Substitution and chemical environment effects on the absorption spectrum of indigo

Photochromic derivatives of indigo: historical overview of development, challenges and applications

The importance of indigo dyes is constantly increasing with the evolution of novel textile materials and photochromic material technologies. The aim of this review article is to provide a comprehensive overview of the development of photochromic indigo derivatives from the first report on the photochromic N,N'-diacetylindigo in 1954 until now. We begin with the list of historical milestones in the development of photochromic indigo derivatives. Further, we provide a brief description of the synthetic procedures utilised to obtain indigo and its derivatives, outline the structural peculiarities, photophysical and photochemical properties of indigo and proceed with the detailed discussion of the photochromic indigo derivatives. Finally, we highlight the photochromism of the structural isomers of indigo (isoindigo and indirubin) and provide an overview of prospective applications of indigo photoswitches.

Enzymatic synthesis of indigo derivatives by tuning P450 BM3 peroxygenases

Indigoids, a class of bis-indoles, have long been applied in dyeing, food, and pharmaceutical industries. Recently, interest in these 'old' molecules has been renewed in the field of organic semiconductors as functional building blocks for organic electronics due to their excellent chemical and physical properties. However, these indigo derivatives are difficult to access through chemical synthesis. In this study, we engineer cytochrome P450 BM3 from an NADPH-dependent monooxygenase to peroxygenases through directed evolution. A select number of P450 BM3 variants are used for the selective oxidation of indole derivatives to form different indigoid pigments with a spectrum of colors. Among the prepared indigoid organic photocatalysts, a majority of indigoids demonstrate a reduced band gap than indigo due to the increased light capture and improved charge separation, making them promising candidates for the development of new organic electronic devices. Thus, we present a useful enzymatic approach with broad substrate scope and cost-effectiveness by using low-cost H₂O₂ as a cofactor for the preparation of diversified indigoids, offering versatility in designing and manufacturing new dyestuff and electronic/sensor components.

Charge injected proton transfer in indigo derivatives

In analogy with excited-state proton transfer, proton transfer is significantly facilitated in cationic and anionic molecules of indigo derivatives generated in field-effect transistors. We have prepared extended and truncated indigo derivatives and investigated their ambipolar transistor properties. Since the proton transfer reduces the energy gap from 2.2 to 0.4 eV, the proton transferred states are stabilized in the charge injected cationic and anionic states; the energy increase is as small as 0.5 eV, which is half of that in the neutral state. The intermolecular proton transfer enlarges the equilibrium N-H distance typically by 0.03 Å, and improves the donor and acceptor abilities by 0.2-0.4 eV, though the reorganization energy is practically unchanged. In addition, the transfer integrals along the hydrogen bonds are as large as one third of the columnar transfers, to facilitate the two-dimensional carrier conduction. The influence of proton transfer is most significant in indigo and truncated indigo derivatives, though isoindigo and quinacridone exhibit similar properties. Accordingly, indigo derivatives show much better donor and acceptor abilities than those expected from isolated molecules.

Simple Protocol for Capturing Both Linear-Response and State-Specific Effects in Excited-State Calculations with Continuum Solvation Models

We present an effective computational protocol (cLR²) to describe both solvatochromism and fluorosolvatochromism. This protocol, which couples the polarizable continuum model to time-dependent density functional theory, simultaneously accounts for both linear-response and state-specific solvation effects. A series of test cases, including solvatochromic and fluorosolvatochromic compounds and excited-state intramolecular proton transfers, are used to highlight that cLR² is especially beneficial for modeling bright excitations possessing a significant charge-transfer character, as well as cases in which an accurate balance between states of various polarities should be restored.

