Photoisomerization Step Research Articles

A photochromic trinuclear dysprosium(iii) single-molecule magnet with two distinct relaxation processes.

Multifunctional molecules responsive to light are highly desired as components for the construction of remotely controlled nanodevices. Here we present a DyIII single molecule magnet (SMM) comprising dithienylethene (dte) photochromic bridging ligands in the form of a pyridine (py) derivative: 1,2-bis((2-methyl-5-pyridyl)thie-3-yl)perfluorocyclo-pentene (dtepy). The title trinuclear compound {[DyIII(BHT)3]3(dtepy)2}·4C5H12 (1) was synthesized by combining the low-coordinate dysprosium complexes DyIII(BHT)3 (BHT = 2,6-di-tert-butyl-4-methylphenolate) with dtepy bridging ligands in the 'open' form using n-pentane as a completely inert solvent. The trinuclear molecule comprises two different DyIII centers due to its quasi-linear geometry: a central trigonal bipyramidal DyIII ion and two peripheral ones with an approximate trigonal pyramidal geometry. Thanks to that, 1 shows two types of SMM behavior which is slightly affected by the photoisomerization of the photochromic dtepy bridges. The impact of the photoisomerization on the magnetization dynamics was studied by means of alternating current (AC) magnetic susceptibility measurements for the 'open' and 'closed' forms of the molecules. The changes between the 'open' and 'closed' isomers were further investigated by IR and UV-vis spectroscopy, suggesting the co-existence of the ligand-related photochromism and single-molecule magnet behavior in 1. However, the powder X-ray diffraction studies indicate loss of structural order in the first photoisomerization step preventing in-depth studies.

Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin.

When a chromophore embedded in a photoreceptive protein undergoes a reaction upon photoexcitation, the photoreaction triggers structural changes in the protein moiety that are necessary for the function of the protein. It is thus essential to elucidate the coupling between the chromophore and protein moiety to understand the functional mechanism for photoreceptive proteins, but the mechanism by which this coupling occurs remains poorly understood. Here, we show that nonbonded atomic contacts play an essential role in driving functionally important structural changes following photoisomerization of the chromophore in Gloeobacter rhodopsin (GR). Time-resolved ultraviolet resonance Raman spectroscopy revealed that the substitution of Trp222, which contacts with methyl groups of the retinal chromophore, with a Phe residue reduced the extent of structural change. The proton-pumping activity of the GR mutant was as small as 9% of that of the wild type. Time-resolved visible absorption and resonance Raman spectra showed that the photocycle of the mutant proceeded to the L intermediate following the all-trans to 13-cis photoisomerization step but did not result in the deprotonation of the chromophore. The present results demonstrate that the atomic contacts between the chromophore and the Trp222 side chain induce the structural changes necessary for proton transfer. The requirement for dense atomic packing in a protein structure for the efficient propagation of structural changes through a coupling mechanism is discussed.

Effect of Temperature on Photoisomerization Dynamics of a Newly Designed Two-Stroke Light-Driven Molecular Rotary Motor.

The working mechanism of conventional light-driven molecular rotary motors, especially Feringa-type motors, contains two photoisomerization steps and two thermal helix inversion steps. Due to the existence of a thermal helix inversion step, both the ability to work at lower temperatures and the rotation speed are limited. In this work, a two-stroke light-driven molecular rotary motor, 2-(1,5-dimethyl-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene)-1,2-dihydro-3H-pyrrol-3-one (DDPY), is proposed, which is capable of performing unidirectional and repetitive rotation by only two photoisomerization (EP→ZP and ZP→EP) steps. With trajectory surface-hopping simulation at the semi-empirical OM2/MRCI level, the EP→ZP and ZP→EP nonadiabatic dynamics of DDPY were systematically studied at different temperatures. Both EP→ZP and ZP→EP photoisomerizations are on an ultrafast timescale (ca. 200–300 fs). The decay mode of EP→ZP photoisomerization is approximately bi-exponential, while that of ZP→EP photoisomerization is found to be periodic. For EP and ZP isomers of DDPY, after the S→S excitation, the dynamical processes of nonadiabatic decay are both followed by twisting about the central C=C double bond and the pyramidalization of the C atom at the stator-axle linkage. The effect of temperature on the nonadiabatic dynamics of EP→ZP and ZP→EP photoisomerizations of DDPY has been systematically investigated. The average lifetimes of the S excited state and quantum yields for both EP→ZP and ZP→EP photoisomerization are almost temperature-independent, while the corresponding unidirectionality of rotation is significantly increased (e.g., 74% for EP→ZP and 72% for ZP→EP at 300 K vs 100% for EP→ZP and 94% for ZP→EP at 50 K) with lowering the temperature.

