Database of Absorption and Fluorescence Spectra of >300 Common Compounds for use in PhotochemCAD

The design of new molecules for photochemical studies typically requires knowledge of spectral features of pertinent chromophores beginning with the absorption spectrum (λ _abs) and accompanying molar absorption coefficient (ε , m ⁻¹ cm⁻¹) and often extending to the fluorescence spectrum (λ _em) and fluorescence quantum yield (Φ_f), where the fluorescence properties may be of direct relevance or useful as proxies to gain insight into the nature of the first excited singlet state. PhotochemCAD databases, developed over a period of 30 years, are described here. The previous databases for 150 compounds have been expanded to encompass 339 compounds for which absorption spectra (including ε values), fluorescence spectra (including Φ_f values) and references to the primary literature have been included where available (552 spectra altogether). The compounds exhibit spectra in the ultraviolet, visible and/or near‐infrared spectral regions. The compound classes and number of members include acridines (21), aromatic hydrocarbons (41), arylmethane dyes (11), azo dyes (18), biomolecules (18), chlorins/bacteriochlorins (16), coumarins (14), cyanine dyes (19), dipyrrins (7), heterocycles (26), miscellaneous dyes (13), oligophenylenes (13), oligopyrroles (6), perylenes (5), phthalocyanines (11), polycyclic aromatic hydrocarbons (16), polyenes/polyynes (10), porphyrins (34), quinones (24) and xanthenes (15). A database of 31 solar spectra also is included.     

Effects of Substituents on Synthetic Analogs of Chlorophylls. Part 4: How Formyl Group Location Dictates the Spectral Properties of Chlorophylls b,d and f

Photosynthetic organisms are adapted to light characteristics in their habitat in part via the spectral characteristics of the associated chlorophyll pigments, which differ in the position of a formyl group around the chlorin macrocycle (chlorophylls b, d, f) or no formyl group (chlorophyll a). To probe the origin of this spectral tuning, the photophysical and electronic structural properties of a new set of synthetic chlorins are reported. The zinc and free base chlorins have a formyl group at either the 2‐ or 3‐position. The four compounds have fluorescence yields in the range 0.19–0.28 and singlet excited‐state lifetimes of ca 4 ns for zinc chelates and ca 8 ns for the free base forms. The photophysical properties of the 2‐ and 3‐formyl zinc chlorins are similar to those observed previously for 13‐formyl or 3,13‐diformyl chlorins, but differ markedly from those for 7‐formyl analogs. Molecular‐orbital characteristics obtained from density functional theory (DFT) calculations were used as input to spectral simulations employing the four‐orbital model. The analysis has uncovered the key changes in electronic structure engendered by the presence/location of a formyl group at various macrocycle positions, which is relevant to understanding the distinct spectral properties of the natural chlorophylls a, b, d and f.     

The first example of Diels-Alder cycloaddition of ortho-xylylenes to meso-tetraarylporphyrins containing electron-deficient β,β-double bonds

β-Nitro-5,10,15,20-tetraphenylporphyrin and its zinc complex, or 2,7-dinitro-5,10,15,20-tetraphenylporphyrin, react with 1,3-dihydrobenzo[c]thiophene 2,2-dioxide in refluxing 1,2,4-trichlorobenzene, giving rise to chlorins, bacteriochlorins or isobacteriochlorins. The products obtained are attractive intermediates for further functionalization of porphyrins and may be of potential use as sensitizers in photodynamic therapy.     

Photophysical Characterization of the Naturally Occurring Dioxobacteriochlorin Tolyporphin A and Synthetic Oxobacteriochlorin Analogues

