The infrared-driven cis-trans isomerization of HONO. II: Vibrational relaxation and slow isomerization channel

In a recent paper [R. Schanz et al., J. Chem. Phys. 122, 044509 (2005)], we investigated the IR-driven cis-trans isomerization of HONO in a Kr matrix with the help of femtosecond IR spectroscopy. We found that isomerization occurs on a 20 ps time scale, however, with a cis-->trans quantum yield of only 10% that is significantly below the value reported in the literature (close to 100%). At the same time, we concluded that vibrational energy has not completely dissipated out of the molecule at the maximum delay time we reached in this study (500 ps). In order to verify whether additional, slower reaction channels exist, we extend the study here to delay times up to 100 ns. At a temperature of 32 K, we indeed find an additional isomerization channel on a 2 ns timescale, which increases the total cis-->trans quantum yield to approximately 30%. The trans-->cis quantum yield is approximately 7%. There is still a discrepancy between the quantum yields we observe and the literature values, however, we provide experimental evidence that this discrepancy is due to the different temperatures of our study. Vibrational cooling occurs on a 20 ns time scale, and cascades in a highly nonstatistical manner through one single normal mode (most likely the ONO bending mode nu(5)). Intermolecular energy dissipation into the rare gas matrix is more efficient than intramolecular vibrational energy redistribution and the matrix environment can certainly not be considered a weak perturbation.     

Time-dependent wave packet study on trans-cis isomerization of HONO

Using a full six-dimensional ab initio potential energy surface and nuclear motion Hamiltonian, time-dependent computations were performed for the cis-trans isomerization of HONO. The multiconfiguration time-dependent Hartree method was used to propagate the six-dimensional wave packets. The initial excitations were chosen to be excitations of the local stretch modes and the HON local bend mode. The energy redistribution within 2 to 5 ps in the energy region of the OH stretching modes in both isomers was analyzed. The Fourier transformed frequency domain spectra were attributed to the eigenstates calculated previously by the time-independent variational approach. The results are also compared with classical trajectory computations of Thomson et al. on empirical surfaces. In agreement with matrix experiments, the cis-->trans isomerization was found to be much faster than the opposite interconversion. The intramolecular dynamics were found to be very complex involving numerous weakly excited delocalized eigenstates and anharmonic resonances. Particularly in the cis-isomer, the excitation of the HON bending local mode leads to fast energy redistribution in cis-trans delocalized modes. Neither the excitation of the OH stretching local mode in the cis nor in the trans form produces a fast isomerization, in agreement with the strongly localized characters of the corresponding eigenstates calculated variationally by Richter et al. and the gas phase spectra of HONO.     

Time-resolved IR spectroscopy of N-methylthioacetamide: trans-->cis isomerization upon n-pi and pi-pi excitation and cis-->trans photoreaction

Time-resolved infrared spectroscopy was used to study the photoisomerization of N-Methylthioacetamide (NMTAA) in D2O in both the cis-->trans and the trans-->cis direction upon selective excitation of the n-pi (S1) and pi-pi (S2) electronic transitions. While isomerization and the return to the ground state takes place on two distinct time scales (cis isomerization is 30-40%, independent of the electronic state excited, while the cis-->trans isomerization proceeds with a 60-70% quantum efficiency. These results support a mechanism by which isomerization takes place via one common intermediate state independent of electronic excitation energy and initial conformation.     

Rotational dynamics of nitrous acid (HONO) in Kr matrix

With the help of ultrafast time-resolved infrared spectroscopy, we investigate rotational diffusion of cis- and trans-nitrous acid (HONO) in solid Kr at 30 K, as well as its reorientation upon the IR-driven cis-->trans isomerization. We find different mobilities for the two isomers: cis-HONO is pinned to the matrix with no decay of the anisotropy on the 100 ns time scale, whereas trans-HONO rotates around its long axis, reducing its anisotropy partially on that time scale. The long axis itself, defined by the terminal oxygen and hydrogen atoms of HONO, stays fixed on even a minute time scale. Accompanying molecular dynamics simulations reproduce the anisotropic rotational diffusion of trans-HONO correctly, although on a completely wrong time scale, whereas they would predict complete reorientation of cis-HONO within approximately 10 ps, in harsh disagreement with the experiment. We attribute the mismatch of orientational time scales to either too soft interaction potentials or to the fact that HONO occupies an interstitial rather than a monosubstitutional matrix site. The experiments furthermore show that the direction of the OH bond hardly changes during the IR-driven cis-->trans isomerization, in contrast to the intuitive picture that it is mostly the light hydrogen which moves. Rather, it is the two central nitrogen and oxygen atoms that are removed during isomerization in a hula hoop fashion, whereas the terminal atoms are still pinned to the matrix cage.     

