Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

The absorption properties of chromophores in biomolecular systems are subject to several fine‐tuning mechanisms. Specific interactions with the surrounding protein environment often lead to significant changes in the excitation energies, but bulk dielectric effects can also play an important role. Moreover, strong excitonic interactions can occur in systems with several chromophores at close distances. For interpretation purposes, it is often desirable to distinguish different types of environmental effects, such as geometrical, electrostatic, polarization, and response (or differential polarization) effects. Methods that can be applied for theoretical analyses of such effects are reviewed herein, ranging from continuum and point‐charge models to explicit quantum chemical subsystem methods for environmental effects. Connections to physical model theories are also outlined. Prototypical applications to optical spectra and excited states of fluorescent proteins, biomolecular photoreceptors, and photosynthetic protein complexes are discussed.     

Synthesis of Dibenzochalcogenaborins and Systematic Comparisons of Their Optical Properties by Changing a Bridging Chalcogen Atom

Novel hetero‐π‐conjugated compounds (dibenzochalcogenaborins) with the same molecular framework, bearing a boron atom as an acceptor and chalcogen atoms as a donor, were synthesized, and systematic comparisons among these molecules were performed. X‐ray crystallographic analysis of these molecules showed similar structures with high planarity. UV/Vis spectroscopy and theoretical calculations revealed that the absorption maxima and the HOMO–LUMO gap changed by systematically changing the bridging chalcogen atom. Dibenzooxaborin and dibenzothiaborin showed fluorescence emission both in solution and in the solid state with a small Stokes shift, indicating the high rigidity of these compounds. On the other hand, dibenzoselenaborin exhibited a very weak fluorescence as a result of the heavy atom effect.     

Characterisation of Nanohybrids of Porphyrins with Metallic and Semiconducting Carbon Nanotubes by EPR and Optical Spectroscopy

Single‐walled carbon nanotubes (SWCNTs) are noncovalently functionalised with octaethylporphyrins (OEPs) and the resulting nanohybrids are isolated from the free OEPs. Electron paramagnetic resonance (EPR) spectroscopy of cobalt(II)OEP, adsorbed on the nanotube walls by π–π‐stacking, demonstrates that the CNTs act as electron acceptors. EPR is shown to be very effective in resolving the different interactions for metallic and semiconducting tubes. Moreover, molecular oxygen is shown to bind selectively to nanohybrids with semiconducting tubes. Water solubilisation of the porphyrin/CNT nanohybrids using bile salts, after applying a thorough washing procedure, yields solutions in which at least 99 % of the porphyrins are interacting with the CNTs. Due to this purification, we observe, for the first time, the isolated absorption spectrum of the interacting porphyrins, which is strongly red‐shifted compared to the free porphyrin absorption. In addition a quasi‐complete quenching of the porphyrin fluorescence is also observed.     

Spectroscopy of Dibenzorubicene: Experimental Data for a Search in Interstellar Spectra

We report on the characterization of dibenzo[cde,opq]rubicene (C₃₀H₁₄). The molecule was studied in solution at room temperature with absorption spectroscopy in the visible (vis) and ultraviolet (UV) wavelength ranges, and with emission spectroscopy. The infrared (IR), visible, ultraviolet, and vacuum ultraviolet (VUV) absorption spectra of a thin film were measured also at room temperature. In addition, the UV/vis absorption spectrum was measured at cryogenic temperatures using the matrix isolation spectroscopy technique. The interpretation of spectra was supported by theoretical calculations based on semiempirical and ab initio models, as well as on density functional theory. Finally, the results of the laboratory study were compared with interstellar spectra.     

