Kinetic analysis of the thermal isomerisation pathways in an asymmetric double azobenzene switch

Here we report a photochemical and kinetic study of the thermal relaxation reaction of a double azobenzene system, in which two azobenzene photochromic units are connected via a phenyl ring. Upon UV irradiation, three thermally unstable isomers are formed. Kinetic studies using arrayed (1)H-NMR spectroscopy revealed four distinct barriers for the thermal reversion to the stable isomer. The double isomerised Z,Z-2 can revert thermally to the E,E-2 isomer via either of two isomerisation pathways. The thermal Z to E isomerisations are not significantly affected by the state of the neighbouring azo-switching unit in the meta position. These findings are supported by quantum chemical calculations on the thermal Z to E isomerisation.     

Evidence for the isomerization and decarboxylation in the photoconversion of the red fluorescent protein DsRed

Recently, it has been shown that the red fluorescent protein DsRed undergoes photoconversion on intense irradiation, but the mechanism of the conversion has not yet been elucidated. Upon irradiation with a nanosecond-pulsed laser at 532 nm, the chromophore of DsRed absorbing at 559 nm and emitting at 583 nm (R form) converts into a super red (SR) form absorbing at 574 nm and emitting at 595 nm. This conversion leads to a significant change in the fluorescence quantum yield from 0.7 to 0.01. Here we demonstrate that the photoconversion is the result of structural changes of the chromophore and one amino acid. Absorption, fluorescence, and vibrational spectroscopy as well as mass spectrometry suggest that a cis-to-trans isomerization of the chromophore and decarboxylation of a glutamate (E215) take place upon irradiation to form SR. At the same time, another photoproduct (B) with an absorption maximum at 386 nm appears upon irradiation. This species is assigned as a protonated form of the DsRed chromophore. It might be a mixture of several protonated DsRed forms as there is at least two ways of formation. Furthermore, the photoconversion of DsRed is proven to occur through a consecutive two-photon absorption process. Our results demonstrate the importance of the chromophore conformation in the ground state on the brightness of the protein as well as the importance of the photon flux to control/avoid the photoconversion process.     

Insight into the common mechanism of the chromophore formation in the red fluorescent proteins: the elusive blue intermediate revealed

Understanding the chromophore maturation process in fluorescent proteins is important for the design of proteins with improved properties. Here, we present the results of electronic structure calculations identifying the nature of a blue intermediate, a key species in the process of the red chromophore formation in DsRed, TagRFP, fluorescent timers, and PAmCherry. The chromophore of the blue intermediate has a structure in which the π-system of the imidazole ring is extended by the acylimine bond, which can be represented by the model N-[(5-hydroxy-1H-imidazole-2yl)methylidene]acetamide (HIMA) compound. Ab initio and QM/MM calculations of the isolated model and protein-bound (mTagBFP) chromophores identify the anionic form of HIMA as the only structure that has absorption that is consistent with the experiment and is stable in the protein binding pocket. The anion and zwitterion are the only protonation forms of HIMA whose absorption (421 and 414 nm, or 2.95 and 3.00 eV) matches the experimental spectrum of the blue form in DsRed (the absorption maximum is 408 nm or 3.04 eV) and mTagBFP (400 nm or 3.10 eV). The QM/MM optimization of the protein-bound anionic form results in a structure that is close to the X-ray one, whereas the zwitterionic chromophore is unstable in the protein binding pocket and undergoes prompt proton transfer. The computed excitation energy of the protein-bound anionic form of the mTagBFP-like chromophore (3.04 eV) agrees with the experimental absorption spectrum of the protein. The DsRed-like chromophore formation in red fluorescent proteins is revisited on the basis of ab initio results and verified by directed mutagenesis revealing a key role of the amino acid residue 70, which is the second after the chromophore tripeptide, in the formation process.     

Revised structure of a purported 1,2-dioxin: a combined experimental and theoretical study

3,6-Bis(p-tolyl)-1,2-dioxin (1g) was suggested by Shine and Zhao as a product in an electron-transfer (ET) photochemical reaction. This photoproduct is instead shown to be (E)-1,4-di-p-tolylbut-2-ene-1,4-dione ((E)-4a). Ab initio and DFT calculations indicate that ring-closed 1,2-dioxin is thermodynamically far less stable than open-chain but-2-ene-1,3-dione. These calculations indicate that (E)-4a is formed via the cation radical of 1g, which sequentially isomerizes to a novel sigma-radical with an O,O 3e bond [(Z)-4a](+)(*), undergoes ET to give (Z)-4a, and then photoisomerizes to (E)-4a.     

