Cis-trans photoisomerization of fluorescent-protein chromophores

Photochromic variants of fluorescent proteins are opening the way to a number of opportunities for high-sensitivity regioselective studies in the cellular environment and may even lead to applications in information and communication technology. Yet, the detailed photophysical processes at the basis of photoswitching have not been fully clarified. In this paper, we used synthetic FP chromophores to clarify the photophysical processes associated with the photochromic behavior. In particular, we investigated the spectral modification of synthetic chromophore analogues of wild-type green fluorescent protein (GFP), Y66F GFP (BFPF), and Y66W GFP (CFP) upon irradiation in solutions of different polarities. We found that the cis-trans photoisomerization mechanism can be induced in all the chromophores. The structural assignments were carried out both by NMR measurements and DFT calculations. Remarkably, we determined for the first time the spectra of neutral trans isomers in different solvents. Finally, we calculated the photoconversion quantum yields by absorption measurements under continuous illumination at different times and by a nanosecond laser-flash photolysis method. Our results indicate that cis-trans photoisomerization is a general mechanism of FP chromophores whose efficiency is modulated by the detailed mutant-specific protein environment.     

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm-Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results).     

Optical absorption and emission properties of fluoranthene, benzo[k]fluoranthene, and their derivatives. A DFT study

Fluoranthene and benzo[k]fluoranthene-based oligoarenes are good candidates for organic light-emitting diodes (OLEDs). In this work, the electronic structure and optical properties of fluoranthene, benzo[k]fluoranthene, and their derivatives have been studied using quantum chemical methods. The ground-state structures were optimized using the density functional theory (DFT) methods. The lowest singlet excited state was optimized using time-dependent density functional theory (TD-B3LYP) and configuration interaction singles (CIS) methods. On the basis of ground- and excited-state geometries, the absorption and emission spectra have been calculated using the TD-DFT method with a variety of exchange-correlation functionals. All the calculations were carried out in chloroform medium. The results show that the absorption and emission spectra calculated using the B3LYP functional is in good agreement with the available experimental results. Unlikely, the meta hybrid functionals such as M06HF and M062X underestimate the absorption and emission spectra of all the studied molecules. The calculated absorption and emission wavelength are more or less basis set independent. It has been observed that the substitution of an aromatic ring significantly alters the absorption and emission spectra.     

The case of the missing ring: radical cleavage of a carbon-carbon bond and implications for GFP chromophore biosynthesis

The green fluorescent protein (GFP) creates its fluorophore by promoting spontaneous peptide backbone cyclization and amino acid oxidation chemistry on its own Ser65, Tyr66, Gly67 tripeptide sequence. Here we use high-resolution crystallography and mutational analyses to characterize GFP variants that undergo backbone cyclization followed by either anticipated chromophore synthesis via Y66F Calpha-Cbeta double-bond formation or unprecedented loss of a Y66F benzyl moiety via Calpha-Cbeta bond cleavage. We discovered a Y66F cleavage variant that subsequently incorporates an oxygen atom, likely from molecular oxygen, at the Y66 Calpha position. The post-translational products identified from these Y66F GFP structures support a common intermediate that partitions between Calpha-Cbeta oxidation and homolytic cleavage pathways. Our data indicate that Glu222 is the branchpoint control for this partitioning step and also influences subsequent oxygen incorporation reactions. From these results, we propose mechanisms for Y66F Calpha-Cbeta cleavage, oxygen incorporation, and chromophore biosynthesis with shared features that include radical chemistry. By revealing how GFP and RFP protein environments steer chemistry to favor fluorophore biosynthesis and disfavor alternative reactivity, we identify strategies for protein design. The proposed, common, one-electron oxidized, radical intermediate for post-translation modifications in the GFP family has general implications for how proteins drive and control spontaneous post-translational chemical modifications in the absence of metal ions.     

