Improving the second-order nonlinear optical response of fluorescent proteins: the symmetry argument

Goharshadi E, Boghossian AA. Micropreparative Gel Electrophoresis for Purification of Nanoscale Bioconjugates

Conventional techniques for purifying macromolecular conjugates often require complex and costly installments that are inaccessible to most laboratories. In this work, we develop a one-step micropreparative method based on a trilayered polyacrylamide gel electrophoresis (MP-PAGE) setup to purify biological samples, synthetic nanoparticles, as well as biohybrid complexes. We apply this method to recover DNA from a ladder mixture with yields of up to 90%, compared to the 58% yield obtained using the conventional crush-and-soak method. MP-PAGE was also able to isolate enhanced yellow fluorescence protein (EYFP) from crude cell extract with 90% purity, which is comparable to purities achieved through a more complex two-step purification procedure involving size exclusion and immobilized metal-ion affinity chromatography. This technique was further extended to demonstrate size-dependent separation of a commercial mixture of graphene quantum dots (GQDs) into three different fractions with distinct optical properties. Finally, MP-PAGE was used to isolate DNA-EYFP and DNA-GQD bioconjugates from their reaction mixture of DNA and EYFP and GQD precursors, samples that otherwise could not be effectively purified by conventional chromatography. MP-PAGE thus offers a rapid and versatile means of purifying biological and synthetic nanomaterials without the need for specialized equipment.

Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes

A multistep computational approach has been employed to study a multimillion all-atom dyed plasma membrane, with no less than 42 different lipid species spanning the major head groups and a variety of fatty acids, as well as cholesterol, with the objective of investigating its structure and dynamics, as well as its impact on the embedded di-8-ANEPPS dyes. The latter are commonly used as bioimaging probes and serve as local microscopes. So, they provide information on membrane morphology via their second harmonic nonlinear optical (NLO) responses, which have the advantage of being specific to interface regions and sensitive to the chromophore environment. In previous studies, this chromophore has only been studied in simpler membrane models, far from the complexity of real lipid bilayers, while, owing to the ever-increasing computational resources, multimillion lipid bilayers have been studied, giving access to the effects of its heterogeneity. First, using molecular dynamics (MD) simulations, it is found that the combination of lipids produces a more ordered and denser membrane compared to its homogeneous model counterparts, while the local environment of the embedded dyes becomes enriched in phosphatidylcholine. Subsequently, the second harmonic first hyperpolarizability of the probes was calculated at the TDDFT level on selected frames of MD, highlighting the influence of the lipid environment. Due to the complexity of the system, machine learning (ML) tools have been employed to establish relationships between the membrane structural parameters, the orientation of the probes, and their NLO responses. These ML approaches have revealed influential features, including the presence of diacylglycerol lipids close to the dye. On the whole, this work provides a first step toward understanding the cooperation, synergy, and interactions that occur in such complex guest-host environments, which have emerged as new targets for drug design and membrane lipid therapy.

Polarization-dependent second harmonic generation in peptide crystals: effects of molecular packing

A series of chiral peptide luminophores containing the coumarin moiety was synthesized via a simple and efficient solution-based procedure. The peptides, containing either L-Phe, or L-Ala, or L-Leu (designated, respectively, as p1, p2, and p3), self-aggregate to form anti-parallel sheet-like structures. The self-assembly of the peptide luminophores leads to non-centrosymmetric crystals which display significant second harmonic generation (SHG). The dependence of the SHG intensity on the input laser polarization revealed a strong correlation between the SHG and the crystal packing. In the polar plots, the SHG intensity as a function of the linear polarization orientation of the input laser beam gave a four-petal pattern for p1, a predominantly two-petal pattern for p2, and a dumbbell-shaped pattern for p3. This reflects the dependence of the second order optical susceptibility tensor on the crystal symmetry. The polar plots can be fitted very well with the theoretical expressions derived from the second order polarization equation after incorporating crystal symmetry in the second order optical susceptibility tensor. The strong polarization-dependent SHG from organic crystals may be interesting for polarization controlled nonlinear optical switches, sensors, and actuators.