Design and Nonadiabatic Photoisomerization Dynamics Study of a Three-Stroke Light-Driven Molecular Rotary Motor.

Working cycle of conventional light-driven molecular rotary motors (LDMRMs), especially Feringa-type motors, usually have four steps, two photoisomerization steps, and two thermal helix inversion (THI) steps. THI steps hinder the ability of the motor to operate at lower temperatures and limit the rotation speed of LDMRMs. A three-stroke LDMRM, 2-(2,7-dimethyl-2,3-dihydro-1H-inden-1-ylidene)-1,2-dihydro-3H-pyrrol-3-one (DDIY), is proposed, which is capable of completing an unidirectional rotation by two photoisomerization steps and one thermal helix inversion step at room temperature. On the basis of trajectory surface-hopping simulation at the semi-empirical OM2/MRCI level, the EP→ZP and ZP→EM nonadiabatic photoisomerization dynamics of DDIY were systematically analyzed. Quantum yields of EP→ZP and ZP→EM photoisomerization of DDIY are ca. 34% and 18%, respectively. Both EP→ZP and ZP→EM photoisomerization processes occur on an ultrafast time scale (ca. 100–300 fs). This three-stroke LDMRM may stimulate further research for the development of new families of more efficient LDMRMs.

Photochemistry of 3,6-Didehydropyridazine Biradical─An Untraceable Para Benzyne Analogue.

We report matrix isolation infrared spectroscopic studies to characterize 3,6-didehydropyridazine 6, a heterocyclic analogue of para benzyne, combined with computations. In this regard, we have utilized 3,6-diiodopyridazine 11 as a photolytic precursor. The experiments toward the generation of the biradical are carried out in argon and nitrogen matrices at 4 K. Instead of the elusive biradical, we have observed a ring-opening product maleonitrile (Z)-7 upon irradiation at 254 nm. In contrast, prolonged irradiation at 254 nm leads only to Z-E isomerization, forming fumaronitrile (E)-7. The mechanistic aspects of ring-opening, product selectivity, and Z-E photoisomerization steps have been investigated in detail using high-level ab initio computations. These studies have found that 3,6-didehydropyridazine 6 is an untraceable intermediate, and the ring-opening step leading to maleonitrile is barrierless. In addition, we have proposed the involvement of the S1 (π-π*) state via conical intersection in the Z-E photoisomerization of maleonitrile.

NaBr-Assisted Photoelectrochemical and Photochemical Integrated Process for Isomerization of Maleate Esters to Fumarate Esters

We developed a NaBr-assisted photoelectrochemical and photochemical integrated process for the complete isomerization of dimethyl maleate to dimethyl fumarate under solar-simulated light irradiation. This process also produced bulky fumarate ester derivatives at high yields (85–100%). A plausible mechanism of the bromine-initiated radical chain reaction was suggested by the results of the experimental data and density function theory calculations. The photoelectrochemical oxidation of NaBr generated the oxidized bromine species, which were then photolyzed to produce the bromine radical initiators induced by the photochemical process. This resulted in the high faradaic efficiency (98%) in the photoelectrochemical step and internal quantum yield (>100%) in the photoisomerization step. This newly developed process is an innovative and environmentally friendly strategy that goes beyond the conventional thermochemical process to achieve the precise synthesis of fumarate derivatives under mild conditions.

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations.

