Model Chromophore Research Articles

The effects of resonance delocalization and the extent of π system on ionization energies of model fluorescent proteins chromophores

Recent advances in the design and application of redox‐active fluorescent proteins (FPs) stimulated an interest in the electronic structure of the ionized/electron‐detached FP chromophores. Here, we report the results of a computational study of the electron‐detached and ionized states of model chromophores of green and red FPs. We focus on the analysis of the effects of the phenolate OH group position (ortho, meta, and para) on relative energies of the chromophores in the ground as well as in the ionized/detached electronic states. We found that, similarly to the green chromophore, the red chromophores with the OH group in meta position have lower vertical detachment energies (DE) and greater ionization energies relative to the ortho and para forms. Moreover, the effect is stronger for the red anionic chromophores. The differences in DE in meta species relative to their para counterparts are 0.47 and 0.25 eV for the red and green chromophores, respectively. The observed trends are due to a combined effect of resonance stabilization and the electronegativity of the acylimine group in the red chromophores. The analysis is supported by the computed charge and spin density delocalization patterns. © 2014 Wiley Periodicals, Inc.

Human infrared vision is triggered by two-photon chromophore isomerization.

Vision relies on photoactivation of visual pigments in rod and cone photoreceptor cells of the retina. The human eye structure and the absorption spectra of pigments limit our visual perception of light. Our visual perception is most responsive to stimulating light in the 400- to 720-nm (visible) range. First, we demonstrate by psychophysical experiments that humans can perceive infrared laser emission as visible light. Moreover, we show that mammalian photoreceptors can be directly activated by near infrared light with a sensitivity that paradoxically increases at wavelengths above 900 nm, and display quadratic dependence on laser power, indicating a nonlinear optical process. Biochemical experiments with rhodopsin, cone visual pigments, and a chromophore model compound 11-cis-retinyl-propylamine Schiff base demonstrate the direct isomerization of visual chromophore by a two-photon chromophore isomerization. Indeed, quantum mechanics modeling indicates the feasibility of this mechanism. Together, these findings clearly show that human visual perception of near infrared light occurs by two-photon isomerization of visual pigments.

Locally-excited (LE) versus charge-transfer (CT) excited state competition in a series of para-substituted neutral green fluorescent protein (GFP) chromophore models.

In this paper, I provide a characterization of the low-energy electronic structure of a series of para-substituted neutral green fluorescent protein (GFP) chromophore models using a theoretical approach that blends linear free energy relationships (LFERs) with state-averaged complete-active-space self-consistent field (SA-CASSCF) theory. The substituents are chosen to sample the Hammett σ(p) scale from R = F to NH2, and a model of the neutral GFP chromophore structure (R = OH) is included. I analyze the electronic structure for different members of the series in a common complete-active-space valence-bond (CASVB) representation, exploiting an isolobal analogy between active-space orbitals for different members of the series. I find that the electronic structure of the lowest adiabatic excited state is a strong mixture of weakly coupled states with charge-transfer (CT) or locally excited (LE) character and that the dominant character changes as the series is traversed. Chromophores with strongly electron-donating substituents have a CT-like excited state such as expected for a push-pull polyene or asymmetric cyanine. Chromophores with weakly electron-donating (or electron-withdrawing) substituents have an LE-like excited state with an ionic biradicaloid structure localized to the ground-state bridge π bond.

Time-resolved pump-probe spectroscopy to follow valence electronic motion in molecules: Application

Numerical experiments are performed using a recently published formalism [Phys. Rev. A 88, 013419 (2013)] for computing the transient absorption of an attosecond x-ray probe by a molecule in a nonstationary valence-excited state. This study makes use of an all-electron correlated electronic-structure model to compute electronic dynamics ensuing after a localized excitation on a model chromophore group. Simulated absorption of a delayed attosecond pulse is then used to investigate the presence of an extra valence electron or vacancy around atoms of a given element as a function of time, by tuning the carrier frequency to the associated core-valence energy gap. We show correlations between the predicted absorption of such pulses and visualizations of the particle and hole locations in test molecules. Given the strong role played by the relative orientation of the molecules and the probe polarization, results are presented for a few different alignment schemes. For the molecules studied, effective pump-induced alignment is sufficient to recover easily interpreted information.