First-principles evaluation of the second harmonic generation response of reference organic and inorganic crystals

Using the CRYSTAL17 package at the coupled-perturbed Kohn-Sham (CPKS) level, periodic boundary conditions first-principles calculations are enacted to predict the second harmonic generation second-order nonlinear optical (NLO) susceptibility, χ⁽²⁾, values of six historical NLO crystals. This selection allowed the comparison between state-of-the-art calculations and experiment. Several computational aspects are tackled to define conditions where the results are converged with respect to the range of lattice summations, to the number of k-points in the first Brillouin zone, to the order of the multipole expansions for evaluating the long-range part of the electrostatic interactions, as well as to the atomic basis set size. A valence triple zeta basis set supplemented with polarization functions has been selected. Then, χ⁽²⁾ calculations have been performed using a range of exchange-correlation functionals (XCFs). Results show the large impact of the amount of Hartree-Fock (HF) exchange on the amplitude but also on the sign on the χ⁽²⁾ tensor components. To a given extent, these amplitude effects are consistent with results on molecules, but the sign reversal effects and the non-monotonic behavior of the χ⁽²⁾ tensor components as a function of the amount of HF exchange are scarcely found for molecules. Then, using the recommended range-separated hybrid XCFs, the CPKS scheme leads to good agreement with experimental data for potassium dihydrogenophosphate, urea, and χ_ZXX ⁽²⁾ of LiNbO₃. The agreement is more questionable for χ_ZZZ ⁽²⁾ of LiNbO₃ whereas it remains poor for ammonium dihydrogenophosphate and 2-methyl-4-nitroaniline, with large underestimations by about a factor of 3, opening a path to further fine-tuning of the ranges of inclusion of HF exchange.

Influence of the Nature of the Lipid Building Blocks on the Second-Order Nonlinear Optical Responses of an Embedded Di-8-ANEPPS Probe

The extensive collection of lipids found in cell membranes is justified by the fact that each lipid contributes to their overall structure, dynamics, and properties and so to the biological processes taking place within them. It also showcases that, in order to deepen our understanding of membranes, we need to have a tool to differentiate lipid bilayers of varying composition. In this work, we investigate a suite of single-component saturated glycerophospholipids varying only in their headgroup structure by analyzing the second harmonic generation (SHG) nonlinear optical (NLO) response of a probe, di-8-ANEPPS, embedded into the membranes. The seven hydrophilic heads chosen (phosphatidylcholine (PC), phosphatidylethanolamine (PE), diaglycerol (GL), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), and phosphatidyc acid (PA)) represent all the major headgroups that are part of mammalian plasma membranes and provide an assortment of neutral, zwiterrionic, and charged species. First, molecular dynamics simulations revealed that the lipidic arrangement is strongly sensitive to the nature of the hydrophilic head and less to the variety in the hydrophobic region. Membranes exhibiting drastically opposite structural properties can be pointed out: 1,2-dihexadecanoyl-rac-glycerol (DPGL) is the thickest and most ordered and aligned system, whereas 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) (DPPG) is thinnest and least ordered and aligned system. The structural analyses are then confronted with the molecular NLO responses, β, computed at the time-dependent density functional theory (TDDFT) level. As the orientation of the chromophore is impacted by the various degrees of order within the lipid bilayers, the diagonal component of the β tensor parallel to the bilayer normal, β_ZZZ, is as well. In the end, this computational approach provides insights into the link between lipid building blocks and the NLO responses of the embedded dye.

