Effect of Leaving Centrosymmetric Character on Spectral Properties in Mono-, Bi-, and Triphotonic Absorption Spectroscopies.

Numerical simulations of the absorption bands of photoswitch --tetrafluoroazobenzene in DMSO solution under one-, two-, and three-photon absorption conditions combined with the analysis of the behavior of transition probability under distortion of planarity reveal many similarities between the mono- and triphoton spectroscopic behaviors with a two-photon spectrum being set apart. The position of the absorption peak for the studied nπ* and ππ* transitions appears shifted to lower energies (longer wavelengths) than the conventional estimate based on vertical excitation from the ground-state potential energy minimum.

Three-Photon Infrared Stimulation of Endogenous Neuroreceptors in Vivo.

To interrogate neural circuits and crack their codes, in vivo brain activity imaging must be combined with spatiotemporally precise stimulation in three dimensions using genetic or pharmacological specificity. This challenge requires deep penetration and focusing as provided by infrared light and multiphoton excitation, and has promoted two-photon photopharmacology and optogenetics. However, three-photon brain stimulation in vivo remains to be demonstrated.

Predicting the Electronic Absorption Band Shape of Azobenzene Photoswitches.

Simulations based on molecular dynamics coupled to excitation energy calculations were used to generate simulated absorption spectra for a family of halide derivatives of azobenzene, a family of photoswitch molecules with a weak absorption band around 400-600 nm and potential uses in living tissue. This is a case where using the conventional approach in theoretical spectroscopy (estimation of absorption maxima based on the vertical transition from the potential energy minimum on the ground electronic state) does not provide valid results that explain how the observed band shape extends towards the low energy region of the spectrum. The method affords a reasonable description of the main features of the low-energy UV-Vis spectra of these compounds.

On the Computational Design of Azobenzene-Based Multi-State Photoswitches.

In order to theoretically design multi-state photoswitches with specific properties, an exhaustive computational study is first carried out for an azobenzene dimer that has been recently synthesized and experimentally studied. This study allows for a full comprehension of the factors that govern the photoactivated isomerization processes of these molecules so to provide a conceptual/computational protocol that can be applied to generic multi-state photoswitches. From this knowledge a new dimer with a similar chemical design is designed and also fully characterized.

A high-throughput computational approach to UV-Vis spectra in protein mutants.

In this work we present a high-throughput approach to the computation of absorption UV-Vis spectra tailored to mutagenesis studies. The scheme makes use of a single molecular dynamics trajectory of a reference (non-mutated) species. The shifts in absorption energy caused by a residue mutation are evaluated by building an effective potential of the environment and computing a correction term based on perturbation theory.

Deciphering the grounds of the suitability of acylhydrazones as efficient photoswitches.

Many efforts are currently being devoted to designing molecular photoswitches with specific properties. In this sense, a recent publication [D. J.

Rationally designed azobenzene photoswitches for efficient two-photon neuronal excitation.

Manipulation of neuronal activity using two-photon excitation of azobenzene photoswitches with near-infrared light has been recently demonstrated, but their practical use in neuronal tissue to photostimulate individual neurons with three-dimensional precision has been hampered by firstly, the low efficacy and reliability of NIR-induced azobenzene photoisomerization compared to one-photon excitation, and secondly, the short cis state lifetime of the two-photon responsive azo switches. Here we report the rational design based on theoretical calculations and the synthesis of azobenzene photoswitches endowed with both high two-photon absorption cross section and slow thermal back-isomerization. These compounds provide optimized and sustained two-photon neuronal stimulation both in light-scattering brain tissue and in Caenorhabditis elegans nematodes, displaying photoresponse intensities that are comparable to those achieved under one-photon excitation.

Ultrafast action chemistry in slow motion: atomistic description of the excitation and fluorescence processes in an archetypal fluorescent protein.

We report quantum mechanical/molecular mechanical non-adiabatic molecular dynamics simulations on the electronically excited state of green fluorescent protein mutant S65T/H148D. We examine the driving force of the ultrafast (τ < 50 fs) excited-state proton transfer unleashed by absorption in the A band at 415 nm and propose an atomistic description of the two dynamical regimes experimentally observed [Stoner Ma et al., J.

Diel variation in the catch of the shrimp Farfantepenaeus duorarum (Decapoda, Penaeidae) and length-weight relationship, in a nursery area of the Terminos Lagoon, Mexico.

The pink shrimp, Farfantepenaeus duorarum is an important commercial species in the Gulf of Mexico, which supports significant commercial fisheries near Dry Tortugas, in Southern Florida and in Campeche Sound, Southern Gulf of Mexico. There is information about the nictemeral behavior of the pink shrimp related to sunset, what is crucial to more accurate estimation of shrimp population biomass, and to assess the potential of this resource and its proper management. To contribute to the knowledge and the population dynamics of the species, shrimp surveys were conducted in a nursery area near “El Cayo” in the Northeastern part of Terminos Lagoon, Mexico during October 2010.