Chirality transfer from chiral solvents and its memory in an azobenzene derivative exhibiting photo-switchable racemization

The transfer and dynamic fixation of chirality in cyclic azobenzenes using R-(+)-1-phenylethylalcohol (R-PEA) and S-(-)-1-phenylethylalcohol (S-PEA) as solvents or additives are investigated. The cyclic azobenzenes used in this study carry a 1,5-dioxynaphthalene moiety as rotating unit, connected to the photoisomerizing (E-Z) azobenzene unit with spacers of varying lengths. With suitable lengths of the spacers the molecules exhibit stable enantiomers originated from the element of planar chirality in the E form due to the stopped rotation of the rotor, while in the Z form the allowed rotation results in racemization. The CD spectra of racemic compounds in the E form in chiral solvents were inert or almost negligible before irradiation, while 366 nm irradiation causing E-Z photoisomerization resulted in induction of clear CD bands. The thermal or photochemical reverse Z-E isomerization causes a change in the CD spectra to new ones which are reasonably matching with the spectra of the pure enantiomers recorded in non-chiral solvents. The obtained new CD spectra are maintained even in a racemic solvent system attained by the dilution with an equal amount of chiral solvent of opposite stereostructure. These results indicate that the chirality is transferred from the chiral solvents or additives to the racemizing Z form of cyclic azobenzene and it is fixed in the non-racemizing E form. The molecule without racemization in both E and Z forms did not show any significant induced CD bands irrespective of E-Z isomerizations. The molecule showing racemization in E and Z forms just shows the non-fixed induced CD. The property of photo-switchable racemization is necessary for the effective transfer and temporal fixation of the chirality in this type of chirality sensors.     

Stereoselective isomerisation of N-allyl aziridines into geometrically stable Z enamines by using rhodium hydride catalysis

In the presence of rhodium(I) hydride catalysts, tertiary N-allylamines are known to isomerise into E enamines. In contrast, we have recently found that N-allylaziridines isomerise to form Z enamines. On the basis of literature data, the most likely mechanism of isomerisation would involve a rhodium hydride addition/beta-hydride elimination sequence. We show that the observed selectivity cannot be adequately explained by this pathway and is more consistent with initial CH-activation followed by rearrangement to form a five-membered cyclometallated rhodium intermediate. This intermediate subsequently undergoes reductive elimination to form a C--H bond. The resulting geometrically stable Z enamines are useful building blocks for stereoselective synthesis.     

An alternate proton acceptor for excited-state proton transfer in green fluorescent protein: rewiring GFP

The neutral form of the chromophore in wild-type green fluorescent protein (wtGFP) undergoes excited-state proton transfer (ESPT) upon excitation, resulting in characteristic green (508 nm) fluorescence. This ESPT reaction involves a proton relay from the phenol hydroxyl of the chromophore to the ionized side chain of E222, and results in formation of the anionic chromophore in a protein environment optimized for the neutral species (the I* state). Reorientation or replacement of E222, as occurs in the S65T and E222Q GFP mutants, disables the ESPT reaction and results in loss of green emission following excitation of the neutral chromophore. Previously, it has been shown that the introduction of a second mutation (H148D) into S65T GFP allows the recovery of green emission, implying that ESPT is again possible. A similar recovery of green fluorescence is also observed for the E222Q/H148D mutant, suggesting that D148 is the proton acceptor for the ESPT reaction in both double mutants. The mechanism of fluorescence emission following excitation of the neutral chromophore in S65T/H148D and E222Q/H148D has been explored through the use of steady state and ultrafast time-resolved fluorescence and vibrational spectroscopy. The data are contrasted with those of the single mutant S65T GFP. Time-resolved fluorescence studies indicate very rapid (< 1 ps) formation of I* in the double mutants, followed by vibrational cooling on the picosecond time scale. The time-resolved IR difference spectra are markedly different to those of wtGFP or its anionic mutants. In particular, no spectral signatures are apparent in the picosecond IR difference spectra that would correspond to alteration in the ionization state of D148, leading to the proposal that a low-barrier hydrogen bond (LBHB) is present between the phenol hydroxyl of the chromophore and the side chain of D148, with different potential energy surfaces for the ground and excited states. This model is consistent with recent high-resolution structural data in which the distance between the donor and acceptor oxygen atoms is < or = 2.4 A. Importantly, these studies indicate that the hydrogen-bond network in wtGFP can be replaced by a single residue, an observation which, when fully explored, will add to our understanding of the various requirements for proton-transfer reactions within proteins.     