Photomagnetic and nonlinear optical properties in cis‐trans green fluoroprotein chromophore coupled Bis‐imino nitroxide diradicals

The current study extends an earlier investigation (Bhattacharya, et al., Phys. Chem. Chem. Phys. 2012, 14, 6905) to further explore various photomagnetic and optical properties of bis‐imino nitroxide, that is, (IN)₂‐based green fluorescent protein (GFP) chromophore coupled diradicals revealing new significant features. The conversion mechanisms of selected trans‐isomers into their corresponding cis‐conformers are discussed in detailed using a number of recently‐developed density functional theory (DFT) functionals based on the Minnesota suite of DFT‐models as well as using some other DFT functionals developed earlier. To provide a more in‐depth analysis of variations in magnetic properties as trans‐conformers (singlet ground‐state) convert into their cis‐analogues (triplet ground‐state), the changes in exchange magnetic coupling constants J are compared with the variation of the selected aromaticity indices. The aromaticity indices include the nuclear independent chemical shift [NICS(0)] values calculated at the center of ring structures and the harmonic oscillator model of aromaticity. Furthermore, the investigation of static nonlinear optical response properties in the (IN)₂‐based GFP chromophore coupled diradicals reveal unusually large static first hyperpolarizabilities for these systems which is highly significant for practical applications in optics and optoelectronics. © 2015 Wiley Periodicals, Inc.     

Electronic structure and optical properties of chelating heteroatomic conjugated molecules: a SAC-CI study

The electronic structure and optical properties of 13 chelating heteroatomic conjugated molecules such as pyridine, benzoxazole, and benzothiazole derivatives, which are used as C–N ligands in organometallic compounds, have been investigated. The geometries of the ground and first excited states were obtained by the DFT and CIS methods, respectively, followed by the SAC-CI calculations of the transition energies for absorption and emission. For six compounds whose experimental data are available, the SAC-CI calculations reproduced the experimental values satisfactorily with deviations of less than 0.3 eV for absorption and 0.1 eV for emission except for benzoxazoles. For other molecules, the theoretical absorption and emission spectra were predicted. The lowest ππ* excited-state geometries was calculated to be planar for most of the molecules with two or three conjugated rings connected by single bond. The geometry change due to the ππ* excitation was qualitatively interpreted by electrostatic force theory based on SAC/SAC-CI electron density difference. The excitations are relatively localized in the central region and in the lowest ππ* excited state, the inter-ring single bond shows large change, with a contraction of 0.05–0.09 Å. The present calculations provide reliable information regarding the energy levels of these chelating heteroatomic conjugated compounds.     

Optical excitations of defects in realistic nanoscale silica clusters: comparing the performance of density functional theory using hybrid functionals with correlated wavefunction methods

Optical excitations of low energy silica (SiO(2))(4) clusters obtained by global optimization, as opposed to constructed by hand, are studied using a range of theoretical methods. By focusing on the lowest energy silica clusters we hope to capture at least some of the characteristic ways by which the dry surfaces of silica nanosystems preferentially terminate. Employing the six lowest energy (SiO(2))(4) cluster isomers, we show that they exhibit a surprisingly wide range of geometries, defects, and associated optical excitations. Some of the clusters show excitations localized on isolated defects, which are known from previous studies using hydrogen-terminated versions of the defect in question. Other clusters, however, exhibit novel charge-transfer excitations in which an electron transfers between two spatially separated defects. In these cases, because of the inherent proximity of the constituent defects due to the small cluster dimensions, the excitation spectrum is found to be very different from that of the same defects in isolation. Excitation spectra of all clusters were calculated using time-dependent density functional theory (TD-DFT) and delta-SCF DFT (DeltaDFT) methods employing two different hybrid density functionals (B3LYP and BB1K) differing essentially in the amount of incorporated Hartree-Fock-like exchange (HFLE). In all cases the results were compared with CASPT2 calculated values which are taken as a benchmark standard. In line with previous work, the spatially localized excitations are found to be well described by TD-DFT/B3LYP but which gives excitation energies that are significantly underestimated in the case of the charge-transfer excitations. The TD-DFT/BB1K combination in contrast is found to give generally good excitation energies for the lowest excited states of both localized and charge-transfer excitations. Finally, our calculations suggest that the increased quality of the predicted excitation spectra by adding larger amounts of HFLE is mainly due to an increased localization of the excited state associated with the elimination of spurious self-interaction inherent to (semi-)local DFT functionals.     