The Quest for Photoswitches Activated by Near-Infrared Light: A Theoretical Study of the Photochemistry of BF2 -Coordinated Azo Derivatives.

Recently synthesized BF2 -coordinated azo derivatives have been proposed as photoswitches that operate in the optical window (λ=600-1200 nm) for use in bioimaging applications. Herein, we have theoretically analyzed these compounds and modified some substituents to analyze which properties of the molecule govern its photochemistry. Our results compare rather well with the available experimental data, so our methodology, based on density functional theory (DFT) calculations for the ground electronic state and time-dependent-DFT for the first excited electronic state, is validated.

Chromophore interactions leading to different absorption spectra in mNeptune1 and mCardinal red fluorescent proteins.

Extensive MD simulations combined with QM/MM calculations have been performed on mNeptune1 and mCardinal red fluorescent proteins to establish the reasons behind the red shift of the excitation wavelength of mCardinal with respect to mNeptune1. In both cases, it is seen that Arg197 stabilizes the chromophore but cannot be described as stabilizing preferentially the excited state because of the anchor point of the interaction. The interactions of the linking bonds to the α-helix of both proteins to the chromophore have been analyzed.

Molecular modelling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein.

Classical molecular dynamics (MD) simulations are carried out for the recently developed TagRFP675 fluorescent protein (FP), which is specifically designed to fully absorb and emit in the near infrared (NIR) region of the electromagnetic spectrum. Since the X-ray data of TagRFP675 reveal that the chromophore exists in both the cis and trans configuration and it can also be neutral (protonated) or anionic (deprotonated) depending on the pH of the media, a total of 8 molecular dynamic simulations have been run to simulate all the possible states of the chromophore. Time-dependent DFT (TDDFT) single point calculations are performed at selected points along the simulation to theoretically mimic the absorption spectrum of the protein.

Transient low-barrier hydrogen bond in the photoactive state of green fluorescent protein.

In this paper, we have analyzed the feasibility of spontaneous proton transfer in GFP at the Franck-Condon region directly after photoexcitation. Computation of a sizeable portion of the potential energy surface at the Franck-Condon region of A the structure shows the process of proton transfer to be unfavorable by 3 kcal mol(-1) in S1 if no further structural relaxation is permitted. The ground vibrational state is found to lie above the potential energy barrier of the proton transfer in both S0 and S1.

Theoretical Computer-Aided Mutagenic Study on the Triple Green Fluorescent Protein Mutant S65T/H148D/Y145F.

Green fluorescent protein (GFP) mutant S65T/H148D has been proposed to host a photocycle that involves an excited-state proton transfer between the chromophore (Cro) and the Asp148 residue and takes place in less than 50 fs without a measurable kinetic isotope effect. It has been suggested that the interaction between the unsuspected Tyr145 residue and the chromophore is needed for the ultrafast sub-50 fs rise in fluorescence. To verify this, we have performed a computer-aided mutagenic study to introduce the additional mutation Y145F, which eliminates this interaction.

New insights into the structure-spectrum relationship in S65T/H148D and E222Q/H148D green fluorescent protein mutants: a theoretical assessment.

The green fluorescent protein (GFP) variant S65T/H148D recovers the A-band fluorescence lost in the single mutant S65T, and it has been established that Asp148 is the alternate proton acceptor for the excited state proton transfer (ESPT). This mutant has been widely studied and presents unique spectroscopic properties, such as an ultrafast rise in the fluorescence (<50 fs). Also it exhibits a red-shift of the A absorption band of 20 nm with respect to wt-GFP's.

Unveiling how an archetypal fluorescent protein operates: theoretical perspective on the ultrafast excited state dynamics of GFP variant S65T/H148D.

Green fluorescent protein variant S65T/H148D has been reported to host a photocycle involving the photoinduced proton transfer reaction between the chromophore and residue Asp148 under 50 fs and without a measurable kinetic isotope effect, and experimental evidence is suggestive of the existence of a highly delocalized proton between these residues. The blinding speed at which this biological system undergoes proton transfer has been ascribed to the extreme increase of acidity of the GFP chromophore in the electronic excited state where proton transfer takes place. This work strives to present a coherent, complete, and balanced description of the dynamics of this specific variant of GFP in which it will be shown that this increase of acidity is insufficient to explain the behavior observed.

Are there really low-barrier hydrogen bonds in proteins? The case of photoactive yellow protein.