Photoisomerization of arylstilbazolium ligands in the presence of DNA

The ability of the DNA duplex to behave as an efficient organized medium for trans-cis photoisomerization has been explored. The presence of DNA affected isomerization in a variety of ways depending on the aryl moiety properties of the ligand and its DNA-binding mode. Contrary to intercalating ligands, 9-[2-(N-methylpyridinium-4-yl)vinyl]phenanthrene (2) and 9-[2-(N-methylpyridinium-4-yl)vinyl]anthracene (3), which gave only cis and trans isomers, the additional products--cyclobutane photodimers--were detected for 2-[2-(N-methylpyridinium-4-yl)vinyl]naphthalene (1), which binds cooperatively to the minor groove of DNA. Photostationary states (pss) for all ligands were seriously affected by the presence of DNA. A trans isomer-rich pss and restriction of trans --> cis process, observed for ligands 1 and 2, were explained in terms of a different binding affinity of DNA toward particular isomers. On the contrary, 9-anthryl derivative 3 isomerized against the isomer-binding preferences, showing cis isomer-rich pss and enhanced quantum yield of isomerization. The unique behavior of ligand 3-DNA complex was attributed to different isomerization mechanism that consists in quantum chain isomerization from an excited singlet state possessing a charge transfer character. This is the first example of ligand, which undergoes DNA-mediated cis-trans isomerization in the opposite direction than expected from DNA-binding preferences. The analysis of pss data based on two alternative pathways of photoisomerization showed that investigated ligands follow the model that allows isomerization of both free and DNA-bound ligands.     

Electronic spectroscopy and photoisomerization of trans-urocanic acid in a supersonic jet.

trans-Urocanic acid (trans-UA), a component of the epidermal layer of skin, exhibits wavelength-dependent photochemistry. The quantum efficiency of isomerization to cis-UA is greatest when the molecule is excited on the long wavelength tail of its absorption profile in solution (300-320 nm). However, exciting the molecule where it absorbs UV light most efficiently (260-285 nm) causes almost no isomerization. We have used fluorescence excitation and dispersed emission methods in a supersonic jet to investigate the electronic states involved in this complex and interesting photochemistry. Three distinct regions are present in the excitation spectrum. Region I, which is below the isomerization barrier, contains sharp, well-resolved peaks that upon excitation emit from the S(1) state of trans-UA. Region II exhibits peaks that increase in broadness and decrease in intensity with increasing excitation energy. Upon excitation these peaks produce dual emission from the S(1) states of both trans- and cis-UA. The trans to cis isomerization barrier is estimated to be 1400 cm(-1). Region III exhibits excitation to the S(2) electronic state and has a broad structure that spans 3000 cm(-1) and occurs 4000 cm(-1) above S(1). S(2) excitation results in essentially no trans to cis isomerization.     

ANALYSIS OF PRIMARY PHOTOCHEMICAL PROCESSES IN BACTERIORHODOPSIN

Abstract— The sequence of primary events following light absorption by light adapted bacteriorhodopsin (bR₅₇₀) is considered by analyzing recent picosecond absorption and emission data. The analysis is facilitated by theoretical calculations which allow us to characterize the properties of the first excited singlet state. It is concluded that excitation leads to the eventual population of a photochemically important nonfluorescent excited state (I) which decays into a photoproduct (J₆₂₅)- In J₆₂₅, which is most probably a ground state molecule, the chromophore has undergone a structural change, presumably trans → 13- cis isomerization. It is suggested that the subsequent process

reflects a relaxation of the protein environment involving proton transfer.     