Synthesis and Characterization of New Organic Dyes Containing the Indigo Core

A new series of symmetrical organic dyes containing an indigo central core decorated with different electron donor groups have been prepared, starting from Tyrian Purple and using the Pd-catalyzed Stille-Migita coupling process. The effect of substituents on the spectroscopic properties of the dyes has been investigated theoretically and experimentally. In general, all dyes presented intense light absorption bands, both in the blue and red regions of the visible spectrum, conferring them a bright green color in solution. Using the same approach, an asymmetrically substituted D-A-π-A green dye, bearing a triarylamine electron donor and the cyanoacrylate acceptor/anchoring group, has been synthesized for the first time and fully characterized, confirming that spectroscopic and electrochemical properties are consistent with a possible application in dye-sensitized solar cells (DSSC).

Molecular Structures and Spectral Properties of Natural Indigo and Indirubin: Experimental and DFT Studies

This paper presents a comparative study on natural indigo and indirubin in terms of molecular structures and spectral properties by using both computational and experimental methods. The spectral properties were analyzed with Fourier transform infrared (FTIR), Raman, UV-Visible, and fluorescence techniques. The density functional theory (DFT) method with B3LYP using 6-311G(d,p) basis set was utilized to obtain their optimized geometric structures and calculate the molecular electrostatic potential, frontier molecular orbitals, FTIR, and Raman spectra. The single-excitation configuration interaction (CIS), time-dependent density functional theory (TD-DFT), and polarization continuum model (PCM) were used to optimize the excited state structure and calculate the UV-Visible absorption and fluorescence spectra of the two molecules at B3LYP/6-311G(d,p) level. The results showed that all computational spectra agreed well with the experimental results. It was found that the same vibrational mode presents a lower frequency in indigo than that in indirubin. The frontier molecular orbital analysis demonstrated that the UV-Visible absorption and fluorescence bands of indigo and indirubin are mainly derived from π → π* transition. The results also implied that the indigo molecule is more conjugated and planar than indirubin, thereby exhibiting a longer maximum absorption wavelength and stronger fluorescence peak.

Protoisomerization of Indigo and Isoindigo Dyes Confirmed by Gas-Phase Infrared Ion Spectroscopy

Gas-phase infrared multiple-photon dissociation (IRMPD) spectra are recorded for the protonated dye molecules indigo and isoindigo by using a quadrupole ion trap (QIT) mass spectrometer coupled to the free electron laser for infrared experiments (FELIX). From their fingerprint IR spectra (600—1800 cm^–1) and comparison with quantum-chemical calculations at the density functional level of theory (B3LYP/6-31++G(d,p)), we derive their structures. We focus particularly on the question of whether trans-to-cis isomerization occurs upon protonation and transfer to the gas phase. The trans-configuration is energetically favored in the neutral forms of the dyes in solution and in the gas phase. Instead, the cis-isomer is lower in energy for the protonated forms of both species, but indigo is also notorious for not undergoing double-bond trans-to-cis isomerization, in contrast to many other conjugated systems. The IR spectra suggest that protoisomerization from trans to cis indeed occurs for both dyes. To estimate the extent of isomerization, on-resonance kinetics are measured on diagnostic and common vibrational frequencies to determine the ratio of cis-to-trans isomers. We find ratios of 65–70% cis and 30–35% trans for indigo versus 75–80% cis and 20–25% trans for isoindigo. Transition-state calculations for the isomerization reactions have been carried out, which indeed suggest a lower barrier for protonated isoindigo, qualitatively explaining the more efficient isomerization.

The Bethe-Salpeter formalism with polarisable continuum embedding: reconciling linear-response and state-specific features

The Bethe-Salpeter equation (BSE) formalism has been recently shown to be a valuable alternative to time-dependent density functional theory (TD-DFT) with the same computing time scaling with system size. In particular, problematic transitions for TD-DFT such as charge-transfer, Rydberg and cyanine-like excitations were shown to be accurately described with BSE. We demonstrate here that combining the BSE formalism with the polarisable continuum model (PCM) allows us to include simultaneously linear-response and state-specific contributions to solvatochromism. This is confirmed by exploring transitions of various natures (local, charge-transfer, etc.) in a series of solvated molecules (acrolein, indigo, p-nitro-aniline, donor-acceptor complexes, etc.) for which we compare BSE solvatochromic shifts to those obtained by linear-response and state-specific TD-DFT implementations. Such a remarkable and unique feature is particularly valuable for the study of solvent effects on excitations presenting a hybrid localised/charge-transfer character.