We analyze light-driven overcrowded alkene-based molecular motors, an intriguing class of small molecules that have the potential to generate MHz-scale rotation rates. The full rotation process is simulated at multiple scales by combining quantum surface-hopping molecular dynamics (MD) simulations for the photoisomerization step with classical MD simulations for the thermal helix inversion step. A Markov state analysis resolves conformational substates, their interconversion kinetics, and their roles in the motor's rotation process. Furthermore, motor performance metrics, including rotation rate and maximal power output, are computed to validate computations against experimental measurements and to inform future designs. Lastly, we find that to correctly model these motors, the force field must be optimized by fitting selected parameters to reference quantum mechanical energy surfaces. Overall, our simulations yield encouraging agreement with experimental observables such as rotation rates, and provide mechanistic insights that may help future designs.

Effect of the PHY Domain on the Photoisomerization Step of the Forward Pr →Pfr Conversion of a Knotless Phytochrome.

Phytochrome photoreceptors operate via photoisomerization of a bound bilin chromophore. Their typical architecture consists of GAF, PAS and PHY domains. Knotless phytochromes lack the PAS domain, while retaining photoconversion abilities, with some being able to photoconvert with just the GAF domain. Therefore, we investigated the ultrafast photoisomerization of the Pr state of a knotless phytochrome to reveal the effect of the PHY domain and its “tongue” region on the transduction of the light signal. We show that the PHY domain does not affect the initial conformational dynamics of the chromophore. However, it significantly accelerates the consecutively induced reorganizational dynamics of the protein, necessary for the progression of the photoisomerization. Consequently, the PHY domain keeps the bilin and its binding pocket in a more reactive conformation, which decreases the extent of protein reorganization required for the chromophore isomerization. Thereby, less energy is lost along nonproductive reaction pathways, resulting in increased efficiency.

Mechanistic Interplay between Light Switching and Guest Binding in Photochromic [Pd2Dithienylethene4] Coordination Cages.

Photochromic [Pd2L4] coordination cages based on dithienylethene (DTE) ligands L allow triggering guest uptake and release by irradiation with light of different wavelengths. The process involves four consecutive electrocyclic reactions to convert all chromophores between their open and closed photoisomeric forms. So far, guest affinity of the fully switched species was elucidated, but mechanistic details concerning the intermediate steps remained elusive. Now, a new member of the DTE cage family allows unprecedented insight into the interplay between photoisomerization steps and guest location inside/outside the cavity. Therefore, the intrinsic chirality of the DTE backbones was used as reporter for monitoring the fate of a chiral guest. In its "open" photoisomeric form ( o-L, [Pd2( o-L)4] = o-C), the C2-symmetric DTE chromophore quickly converts between energetically degenerate P and M helical conformations. After binding homochiral 1 R-( -) or 1 S-( +) camphor sulfonate ( R-CSA or S-CSA), guest-to-host chirality transfer was observed via a circular dichroism (CD) signal for the cage-centered absorption. Irradiating the R/S-CSA@ o-C host-guest complexes at 313 nm produced configurationally stable "closed" photoisomers, thus locking the induced chirality with an enantiomeric excess close to 25%. This value (corresponding to chiral induction for one out of four ligands), together with DOSY NMR, ion mobility mass spectrometry, and X-ray structure results, shows that closure of the first photoswitch is sufficient to expel the guest from the cavity.

Fulgides as Light-Driven Molecular Rotary Motors: Computational Design of a Prototype Compound.

A new family of light-driven molecular rotary motors utilizing the fulgide motif is proposed and its prototype molecule is studied by quantum chemical calculations and nonadiabatic molecular dynamics simulations. The new motor performs pure unidirectional axial rotation of the rotor blade with high quantum efficiency (ϕ ∼ 0.55-0.68) and ultrafast dynamics (⟨ t⟩ S1 ∼ 200-300 fs) of its successive photoisomerization steps. The photocyclization reaction typical of fulgide compounds is blocked by the design of the new motor and never occurred in the molecular dynamics simulations. The new motors can be synthesized from easily available precursors. In view of its remarkable photoisomerization ability, the new motor represents a prospective class of compounds for the use in nanosized molecular devices.