Modulating the electronic structure of chromophores by chemical substituents for efficient energy transfer: application to fluorone.

Strong electron correlation within a quasi-spin model of chromophores was recently shown to enhance exciton energy transfer significantly. Here we investigate how the modulation of the electronic structure of the chromophores by chemical substitution can enhance energy-transfer efficiency. Unlike previous work that does not consider the direct effect of the electronic structure on exciton dynamics, we add chemical substituents to the fluorone dimer to study the effect of electron-donating and electron-withdrawing substituents on exciton energy transfer. The exciton dynamics are studied from the solution of a quantum Liouville equation for an open system whose model Hamiltonian is derived from excited-state electronic structure calculations. Both van der Waals energies and coupling energies, arising from the Hellmann-Feynman force generated upon transferring the dimers from infinity to a finite separation, are built into the model Hamiltonian. Though these two effects are implicitly treated in dipole-based models, their explicit and separate treatment as discussed here is critical to forging the correct connection with the electronic structure calculations. We find that the addition of electron-donating substituents to the fluorone system results in an increase in exciton-transfer rates by factors ranging from 1.3-1.9. The computed oscillator strength is consistent with the recent experimental results on a larger heterodimer system containing fluorone. The oscillator strength increases with the addition of electron-donating substituents. Our results indicate that the study of chromophore networks via electronic structure will help in the future design of efficient synthetic light-harvesting systems.

Photochemistry of Pheomelanin Building Blocks and Model Chromophores: Excited-State Intra- and Intermolecular Proton Transfer.

Pheomelanins, the epidermal pigments of red-haired people responsible for their enhanced UV susceptibility, contain 1,4-benzothiazines and 1,3-benzothiazole as main structural components. Despite the major role played in pheomelanin phototoxicity, the photoreactivity of these species has so far remained unexplored. Static and time-resolved fluorescence spectroscopy was used to identify excited-state reactions of the two main pheomelanin benzothiazole building blocks, namely, the 6-(2-amino-2-carboxyethyl)-4-hydroxy-1,3-benzothiazole (BT) and the 2-carboxy derivative (BTCA) together with model chromophores lacking some of the ionizable functions. The results show that in aqueous buffer solution the OH at 4-position and the benzothiazole nitrogen atom control the photochemistry of both BT and BTCA via excited-state proton transfer to solvent (ESPT) and excited-state intramolecular proton transfer (ESIPT), while the amino acidic groups of the alanyl chain have a minor influence on the photochemistry. The ESPT and ESIPT produce several different excited-state ionic species with lifetimes ranging from ∼100 ps to ∼3 ns.