Luminescent compounds diphenylboron analogs of Alq3 and its methyl substituents: A theoretical investigation of their electronic and spectroscopic properties

The absorption and emission energies for diphenylboron analogs of Alq₃ (Ph₂Bq) and its methyl substituents (Ph₂Bmq) were systematically investigated at the Zerner's intermediate neglect of differential overlap (ZINDO), configuration interaction singles (CIS), and time‐dependent density functional theory (TD‐DFT) levels of theory. The lowest excited‐state geometries were optimized at the ab initio CIS level. The TD‐DFT method provides the most reliable results for the absorption and emission transition energies, compared with other methods. Moreover, the TD‐DFT calculations reliably estimate the changes of absorption and emission λ_max values upon methyl substitution, with errors of 1.2% and 1.8%, respectively. The Stokes shifts are well reproduced by TD‐DFT calculations. Various density functional theory methods have been tested and the B3LYP functional clearly seems to be the best choice for this class of compounds. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical investigation of substituted anthraquinone dyes

We have investigated with computational chemistry techniques the visible spectra of substituted anthraquinones. A wide panel of theoretical methods has been used, with various basis sets and density functional theory (DFT) functionals, in order to assess a level of theory that would lead to converged excitation energies. It turns out that the hybrid Becke-Lee-Yang-Parr and Perdew-Burke-Erzenrhof functionals with the 6-31G (d,p) atomic basis set provide reliable lambda(max) when the solvent effects are included in the model. Combining the results of both DFT schemes allows the prediction of lambda(max) with a standard deviation limited to 13 nm.     

Theoretical investigation of the energies and geometries of photoexcited uranyl(VI) ion: a comparison between wave-function theory and density functional theory

In order to assess the accuracy of wave-function and density functional theory (DFT) based methods for excited states of the uranyl(VI) UO2(2+) molecule excitation energies and geometries of states originating from excitation from the sigma(u), sigma(g), pi(u), and pi(g) orbitals to the nonbonding 5f(delta) and 5f(phi) have been calculated with different methods. The investigation included linear-response CCSD (LR-CCSD), multiconfigurational perturbation theory (CASSCFCASPT2), size-extensivity corrected multireference configuration interaction (MRCI) and AQCC, and the DFT based methods time-dependent density functional theory (TD-DFT) with different functionals and the hybrid DFTMRCI method. Excellent agreement between all nonperturbative wave-function based methods was obtained. CASPT2 does not give energies in agreement with the nonperturbative wave-function based methods, and neither does TD-DFT, in particular, for the higher excitations. The CAM-B3LYP functional, which has a corrected asymptotic behavior, improves the accuracy especially in the higher region of the electronic spectrum. The hybrid DFTMRCI method performs better than TD-DFT, again compared to the nonperturbative wave-function based results. However, TD-DFT, with common functionals such as B3LYP, yields acceptable geometries and relaxation energies for all excited states compared to LR-CCSD. The structure of excited states corresponding to excitation out of the highest occupied sigma(u) orbital are symmetric while that arising from excitations out of the pi(u) orbitals have asymmetric structures. The distant oxygen atom acquires a radical character and likely becomes a strong proton acceptor. These electronic states may play an important role in photoinduced proton exchange with a water molecule of the aqueous environment.     

Scaled second-order perturbation corrections to configuration interaction singles: efficient and reliable excitation energy methods

Two modifications of the perturbative doubles correction to configuration interaction with single substitutions (CIS(D)) are suggested, which are excited state analogues of ground state scaled second-order M?ller-Plesset (MP2) methods. The first approach employs two parameters to scale the two spin components of the direct term of CIS(D), starting from the two-parameter spin-component scaled (SCS) MP2 ground state, and is termed SCS-CIS(D). An efficient resolution-of-the-identity (RI) implementation of this approach is described. The second approach employs a single parameter to scale only the opposite-spin direct term of CIS(D), starting from the one-parameter scaled opposite-spin (SOS) MP2 ground state, and is called SOS-CIS(D). By utilizing auxiliary basis expansions and a Laplace transform, a fourth-order algorithm for SOS-CIS(D) is described and implemented. The parameters that describe SCS-CIS(D) and SOS-CIS(D) are optimized based on a training set that includes valence excitations of various organic molecules and Rydberg transitions of water and ammonia, and they significantly improve upon CIS(D) itself. The accuracy of the two methods is found to be comparable. This arises from a strong correlation between the same-spin and the opposite-spin portions of the excitation energy terms. The methods are successfully applied to the zincbacteriochlorin-bacteriochlorin charge-transfer transition, for which time-dependent density functional theory, with presently available exchange-correlation functionals, is known to fail. The methods are also successfully applied to describe various electronic transitions outside of the training set. The efficiency of the SOS-CIS(D) and the auxiliary basis implementation of CIS(D) and SCS-CIS(D) are confirmed with a series of timing tests.     