PHOTOMODULATION OF AZOALDOLASE ACTIVITY

Abstract— Rabbit muscle aldolase, modified by azo groups covalently bound to cysteinyl residues 237 and 287, shows activation of the fructose-1,6 diphosphate cleavage reaction at 30T, after preirradiation with visible light. When the light treatment is carried out under an atmosphere of Ar to avoid oxidation, there is a reversible diminution of the Michaelis-Menten constant, with no change in the turnover number. The direct effect of the light is the E → Z geometric isomerization of the azochromophore; thereafter the Z isomer is thermally converted to the more stable E isomer. Both regulation at the level of the enzyme-substrate interaction and the involvement of the geometry of the chromophore have been demonstrated. The substrate, added to azoaldolase in the dark, causes E to Z isomerization of part of the extrinsic protein chromophores leading to a different isomeric composition at the thermal equilibrium. This result is consistent with higher binding energy of the enzymesubstrate complex when the modified enzyme contains azo chromophores in the Z configuration, as compared with the same chromophores in the E configuration. Azoaldolase has been discussed as a model for direct photoregulation of enzyme activity at the level of enzyme-substrate interaction.     

New light on the ring-chain equilibrium of a hydrogen-bonded supramolecular polymer based on a photochromic dithienylethene unit and its energy-transfer properties as a storage material

A novel, bifunctional, quadruple hydrogen-bonding ureido-pyrimidinone (UPy) unit bridged by photochromic dithienylethene (1) has been synthesized, which affords linear assemblies in solution and undergoes concentration-dependent ring-opening polymerization. The two UPy functional groups of 1 can dimerize intramolecularly to form a cyclic monomer with the two thienyl rings fixed in a parallel conformation, which prohibits its photocyclization. We exploited the photochemical reactivity and resonance difference of the linker of the bis-UPy derivative as well as using the more typical (1)H NMR, DOSY, and Ubbelohde viscometry methods to investigate for the first time the ring-chain polymerization mechanism. Moreover, we fabricated a mixed polymer film with a fluorescent dye noncovalently endcapping the linear photochromic assemblies through quadruple hydrogen bonds, which showed nondestructive fluorescent read-out ability for data storage by fluorescence resonance energy transfer (FRET) from the fluorescent dye to the closed form of the diarylethene.     

Common pathway for the red chromophore formation in fluorescent proteins and chromoproteins

The mechanism of the chromophore maturation in members of the green fluorescent protein (GFP) family such as DsRed and other red fluorescent and chromoproteins was analyzed. The analysis indicates that the red chromophore results from a chemical transformation of the protonated form of the GFP-like chromophore, not from the anionic form, which appears to be a dead-end product. The data suggest a rational strategy to achieve the complete red chromophore maturation utilizing substitutions to favor the formation of the neutral phenol in GFP-like chromophore. Our approach to detect the neutral chromophore form expands the application of fluorescent timer proteins to faster promoter activities and more spectrally distinguishable fluorescent colors. Light sensitivity found in the DsRed neutral form, resulting in its instant transformation to the mature red chromophore, could be exploited to accelerate the fluorescence acquisition.     