SORCI for photochemical and thermal reaction paths: A benchmark study

Dynamic electron correlation is very important for the correct description of potential energy surfaces, especially surface with differential dynamic electron correlation. Moreover, an accurate description of both the ground and excited state potential energy surfaces is essential to understand thermal and photochemical reactions of molecular systems. In the present work we test the performance of the Spectroscopy ORiented Configuration Interaction (SORCI) method that was originally designed to account for the dynamic electron correlation in an efficient manner at fixed geometry. Here, we assess the performance of SORCI along several paths on the ground and excited state potential energy surfaces that are related to the thermal and photochemical isomerization of a reduced retinal chromophore model. The ground state mapping involves three paths. Two of them are minimum energy paths that lead through different transitions states from one cis/trans stereoisomer to the other. One transition state has a diradical (open-shell) character while the other one has a charge-transfer character. The third ground state path connects these two transition states via a conical intersection. In addition, we assess the performance of SORCI for three excited state paths that comprise a minimum energy path starting from each of the cis and from the trans chromophore. These two pathways arrive at different conical intersections that are part of one seam of conical intersections. The third excited state path presents a profile along this seam.Despite the high complexity and varying mixture of different electronic structures involved in this benchmark, SORCI produces energy differences and energy profiles in good agreement with the multireference configuration interaction plus quadruples correction (MRCISD+Q) reference along all six paths. We find that SORCI is capable of producing smooth energy profiles, which require tighter thresholds than the present default. A further tightening of these thresholds by one order of magnitude yields converged SORCI values as compared to the limit of the method obtained by setting the three cutoffs to zero. However, we note also some deficiencies relative to MRCISD+Q in the description of relative energy differences. When comparing energies of structures that have very different geometries on the same potential energy surface we find that SORCI underestimates the reference values. Here SORCI underestimates the corresponding MRCISD+Q reference values thus indicating a non-negligible effect of the inactive double excitations. In addition we observe some artifacts at conical intersections due to the Davidson correction for higher excitations. Ways to overcome these drawbacks are discussed.

Molecular‐Level Understanding of Ground‐ and Excited‐State OH⋅⋅⋅O Hydrogen Bonding Involving the Tyrosine Side Chain: A Combined High‐Resolution Laser Spectroscopy and Quantum Chemistry Study

The present study combines both laser spectroscopy and ab initio calculations to investigate the intermolecular OH⋅⋅⋅O hydrogen bonding of complexes of the tyrosine side chain model chromophore compounds phenol (PH) and para-cresol (pCR) with H2 O, MeOH, PH and pCR in the ground (S0 ) state as well as in the electronic excited (S1 ) state. All the experimental and computational findings suggest that the H-bond strength increases in the S1 state and irrespective of the hydrogen bond acceptor used, the dispersion energy contribution to the total interaction energy is about 10-15 % higher in the S1 state compared to that in the S0 state. The alkyl-substituted (methyl; +I effect) H-bond acceptor forms a significantly stronger H bond both in the S0 and the S1 state compared to H2 O, whereas the aryl-substituted (phenyl; -R effect) H-bond donor shows a minute change in energy compared to H2 O. The theoretical study emphasizes the significant role of the dispersive interactions in the case of the pCR and PH dimers, in particular the CH⋅⋅⋅O and the CH⋅⋅⋅π interactions between the donor and acceptor subunits in controlling the structure and the energetics of the aromatic dimers. The aromatic dimers do not follow the acid-base formalism, which states that the stronger the base, the more red-shifted is the XH stretching frequency, and consequently the stronger is the H-bond strength. This is due to the significant contribution of the dispersion interaction to the total binding energy of these compounds.

Assessment of Density Functional Methods for Obtaining Geometries at Conical Intersections in Organic Molecules

A number of commonly available density functionals have been tested for their ability to describe the energetics and the geometry at conical intersections in connection with the spin-restricted ensemble referenced Kohn–Sham (REKS) method. The minimum energy conical intersections have been optimized for several molecular systems, which are widely used as paradigmatic models of photochemical rearrangements and models of biological chromophores. The results of the calculations are analyzed using the sign-change theorem of Longuet-Higgins and a method of elementary reaction coordinates of Haas et al. The latter approach helps to elucidate the differences between the geometries at conical intersections as predicted by the multireference wave function ab initio methods and by the density functional methods. Overall, the BH&HLYP density functional yields the best results for the conical intersection geometries and energetics.

Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods.