Effect of different physico-chemical parameters for natural indigo production during fermentation of Indigofera plant biomass

Natural indigo production from Indigofera plant biomass requires fermentation of biomass, oxidation of fermented broth, settling of oxidized product (indigo), filtration and recovery. In this study, we have investigated roles of physico-chemical parameters during fermentation with respect to product yield. The study showed that water-to-biomass ratio (1:10), fermentation duration (0, 6, 12, 18, 24 h), pH (6-7.5), dissolved oxygen concentration; DO (0.5-3 mg ml^-1), oxidation reduction potential ORP (+50 to -300 mV) and temperature (25-40 °C) during fermentation, oxidation and dye recovery from the broth are directly or indirectly related to indigo yield. Biomass fermentation for 12 h at 40 °C incubation temperature yields the highest biogenic indigo (2.84 mg g^-1) out of the different experimental conditions.

General C-H Arylation Strategy for the Synthesis of Tunable Visible Light-Emitting Benzo[a]imidazo[2,1,5-c,d]indolizine Fluorophores

Herein we report the discovery of the benzo[a]imidazo[2,1,5-c,d]indolizine motif displaying tunable emission covering most of the visible spectrum. The polycyclic core is obtained from readily available amides via a chemoselective process involving Tf₂O-mediated amide cyclodehydration, followed by intramolecular C-H arylation. Additionally, these fluorescent heterocycles are easily functionalized using electrophilic reagents, enabling divergent access to varied substitution. The effects of said substitution on the compounds' photophysical properties were rationalized by density functional theory calculations. For some compounds, emission wavelengths are directly correlated to the substituent's Hammett constants. Easily introduced nonconjugated reactive functional groups allow the labeling of biomolecules without modification of emissive properties. This work provides a straightforward platform for the synthesis of new moderately bright fluorescent dyes remarkable for their chemical stability, predictability, and unusually high excitation-emission differential.

A Computational Study of the Protoisomerization of Indigo and Its Imine Derivatives

The protoisomerization (isomerization induced by protonation) mechanisms of indigo as well as indigo di- and monoimine derivatives were investigated using computational chemistry. Both density functional theory (M06-2X) and wave function theory (GMC-QDPT) methods were used to obtain reliable results. A solvation model (C-PCM with CH2Cl2 solvent) was employed to mimic the actual environment of the isomerization. The calculations reveal that the protoisomerizations of both the indigo and its imine derivatives are thermodynamically favorable. However, the energy barriers for rotating the double bonds in the derivatives are found to be lower than the one for indigo. More importantly, the imine derivatives undergo one-step isomerization, whereas a two-step process is predicted for indigo itself. The computational results provide insightful explanation for the different protoisomerization propensities of the parent indigo and its imine derivatives observed in experiment.

Indirubin derivatives: a patent review (2010 - present)

INTRODUCTION

Indirubins are bisindole alkaloids naturally occurring in indigo-bearing plants or in mollusks from the Muricidae family. They belong to the rather small family of indigoids, which has nevertheless found an extreme importance in the fields of dyes and medicinal chemistry. Indirubin has been found to be the active ingredient of a traditional Chinese Medicine used to treat the symptoms of leukemia. Further biological explorations revealed the ability of indirubin to bind cyclin-dependent kinases and 6-bromoindirubin, extracted from mollusks, to bind glycogen synthase kinase-3. The high affinity displayed by the two natural products has opened a vast field of research and triggered the development of hundred of derivatives with biological activities.

