophore. In this work, a range of GFP chromophores with different alkyl substituents are synthesized and their electronic spectra, pH dependence, and ultrafast fluorescence decay kinetics are investigated. The weakly electron donating character of the alkyl substituents leads to dramatic red shifts in the electronic spectra of the anions, which are accompanied by increased fluorescence decay times. This high sensitivity of electronic structure to substitution is also characteristic of some fluorescent proteins. The solvent viscosity dependence of the decay kinetics are investigated, and found to be consistent with a bimodal radiationless relaxation coordinate. Some substituents are shown to distort the planar structure of the chromophore, which results in a blue shift in the electronic spectra and a strong enhancement of the radiationless decay. The significance of these data for the rational design of novel fluorescent proteins is discussed.

Butadiene-based photoresponsive soft materials

The creation of stimuli-responsive materials offers considerable challenges in the area of material science. The use of light as an external stimulus has particular advantages because it can bring about rapid transformations in remote regions in a very precise manner. Naturally occurring photoresponsive systems provide the motivation for developing corresponding artificial systems using molecular self-assembly to address issues such as quantum efficiency, selectivity, and amplification. A practical strategy for developing photoresponsive materials is to utilize molecules that can undergo considerable change in shape on photoisomerization. Although the photoisomerization of polyenes between their linear all-trans isomer and bent cis isomers has been extensively investigated in solution and in organized media because of its relevance to naturally occurring photoresponsive systems, its use in developing artificial photoresponsive systems has not been well explored. This feature article provides an overview of photoresponsive soft materials such as liquid crystals and gels with special emphasis on our recent studies related to the use of the butadiene chromophore for the design of such materials. The role of molecular self-assembly in controlling the photochemical and photophysical properties of these molecules is also discussed.

Alloprenols: novel alpha-trans-polyprenols of Allophylus caudatus

A novel type of polyprenols, alloprenols, with an alpha-trans-isoprenoid unit was found in the leaves of Allophylus caudatus (Sapindaceae) besides typical alpha-cis-polyprenols. The polyprenol family (Prenol-11-13, Prenol-12 dominating) was accompanied by traces of dolichols of the same chain-length. Prenol alpha-cis- and alpha-trans-isomers were chromatographically separated and their structure was analyzed by HPLC/ESI-MS, HR-ESI-MS and 1H and 13C NMR spectroscopy. Model compounds, semi-synthetic alpha-isomers of all-trans-Pren-9 and mainly-cis-Pren-11, were obtained using an oxidation-reduction procedure. Comparison of their NMR spectra confirmed the structure of the newly identified polyprenols. The observed pattern of NMR signal shifts may be applied for elucidation of isoprenoid structure.

Cis → trans and trans → cis isomerizations of styrylcoumarins in the solid state. Importance of the location of free volume in crystal lattices

We have examined the photobehavior of a set of isomers of 2-pyranone-annulated stilbenes (6-styrylcoumarin 1, 7-styrylcoumarin 2, 4-methyl-6-styrylcoumarin 3, and 4-methyl-7-styrylcoumarin, 4) in their crystalline phases. While the cis isomers of 1-3 undergo cis-->trans photoisomerizations in the solid state, cis-4 and the trans isomers of 1-3 do not; the trans isomer of 4 undergoes photo-induced intermolecular reactions. Solution-state irradiations of the trans isomers of 1-4 lead to the cis isomers quite readily, as does cis-4 lead to trans-4, which suggests that the absence of geometric isomerization of the trans isomers and the lack of reactivity of cis-4 in the solid state are due to molecular packing effects. X-Ray crystal structural analyses of 1-4 reveal interesting conformational preferences for the styrenic moieties and differences in the total 'free' volumes within the lattices, but neither factor explains satisfactorily why some of the molecules undergo geometric isomerizations in their single crystals and others do not. Using the PLATON program, we have located the sizes and positions of 'void volumes' within the crystal lattices, and identified trajectories necessary for atomic motions to lead to geometric isomerizations to understand the reactivities of 1-4. The voids in the reactive cis isomers of 1-3 crystals are located along the trajectories needed for geometric isomerization. The relevant voids in the crystals of cis-4 and the trans isomers of 1 and 2 (the non-isomerizing molecules for which suitable crystals could be grown for X-ray analyses) are located along a trajectory that does not permit isomerization. We hypothesize that the classical momentum gained from the initial motions that are facilitated due to the voids in the crystals of the cis isomers of 1-3, as well as the heat dissipated to the local environment by internal conversions and vibronic cascade of the Franck-Condon states, helps to drive the system over potential energy barriers that would not be possible otherwise. Cis-4 and the trans isomers of 1 and 2, as well as other examples from the literature in which geometric isomerizations do or do not occur in the solid state, also follow the predictions based upon the PLATON analyses. On these bases, it is suggested that the methodology described may be generally applicable for predicting when geometric isomerizations (and possibly other reactive processes) in crystalline materials will occur.

Crystalline-State Z,E-Photoisomerization of a Series of (Z,E,Z)-1,6-Diphenylhexa-1,3,5-triene 4,4‘-Dicarboxylic Acid Dialkyl Esters. Chain Length Effects on the Crystal Structure and Photoreactivity

[reaction: see text] Crystalline-state Z,E-photoisomerization of a series of (Z,E,Z)-1,6-diphenylhexa-1,3,5-triene 4,4'-dicarboxylic acid dialkyl (R) esters [(Z,E,Z)-1a, R = Me; (Z,E,Z)-1b, R = Et; (Z,E,Z)-1c, R = n-Pr; (Z,E,Z)-1d, R = n-Bu] was investigated. All Z,E,Z isomers underwent one-way isomerization to the corresponding E,E,E isomers. The reaction efficiency was strongly enhanced as the length of the alkyl chain increased. Single-crystal X-ray analyses of (Z,E,Z)-1a-d showed that the alkyl chain part of the crystals became larger as the chain length increased. The conformational flexibility of the alkyl chains made the large change in the triene geometry in the lattice possible, leading to the enhancement of the photoreactivity in the crystalline state.

A Multireference Configuration Interaction Investigation of the Excited-State Energy Surfaces of Fluoroethylene (C2H3F)

Multireference configuration interaction with singles and doubles (MR-CISD) calculations has been performed for the optimization of conical intersections and stationary points on the fluoroethylene excited-state energy surfaces. For the planar ground state geometry, the vertical spectrum including 3s and 3p Rydberg states was calculated. From this geometry, a rigid torsion around the CC bond strongly reduces the energy gap between S0 and S1 states. Furthermore, a search for the minimum of the crossing seam shows that there exists a conical intersection close to the twisted structure and two additional ones for cis and trans pyramidalized structures. These three intersections are connected by the same seam. We have shown that the Hula-Twist process is an alternative way to the direct CC twisting in order to reach this part of the seam. Other conical intersections were also located in the CH3CF and CH2FCH, H-migration, and C(3v) structures. The photodynamics of the system is discussed based on topological features of these intersections.

Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds

Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.