Tolyporphins are tetrapyrrole macrocycles produced by a cyanobacterium‐containing culture known as HT‐58‐2. Tolyporphins A–J are free base dioxobacteriochlorins, whereas tolyporphin K is an oxochlorin. Here, the photophysical characterization is reported of tolyporphin A and two synthetic analogues, an oxobacteriochlorin and a dioxobacteriochlorin. The characterization (in toluene, diethyl ether, ethyl acetate, dichloromethane, 1‐pentanol, 2‐butanone, ethanol, methanol, N,N‐dimethylformamide and dimethylsulfoxide) includes static absorption and fluorescence spectra, fluorescence quantum yields and time‐resolved data. The data afford the lifetime of the lowest singlet excited state and the yields of the nonradiative decay pathways (intersystem crossing and internal conversion). The three macrocycles exhibit only modest variation in spectroscopic and excited‐state photophysical parameters across the solvents. The long‐wavelength (Q_y) absorption band of tolyporphin A appears at ~680 nm and is remarkably narrow (full‐width‐at‐half‐maximum ~7 nm). The position of the long‐wavelength (Q_y) absorption band of tolyporphin A (~680 nm) more closely resembles that of chlorophyll a (662 nm) than bacteriochlorophyll a (772 nm). The absorption spectra of tolyporphins B–I, K (which were available in minute quantities) are also reported in methanol; the spectra of B–I closely resemble that of tolyporphin A. Taken together, tolyporphin A generally exhibits spectral and photophysical features resembling those of chlorophyll a.     

Self-Assembly of Synthetic Zinc Chlorins in Aqueous Microheterogeneous Media to an Artificial Supramolecular Light-Harvesting Device

Self-assembled aggregates of a synthetic zinc chlorin in an aqueous suspension with either α-lecithin or Triton X-100 exhibit unique structural and functional properties. Absorption, circular dichroism, fluorescence, and resonance Raman spectra indicate that the supramolecular structure in an aqueous microheterogeneous medium is very similar to that of the bacteriochlorophyll c aggregates in non-polar organic solvents and in chlorosomes, the main light-harvesting antennae of green photosynthetic bacteria. The nature of the aggregates is controlled by structure and/or concentration of the added surfactants. When a small amount of metal-free bacteriochlorin is present it acts as an efficient energy acceptor from the aggregated zinc chlorins. Thus, self-assembly of synthetic zinc chlorins, doped with appropriate energy acceptors and surrounded with surfactants, affords an artificial supramolecular light-harvesting device in aqueous environment.     

Synthesis of New Derivatives of Protoporphyrin IX and Chlorophyll <Emphasis Type="Italic">a</Emphasis>

The vinyl groups in protoporphyrin IX and chlorophyll a derivatives were selectively transformed into hydroxymethyl and acetoxymethyl substituents. The reactivities of β-hydroxymethyl and β-acetoxymethyl groups in porphyrins and chlorins toward nucleophilic reagents were compared for the first time using the reaction with acetylacetone as an example. Peripheral acetylacetone moieties in porphyrins and chlorins were shown to be promising as building blocks for generation of exo heterocyclic structures.     

AQUEOUS AGGREGATES OF BACTERIOCHLOROPHYLL c AS A MODEL FOR PIGMENT ORGANIZATION IN CHLOROSOMES

Chlorosomes isolated from Chloroflexus aurantiacus were extracted with chloroform/methanol. The extract contained bacteriochlorophylls c and a and lipids, but was devoid of proteins. This crude extract spontaneously formed aggregates when a methanol solution was dispersed in aqueous buffer. The aggregates could be sedimented by ultracentrifugation and appeared in electron micrographs as stain-excluding bodies with diameters between 70 and 170 nm. The absorption spectrum is remarkably similar to that of intact chlorosomes with an absorption maximum of bacteriochlorophyll c at around 740 nm. The circular dichroism spectrum of the aggregate is also very similar to that of intact chlorosomes. A conservative (±) band centered at 740 nm confirms the highly aggregated state of bacteriochlorophyll c in both systems. Steady-state fluorescence studies showed that in the aggregate energy-transfer from bacteriochlorophyll c to a component emitting at 830 nm took place. When the aggregate was suspended in buffer saturated with 1-hexanol the 740 nm form of bacteriochlorophyll c was reversibly converted to a form with spectral properties resembling the monomer absorbing at 670 nm but still in an aggregated state. This form of bacteriochlorophyll c showed no circular dichroism signal.     