Conversion of red fluorescent protein into a bright blue probe

We used a red chromophore formation pathway, in which the anionic red chromophore is formed from the neutral blue intermediate, to suggest a rational design strategy to develop blue fluorescent proteins with a tyrosine-based chromophore. The strategy was applied to red fluorescent proteins of the different genetic backgrounds, such as TagRFP, mCherry, HcRed1, M355NA, and mKeima, which all were converted into blue probes. Further improvement of the blue variant of TagRFP by random mutagenesis resulted in an enhanced monomeric protein, mTagBFP, characterized by the substantially higher brightness, the faster chromophore maturation, and the higher pH stability than blue fluorescent proteins with a histidine in the chromophore. The detailed biochemical and photochemical analysis indicates that mTagBFP is the true monomeric protein tag for multicolor and lifetime imaging, as well as the outstanding donor for green fluorescent proteins in F?rster resonance energy transfer applications.     

Opening a spiropyran ring by way of an exciplex intermediate

A molecular dyad has been synthesized in which the main chromophore is a 1,4-diethynylated benzene residue terminated with pyrene moieties, this latter unit acting as a single chromophore. A spiropyran group has been condensed to the central phenylene ring so as to position a weak electron donor close to the pyrene unit. Illumination of the pyrene-based chromophore leads to formation of a fluorescent exciplex in polar solvents but pyrene-like fluorescence is observed in nonpolar solvents. The exciplex has a lifetime of a few nanoseconds and undergoes intersystem crossing to the pyrene-like triplet state with low efficiency. Attaching a 4-nitrobenzene group to the open end of the spiropyran unit creates a new route for decay of the exciplex whereby the triplet state of the spiropyran is formed. Nonradiative decay of this latter species results in ring opening to form the corresponding merocyanine species. Rate constants for the various steps have been obtained from time-resolved fluorescence spectroscopy carried out over a modest temperature range. Under visible light illumination, the merocyanine form reverts to the original spiropyran geometry so that the cycle is closed. Energy transfer from the pyrene chromophore to the merocyanine unit leads to an increased rate of ring closure and serves to push the steady-state composition in favor of the spiropyran form.     

Thermal [2 + 2] cycloreversion of a cyclobutane moiety via a biradical reaction

The nature of the Woodward-Hoffmann-forbidden, thermal activated cycloreversion mechanism of cyclobutane has long been the subject of speculation and intense research. We were now able to prove the theoretically postulated biradicalic mechanism directly from radical scavenging reactions and electron paramagnetic resonance (EPR) experiments on [2 + 2] heterodimers of 5-fluoro-1-heptanoyluracil and 7-methoxy-1,1-dimethylnaphthalenon. The dimers show both the "allowed" photochemically as well as the "forbidden" thermally triggered [2 + 2] cycloreversion of the cyclobutane ring. The quantum efficiency of the photochemical cleavage is about 1%. The thermal cycloreversion reaction is independent from solvent and occurs at low activation energies of about 13 kcal/mol, even in the solid state. The radical scavenger and EPR results are further supported by the finding, that the reaction products are solely the educts for the anti-head-to-tail heterodimer. But for the syn-head-to-head heterodimer two additional products are observed, which require a sufficiently stable biradical intermediate to facilitate the required intramolecular rearrangements. Because of the surprisingly high lifetime of the radical species of these heterodimers it was possible to prove the long-discussed biradical mechanism experimentally.     

New open-chain tetrapyrroles as chromophores in the plant photoreceptor phytochrome

A series of six open-chain tetrapyrroles has been synthesized and used as chromophores for the plant photoreceptor protein phytochrome. The novel chromophores vary in the size of substituents 17 and 18 at ring D. This ring undergoes maximal conformational change upon light excitation ( Z --> E photoisomerization of the 15,16-double bond). Instead of methyl and vinyl substituents (positions 17, 18) as present in the native chromophore phytochromobilin, dimethyl, methyl and isopropyl, methyl and tert-butyl, ethyl and methyl, vinyl and methyl, and isopropyl and methyl substituents have been generated. All novel chromophores assemble with the apoprotein. The obtained chromoproteins show hypsochromic shifts of the absorbance maxima by 10 nm maximally, compared to the native pigment, except for the 17-isopropyl-18-methyl-substituted compound which showed a 100 nm hypsochromic shift of selectively the P r form. The assembly kinetics were slowed down in correlation to the increasing size of the substituents, with stronger effects for modified substituents at position 17. The thermal stability of the photoinduced P fr form for the 18-isopropyl and the 18- tert butyl substituents was even greater than that of the native pigments. Those chromophores carrying substituents at position 17 larger than the methyl group (ethyl and isopropyl) showed a very low stability of the respective P fr forms. Time-resolved detection of the P r to P fr conversion (laser-induced flash photolysis) revealed a slower formation of the P fr form for those chromophores carrying larger substituents at position 18, whereas the rise and decay kinetics of the early intermediates are only moderately changed. Introduction of larger substituents at position 17 (ethyl, vinyl, and isopropyl) causes drastic changes in the kinetics; in particular the formation of the first thermally stable intermediate, I 700, is significantly slowed, making a detection of its rise possible.     