Different conical intersections control nonadiabatic photochemistry of fluorene light-driven molecular rotary motor: A CASSCF and spin-flip DFT study

We report the light-driven isomerization mechanism of a fluorene-based light-driven rotary motor (corresponding to Feringa's 2nd generation rotary motor, [M. M. Pollard et al., Org. Biomol. Chem. 6, 507-512 (2008)]) at the complete active space self-consistent field (CASSCF) and spin-flip time-dependent density functional theory (TDDFT) (SFDFT) levels, combined with the complete active space second-order perturbation theory (CASPT2) single-point energy corrections. The good consistence between the SFDFT and CASSCF results confirms the capability of SFDFT in investigating the photoisomerization step of the light-driven molecular rotary motor, and proposes the CASPT2//SFDFT as a promising and effective approach in exploring photochemical processes. At the mechanistic aspect, for the fluorene-based motor, the S1/S0 minimum-energy conical intersection (MECIs) caused by pyramidalization of a fluorene carbon have relatively low energies and are easily accessible by the reactive molecule evolution along the rotary reaction path; therefore, the fluorene-type MECIs play the dominant role in nonadiabatic decay, as supported by previous experimental and theoretical works. Comparably, the other type of MECIs that results from pyramidalization of an indene carbon, which has been acting as the dominant nonadiabatic decay channel in the stilbene motor, is energetically inaccessible, thus the indene-type MECIs are "missing" in previous mechanistic studies including molecular dynamic simulations. A correlation between the geometric and electronic factors of MECIs and that of the S1 energy profile along the C═C rotary coordinate was found. The findings in current study are expected to deepen the understanding of nonadiabatic transition in the light-driven molecular rotary motor and provide insights into mechanistic tuning of their performance.

Surface Hopping Excited-State Dynamics Study of the Photoisomerization of a Light-Driven Fluorene Molecular Rotary Motor.

We report a theoretical study of the photoisomerization step in the operating cycle of a prototypical fluorene-based molecular rotary motor (1). The potential energy surfaces of the ground electronic state (S0) and the first singlet excited state (S1) are explored by semiempirical quantum-chemical calculations using the orthogonalization-corrected OM2 Hamiltonian in combination with a multireference configuration interaction (MRCI) treatment. The OM2/MRCI results for the S0 and S1 minima of the relevant 1-P and 1-M isomers and for the corresponding S0 transition state are in good agreement with higher-level calculations, both with regard to geometries and energetics. The S1 surface is characterized at the OM2/MRCI level by locating two S0-S1 minimum-energy conical intersections and nearby points on the intersection seam and by computing energy profiles for pathways toward these MECIs. Semiclassical Tully-type trajectory surface hopping (TSH) simulations with on-the-fly OM2/MRCI calculations are carried out to study the excited-state dynamics after photoexcitation to the S1 state. Fast relaxation to the ground state is observed through the conical intersection regions, predominantly through the lowest-energy one with a strongly twisted central C═C double bond and pyramidalized central carbon atom. The excited-state lifetimes for the direct and inverse photoisomerization reactions (1.40 and 1.79 ps) and the photostationary state ratio (2.7:1) from the TSH-OM2 simulations are in good agreement with the available experimental data (ca. 1.7 ps and 3:1). Excited-state lifetimes, photostationary state ratio, and dynamical details of the TSH-OM2 simulations also agree with classical molecular dynamics simulations using a reparametrized optimized potentials for liquid simulations (OPLS) all-atom force field with ad-hoc surface hops at predefined conical intersection points. The latter approach allows for a more extensive statistical sampling.

Fluorenylidene−Pyrroline Biomimetic Light-Driven Molecular Switches

A new family of biomimetic photoactivated molecular switches based in the retinal chromophore is described. Expedient synthesis allows a library of compounds with a different substitution pattern, including chiral substituents, to be obtained. The effect of substitution, solvent, and light source on the photoisomerization step has been assessed. The absorption maximum has been red-shifted ca. 50 nm with respect to related systems and rotation is now easily achieved by using visible light.