AREAS COVERED

The traditional use of indirubin for the treatment of leukemia has prompted different research groups to study the cytotoxic effect of indirubin derivatives on both solid tumors and leukemia. Moreover, the affinity of indirubins for kinases also allowed the exploration of their activity towards stem cells.

EXPERT OPINION

The derivatives presented are in accordance with first discoveries and establish the close relation between activity and kinase inhibition. New derivatives have been patented and new interferences in signaling pathways are described. However, few in vivo studies have been performed and more efficient solutions are needed to unravel the major issue of solubility.

Virtual eyes for technology and cultural heritage: toward computational strategy for new and old indigo-based dyes

A cost-effective, robust, and reliable computational strategy is applied to simulate peak positions and band-shapes of UV-vis spectra together with the dye colours perceived by human eyes. The features of our virtual multifrequency spectrometer (VMS) relevant to this topic are sketched with special focus on the selection of density functional, vibronic model, and solvent description. Furthermore, the new VMS-Draw graphical user interface (GUI) is employed for user-friendly pre- and post-processing of the computed data. The family of indigo dyes is used as case study in view of their continued use in the field of cultural heritage, together with new promising applications for photonics and sustainable energy. After assessment of different simplified models employed in previous studies, the role of several substituents and of dimerization in tuning the colour and spectral features are analyzed in detail by means of both accurate computations and interpretative models. The results are in remarkable agreement with experiment and allow to rationalize the behaviour of this class of dyes.

Kristall- und Molekülstruktur von „Urindigo“ (4,4,4′,4′-Tetramethyl-2,2′-bipyrrolidinyliden-3,3′-dion) und die Strukturverwandtschaft zum Indigo

The crystal structure of 4,4,4′,4′-tetramethyl-2,2′-bipyrrolidinyliden-3,3′-dione (3) („urindigo“ = primordial indigo) was determined by X-ray diffraction. The molecule has thetrans-configuration as indigo itself. Within the parent grouptrans-(OC)(HN)C=C(CO)(NH) the distances and angles of3are very similar to that in indigo: C=C (136.6 pm), C–N (140.9 pm), C–C (145.6 pm), C=O (122.6 pm). The intramolecular N–H···O bonds in3and indigo are similar whereas the intermolecular hydrogen bonds in the former are substantially weaker. The latter observation finds its interesting parallel in the markedly smaller difference between the Vis absorptions of the gaseous and the solid primordial indigo in comparison to that of indigo. The present results support the early view by Lüttke and Klessinger that thetrans-(OC)(HN)C=C(CO)(NH) fragment is the parent chromophor of indigo dyes.

Dye chemistry with time-dependent density functional theory

In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.

An explicit account of solvation is essential for modeling Suzuki–Miyaura coupling in protic solvents

We compared explicit and implicit solvation approaches in modeling the free energy profile of the final step of Suzuki–Miyaura coupling.

Synthesis, characterization, optical properties and theoretical calculations of 6-fluoro coumarin

6-Fluoro coumarin is synthesized and characterized by (1)H NMR and (13)C NMR. The optical properties of the title compound are investigated by UV-vis absorption and fluorescence emission spectra, the results show the title compound can absorb UV-vis light at 319, 269 and 215nm, moreover it exhibits blue-purple fluorescence emission at 416nm. Theoretical studies on molecular structure, infrared spectra (IR), nuclear magnetic resonance ((1)H NMR, (13)C NMR) chemical shifts, UV-vis absorption and fluorescence emission of the synthesized compound have been worked out. Most chemical calculations were performed by density functional theory (DFT) method at the B3LYP/6-311G(d,p) level (NMR at B3LYP/Aug-CC-Pvdz level) using Gaussian 09 program. The compared results reveal that the scaled theoretical vibrational frequencies are in good accordance with the observed spectra; computational chemical shifts are consistent with the experimental values in most parts, except for some minor deviations; the UV-vis absorption calculated matches the experimental one very well, and the fluorescence emission spectrum is in good agreement with the experimental one when the solute-solvent hydrogen-bonding interaction is considered. These good coincidences prove that the computational methods selected can be used to predict these properties of other similar materials where it is difficult to arrive at experimental results.