Squaraine-derived rotaxanes: highly stable, fluorescent near-IR dyes

Squaraines are fluorescent, near-IR dyes with promising photophysical properties for biomedical applications. A limitation with these dyes is their inherent reactivity with nucleophiles, which leads to loss of the chromophore. Another drawback is their tendency to form nonfluorescent aggregates in water. Both problems can be greatly attenuated by encapsulating the dye inside an amide-containing macrocycle. In other words, the squaraine becomes the thread component in a Leigh-type rotaxane, a permanently interlocked molecule. Two new rotaxanes are described: an analogue with four tri(ethyleneoxy) chains on the squaraine to enhance water solubility, and a rotaxane that has an encapsulating macrocycle with transposed carbonyl groups. An X-ray crystal structure of the latter rotaxane shows that the macrocycle provides only partial protection of the electrophilic cyclobutene core of the squaraine thread. The stabilities of each compound in various solvents, including serum, were compared with a commercially available cyanine dye. The squaraine rotaxane architecture is remarkably resistant to chemical and photochemical degradation, and likely to be very useful as a versatile fluorescent scaffold for constructing various types of highly stable, near-IR imaging probes.     

Protein-bound chromophores astaxanthin and phytochromobilin: excited state quantum chemical studies

We present an overview of excited state quantum chemical calculations aimed at elucidating controversial issues regarding the photochemistry of the protein-bound chromophores astaxanthin and phytochromobilin. In particular, we show how the application of time-dependent density functional theory and other single-reference quantum chemical excited state methods have contributed to shed new light on the origin of the >0.5 eV bathochromic shift of the electronic absorption by the carotenoid astaxanthin in the protein macromolecular complex crustacyanin, and the mechanism for C15-Z,syn --> C15-E,anti isomerization of the tetrapyrrole phytochromobilin that underlies the photoactivation of the plant photoreceptor phytochrome. Within the approximation that exciton coupling is neglected, the calculations on astaxanthin provide support for the notion that the bathochromic shift, which is responsible for the slate-blue coloration of lobster shell, is due to polarization rather than a conformational change of the chromophore in the protein-bound state. Furthermore, the polarization is attributed to a hydrogen-bonded protonated histidine residue. The calculations on phytochromobilin, in turn, suggest that a stepwise C15-Z,syn --> C15-E,syn (photochemical), C15-E,syn --> C15-E,anti (thermal) mechanism is much more favorable than a concerted, fully photochemical mechanism, and that neutral forms of the chromophore are much less likely to photoisomerize than the parent, protonated form. Accordingly, the calculations indirectly support the view that the photoactivation of phytochrome does not involve a proton transfer from the chromophore to the surrounding protein.     

Single oligomer spectra probe chromophore nanoenvironments of tetrameric fluorescent proteins

When analyzing the emission of a large number of individual chromophores embedded in a matrix, the spread of the observed parameters is a characteristic property for the particular chromophore-matrix system. To quantitatively assess the influence of the matrix on the single molecule emission parameters, it is imperative to have a system with a well-defined chromophore nanoenvironment and the possibility to alter these surroundings in a precisely controlled way. Such a system is available in the form of the visible fluorescent proteins, where the chromophore nanoenvironment is defined by the specific protein sequence. We analyze the influence of the chromophore embedding within this defined protein environment on the distribution of the emission maximum wavelength for a number of variants of the fluorescent protein DsRed, and show that this parameter is characteristic of the chromophore-protein matrix combination and largely independent of experimental conditions. We observe that the chemical changes in the vicinity of the chromophore of different variants do not account for the different distributions of emission maximum positions but that the flexibility of the chromophore surrounding has a dominant role in determining the distribution. We find, surprisingly, that the more rigid the chromophore surrounding, the broader the distribution of observed maximum positions. We hypothesize that, after a thermally induced reorientation in the chromophore surrounding, a more flexible system can easily return to its energetic minimum position by fast reorientation, while in more rigid systems the return to the energetic minimum occurs in a stepwise fashion, leading to the broader distribution observed.     