Characterization of porphyrins, chlorins, and bacteriochlorins formed via allomerization of bacteriochlorophyll a. Synthesis of highly stable bacteriopurpurinimides and their metal complexes

Allomerization of bacteriochlorophyll a (Bchl a) was studied under various reaction conditions. Bchl a on stirring with KOH/propanol produced an "unstable bacteriochlorin", which decomposed in acidic conditions to give a complex mixture containing bacteriopurpurin a as a principal component. The yields of other compounds varied and were found to be dependent on reaction condition. The structures of the isolated porphyrins, chlorins, and bacteriochlorins, related to Bchl a, were assigned on the basis of 1D, 2D NMR (ROESY), and mass spectroscopy analyses. The presence of fused anhydride rings in porphyrin, chlorin, and bacterichlorin systems showed a significant influence on their optical properties. Compared to bacteriochlorophyll a and bacteriopheophytin, the related structurally modified analogues, e.g., the bacteriopurpurin a, 13(1)/15(1)-N-alkyl isoimide, and the imide analogues were found to be more stable with a significant difference in spectroscopic properties. Bacteriochlorins containing anhydride, imide, or isoimide cyclic rings demonstrated a significant bathochromic shift of their Q bands in their electronic absorption spectra. Under basic conditions the formation of the 12-hydroxymethyl, 12-formyl, and 12-methylene analogues as byproducts from the 12-methyl-bacteriopurpurin-N-hexylimide could be due to subsequent oxidation of the vinylogous enolate intermediates. To investigate the effect of the central metal in the electronic spectra, the stable bacteriopurpurin-18-N-hexylimide was converted to a series of metal complexes [Zn(II), Cd(II), and Pd(II)] by following the direct or transmetalation approaches. Compared to the free-base analogue, these complexes showed a remarkable shift in their electronic absorption spectra.     

Photophysical Properties and Electronic Structure of Bacteriochlorin–Chalcones with Extended Near‐Infrared Absorption

Synthetic bacteriochlorins enable systematic tailoring of substituents about the bacteriochlorin chromophore and thereby provide insights concerning the native bacteriochlorophylls of bacterial photosynthesis. Nine free‐base bacteriochlorins (eight prepared previously and one prepared here) have been examined that bear diverse substituents at the 13‐ or 3,13‐positions. The substituents include chalcone (3‐phenylprop‐2‐en‐1‐onyl) derivatives with groups attached to the phenyl moiety, a “reverse chalcone” (3‐phenyl‐3‐oxo‐1‐enyl), and extended chalcones (5‐phenylpenta‐2,4‐dien‐1‐onyl, retinylidenonyl). The spectral and photophysical properties (τ_s, Φ_f, Φ_ic, Φ_isc, τ_T, k_f, k_ic, k_isc) of the bacteriochlorins have been characterized. The bacteriochlorins absorb strongly in the 780–800 nm region and have fluorescence quantum yields (Φ_f) in the range 0.05–0.11 in toluene and dimethylsulfoxide. Light‐induced electron promotions between orbitals with predominantly substituent or macrocycle character or both may give rise to some net macrocycle ? substituent charge‐transfer character in the lowest and higher singlet excited states as indicated by density functional theory (DFT) and time‐dependent DFT calculations. Such calculations indicated significant participation of molecular orbitals beyond those (HOMO ? 1 to LUMO + 1) in the Gouterman four‐orbital model. Taken together, the studies provide insight into the fundamental properties of bacteriochlorins and illustrate designs for tuning the spectral and photophysical features of these near‐infrared‐absorbing tetrapyrrole chromophores.     

Self‐aggregation of Synthetic Zinc Chlorophyll Derivatives Possessing 31‐Hydroxy or Methoxy Group and 131‐Mono‐ or Dicyanomethylene Moiety in Nonpolar Organic Solvents as Models of Chlorosomal Bacteriochlorophyll‐d Aggregates

Methyl 13¹‐(di)cyanomethylene‐pyropheophorbides were synthesized by Knoevenagel reactions of the corresponding 13¹‐oxo‐chlorins prepared from modifying chlorophyll‐a with malononitrile or cyanoacetic acid. Alternatively, methyl 13¹‐cyanomethylene‐pyropheophorbides were produced by Wittig reactions of 13¹‐oxo‐chlorins with Ph₃P=CHCN. Self‐aggregation of zinc complexes of the semi‐synthetic chlorophyll derivatives possessing a hydroxy or methoxy group at the 3¹‐position was examined in 1%(v/v) tetrahydrofuran or dichloromethane and hexane by electronic absorption and circular dichroism spectroscopy. Although intermolecular hydrogen‐bonding between the 3¹‐hydroxy and 13¹‐oxo groups of bacteriochlorophylls‐c/d/e/f was essential for their self‐aggregation in natural light‐harvesting antenna systems (=chlorosomes), zinc 3¹‐hydroxy‐13¹‐di/monocyanomethylene‐chlorins self‐aggregated in the less/lesser polar organic solvents to form chlorosome‐like large oligomers in spite of lacking the 13¹‐oxo moiety as the hydrogen‐bonding acceptor. Zinc 3¹‐methoxy‐13¹‐dicyanomethylene‐chlorin gave similar self‐aggregates regardless of lack of both the 3¹‐hydroxy and 13¹‐oxo groups. The present self‐aggregation was ascribable to stronger coordination of the 3¹‐oxygen atom to the central zinc than the conventional systems, where the electron‐withdrawing cyano group(s) increased the coordinative ability of the central zinc through the chlorin π‐system.     