TDDFT Investigation of the Raman and Resonant Raman Spectra of Fluorescent Protein Chromophore Models

The off-resonance and resonant Raman spectra have been simulated for models of fluorescent protein chromophores, those of the green fluorescent protein (GFP, called FP1) and of DsRed (called FP2), which presents a longer π-conjugated path, with the aim of providing a systematic investigation of structural but also computational aspects. These were performed at the (time-dependent) density functional theory [(TD)DFT] level. The off-resonance intensities have been calculated from the derivatives of the frequency-dependent polarizability with respect to the normal coordinates while the resonant ones have been evaluated using Huang-Rhys factors determined from the gradients of the excitation energies with respect to the normal coordinates. When applied with the M05 meta-GGA exchange-correlation functional, this simple computational scheme can reproduce most of the experimental Raman signatures of FP1 in its protonated and deprotonated forms, the differences of vibrational signatures of the cis (Z) and trans (E) isomers, as well as their changes as a function of the excitation wavelength. On the other hand, testing the predictions made for FP2 would require new experimental work. It was also observed that simulations with methods that inadequately predict the resonant Raman spectra could nevertheless produce a UV-vis absorption spectrum that is quite similar to the one obtained with better methods, once realistic peak broadening has been applied.

Stimuli-Responsive Zinc (II) Coordination Polymers: A Novel Platform for Supramolecular Chromic Smart Tools

The unique role of the zinc (II) cation prompted us to cut a cross-section of the large and complex topic of the stimuli-responsive coordination polymers (CPs). Due to its flexible coordination environment and geometries, easiness of coordination-decoordination equilibria, "optically innocent" ability to "clip" the ligands in emissive architectures, non-toxicity and sustainability, the zinc (II) cation is a good candidate for building supramolecular smart tools. The review summarizes the recent achievements of zinc-based CPs as stimuli-responsive materials able to provide a chromic response. An overview of the past five years has been organised, encompassing 1, 2 and 3D responsive zinc-based CPs; specifically zinc-based metallorganic frameworks and zinc-based nanosized polymeric probes. The most relevant examples were collected following a consequential and progressive approach, referring to the structure-responsiveness relationship, the sensing mechanisms, the analytes and/or parameters detected. Finally, applications of highly bioengineered Zn-CPs for advanced imaging technique have been discussed.

All-Atom Quantum Mechanical Calculation of the Second-Harmonic Generation of Fluorescent Proteins

Fluorescent proteins (FPs) are biotags of choice for second-harmonic imaging microscopy (SHIM). Because of their large size, computing their second-harmonic generation (SHG) response represents a great challenge for quantum chemistry. In this contribution, we propose a new all-atom quantum mechanics methodology to compute SHG of large systems. This is now possible because of two recent implementations: the tight-binding GFN2-xTB method to optimize geometries and a related version of the simplified time-dependent density functional theory (sTD-DFT-xTB) to evaluate quadratic response functions. In addition, a new dual-threshold configuration selection scheme is introduced to reduce the computational costs while retaining overall similar accuracy. This methodology was tested to evaluate the SHG of the proteins iLOV and bacteriorhodopsin (bR). In the case of bR, quantitative agreement with respect to experiment was reached for the out-of-resonance low-energy part of the β_HRS frequency dispersion. This work paves the way toward an accurate prediction of the SHG of large structures-a requirement for the design of new and improved SHIM biotags.

Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology

Chimeric fusion proteins are essential tools for protein nanotechnology. Non-optimized protein-protein connections are usually flexible and therefore unsuitable as structural building blocks. Here we show that the ER/K motif, a single α-helical domain (SAH), can be seamlessly fused to terminal helices of proteins, forming an extended, partially free-standing rigid helix. This enables the connection of two domains at a defined distance and orientation. We designed three constructs termed YFPnano, T4Lnano, and MoStoNano. Analysis of experimentally determined structures and molecular dynamics simulations reveals a certain degree of plasticity in the connections that allows the adaptation to crystal contact opportunities. Our data show that SAHs can be stably integrated into designed structural elements, enabling new possibilities for protein nanotechnology, for example, to improve the exposure of epitopes on nanoparticles (structural vaccinology), to engineer crystal contacts with minimal impact on construct flexibility (for the study of protein dynamics), and to design novel biomaterials.