Femtosecond studies of charge-transfer mediated proton transfer in 2-butylamino-6-methyl-4-nitropyridine N-oxide

We have unraveled the effects of an amino substituent in the ortho position on the excited-state dynamics of 4-nitropyridine N-oxide by studying the picosecond fluorescence kinetics and femtosecond transient absorption of a newly synthesized compound, 2-butylamino-6-methyl-4-nitropyridine N-oxide, and by quantum chemical calculations. Similar to the parent compound, the S(1) state of the target molecule has significant charge-transfer character and shows a large (approximately 8000 cm(-1)) static Stokes shift in acetonitrile. Analysis of the experimental and the theoretical results leads, however, to a new scenario in which this intramolecular charge transfer triggers in polar, aprotic solvents an ultrafast (around 100 fs) intramolecular proton transfer between the amino and the N-O group. The electronically excited N-OH tautomer is subsequently subject to solvent relaxation and decays with a lifetime of approximately 150 ps to the ground state.     

Hydrogen molecule in the small dodecahedral cage of a clathrate hydrate: quantum five-dimensional calculations of the coupled translation-rotation eigenstates

We report quantum five-dimensional (5D) calculations of the energy levels and wave functions of the hydrogen molecule, para-H2 and ortho-H2, confined inside the small dodecahedral (H2O)20 cage of the sII clathrate hydrate. All three translational and the two rotational degrees of freedom of H2 are included explicitly, as fully coupled, while the cage is treated as rigid. The 5D potential energy surface (PES) of the H2-cage system is pairwise additive, based on the high-quality ab initio 5D (rigid monomer) PES for the H2-H2O complex. The bound state calculations involve no dynamical approximations and provide an accurate picture of the quantum 5D translation-rotation dynamics of H2 inside the cage. The energy levels are assigned with translational (Cartesian) and rotational quantum numbers, based on calculated root-mean-square displacements and probability density plots. The translational modes exhibit negative anharmonicity. It is found that j is a good rotational quantum number, while the threefold degeneracy of the j = 1 level is lifted completely. There is considerable translation-rotation coupling, particularly for excited translational states.     

A fast photoswitch for minimally perturbed peptides: investigation of the trans-->cis photoisomerization of N-methylthioacetamide

Thio amino acids can be integrated into the backbone of peptides without significantly perturbing their structure. In this contribution we use ultrafast infrared and visible spectroscopy as well as state-of-the-art ab initio computations to investigate the photoisomerization of the trans form of N-methylthioacetamide (NMTAA) as a model conformational photoswitch. Following the S2 excitation of trans-NMTAA in water, the return of the molecule into the trans ground state and the formation of the cis isomer is observed on a dual time scale, with a fast component of 8-9 ps and a slow time constant of approximately 250 ps. On both time scales the probability of isomerization to the cis form is found to be 30-40%, independently of excitation wavelength. Ab initio CASPT2//CASSCF photochemical reaction path calculations indicate that, in vacuo, the trans-->cis isomerization event takes place on the S1 and/or T1 triplet potential energy surfaces and is controlled by very small energy barriers, in agreement with the experimentally observed picosecond time scale. Furthermore, the calculations identify one S2/S1 and four nearly isoenergetic S1/S0 conical intersection decay channels. In line with the observed isomerization probability, only one of the S1/S0 conical intersections yields the cis conformation upon S1-->S0 decay. A substantially equivalent excited-state relaxation results from four T1/S0 intersystem crossing points.     

Probing highly efficient photoisomerization of a bridged azobenzene by a combination of CASPT2//CASSCF calculation with semiclassical dynamics simulation