Pairing of Isolated Nucleobases: Double Resonance Laser Spectroscopy of Adenine–Thymine

The vibronic spectrum of the adenine–thymine (A–T) base pair was obtained by one‐color resonant two‐photon ionization (R2PI) spectroscopy in a free jet of thermally evaporated A and T under conditions favorable for formation of small clusters. The onset of the spectrum at 35 064 cm^?1 exhibits a large red shift relative to the π–π* origin of 9H‐adenine at 36 105 cm^?1. The IR–UV spectrum was assigned to cluster structures with HNH???O?C/N???HN hydrogen bonding by comparison with the IR spectra of A and T monomers and with ab initio calculated vibrational spectra of the most stable A–T isomers. The Watson–Crick A–T base pair is not the most stable base‐pair structure at different levels of ab initio theory, and its vibrational spectrum is not in agreement with the observed experimental spectrum. Experiments with methylated A and T were performed to further support the structural assignment.     

Aggregation of 2‐Aminobenzimidazole—A Combined Experimental and Theoretical Investigation

An investigation of 2‐aminobenzimidazole was carried out by calculations at HF, MP2, and DFT levels of theory and also by UV and IR spectroscopy. The quantum chemical calculations predict a full shift of the equilibrium towards the amino form, but the absorption spectra in different solvents distinctly show a two‐component equilibrium system. Examination of possible equilibria in solution shows that an equilibrium between two dimeric forms of the amino tautomer of 2‐aminobenzimidazole explains the spectral observations.     

Spectral Properties of Foams and Emulsions

The optical and spectral properties of foams and emulsions provide information about their micro-/nanostructures, chemical and time stability and molecular data of their components. Foams and emulsions are collections of different kinds of bubbles or drops with particular properties. A summary of various surfactant and emulsifier types is performed here, as well as an overview of methods for producing foams and emulsions. Absorption, reflectance, and vibrational spectroscopy (Fourier Transform Infrared spectroscopy-FTIR, Raman spectroscopy) studies are detailed in connection with the spectral characterization techniques of colloidal systems. Diffusing Wave Spectroscopy (DWS) data for foams and emulsions are likewise introduced. The utility of spectroscopic approaches has grown as processing power and analysis capabilities have improved. In addition, lasers offer advantages due to the specific properties of the emitted beams which allow focusing on very small volumes and enable accurate, fast, and high spatial resolution sample characterization. Emulsions and foams provide exceptional sensitive bases for measuring low concentrations of molecules down to the level of traces using spectroscopy techniques, thus opening new horizons in microfluidics.     

IR,Raman, and UV/Vis Spectra of Corannulene for Use in Possible Interstellar Identification

The spectroscopic characterization of corannulene (C₂₀H₁₀) is carried out by several techniques. The high purity of the material synthesized for this study was confirmed by gas chromatography‐mass spectrometry (GC‐MS). During a high‐performance liquid chromatography (HPLC) process, the absorption spectrum of corannulene in the ultraviolet (UV) and visible (vis) ranges is obtained. The infrared (IR) absorption spectrum is measured in CsI pellets, and the Raman scattering spectrum is recorded for pure crystal grains. In addition to room temperature measurements, absorption spectroscopy in an argon matrix at 12 K is also performed in the IR and UV/Vis ranges. The experimental spectra are compared with theoretical Raman and IR spectra and with calculated electronic transitions. All calculations are based on the density functional theory (DFT), either normal or time‐dependent (TDDFT). Our results are discussed in view of their possible application in the search for corannulene in the interstellar medium.     

Effect of peripheral substitution on the electronic absorption and fluorescence spectra of metal-free and zinc phthalocyanines