The photoisomerization of the retinal chromophore of visual pigments proceeds along a complex reaction coordinate on a multidimensional surface that comprises a hydrogen-out-of-plane (HOOP) coordinate, a bond length alternation (BLA) coordinate, a single bond torsion and, finally, the reactive double bond torsion. These degrees of freedom are coupled with changes in the electronic structure of the chromophore and, therefore, the computational investigation of the photochemistry of such systems requires the use of a methodology capable of describing electronic structure changes along all those coordinates. Here, we employ the penta-2,4-dieniminium (PSB3) cation as a minimal model of the retinal chromophore of visual pigments and compare its excited state isomerization paths at the CASSCF and CASPT2 levels of theory. These paths connect the cis isomer and the trans isomer of PSB3 with two structurally and energetically distinct conical intersections (CIs) that belong to the same intersection space. MRCISD+Q energy profiles along these paths provide benchmark values against which other ab initio methods are validated. Accordingly, we compare the energy profiles of MRPT2 methods (CASPT2, QD-NEVPT2, and XMCQDPT2) and EOM-SF-CC methods (EOM-SF-CCSD and EOM-SF-CCSD(dT)) to the MRCISD+Q reference profiles. We find that the paths produced with CASSCF and CASPT2 are topologically and energetically different, partially due to the existence of a "locally excited" region on the CASPT2 excited state near the Franck-Condon point that is absent in CASSCF and that involves a single bond, rather than double bond, torsion. We also find that MRPT2 methods as well as EOM-SF-CCSD(dT) are capable of quantitatively describing the processes involved in the photoisomerization of systems like PSB3.

Assessment of Density Functional Theory for Describing the Correlation Effects on the Ground and Excited State Potential Energy Surfaces of a Retinal Chromophore Model.

In the quest for a cost-effective level of theory able to describe a large portion of the ground and excited potential energy surfaces of large chromophores, promising approaches are rooted in various approximations to the exact density functional theory (DFT). In the present work, we investigate how generalized Kohn-Sham DFT (GKS-DFT), time-dependent DFT (TDDFT), and spin-restricted ensemble-DFT (REKS) methods perform along three important paths characterizing a model retinal chromophore (the penta-2,4-dieniminium cation) in a region of near-degeneracy (close to a conical intersection) with respect to reference high-level multiconfigurational wave function methods. If GKS-DFT correctly describes the closed-shell charge transfer state, only TDDFT and REKS approaches give access to the open-shell diradical, one which sometimes corresponds to the electronic ground state. It is demonstrated that the main drawback of the usual DFT-based methods lies in the absence of interactions between the charge transfer and the diradicaloid configurations. Hence, we test a new computational scheme based on the State-averaged REKS (SA-REKS) approach, which explicitly includes these interactions into account. The State-Interaction SA-REKS (SI-SA-REKS) method significantly improves on the REKS and the SA-REKS results for the target system. The similarities and differences between DFT and wave function-based approaches are analyzed according to (1) the active space dimensions of the wave function-based methods and (2) the relative electronegativities of the allyl and protonated Schiff base moieties.

Photo-isomerization upshifts the pKa of the Photoactive Yellow Protein chromophore to contribute to photocycle propagation

a b s t r a c t The influence of chromophore structure on the protonation constant of the Photoactive Yellow Protein chromophore is explored with isolated para-coumaric acid (pCA) and thiomethyl-para-coumaric acid model chromophores in solution. pH titration coupled with visible absorption spectra of the trans and photogenerated cis conformer of isolated pCA demonstrates that the isomerization of the chromophore increases the pKa of the phenolate group by 0.6 units (to 10.1 ± 0.22). Formation of the pCA thioester reduces the pKa of the phenolic group by 0.3 units (from 9.5 ± 0.15 to 9.2 ± 0.16). Unfortunately, a macro- scopic cis-TMpCA population was not achieved via photoexcitation. Both trends were explained with electronic structure calculations including a Natural Bond Orbital analysis that resolves that the pKa upshift for the cis configuration is attributed to increased Columbic repulsion between the coumaryl tail and the phenolate moieties. This structurally induced pKa upshift after isomerization is argued to aid in the protonation of the chromophore within the PYP protein environment and the subsequent propagation of the photocycle response and in vivo photo-activity. © 2013 Elsevier B.V. All rights reserved.