Mechanism of phototriggered isomerization of azobenzene and its derivatives is of broad interest. In this paper, the S(0) and S(1) potential energy surfaces of the ethylene-bridged azobenzene (1) that was recently reported to have highly efficient photoisomerization were determined by ab initio electronic structure calculations at different levels and further investigated by a semiclassical dynamics simulation. Unlike azobenzene, the cis isomer of 1 was found to be more stable than the trans isomer, consistent with the experimental observation. The thermal isomerization between cis and trans isomers proceeds via an inversion mechanism with a high barrier. Interestingly, only one minimum-energy conical intersection was determined between the S(0) and S(1) states (CI) for both cis → trans and trans → cis photoisomerization processes and confirmed to act as the S(1) → S(0) decay funnel. The S(1) state lifetime is ～30 fs for the trans isomer, while that for the cis isomer is much longer, due to a redistribution of the initial excitation energies. The S(1) relaxation dynamics investigated here provides a good account for the higher efficiency observed experimentally for the trans → cis photoisomerization than the reverse process. Once the system decays to the S(0) state via CI, formation of the trans product occurs as the downhill motion on the S(0) surface, while formation of the cis isomer needs to overcome small barriers on the pathways of the azo-moiety isomerization and rotation of the phenyl ring. These features support the larger experimental quantum yield for the cis → trans photoisomerization than the trans → cis process.     

Ultrafast excited-state dynamics preceding a ligand trans-cis isomerization of fac-[Re(Cl)(CO)3(t-4-styrylpyridine)2] and fac-[Re(t-4-styrylpyridine)(CO)3(2,2'-bipyridine)]+

UV-vis absorption and resonance Raman spectra of the complexes fac-[Re(Cl)(CO)3(stpy)2] and fac-[Re(stpy)(CO)3(bpy)]+ (stpy = t-4-styrylpyridine, bpy = 2,2'-bipyridine) show that their lowest absorption bands are dominated by stpy-localized intraligand (IL) pi pi* transitions. For the latter complex a Re --> bpy transition contributes to the low-energy part of the absorption band. Optical population of the 1IL excited state of fac-[Re(Cl)(CO)3(stpy)2] is followed by an intersystem crossing (< or =0.9 ps) to an 3IL state with the original planar trans geometry of the stpy ligand. This state undergoes a approximately 90 degrees rotation around the stpy C=C bond with a 11 ps time constant. An electronically excited species with an approximately perpendicular orientation of the phenyl and pyridine rings of the stpy ligand is formed. Conversion to the ground state and isomerization occurs in the nanosecond range. Intraligand excited states of fac-[Re(stpy)(CO)3(bpy)]+ show the same behavior. Moreover, it was found that the planar reactive 3IL excited state is rapidly and efficiently populated after optical excitation into the Re --> bpy 1MLCT excited state. A 1MLCT --> 3MLCT intersystem crossing takes place first with a time constant of 0.23 ps followed by an intramolecular energy transfer from the ReI(CO)3(bpy) chromophore to a stpy-localized 3IL state with a 3.5 ps time constant. The fast rate ensures complete conversion. Coordination of the stpy ligand to the ReI center thus switches the ligand trans-cis isomerization mechanism from singlet to triplet (intramolecular sensitization) and, in the case of fac-[Re(stpy)(CO)3(bpy)]+, opens an indirect pathway for population of the reactive 3IL excited state via MLCT states.     

Photoproperties of isolated cis and trans stilbene molecules

A detailed account is given of the experimental approach to measuring transient spectra of dilute gases using picosecond pulses. The picosecond continuum generated by Nd:glass laser pulses is used to probe gaseous samples and spectra are recorded in a double beam arrangement. The pump and probe pulses interact with the sample over a few centimeters by means of a dielectric waveguide. Picosecond time resolved spectra, relative fluorescence quantum yield measurements, and fluorescence spectra are reported for trans-stilbene under collision free conditions. The lifetime of the optically prepared states at 265 nm and 287 nm are 15 ps and 55 ps respectively, measured by the decay of the transient absorption. The deuteration effect is less than 20%. The variation of the fluorescence yield with vibrational energy excess in the excited state of trans is fitted to these lifetime measurements to yield the variation of nonradiative decay due to twisting of trans-stilbene. Cis-stilbene is suggested to twist in less than 1 ps. Consideration of the spectral results yields new information about the isomerization of stilbene, in particular that there exists a barrier to twisting in the isolated molecule and that vibrational energy redistribution at the trans configuration is probably not complete on the time scale of our experiments. A pictorial model for discussing constant energy relaxation phenomena is introduced.     