具有亲油性及近红外光吸收特性的金属细菌卟吩的合成与表征

在四氢呋喃中加入金属卟吩、 强碱(无水氢化钠)和金属盐MX_n(M=Cu, Ni, Pd), 合成了细菌卟吩的5种过渡金属配合物, 该方法减少了反应时间, 提高了反应产率. 通过紫外-可见光谱、 核磁共振氢谱、 质谱等方法对所合成的化合物进行了表征, 并研究了其光学性质. 结果表明, 细菌卟吩在近红外区有明显的吸收峰, 且具有较高的强度, 相比于细菌卟吩配体, 金属配合物吸收光谱中的Q_x和Q_y带均发生了明显的红移. 细菌卟吩配体与锌配合物具有发光性质, 为Q_y(0,0)荧光, 而铜、 镍等金属配合物并没有检测到荧光峰.     

Self-assembly of zinc chlorophyll derivatives possessing a pyrenyl group at the 17-propionate residue and effects of additional γ-cyclodextrins on their optical properties

Two kinds of zinc 3¹-hydroxy-13¹-oxo-chlorins 1 and 2 possessing a pyrenyl group at the 17-propionate residue, of which the linker length between the chlorin and the pyrene moieties was varied, were synthesised from naturally occurring chlorophyll a, and were self-assembled in an aqueous solution. Both zinc chlorins 1 and 2 exhibited Q_y absorption bands around 720 nm accompanying circular dichroism signals in the Q_y region, indicating that these zinc chlorins could form self-aggregates like chlorosomes of green photosynthetic bacteria. Addition of γ-cyclodextrin into an aqueous solution containing the self-aggregates of zinc chlorin 1 esterified with 1-pyrenylmethanol induced the appearance of excimer emission of the pyrene moieties around 480 nm as well as increased the fluorescence intensities of the pyrene monomers at 378 and 396 nm, while only an increase in fluorescence from the monomeric pyrene moiety was observed in the case of 2 esterified with 4-(1-pyrenyl)butanol. Exogenous γ-cyclodextrin unchanged the spectral features derived from the chlorin moieties of 1 and 2 in the aqueous phase. These suggest that the encapsulation of the pyrenyl groups in the zinc chlorins unchanged their assembling states under the present conditions.     

Characterization of chlorins within a natural chlorin mixture using electrospray/ion trap mass spectrometry

Chlorins in a sedimentary mixture were characterized, without prior isolation of individual components, using electrospray ionization combined with ion trap mass spectrometry. Collision-induced dissociation in the atmospheric sampling interface and multi-step mass spectrometry (i.e. MSⁿ where n ? 2) were used in order to obtain structural information about the macrocycle. Fragmentation pathways are proposed for different macrocycle types based on data from model chlorins. Three unknown chlorins (RMM = 888, 844 and 790) are assigned as having bacteriochlorophyll macrocycle types esterifled to unusual side-chains (i.e. dihydrophytol for the unknown with a bacteriopheophorbide a structure, phytol and an alcohol with a molecular mass of 242 u for the two unknowns with a proposed bacteriopyropheophorbide d structure).     

Integration of Cyanine,Merocyanine and Styryl Dye Motifs with Synthetic Bacteriochlorins