Unravelling the Effects of Cholesterol on the Second-Order Nonlinear Optical Responses of Di-8-ANEPPS Dye Embedded in Phosphatidylcholine Lipid Bilayers

Cholesterol is known for its role in maintaining the correct fluidity and rigidity of the animals cell membranes and thus their functions. Assessing the content and the role of cholesterol in lipid bilayers is therefore of crucial importance for a deeper understanding and control of membrane functioning. In this computational work, we investigate bilayers built from three types of glycerophospholipid phosphatidylcholine (PC) lipids, namely dipalmitoylphosphatidylcholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and dioleoylphosphatidylcholine (DOPC), and containing different amounts of cholesterol by analyzing the second-harmonic generation (SHG) nonlinear optical (NLO) response of a probe molecule, di-8-ANEPPS, inserted into the membranes. This molecular property presents the advantage to be specific to interfacial regions such as lipid bilayers. To unravel these effects, Molecular Dynamics (MD) simulations have been performed on both DPPC and DOPC lipids by varying the cholesterol mole fraction (from 0 to 0.66), while POPC was only considered as a pure bilayer. In the case of the structural properties of the bilayers, all the analyses converge toward the same conclusion: as the mole fraction of cholesterol increases, the systems become more rigid, confirming the condensing effect of cholesterol. In addition, the chromophore is progressively more aligned with respect to the normal to the bilayer. On the contrary, addition of unsaturation disorders the lipid bilayers, with barely no impact on the alignment of the chromophore. Then, using the frames obtained from the MD simulations, the first hyperpolarizability β of the dye in its environment has been computed at the TDDFT level. On the one hand, the addition of cholesterol induces a progressive increase of the diagonal component the β tensor parallel to the bilayer normal. On the other hand, larger β values have been calculated for the unsaturated than for the saturated lipid systems. In summary, this study illustrates the relationship between the composition and structure of the bilayers and the NLO responses of the embedded dye.

Visual pH Sensors: From a Chemical Perspective to New Bioengineered Materials

Many human activities and cellular functions depend upon precise pH values, and pH monitoring is considered a fundamental task. Colorimetric and fluorescence sensors for pH measurements are chemical and biochemical tools able to sense protons and produce a visible signal. These pH sensors are gaining widespread attention as non-destructive tools, visible to the human eye, that are capable of a real-time and in-situ response. Optical “visual” sensors are expanding researchers’ interests in many chemical contexts and are routinely used for biological, environmental, and medical applications. In this review we provide an overview of trending colorimetric, fluorescent, or dual-mode responsive visual pH sensors. These sensors include molecular synthetic organic sensors, metal organic frameworks (MOF), engineered sensing nanomaterials, and bioengineered sensors. We review different typological chemical entities of visual pH sensors, three-dimensional structures, and signaling mechanisms for pH sensing and applications; developed in the past five years. The progression of this review from simple organic molecules to biological macromolecules seeks to benefit beginners and scientists embarking on a project of pH sensing development, who needs background information and a quick update on advances in the field. Lessons learned from these tools will aid pH determination projects and provide new ways of thinking for cell bioimaging or other cutting-edge in vivo applications.

Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design

For the whole GFP family, a few cases, when a single mutation in the chromophore environment strongly inhibits maturation, were described. Here we study EYFP-F165G - a variant of the enhanced yellow fluorescent protein - obtained by a single F165G replacement, and demonstrated multiple fluorescent states represented by the minor emission peaks in blue and yellow ranges (~470 and ~530 nm), and the major peak at ~330 nm. The latter has been assigned to tryptophan fluorescence, quenched due to excitation energy transfer to the mature chromophore in the parental EYFP protein. EYFP-F165G crystal structure revealed two general independent routes of post-translational chemistry, resulting in two main states of the polypeptide chain with the intact chromophore forming triad (~85%) and mature chromophore (~15%). Our experiments thus highlighted important stereochemical role of the 165th position strongly affecting spectral characteristics of the protein. On the basis of the determined EYFP-F165G three-dimensional structure, new variants with ~ 2-fold improved brightness were engineered.