Photochromic fulgides: Transformation of the non‐photochromic (Z)‐isomer of a fulgide into a highly photochromic (E)‐isomer via structural modification involving enhanced conjugation

The non‐photochromic fulgide (1‐Z) has been successfully converted into the highly photochromic ( 3‐Z ) analogue. A dicyanomethylene group was introduced at the 5‐position of 1‐Z in order to enhance the latter's conjugation properties that would facilitate the photochemical Z→E isomerization process. The irradiation of the product 3‐Z with a UV light at λ_max 350 nm formed a bluish green solution which absorbed at λ_max 620 nm, corresponding to the ring‐closed product 4. The latter was also formed from the reference dicyanomethylene product 3‐E synthesized from 1‐E. The irradiation of 4 at λ_max 532 nm produced the reversion to the original pale yellow color of 3‐E.     

A pentiptycene-derived molecular brake: photochemical E→Z and electrochemical Z→E switching of an enone module

The synthesis and brakelike performance of a new molecular system (1) consisting of a pentiptycene rotor and a 2-methyleneindanone brake are reported. The rotation kinetics of the rotor was probed by both variable-temperature (1)H and (13)C NMR spectroscopy and DFT calculations, and the switching between the brake-on and brake-off states was conducted by a combination of photochemical and electrochemical isomerization. Because of the greater steric hindrance between the rotor and the brake units in the Z form ((Z)-1) than in the E form ((E)-1), rotation of the rotor is slowed down 500-fold at room temperature (298 K) on going from (E)-1 to (Z)-1, corresponding to the brake-off and brake-on states, respectively. The (E)-1→(Z)-1 photoisomerization in acetonitrile is efficient and reaches an (E)-1/(Z)-1 ratio of 11:89 in the photostationary state upon excitation at 290 nm, attributable to a much larger isomerization quantum efficiency for (E)-1 versus (Z)-1. An efficient (Z)-1→(E)-1 isomerization (96%) was also achieved by electrochemical treatment through the radical anionic intermediates. Consequently, the reversibility of the E-Z switching of 1 is as high as 85%. The repeated E-Z switching of 1 with alternating photochemical and electrochemical treatments is also demonstrated.     

Chemistry of the diazeniumdiolates: Z right harpoon over left harpoon E isomerism

Here, we explore the chemistry of the previously undocumented E form of diazeniumdiolates having the structure R(1)R(2)NN(O)=NOR(3). Reported crystallographic studies have uniformly revealed the Z configuration, and our attempts to observe a Z --> E conversion through thermal equilibration or photochemical means have, until now, consistently failed to reveal a significant amount of a second conformer. As a typical example, the NMR spectrum of trimethyl derivative Me(2)NN(O)=NOMe revealed no evidence for a second configuration. Electronic structure calculations attribute this finding to a prohibitively high interconversion barrier of approximately 40 kcal/mol. A similar result was obtained when we considered the case of R(1) = Me = R(3) and R(2) = H at the same levels of theory. However, when MeHNN(O)=NOMe was ionized by dissociating the N-H bond, the barrier was calculated to be lower by approximately 20 kcal/mol, with the E form of the anion being favored over Z. This circumstance suggested that an E isomer might be isolable if a Z anion were formed and given sufficient time to assume the E configuration, then quenched by reaction with an electrophile to trap and neutralize the E form and restore the putatively high interconversion barrier. Consistent with this prediction, basifying iPrHNN(O)=NOCH(2)CH(2)Br rapidly led to a six-membered heterocycle that was crystallographically characterized as containing the -N(O)=NO- functional group in the E configuration. The results suggest an approach for generating pairs of Z and E diazeniumdiolates for systematic comparison of the rates at which the individual isomers release bioactive NO and of other physicochemical determinants of their biomedical utility.