Vibrational energy flow rates for cis- and trans-stilbene isomers in solution

Transient electronic absorption following excitation of the first C-H stretching overtone (2nu(CH)) or a C-H stretch-bend combination (nu(CH) + nu(bend)) monitors the flow of vibrational energy in cis-stilbene and in trans-stilbene. Following a rapid initial rise as energy flows into states interrogated by the probe pulse, the absorption decays with two time constants, which are about a factor of 2 longer for the cis-isomer than for the trans-isomer. The decay times for cis-stilbene are tau2(cis) = (2.6 +/- 1.5) ps and tau3(cis) = (24.1 +/- 2.1) ps, and those for trans-stilbene are tau2(trans) = (1.4 +/- 0.6) ps and tau3(trans) = (10.2 +/- 1.1) ps. The decay times are essentially the same in different solvents, suggesting that the relaxation is primarily intramolecular. The two decay times are consistent with the sequential flow of energy through sets of coupled states within the molecule, and the difference in the rates for the two isomers likely reflects differences in coupling among the states arising from the different structures of the isomers. The similarity of the time evolution following excitation of the first C-H overtone at 5990 cm(-1) and the stretch-bend combination at 4650 cm(-1) is consistent with a subset of states, whose structure is similar for the two vibrational excitation energies, controlling the observed flow of energy.     

Picosecond isomerization in photochromic ruthenium-dimethyl sulfoxide complexes

The complexes [Ru(tpy)(bpy)(dmso)](OSO(2)CF(3))(2) and trans-[Ru(tpy)(pic)(dmso)](PF(6)) (tpy is 2,2':6',2' '-terpyridine, bpy is 2,2'-bipyridine, pic is 2-pyridinecarboxylate, and dmso is dimethyl sulfoxide) were investigated by picosecond transient absorption spectroscopy in order to monitor excited-state intramolecular S-->O isomerization of the bound dmso ligand. For [Ru(tpy)(bpy)(dmso)](2+), global analysis of the spectra reveals changes that are fit by a biexponential decay with time constants of 2.4 +/- 0.2 and 36 +/- 0.2 ps. The first time constant is assigned to relaxation of the S-bonded (3)MLCT excited state. The second time constant represents both excited-state relaxation to ground state and excited-state isomerization to form O-[Ru(tpy)(bpy)(dmso)](2+). In conjunction with the S-->O isomerization quantum yield (Phi(S)(-->)(O) = 0.024), isomerization of [Ru(tpy)(bpy)(dmso)](2+) occurs with a time constant of 1.5 ns. For trans-[Ru(tpy)(pic)(dmso)](+), global analysis of the transient spectra reveals time constants of 3.6 +/- 0.2 and 118 +/- 2 ps associated with these two processes. In conjunction with the S-->O isomerization quantum yield (Phi(S)(-->)(O) = 0.25), isomerization of trans-[Ru(tpy)(pic)(dmso)](+) occurs with a time constant of 480 ps. In both cases, the thermally relaxed excited states are assigned as terpyridine-localized (3)MLCT states. Electronic state diagrams are compiled employing these data as well as electrochemical, absorption, and emission data to describe the reactivity of these complexes. The data illustrate that rapid bond-breaking and bond-making reactions can occur from (3)MLCT excited states formed from visible light irradiation.     

Photoisomerization of disperse red 1 studied with transient absorption spectroscopy and quantum chemical calculations

The photoisomerization of the push-pull substituted azo dye Disperse Red 1 is studied using femtosecond time-resolved absorption spectroscopy and other spectroscopic and computational techniques. In comparison with azobenzene, the pipi* state is more stabilized by the effects of push-pull substitution than the npi* state, but the latter is probably still the lowest in energy. This conclusion is based on the kinetics, anisotropy of the excited state absorption spectrum, the spectra of the ground states, and quantum chemical calculations. The S(1)(npi*) state is formed from the initially excited pipi* state in <0.2 ps, and decays to the ground state with time constants of 0.9 ps in toluene, 0.5 ps in acetonitrile, and 1.4 ps in ethylene glycol. Thermal isomerization transforms the Z isomer produced to the more stable E isomer with time constants of 29 s (toluene), 28 ms (acetonitrile), and 2.7 ms (ethylene glycol). The pathway of photoisomerization is likely to be rotation about the N=N bond. Quantum chemical calculations indicate that along the inversion pathway ground and excited state energy surfaces remain well separated, whereas rotation leads to a region where conical intersections can occur. For the ground-state Z to E isomerization, conclusive evidence is lacking, but inversion is more probably the favored pathway in the push-pull substituted systems than in the parent azobenzene.     