Cover Picture: Visible-Light-Induced Photodimerization of a Photoactive Yellow Protein (PYP) Chromophore Model in a Single Crystal (Chem. Eur. J. 25/2013)

Cover Picture: Visible-Light-Induced Photodimerization of a Photoactive Yellow Protein (PYP) Chromophore Model in a Single Crystal (Chem. Eur. J. 25/2013)

On the Photodetachment from the Green Fluorescent Protein Chromophore

Motivated by the discrepancies in recent experimental and theoretical studies of photodetachment from isolated model chromophores of the green fluorescent protein (GFP), this study reports calculations of the electron detachment energies and photoelectron spectra of the phenolate and deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) anions. The spectra were computed using double-harmonic parallel normal mode approximation. High-level coupled-cluster methods as well as density functional theory were used to compute vertical and adiabatic detachment energies of the phenolate anion serving as a model system representing anionic GFP-like chromophores (HBDI). The benchmark calculations reveal that the basis set has significant effect on the computed detachment energies, whereas the results are less sensitive to the level of electron correlation treatment. At least aug-cc-pVTZ basis set is required. The best ωB97X-D and CCSD(T) estimates of phenolate's adiabatic detachment energy are 2.12 and 2.19 eV; these values are very close to the experimental value, 2.253 eV [Gunion et al. Int. J. Mass Spectrom. Ion Proc. 1992, 117, 601]. The best estimate of the vertical detachment energy of deprotonated HBDI is 2.76 eV, which supports bound character of the bright excited state in the Franck-Condon region. The most intense transition in the computed photoelectron spectra of both phenolate and deprotonated HBDI is the 0-0 S0-D0 transition, which is 0.11 eV below vertical detachment energy. Therefore, the position of the maximum of the photoelectron spectrum does not represent vertical detachment energy, and the direct comparison between theory and experiment must involve spectrum modeling.

Visible-Light-Induced Photodimerization of a Photoactive Yellow Protein (PYP) Chromophore Model in a Single Crystal

The chromophore of the photoactive yellow protein (PYP), the photoreceptor in the photomotility of the bacterium Halorhodospira halophila, is a deprotonated para-coumaric thioester linked to the side residue of a cysteine residue. The photophysics of the PYP chromophore is conveniently modeled with para-hydroxycinnamic thiophenyl esters. Herein, we report the first direct evidence, obtained with X-ray diffraction, of photodimerization of a para-hydroxycinnamic thiophenyl ester in single crystalline state. This result represents the first direct observation of [2+2] dimerization of a model PYP chromophore, and demonstrates that even very weak light in the visible region is capable of inducing parallel radical reactions in PYP from the excited state of the chromophore, in addition to the main reaction pathway (trans-cis isomerization). This PYP model system adds an interesting example to the known solid-state photodimerizations, because unlike the anhydrous crystal (which is not capable of sustaining the stress and disintegrates in the course of photodimerization), a single water molecule "dilutes" the structure to the extent sufficient for single-crystal-to-single-crystal reaction.

Conformational Heterogeneity of Methyl 4-Hydroxycinnamate: A Gas-Phase UV–IR Spectroscopic Study

UV excitation and IR absorption spectroscopy on jet-cooled molecules is used to study the conformational heterogeneity of methyl 4-hydroxycinnamate, a model chromophore of the Photoactive Yellow Protein (PYP), and to determine the spectroscopic properties of the various conformers. UV-UV depletion spectroscopy identifies four different species with distinct electronic excitation spectra. Quantum chemical calculations argue that these species are associated with different conformers involving the s-cis/s-trans configuration of the ester with respect to the propenyl C-C single bond and the syn/anti orientation of the phenolic OH group. IR-UV hole-burning spectroscopy is used to record their IR absorption spectra in the fingerprint region. Comparison with IR absorption spectra predicted by quantum chemical calculations provides vibrational markers for each of the conformers, on the basis of which each of the species observed with UV-UV depletion spectroscopy is assigned. Although both DFT and wave function methods reproduce experimental frequencies, we find that calculations at the MP2 level are necessary to obtain agreement with experimentally observed intensities. To elucidate the role of the environment, we compare the IR spectra of the isolated conformers with IR spectra of methyl 4-hydroxycinnamate-water clusters, and with IR spectra of methyl 4-hydroxycinnamate in solution.