Preparation and Chemical Properties of π-Conjugated Polymers Containing Indigo Unit in the Main Chain

π-Conjugated polymers based on indigo unit were prepared. Dehalogenative polycondensation of N-hexyl-6,6′-dibromoindigo with a zerovalent nickel complex gave a homopolymer, P(HexI), in 77% yield. Copolymer of N-hexyl-indigo and pyridine, P(HexI-Py), was also prepared in 50% yield. P(HexI) showed good solubility in organic solvents, whereas P(HexI-Py) was only soluble in acids such as HCOOH. The weight-average molecular weights (M_w) of P(HexI) and P(HexI-Py) were determined to be 10,000 and 40,000, respectively, by a light scattering method. Pd-catalyzed polycondensation between 6,6′-dibromoindigo with N-BOC (BOC = t-butoxycarbonyl) substituents and a diboronic compound of 9,9-dioctylfluorene afforded the corresponding alternating copolymer, P(BOCI-Flu), as a deep red solid in 98% yield. P(BOCI-Flu) was soluble in N-methyl-2-pyrroridone and showed an M_w of 29,000 in GPC analysis. Treatment of P(BOCI-Flu) with CF₃COOH smoothly led to a BOC-deprotection reaction to give an insoluble deep green polymer, P(I-Flu), in a quantitative yield. Diffuse reflectance spectra of powdery P(BOCI-Flu) and P(I-Flu) showed peaks at about 580 nm and 630 nm, respectively, which are thought to originate from the indigo unit.

Environmental and complexation effects on the structures and spectroscopic signatures of organic pigments relevant to cultural heritage: the case of alizarin and alizarin-Mg(II)/Al(III) complexes

An integrated computational approach allowed an unbiased analysis of optical and structural properties of alizarin-based pigments, which can be directly compared with experimental results. Madder lake pigments have been modeled by Mg(II)- and Al(III)-coordinated alizarin taking into account solvation and metal-linkage effects, responsible for colour modifications. Moreover, different environmental conditions have been analyzed for free alizarin, showing in all cases semi-quantitative agreement with experimental spectroscopic data (UV-VIS). Our results point out the ability of in silico approaches to unravel the subtle interplay of stereo-electronic, dynamic, and environmental effects in tuning the physico-chemical properties of pigments relevant to cultural heritage.

25th anniversary article: progress in chemistry and applications of functional indigos for organic electronics

Indigo and its derivatives are dyes and pigments with a long and distinguished history in organic chemistry. Recently, applications of this 'old' structure as a functional organic building block for organic electronics applications have renewed interest in these molecules and their remarkable chemical and physical properties. Natural-origin indigos have been processed in fully bio-compatible field effect transistors, operating with ambipolar mobilities up to 0.5 cm(2) /Vs and air-stability. The synthetic derivative isoindigo has emerged as one of the most successful building-blocks for semiconducting polymers for plastic solar cells with efficiencies > 5%. Another isomer of indigo, epindolidione, has also been shown to be one of the best reported organic transistor materials in terms of mobility (∼2 cm(2) /Vs) and stability. This progress report aims to review very recent applications of indigoids in organic electronics, but especially to logically bridge together the hereto independent research directions on indigo, isoindigo, and other materials inspired by historical dye chemistry: a field which was the root of the development of modern chemistry in the first place.

The Indigo Molecule Revisited Again: Assessment of the Minnesota Family of Density Functionals for the Prediction of Its Maximum Absorption Wavelengths in Various Solvents

The Minnesota family of density functionals (M05, M05-2X, M06, M06L, M06-2X, and M06-HF) were evaluated for the calculation of the UV-Vis spectra of the indigo molecule in solvents of different polarities using time-dependent density functional theory (TD-DFT) and the polarized continuum model (PCM). The maximum absorption wavelengths predicted for each functional were compared with the known experimental results.