For a long time, low-barrier hydrogen bonds (LBHBs) have been proposed to exist in many enzymes and to play an important role in their catalytic function, but the proof of their existence has been elusive. The transient formation of an LBHB in a protein system has been detected for the first time using neutron diffraction techniques on a photoactive yellow protein (PYP) crystal in a study published in 2009 (Yamaguchi, S.; et al.

A theoretical study of the photochemistry of indigo in its neutral and dianionic (leucoindigo) forms.

A thorough analysis of the single and double proton transfer and the internal rotations of neutral indigo and its dianionic leucoindigo form has been performed for the ground and first singlet excited electronic states using, respectively, DFT and TDDFT state-of-the-art methods. Our theoretical analysis discloses that the diketo isomer is the most stable one in the ground state of indigo but not in leucoindigo where the dienol minimum is more stable. Single and double proton transfer processes are not energetically favored in the ground electronic state but a single proton transfer gives a more stable tautomer in the excited electronic state of indigo whereas a double proton transfer is energetically favorable in the excited state of leucoindigo.

How Does the Environment Affect the Absorption Spectrum of the Fluorescent Protein mKeima?

The absorption spectrum of a fluorescent protein is determined by its chromophore, but the residues that surround it also have a remarkable role, leading to noticeable spectral shifts. We have theoretically analyzed the monomeric protein Keima (mKeima), a red fluorescent protein most remarkable for an outstanding difference between the absorption and emission frequencies, and potentially suited for multicolor imaging applications. In the present work, we have performed excited state electronic calculations on the chromophore with an increasing number of atoms surrounding it, and we have compared these results with the excited states calculations on an ensemble of structures obtained from a molecular dynamics simulation of the complete protein.

Peek at the potential energy surfaces of the LSSmKate1 and LSSmKate2 proteins.

To determine the energetic feasibility of the mechanisms involved in the generation of the fluorescent species in red fluorescent proteins LSSmKate1 and LSSmKate2 developed by Piatkevich et al. (Proc. Natl.

Photo-deactivation pathways of a double H-bonded photochromic Schiff base investigated by combined theoretical calculations and experimental time-resolved studies.

The photophysics of N,N'-bis(salicylidene)-p-phenylenediamine (BSP) is analyzed both theoretically and experimentally. The alternative intramolecular proton-transfer reactions lead to three different tautomers. We performed DFT and TDDFT calculations to analyze the topography of the reactions connecting the three tautomers.

A method to compute probability current in generic coordinates.

A method to compute probability current and its surface integral, the total flux, for systems of many particles of different masses is presented, based on transforming the wave function and its gradient onto a mass-weighted coordinate system. As a test for this methodology, it has been applied to a nontrivial 6-dimensional quantum dynamics study of a model of the operation of the proton-wire in Green Fluorescent Protein [O. Vendrell, R.

Modulating the photochemistry of bipyridylic compounds by symmetric substitutions.

A quantum electronic study of the effect of substituents on (2,2'-bipyridyl)-3,3'-diol and (2,2'-bipyridyl)-3,3'-diamine is presented. A large difference in the photochemical behavior between the original and the substituted selected systems is expected. For the sake of simplicity, the study is restricted to the symmetrically bi-substituted compounds: fluorine, the more electronegative atom and thus a strong σ-acceptor but also a weak π-donor group, and NO(2), a strong π-acceptor substituent.

Bipyridyl derivatives as photomemory devices: a comparative electronic-structure study.

The two isoelectronic bipyridyl derivatives [2,2'-bipyridyl]-3,3'-diamine (BP(NH(2))(2)) and [2,2'-bipyridyl]-3,3'-diol (BP(OH)(2)) are experimentally known to undergo very different excited-state double proton transfer processes that result in fluorescence quantum yields that differ by four orders of magnitude. Such differences have been theoretically explained in terms of topographical features in the potential energy surface and the likely presence of conical intersections. The hypothetical hybrid compound [2,2'-bipyridyl]-3-amin-3'-ol (BP(OH)(NH(2))) presents intermediate photochemical features of its "ancestors".

A theoretical assessment of factors causing different molecular volumes in isotopologues.

A dynamical study has been performed to determine from first principles the molecular volume of C(6)H(6) and C(6)D(6) in the gas phase, starting from a normal-mode analysis and using anharmonic potential energy profiles at DFT level to determine vibrational eigenfunctions for all 30 degrees of freedom and using a Monte Carlo procedure to determine the appreciable ranges of variation of the coordinates of all atoms. The gas phase study reveals that the intrinsic volume of C(6)D(6) is always the smallest, even though it increases faster with temperature than that of C(6)H(6). In order to explain the experimentally observed fact that C(6)D(6) volume is the largest at high temperatures, the likely effect on molecular motions caused by the crystalline environment of a given molecule has to be considered.