Molecular Spoked Wheels: Synthesis and Self-Assembly Studies on Rigid Nanoscale 2D Objects

We present the efficient synthesis of a new molecular spoked-wheel structure (MSW-3). Two derivatives with diameters of approximately 4 nm have been prepared. By highlighting the importance of pseudo-high-dilution conditions during cyclization, we were able to access the compounds on a several hundred milligram scale. In addition to the standard characterization (NMR spectroscopy, MS), we describe a detailed investigation of the optical properties of the fluorescent MSWs by comparison with appropriate model chromophores. Furthermore, a comprehensive study of the structure in solution by means of light- and X-ray scattering experiments has been conducted. Scanning tunneling microscopy (STM) revealed the two-dimensional organization of the molecules on highly oriented pyrolytic graphite and emphasized the spoked-wheel structure. The diameter of these molecules measured by small-angle X-ray scattering is in very good agreement with that obtained from STM and matches the results of molecular modeling. This confirms the rigidifying effect of the spokes, which results in highly shape-persistent nanometer-sized oblate organic compounds.

Spectral Tuning of the Photoactive Yellow Protein Chromophore by H-Bonding

Gas phase photoabsorption measurements on model chromophores can be useful in shedding light on the issue of spectral tuning within photoactive proteins. In nature, protein pockets holding chromophores often form one or more H-bonds with the chromophore, which almost always participates in the photocycle of the protein. We address the issue of spectral tuning by H-bonds using one of the simplest model systems, the anionic form of trans p-coumaric acid.

Two-photon solvatochromism. I. Solvent effects on two-photon absorption cross section of 4-dimethylamino-4′-nitrostilbene (DANS)

This Letter reports a systematic study of solvent effect on two-photon absorption (2PA) spectra of a model chromophore, 4-dimethylamino-4′-nitrostilbene (DANS). The two-photon solvatochromic behavior of DANS was investigated in selected solvents using the Z-scan measurement technique. The obtained results demonstrate that the examined molecule possesses slightly different 2PA response in solvents of different polarity. A decrease in the two-photon absorption strength is observed when the solvent is changed from chloroform and dichloromethane to the more polar dimethyl sulfoxide.

Toward Understanding the Redox Properties of Model Chromophores from the Green Fluorescent Protein Family: An Interplay between Conjugation, Resonance Stabilization, and Solvent Effects

The redox properties of model chromophores from the green fluorescent protein family are characterized computationally using density functional theory with a long-range corrected functional, the equation-of-motion coupled-cluster method, and implicit solvation models. The analysis of electron-donating abilities of the chromophores reveals an intricate interplay between the size of the chromophore, conjugation, resonance stabilization, presence of heteroatoms, and solvent effects. Our best estimates of the gas-phase vertical/adiabatic detachment energies of the deprotonated (i.e., anionic) model red, green, and blue chromophores are 3.27/3.15, 2.79/2.67, and 2.75/2.35 eV, respectively. Vertical/adiabatic ionization energies of the respective protonated (i.e., neutral) species are 7.64/7.35, 7.38/7.15, and 7.70/7.32 eV, respectively. The standard reduction potentials (E(red)(0)) of the anionic (Chr•/Chr–) and neutral (Chr+•/Chr) model chromophores in acetonitrile are 0.34/1.40 V (red), 0.22/1.24 V (green), and −0.12/1.02 V (blue), suggesting, counterintuitively, that the red chromophore is more difficult to oxidize than the green and blue ones (in both neutral and deprotonated forms). The respective redox potentials in water follow a similar trend but are more positive than the acetonitrile values.