Excited State Intramolecular Proton Transfer in Schiff Bases. Decay of the Locally Excited Enol State Observed by Femtosecond Resolved Fluorescence

Although the late (t>1 ps) photoisomerization steps in Schiff bases have been described in good detail, some aspects of the ultrafast (sub-100 fs) proton transfer process, including the possible existence of an energy barrier, still require experimental assessment. In this contribution we present femtosecond fluorescence up-conversion studies to characterize the excited state enol to cis-keto tautomerization through measurements of the transient molecular emission. Salicylideneaniline and salicylidene-1-naphthylamine were examined in acetonitrile solutions. We have resolved sub-100 fs and sub-0.5 ps emission components which are attributed to the decay of the locally excited enol form and to vibrationally excited states as they transit to the relaxed cis-keto species in the first electronically excited state. From the early spectral evolution, the lack of a deuterium isotope effect, and the kinetics measured with different amounts of excess vibrational energy, it is concluded that the intramolecular proton transfer in the S1 surface occurs as a barrierless process where the initial wave packet evolves in a repulsive potential toward the cis-keto form in a time scale of about 50 fs. The absence of an energy barrier suggests the participation of normal modes which modulate the donor to acceptor distance, thus reducing the potential energy during the intramolecular proton transfer.

Synthesis and Photoisomerization Characteristics of a 2,4,4‘-Substituted Azobenzene Tethered to the Side Chains of Polymethacrylamide

A side-chain methacrylamide copolymer, poly{(N-[3-(4-(4‘-methoxyphenylazo)-2-nitrophenoxy)propyl]-N-[3-(dimethylamino)propyl]methacrylamide)-co-(N-[3-(dimethylamino)propyl]methacrylamide)} (PNA) functionalized with a 2,4,4‘-substituted chromophore, 2-nitro-4‘-methoxyazobenzene was prepared and characterized. The branched structure of the azo chromophore was specifically designed to prevent the aggregate formation by minimizing the ground-state aromatic stacking interactions between the azo molecules. This cationic polyelectrolyte, together with the oppositely charged ι-carrageenan (CAG) polysaccharide, was alternately dip-coated onto a fused silica substrate to produce a multilayered film by layer-by-layer electrostatic self-assembly. A UV/vis spectroscopic study of PNA, performed during both a heating−cooling (25−85 °C) and an E−Z−E photoisomerization cycle, revealed that the maximum absorbance wavelength of the chromophore did not shift in either DMSO/H2O (1:20) solution or the multilayer assembly comprising 10 PNA/CAG bilayers. This result indicates that the PNA chromophores do not undergo aggregation. Monitoring of the E/Z photoisomerization of the solution- and film-based PNA chromophores revealed that the intensity of the π−π* transition band of its E-isomer decreased during irradiation with UV light. Also, the Z/E reverse isomerization induced by visible light (λ > 460 nm) was observed with almost full recovery of the E isomer. The kinetics of the photoisomerization step was determined to be monoexponential, indicating that photoisomerization proceeds via a single pathway. Unlike in general cases, one distinguishable property of the film-based PNA chromophore is the E/Z switching speed under experimental conditions (360 nm, P = 2 mW/cm2), which is remarkably similar to that observed in solution.

Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.

Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound chromophore. The "chemical role" of the protein cavity in the control of the photoisomerization step has been elucidated. Isomerization is facilitated due to preferential electrostatic stabilization of the chromophore's excited state by the guanidium group of Arg52, located just above the negatively charged chromophore ring. In vacuo isomerization does not occur. Isomerization of the double bond is enhanced relative to isomerization of a single bond due to the steric interactions between the phenyl ring of the chromophore and the side chains of Arg52 and Phe62. In the isomerized configuration (ground-state cis), a proton transfer from Glu46 to the chromophore is far more probable than in the initial configuration (ground-state trans). It is this proton transfer that initiates the conformational changes within the protein, which are believed to lead to signaling.

Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin

X-ray and electron diffraction studies of specific reaction intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the primary proton transfer event from the positively charged Schiff base to the negatively charged Asp-85. Here we report the structural changes in bacteriorhodopsin following red light illumination at 150 K. Single crystal microspectrophotometry showed that only the L-intermediate is populated in three-dimensional crystals under these conditions. The experimental difference Fourier electron density map and refined crystallographic structure were consistent with those previously presented (Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol. 74, 794-804). Based on the refined crystallographic structures, molecular dynamic simulations were used to examine the influence of the conformational change of the protein that is associated with the K-to-L transition on retinal dynamics. Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed.

Photoisomerization Kinetics of Cefuroxime Axetil and Related Compounds

The photoisomerization kinetics of aqueous solutions of cefuroxime axetil under irradiation at 254 nm was investigated by HPLC. The overall degradation is the result of a competition between the isomerization of the alkoxyimino group and the photolysis of the β-lactam ring. Cefuroxime axetil exists as a mixture of two diastereomers which are shown to react at different rates. This is true not only for the photoisomerization step but also for ground-state hydrolysis in alkaline conditions. Photoisomerization of the alkoxyimino group is also observed for theantiisomer of cefuroxime axetil and for some of its degradation products. The quantum yields for all these photoisomerizations are always lower than 1%, which explains the relative importance of the photolysis step. A stationarysyntoantiratio of 1 is measured for cefuroxime axetil and of 2.1 for cefuroxime. From this and previous studies, it appears that cefuroxime axetil is the most sensitive under irradiation at 254 nm when compared to other antibiotics bearing the alkoxyimino group. Aztreonam is the most stable followed by cefotaxime, cefuroxime, and cefuroxime axetil.

Preferential and strand-specific DNA repair of (6-4) photoproducts detected by a photochemical method in the hamster DHFR gene.

A non-enzymatic method that was previously shown to create single-strand DNA breaks at the location of (6-4) photoproducts in the overall genome was adapted to measure (6-4) photoproducts at the level of the gene. This approach employs a photoisomerization step that converts the (6-4) photoproduct into the Dewar valence photoisomer, which is more alkaline labile and allows for the creation of a single-strand DNA break at this site. These strand breaks were quantified via Southern analysis and the DNA repair of (6-4) photoproducts was measured over 2, 4 and 8 h after a UV dose of 40 J/m2. A comparison of repair efficiency in the actively transcribed dihydrofolate reductase (DHFR) gene, a transcriptionally inactive genomic region and the overall genome (as measured by radioimmunoassay) showed preferential repair of the active gene. The active DHFR gene showed 59% repair by 8 h compared to 33% repair in the inactive downstream region. Analysis of (6-4) photoproduct repair in the transcribed and non-transcribed strands of the DHFR gene indicate some strand specificity with 62% repair in the transcribed strand at 8 h compared with 43% repair in the non-transcribed strand. However, this strand bias is much less distinct than has been reported for the major UV photoproduct, the cyclobutane pyrimidine dimer.

Photodegradation paths of cefotaxime

The degradation kinetics of cefotaxime sodium salt in aqueous solution, under UV light at 254 nm, was investigated by HPLC and antibiotic activity. This degradation is the result of two competitive processes, an isomerization and a photolysis. This study is mostly about the isomerization step. The measured quantum yields for the cefotaxime to its anti-isomer and anti-isomer to cefotaxime isomerizations are, respectively, 0.10 and 0.12. A photostationary state characterized by an anti:syn ratio of 1.2 is obtained after 30min of irradiation. The competitive photolysis, which actually consists of at least two processes (one on the Δ3-cephem ring and the second on the methoxyimino group), leads to an intense yellowing of the solution corresponding to the destruction of the molecule. The comparative evolution of the absorption spectra, under irradiation at 254 nm, of cefotaxime, thiazoximic acid, and 7-aminocephalosporanic acid shows that it is the Δ3-cephem ring photolysis which gives the yellow color. The major conclusion of this work is to call attention to the photoisomerization step which leads efficiently to the inactive anti-isomer, without giving any visible notice of degradation. Such a process is to be expected in all antibiotics containing an alkoxyimino linkage on the C-7 substitution.