Nanoscale Infrared Spectroscopy and Chemometrics Enable Detection of Intracellular Protein Distribution

Determination of the intracellular location of proteins is one of the fundamental tasks of microbiology. Conventionally, label-based microscopy and super-resolution techniques are employed. In this work, we demonstrate a new technique that can determine intracellular protein distribution at nanometer spatial resolution. This method combines nanoscale spatial resolution chemical imaging using the photothermal-induced resonance (PTIR) technique with multivariate modeling to reveal the intracellular distribution of cell components. Here, we demonstrate its viability by imaging the distribution of major cellulases and xylanases in Trichoderma reesei using the colocation of a fluorescent label (enhanced yellow fluorescence protein, EYFP) with the target enzymes to calibrate the chemometric model. The obtained partial least squares model successfully shows the distribution of these proteins inside the cell and opens the door for further studies on protein secretion mechanisms using PTIR.

Selection enhances protein evolvability by increasing mutational robustness and foldability

Natural selection can promote or hinder a population’s evolvability—the ability to evolve new and adaptive phenotypes—but the underlying mechanisms are poorly understood. To examine how the strength of selection affects evolvability, we subjected populations of yellow fluorescent protein to directed evolution under different selection regimes and then evolved them toward the new phenotype of green fluorescence. Populations under strong selection for the yellow phenotype evolved the green phenotype most rapidly. They did so by accumulating mutations that increase both robustness to mutations and foldability. Under weak selection, neofunctionalizing mutations rose to higher frequency at first, but more frequent deleterious mutations undermined their eventual success. Our experiments show how selection can enhance evolvability by enhancing robustness and create the conditions necessary for evolutionary success.

Harmonic Generation Microscopy 2.0: New Tricks Empowering Intravital Imaging for Neuroscience

Optical harmonic generation, e.g., second- (SHG) and third-harmonic generation (THG), provides intrinsic contrasts for three-dimensional intravital microscopy. Contrary to two-photon excited fluorescence (TPEF), however, they have found relatively specialized applications, such as imaging collagenous and non-specific tissues, respectively. Here we review recent advances that broaden the capacity of SHG and THG for imaging the central nervous system in particular. The fundamental contrast mechanisms are reviewed as they encode novel information including molecular origin, spectroscopy, functional probes, and image analysis, which lay foundations for promising future applications in neuroscience.

Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins

Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.

Excited State Electronic Interconversion and Structural Transformation of Engineered Red-Emitting Green Fluorescent Protein Mutant

Red fluorescent proteins with a large Stokes shift offer a limited autofluorescence background and are used in deep tissue imaging. Here, by introducing the free amino group in Aequorea victoria, the electrostatic charges of the p-hydroxybenzylidene imidazolinone chromophore of green fluorescent protein (GFP) have been altered resulting in an unusual, 85 nm red-shifted fluorescence. The structural and biophysical analysis suggested that the red shift is due to positional shift occupancy of Glu222 and Arg96, resulting in extended conjugation and a relaxed chromophore. Femtosecond transient absorption spectra exhibited that the excited state relaxation dynamics of red-shifted GFP (rGFP) (τ4 = 234 ps) are faster compared to the A. victoria green fluorescent protein (τ4 = 3.0 ns). The nanosecond time-resolved emission spectra of rGFP reveal the continuous spectral shift during emission by a solvent reorientation in the chromophore. Finally, the molecular dynamics simulations revealed the rearrangement of the hydrogen bond interactions in the chromophore vicinity, reshaping the symmetric distribution of van der Waals space to fine tune the GFP structure resulting from highly red-shifted rGFP.