Comparison of DFT methods for molecular orbital eigenvalue calculations

We report how closely the Kohn-Sham highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) eigenvalues of 11 density functional theory (DFT) functionals, respectively, correspond to the negative ionization potentials (-IPs) and electron affinities (EAs) of a test set of molecules. We also report how accurately the HOMO-LUMO gaps of these methods predict the lowest excitation energies using both time-independent and time-dependent DFT (TD-DFT). The 11 DFT functionals include the local spin density approximation (LSDA), five generalized gradient approximation (GGA) functionals, three hybrid GGA functionals, one hybrid functional, and one hybrid meta GGA functional. We find that the HOMO eigenvalues predicted by KMLYP, BH&HLYP, B3LYP, PW91, PBE, and BLYP predict the -IPs with average absolute errors of 0.73, 1.48, 3.10, 4.27, 4.33, and 4.41 eV, respectively. The LUMOs of all functionals fail to accurately predict the EAs. Although the GGA functionals inaccurately predict both the HOMO and LUMO eigenvalues, they predict the HOMO-LUMO gap relatively accurately (approximately 0.73 eV). On the other hand, the LUMO eigenvalues of the hybrid functionals fail to predict the EA to the extent that they include HF exchange, although increasing HF exchange improves the correspondence between the HOMO eigenvalue and -IP so that the HOMO-LUMO gaps are inaccurately predicted by hybrid DFT functionals. We find that TD-DFT with all functionals accurately predicts the HOMO-LUMO gaps. A linear correlation between the calculated HOMO eigenvalue and the experimental -IP and calculated HOMO-LUMO gap and experimental lowest excitation energy enables us to derive a simple correction formula.     

Electronic Structure Characteristics of ESIPT and TICT Fluorescence Emissions and Calculations of Emitting Energies

A scheme of time-dependent density functional theory (TDDFT) combined with the single-excitation configuration interaction (CIS) approach was employed to investigate the first excited singlet state (S₁) for eight salicylanilide derivatives and analogues, which have similar structural formulas. The results showed that fluorescence-emitting mechanisms of these molecules were in two distinct manners (excited-state intramolecular proton transfer (ESIPT) and twisted intramolecular charge transfer (TICT)), which agreed with the well-known experiments. For ESIPT compounds with inconspicuous charge transfer (CT) during electron transition, pure functionals without Hartree-Fock (HF) exchange energy, such as OLYP and BLYP, were suitable to calculate emitting energies. For TICT compounds with large CT during electron transition, hybrid functionals with about 37% HF exchange energy, such as mPW1B95 and MPW1K, performed well. On condition that the exchange-correlation (XC) functionals were chosen properly according to the rules above, reliable emitting energies for salicylanilide derivatives and analogues could be obtained at the TDDFT/6-31G(d)//CIS/3-21G(d) level. The average accuracy reached about 0.2 eV. For the salicylanilides with both proton transfer (PT) and CT reaction channels, only one channel occurred actually according to the principle of energy minimum. This actual reaction decided proper XC functionals, whereas the reaction that did not occur actually was trivial. Eight appendent compounds were calculated to prove that this successful scheme is expected to be suitable for other ESIPT and TICT compounds.     

Prediction of the Efficiency of Phosphorescent Emitters: A Theoretical Analysis of Triplet States in Platinum Blue Emitters

DFT methods are routinely used to predict the excited-state structure of phosphorescent triplet emitters. However, sometimes they fail: different functionals predict diverse lowest adiabatic emissive states. An evaluation is undertaken to determine whether it is possible to use DFT methods to investigate the triplet emitter's hypersurfaces and to explain the experimental observation that similar ligands lead to remarkably diverse phosphorescence quantum yields.