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.     

Photophysical studies of the trans to cis isomerization of the push-pull molecule: 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene (mepepy)

Organic molecules possessing intramolecular charge-transfer properties (D-pi-A type molecules) are of key interest particularly in the development of new optoelectronic materials as well as photoinduced magnetism. One such class of D-pi-A molecules that is of particular interest contains photoswitchable intramolecular charge-transfer states via a photoisomerizable pi-system linking the donor and acceptor groups. Here we report the photophysical and electronic properties of the trans to cis isomerization of 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene ligand (mepepy) in aqueous solution using photoacoustic calorimetry (PAC) and theoretical methods. Density functional theory (DFT) calculations demonstrate a global energy difference between cis and trans isomers of mepepy to be 8 kcal mol(-1), while a slightly lower energy is observed between the local minima for the trans and cis isomers (7 kcal mol(-1)). Interestingly, the trans isomer appears to exhibit two ground-state minima separated by an energy barrier of approximately 9 kcal mol(-1). Results from the PAC studies indicate that the trans to cis isomerization results in a negligible volume change (0.9 +/- 0.4 mL mol(-1)) and an enthalpy change of 18 +/- 3 kcal mol(-1). The fact that the acoustic waves associated with the trans to cis transition of mepepy overlap in frequency with those of a calorimetric reference implies that the conformational transition occurs faster than the approximately 50 ns response time of the acoustic detector. Comparison of the experimental results with theoretical studies provide evidence for a mechanism in which the trans to cis isomerization of mepepy results in the loss of a hydrogen bond between a water molecule and the pyridine ring of mepepy.     

Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions

Green fluorescent proteins (GFPs) are widely used as tools in biochemistry, cell biology, and molecular genetics due to their unusual optical spectroscopic characteristics. The spectrophotometric and fluorescence properties of GFPs are controlled by the protonation states and possibly cis-trans isomerization of the chromophore (p-hydroxybenzylideneimidazolinone). In this work, we have investigated electronic structures, liquid structures, and solvent shifts of the three possible protonated states (neutral, anionic, and zwitterionic) and their cis-trans isomerization of a model compound 4'-hydroxybenzylidene-2-methyl-imidazolin-5-one-3-acetate (HBMIA) in aqueous solutions. Our calculated results suggest that HBMIA could adopt both cis and trans conformations in a solution, and it exists in three different protonation states depending on the pH conditions. The absorption spectrum observed in neutral solution is thus assigned to the electronic excitations within the neutral form and the cis isomer of the zwitterionic form, while the absorption band at 425 nm in the basic solution is due to the excitations within the anionic form and the trans isomer of the zwitterionic form. Some technical problems related to the computation of electronic excitations within the HBMIA at the anionic state are also discussed.     

Characterization of a single molecule DNA switch in free solution

We have studied a donor-acceptor fluorophore-labeled DNA switch where the acceptor is Alexa-647, a carbocyanine dye, in solution at the single molecule level to elucidate the fluorescence switching mechanism. The acceptor, which is in an initial high fluorescence trans state, undergoes a photoisomerization reaction resulting in two additional states during its sub-millisecond transit across the probe volume. These two states are assigned to a nonfluorescent triplet trans state that strongly quenches the donor emission and a singlet cis state that blocks the fluorescence resonance energy transfer (FRET) pathway and gives rise to donor-only fluorescence. The formation of these states is faster than the transit time, so that all three states are approximately equally populated under our experimental conditions. The acceptor dye can stick to the DNA in all these states, with the rate of unsticking determining the rate of isomerization into the other states. Measurement of the rate of change of the FRET signal therefore provides information about the fluorophore-DNA intramolecular dynamics. These results explain the large zero peak in the proximity ratio, often seen in single molecule FRET experiments, and suggest that photoinduced effects may be important in single molecule FRET experiments using carbocyanine dyes. They also suggest that for fast photoinduced switching the interactions of the acceptor dye with the DNA and other surfaces should be prevented.