Nonlinear-response properties in a simplified time-dependent density functional theory (sTD-DFT) framework: Evaluation of the first hyperpolarizability

Recent developments in nonlinear imaging microscopy show the need to implement new theoretical tools, which are able to characterize nonlinear optical properties in an efficient way. For second-harmonic imaging microscopy (SHIM), quantum chemistry could play an important role to design new exogenous dyes with enhanced first hyperpolarizabilities or to characterize the response origin in large endogenous biological systems. Such methods should be able to screen a large number of compounds while reproducing their trends and to treat large systems in reasonable computation times. To fulfill these requirements, we present a new simplified time-dependent density functional theory (sTD-DFT) implementation to evaluate the first hyperpolarizability where the Coulomb and exchange integrals are approximated by short-range damped Coulomb interactions of transition density monopoles. For an ultra-fast computation of the first hyperpolarizability, a tight-binding version (sTD-DFT-xTB) is also proposed. In our implementation, a sTD-DFT calculation is more than 600 time faster with respect to a regular TD-DFT treatment, while the xTB version speeds up the entire calculation further by at least two orders of magnitude. We challenge our implementation on three test cases: typical push-pull π-conjugated compounds, fluorescent proteins, and a collagen model, which were selected to model requirements for SHIM applications.

First principles crystal engineering of nonlinear optical materials. I. Prototypical case of urea

The crystalline materials with nonlinear optical (NLO) properties are critically important for several technological applications, including nanophotonic and second harmonic generation devices. Urea is often considered to be a standard NLO material, due to the combination of non-centrosymmetric crystal packing and capacity for intramolecular charge transfer. Various approaches to crystal engineering of non-centrosymmetric molecular materials were reported in the literature. Here we propose using global lattice energy minimization to predict the crystal packing from the first principles. We developed a methodology that includes the following: (1) parameter derivation for polarizable force field AMOEBA; (2) local minimizations of crystal structures with these parameters, combined with the evolutionary algorithm for a global minimum search, implemented in program USPEX; (3) filtering out duplicate polymorphs produced; (4) reoptimization and final ranking based on density functional theory (DFT) with many-body dispersion (MBD) correction; and (5) prediction of the second-order susceptibility tensor by finite field approach. This methodology was applied to predict virtual urea polymorphs. After filtering based on packing similarity, only two distinct packing modes were predicted: one experimental and one hypothetical. DFT + MBD ranking established non-centrosymmetric crystal packing as the global minimum, in agreement with the experiment. Finite field approach was used to predict nonlinear susceptibility, and H-bonding was found to account for a 2.5-fold increase in molecular hyperpolarizability to the bulk value.

Crystal Structure of Green Fluorescent Protein Clover and Design of Clover-Based Redox Sensors

We have determined the crystal structure of Clover, one of the brightest fluorescent proteins, and found that its T203H/S65G mutations relative to wild-type GFP lock the critical E222 side chain in a fixed configuration that mimics the major conformer of that in EGFP. The resulting equilibrium shift to the predominantly deprotonated chromophore increases the extinction coefficient (EC), opposes photoactivation, and is responsible for the bathochromic shift. Clover's brightness can further be attributed to a π-π stacking interaction between H203 and the chromophore. Consistent with these observations, the Clover G65S mutant reversed the equilibrium shift, dramatically decreased the EC, and made Clover photoactivatable under conditions that activated photoactivatable GFP. Using the Clover structure, we rationally engineered a non-photoactivatable redox sensor, roClover1, and determined its structure as well as that of its parental template, roClover0.1. These high-resolution structures provide deeper insights into structure-function relationships in GFPs and may aid the development of excitation-improved ratiometric biosensors.

Photoswitchable nonlinear optical properties of metal complexes

Incorporating photosensitive molecules into the organic/inorganic hybrid materials can contribute to forming photoresponsive systems.

A series of multifunctional coordination polymers based on terpyridine and zinc halide: second-harmonic generation and two-photon absorption properties and intracellular imaging

How can imaging be improved? Coordination polymers (CPs) show fascinating potential in optoelectronic optics but limited potential in bioimaging. Without doubt, it was very meaningful when CPs were first used in second-harmonic generation (SHG) imaging. Herein, through reasonable design and synthesis, a series of nonlinear optical CPs bearing very good one-photon excited fluorescence (OPEF), two-photon excited fluorescence (TPEF) and very strong SHG properties has been presented. Further study demonstrated that the nanoscale CPs show very strong SHG signals which have been applied in the three-dimensional imaging of thick block tissue with higher spatial resolution through simultaneous multichannel nonlinear optical (NLO) imaging technology. After simple encapsulation by polymeric micelles, the nanoscale CPs were successfully applied in SHG bio-imaging within the living cells. This finding throws light on the design of nanoscale NLO CPs and offers a simple avenue to develop novel effective exogenous SHG imaging agents.