An ab initio simulation of the UV/Visible spectra of substituted chalcones

The electronic absorption spectra of 29 phenyl-ring substituted chalcones have been investigated with the time-dependent density functional theory (TD-DFT) and polarizable continuum TD-DFT (PCM-TD-DFT). It turns out that the hybrid PBE1PBE functional with the 6-31G basis set provide reliable λmax when the solvent effects are included in the model. Comparisons with experimental values lead to a mean absolute error of 12 nm (0.136 eV). Moreover, the observed substituent effects are reproduced by calculation qualitatively. The λmax of substituted chalcone in phenyl ring A is less sensitive to substitution than that in ring B. The linear correlation of Hammett’s substituent constants (σP) with LUMO energies is better with respect to HOMO energies. The calculation reveals that the maximum absorption band mainly results from the π→π* transition from HOMO to LUMO. The analysis of the electron density plots of frontier molecular orbitals show that most transitions should be of valence excitation nature.

Computational chemistry meets cultural heritage: challenges and perspectives

Chemistry is central to addressing topics of interest in the cultural heritage field, offering particular insight into the nature and composition of the original materials, the degradation processes that have occurred over the years, and the attendant physical and chemical changes. On the one hand, the chemical characterization of the constituting materials allows researchers to unravel the rich information enclosed in a work of art, providing insight into the manufacturing techniques and revealing aspects of artistic, chronological, historical, and sociocultural significance. On the other hand, despite the recognized contribution of computational chemistry in many branches of materials science, this tool has only recently been applied to cultural heritage, largely because of the inherent complexity of art materials. In this Account, we present a brief overview of the available computational methods, classified on the basis of accuracy level and dimension of the system to be simulated. Among the discussed methodologies, density functional theory (DFT) and time-dependent DFT represent a good compromise between accuracy and computational cost, allowing researchers to model the structural, electronic, and spectroscopic properties of complex extended systems in condensed phase. We then discuss the results of recent research devoted to the computer simulation of prototypical systems in cultural heritage, namely, indigo and Maya Blue, weld and weld lake, and the pigment minium (red lead). These studies provide insight into the basic interactions underlying the materials properties and, in some cases, permit the assignment of the material composition. We discuss properties of interest in the cultural heritage field, ranging from structural geometries and acid-base properties to IR-Raman vibrational spectra and UV-vis absorption-emission spectra (including excited-state deactivation pathways). We particularly highlight how computational chemistry applications in cultural heritage can complement experimental investigations by establishing or rationalizing structure-property relations of the fundamental artwork components. These insights allow researchers to understand the interdependence of such components and eventually the composition of the artwork materials. As a perspective, we aim to extend the simulations to systems of increasing complexity that are similar to the realistic materials encountered in works of art. A challenge is the computational investigation of materials degradation and their associated reactive pathways; here the possible initial components, intermediates, final materials, and various deterioration mechanisms must all be simulated.

Self-assembly of enantiopure domains: the case of indigo on Cu(111)

The adsorption of indigo molecules on Cu(111) was investigated by low temperature (5 K) scanning tunneling microscopy from the isolated single molecule regime to one monolayer. Structural optimization and image calculations demonstrate that the molecules are in a physisorbed state. Because of the reduced symmetry at the surface, single molecules acquire a chiral character upon adsorption leading to a two-dimensional (2D) chirality. They adopt two adsorption configurations, related by a mirror symmetry of the substrate, each with a distinct molecular orientation. Consequently, the 2D chirality is expressed by the orientation of the molecule. For higher coverage, molecules self-assemble by hydrogen bonding in nearly homochiral molecular chains, whose orientation is determined by the orientation taken by the isolated molecules. When the coverage approaches one monolayer, these chains pack into domains. Finally, the completion of the monolayer induces the expulsion of the molecules of the wrong chirality that are still in these domains, leading to perfect resolution in enantiopure domains.