The effect of substituents on the position and intensity of the electronic absorption and fluorescence spectra of phthalocyanines (Pcs) was examined for 35 Pc compounds. When electron-releasing groups are bound to four alpha-benzo positions of the Pc skeleton, the B and Q bands shift to longer wavelength. Relative to this shift, the effect of introducing the same electron-releasing groups at the other four alpha positions amounts to about 1.6-2.0. Although the effect is not always clearly seen, introduction of electron-releasing groups in the beta-benzo positions of the Pc skeleton generally shifts the Q band to shorter wavelength. The effect of electron-withdrawing groups is exactly the opposite with respect to the alpha and beta positions. These effects can be reasonably explained by considering the magnitude of the atomic orbital coefficients of the carbon atoms derived from molecular orbital (MO) calculations. In addition, the following intriguing phenomena were observed in the experiments, although not all were explained theoretically: 1) the splitting of the Q band of metal-free Pcs decreases with increasing wavelength of the Q band, 2) the ring currents of Pcs with Q bands at longer wavelength are generally smaller, and 3) the absorption coefficients of the Q band of Pc compounds with 16-electron-releasing substituents are larger than those of the corresponding tetra- and octasubstituted Pcs by several tens of percent. 4) Our PPP calculations suggested that the absorption coefficient of the Q band of Pcs with more strongly electron releasing substituents is larger. 5) The second HOMO of the Pcs with the Q band at longer wavelength has b(1u) symmetry, as opposed to the a(2u) symmetry of normal Pcs. 6) Pcs showing S1 emission maxima at wavelengths longer than about 740 nm generally have quantum yields of less than 0.1.     

Rational Molecular Design towards Vis/NIR Absorption and Fluorescence by using Pyrrolopyrrole aza‐BODIPY and its Highly Conjugated Structures for Organic Photovoltaics

Pyrrolopyrrole aza‐BODIPY (PPAB) developed in our recent study from diketopyrrolopyrrole by titanium tetrachloride‐mediated Schiff‐base formation reaction with heteroaromatic amines is a highly potential chromophore due to its intense absorption and fluorescence in the visible region and high fluorescence quantum yield, which is greater than 0.8. To control the absorption and fluorescence of PPAB, particularly in the near‐infrared (NIR) region, further molecular design was performed using DFT calculations. This results in the postulation that the HOMO–LUMO gap of PPAB is perturbed by the heteroaromatic moieties and the aryl‐substituents. Based on this molecular design, a series of new PPAB molecules was synthesized, in which the largest redshifts of the absorption and fluorescence maxima up to 803 and 850 nm, respectively, were achieved for a PPAB consisting of benzothiazole rings and terthienyl substituents. In contrast to the sharp absorption of PPAB, a PPAB dimer, which was prepared by a cross‐coupling reaction of PPAB monomers, exhibited panchromatic absorption across the UV/Vis/NIR regions. With this series of PPAB chromophores in hand, a potential application of PPAB as an optoelectronic material was investigated. After identifying a suitable PPAB molecule for application in organic photovoltaic cells based on evaluation using time‐resolved microwave conductivity measurements, a maximized power conversion efficiency of 1.27 % was achieved.     

UV/Vis Spectroscopy of Copper Formate Clusters: Insight into Metal-Ligand Photochemistry

The electronic structure and photochemistry of copper formate clusters, Cu^I₂(HCO₂)₃⁻ and Cu^II_n(HCO₂)_2n+1⁻, n≤8, are investigated in the gas phase by using UV/Vis spectroscopy in combination with quantum chemical calculations. A clear difference in the spectra of clusters with Cu^I and Cu^II copper ions is observed. For the Cu^I species, transitions between copper d and s/p orbitals are recorded. For stoichiometric Cu^II formate clusters, the spectra are dominated by copper d–d transitions and charge-transfer excitations from formate to the vacant copper d orbital. Calculations reveal the existence of several energetically low-lying isomers, and the energetic position of the electronic transitions depends strongly on the specific isomer. The oxidation state of the copper centers governs the photochemistry. In Cu^II(HCO₂)₃⁻, fast internal conversion into the electronic ground state is observed, leading to statistical dissociation; for charge-transfer excitations, specific excited-state reaction channels are observed in addition, such as formyloxyl radical loss. In Cu^I₂(HCO₂)₃⁻, the system relaxes to a local minimum on an excited-state potential-energy surface and might undergo fluorescence or reach a conical intersection to the ground state; in both cases, this provides substantial energy for statistical decomposition. Alternatively, a Cu^II(HCO₂)₃Cu⁰⁻ biradical structure is formed in the excited state, which gives rise to the photochemical loss of a neutral copper atom.     

Resonance Raman studies of beta-substituted porphyrin systems with unusual electronic absorption properties.