A Series of Imidazole Derivatives: Synthesis, Two-Photon Absorption, and Application for Bioimaging

A new series of D-π-A type imidazole derivatives have been synthesized and characterized. Two corresponding imidazolium salts (iodine and hexafluorophosphate) were prepared from the imidazole compound. Their electron-withdrawing ability can be largely tunable by salt formation reaction or ion exchange. UV-vis absorption and single-photon fluorescence spectra have been systematically investigated in different solvents. The two-photon cross sections (δ 2PA) of the imidazole derivatives are measured by two-photon excited fluorescence (2PEF) method. Compared with those of T-1 (107 GM) and T-3 (96 GM), T-2 (imidazolium iodine salt) has a large two-photon absorption (2PA) cross section value of 276 GM. Furthermore, the cytotoxicity and applications in bioimaging for the imidazole derivatives were carried out. The results showed that T-1 can be used as a lysosomal tracker with high stability and water solubility within pHs of 4-6, while T-2 and T-3 can be used as probes for cell cytoplasm.

Organized chromophoric assemblies for nonlinear optical materials: towards (sub)wavelength scale architectures

Photonic circuits are expected to greatly contribute to the next generation of integrated chips, as electronic integrated circuits become confronted with bottlenecks such as heat generation and bandwidth limitations. One of the main challenges for the state-of-the-art photonic circuits lies in the development of optical materials with high nonlinear optical (NLO) susceptibilities, in particular in the wavelength and subwavelength dimensions which are compatible with on-chip technologies. In this review, the varied approaches to micro-/nanosized NLO materials based on building blocks of bio- and biomimetic molecules, as well as synthetic D-π-A chromophores, have been categorized as supramolecular self-assemblies, molecular scaffolds, and external force directed assemblies. Such molecular and supramolecular NLO materials have intrinsic advantages, such as structural diversities, high NLO susceptibilities, and clear structure-property relationships. These "bottom-up" fabrication approaches are proposed to be combined with the "top-down" techniques such as lithography, etc., to generate multifunctionality by coupling light and matter on the (sub)wavelength scale.

Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field

The aim of this study is to identify the responsible molecular forms for the pH dependent optical properties of the deGFP1 green fluorescent protein mutant. We have carried out static and dynamic type calculations for all four protonation states of the chromophore to unravel the contributions due to finite temperature and the flexible protein backbone on the pH dependent optical properties. In particular, we have used a combined molecular dynamics and density functional-molecular mechanics linear response approach by means of which the optical property calculations were carried out for the chromophore in the explicitly treated solvent and bioenvironment. Two different models were used to describe the environment-electronic embedding and polarizable electronic embedding-accounting for the polarization of the chromophore and the mutual polarization between the chromophore and the environment, respectively. For this purpose a polarizable force field was derived quantum mechanically for the protein environment by use of analytical response theory. While the gas-phase calculations for the chromophore predict that the induced red shift going from low to high pH is attributed to the change of molecular forms from neutral to zwitterionic, the two more advanced models that explicitly account for the protein backbone attribute the pH shift to a neutral to anionic conversion. Some ramifications of the results for the use of GFPs as pH sensors are discussed.

Marine natural products from the deep Pacific as potential non-linear optical chromophores

Theoretical analysis using quadratic response theory within the time-dependent density functional theory (TDDFT) formalism shows that the dermacozines, a group of phenazine-based compounds isolated from cultures of Dermacoccus abyssi found in the Mariana Trench, possess large first hyperpolarisability (β) values at common incident laser wavelengths that are highly sensitive to the degree and type of substitution of the core structure. The phenazine moiety is a versatile and tunable chromophore for non-linear optics and this work serves to highlight the potential that (marine) natural products, even those found in the darkest places on the planet, may have for aiding developments in optical materials design.