Zn(II) and Cu(II) porphyrins with beta-conjugated barbiturate functional groups have low-energy electronic transitions which are unusual in that there are two strong bands in the Soret region. Resonance excitation of the two bands shows that each has features characteristic of both the porphyrin and barbiturate groups, with some perturbation to these features caused by the interaction of the two chromophores. The resonance Raman (RR) spectrum (lambda(exc)=413.1 nm) of the 412 nm band shows two bands at 1722 and 1743 cm(-1) attributable to C==O stretches in the substituent. Changes in frequency of porphyrin core modes due to the differing metal centres are reproduced by density functional theory calculations. The Q band RR spectra show modes with anomalous polarization which may be attributed to A(2g) modes, however no overtone or combination bands are observed.     

Isolation and Spectroscopic Characterization of New Endohedral Fullerenes in the Size Gap of C74 to C76

New alkaline earth metal endohedral fullerenes Sr@C₇₄, Sr@C₇₆‐I, II and Ca@C₇₄, prepared by means of the RF‐method, have been isolated using multistep HPLC. The purity was ascertained by anionic LDI TOF mass spectroscopy, considering the isotopic patterns of the compounds. The influence of the incorporated metal on the electronic structure has been studied by VIS‐NIR and Raman spectroscopy. Photoexcited triplet‐state EPR spectroscopy was used to investigate the structure of these otherwise EPR‐silent fullerenes. Displaying the frequency of the cage vs. encapsulated metal vibrational modes as a function of the square root of the reciprocal masses of the metals clearly separates the M³⁺@C_n^3— and the M²⁺@C_n^2— families. This seems to be a generally applicable tool for monitoring the metal to fullerene charge transfer.     

Identification of Triplet States in Carotenoids by Intracavity Absorption Spectroscopy and Measurements of Delayed Fluorescence

Owing to the low quantum yield of phosphorescence , triplet states of carotenoids have been very difficult to identify. These states can be characterized by intracavity absorption spectroscopy, which allows the direct measurement of the spin-forbidden singlet–triplet transitions in low concentrated solutions, and by delayed fluorescence measurements.     

Synthesis and Optical Properties of Water‐Soluble Polyglycerol‐Dendronized Rylene Bisimide Dyes

Four new water‐soluble polyglycerol‐dendronized perylene, terrylene, and quaterrylene bisimides have been synthesized and characterized with respect to their optical properties in polar organic solvents and water by using UV/Vis and fluorescence spectroscopy. All of these dyes were highly soluble in water, but the size of the chosen polyglycerol dendron was only sufficient to completely suppress dye aggregation for the core‐unsubstituted perylene derivative. Their high solubility in water and their absorption and emission wavelengths up to the NIR region make the core‐unsubstituted perylene and terrylene bisimides ideal candidates for applications in bioimaging, whilst the lack of fluorescence for quaterrylene bisimide in all polar solvents does not warrant further investigation of this chromophore in fluorescence and imaging applications. Likewise, tuning of the emission of rylene bisimides towards longer wavelengths by employing electron‐donating bay substituents is not a promising strategy, owing to the lower fluorescence quantum yields in polar solvents and, in particular, in water.     

Pigmentation of White,Brown, and Green Chicken Eggshells Analyzed by Reflectance,Transmittance, and Fluorescence Spectroscopy

We report on the reflectance, transmittance and fluorescence spectra (λ=200–1200 nm) of four types of chicken eggshells (white, brown, light green, dark green) measured in situ without pretreatment and after ablation of 20–100 μm of the outer shell regions. The color pigment protoporphyrin IX (PPIX) is embedded in the protein phase of all four shell types as highly fluorescent monomers, in the white and light green shells additionally as non-fluorescent dimers, and in the brown and dark green shells mainly as non-fluorescent poly-aggregates. The green shell colors are formed from an approximately equimolar mixture of PPIX and biliverdin. The axial distribution of protein and colorpigments were evaluated from the combined reflectances of both the outer and inner shell surfaces, as well as from the transmittances. For the data generation we used the radiative transfer model in the random walk and Kubelka-Munk approaches.