Understanding the effects of substituents on spectral properties is essential for the rational design of tailored bacteriochlorins for light‐harvesting and other applications. Toward this goal, three new bacteriochlorins containing previously unexplored conjugating substituents have been prepared and characterized. The conjugating substituents include two positively charged species, 2‐(N‐ethyl 2‐quinolinium)vinyl‐ (B‐1) and 2‐(N‐ethyl 4‐pyridinium)vinyl‐ (B‐2), and a neutral group, acroleinyl‐ (B‐3); the charged species resemble cyanine (or styryl) dye motifs whereas the neutral unit resembles a merocyanine dye motif. The three bacteriochlorins are examined by static and time‐resolved absorption and emission spectroscopy and density functional theoretical calculations. B‐1 and B‐2 have Q_y absorption bathochromically shifted well into the NIR region (822 and 852 nm), farther than B‐3 (793 nm) and other 3,13‐disubstituted bacteriochlorins studied previously. B‐1 and B‐2 have broad Q_y absorption and fluorescence features with large peak separation (Stokes shift), low fluorescence yields, and shortened S₁ (Q_y) excited‐state lifetimes (~700 ps and ~100 ps). More typical spectra and S₁ lifetime (~2.3 ns) are found for B‐3. The combined photophysical and molecular‐orbital characteristics suggest the altered spectra and enhanced nonradiative S₁ decay of B‐1 and B‐2 derive from excited‐state configurations in which electron density is shifted between the macrocycle and the substituents.     

Constant time interval method for analysis of reaction rate data

In the study of chemical kinetics, many integrated reaction rate equations have the form In [f(A) + a] = bt + c, where a, b, and c are constants and f(A) is some function of the concentration of a reactant (or product) which can be calculated from the data. The left-hand side of this equation cannot be graphed versus time if the constant a is unknown. However, it is shown that f(A2) varies linearly with f(A₁) if A₂ is the concentration of reactant measured at a constant time interval later than A₁. The constants a and b can be determined from the linear graph. A number of specific examples are considered.     

Investigation of the Scope of Heterogeneous and Homogeneous Procedures for Preparing Magnesium Chelates of Porphyrins, Hydroporphyrins, and Phthalocyanines

A simple method has been developed for metalation of porphyrinic compounds under homogeneous conditions at room temperature using a stable ethereal solution of MgI(2) and N,N-diisopropylethylamine. A previously developed heterogeneous procedure employs a mixture of a magnesium halide and a nonnucleophilic amine in a noncoordinating solvent at room temperature. The scope of the heterogeneous and homogeneous magnesium insertion procedures has been investigated across a family of 19 porphyrinic compounds, including synthetic porphyrins, synthetic or naturally occurring chlorins, and organic-soluble phthalocyanines. The rate of magnesium insertion increased in the series phthalocyanines < chlorins < porphyrins, which parallels the basicity of the ligands. Though phthalocyanines have the smallest core size, the magnesium phthalocyanines were far more stable than magnesium porphyrins to acid-induced demetalation. The heterogeneous method is broadly applicable to porphyrins, chlorins, and phthalocyanines. The homogeneous method is generally slower than the heterogeneous method, though both afford rapid metalation of most porphyrins, including electron-deficient, peripherally coordinating, or facially encumbered meso-substituted tetraarylporphyrins, and the beta-substituted octaethylporphyrin. Chlorin e(6) trimethyl ester and methyl pyropheophorbide a were metalated cleanly under homogeneous but not heterogeneous conditions, while pheophytin a failed with both methods. The homogeneous method failed altogether with phthalocyanines. Several methods in magnesium chemistry have been developed that augment these procedures, including a mild synthesis of tetraphenylchlorin and a streamlined separation of porphyrin, chlorin, and bacteriochlorins based on selective formation of the magnesium chelates. Collectively, these methods should broaden the scope of model systems based on magnesium chelates of porphyrinic compounds.     

Anomalous fluorescence spectra of benz[a]azulene derivatives

The electronic and fluorescence spectra of banz[a]azulene derivatives have been measured. the fluorescence from the second excited singlet state have been observed for these compounds. The fluorescence quantum yields (φ_f) is sensitive to the energy difference between the first excited singlet (S₁) and the second excited singlet state (S₂).     

三苯基咪唑类化合物的合成及其紫外、荧光性质研究

设计合成了四种三苯基咪唑类化合物:4,5-二苯基-2-对甲酰基苯基咪唑(2a),4,5-二(2-硝基苯基)-2-对甲酰基苯基咪唑(2b),N-苄基-4,5-二苯基-2-对甲酰基苯基咪唑(2c)和N-苄基-4,5-二(2-硝基苯基)-2-对甲酰基苯基咪唑(2d),并用FT-IR,NMR和MS进行结构表征.在乙酸乙酯-石油醚溶液中获得了2c的单晶,用X射线单晶衍射法测定了其晶体结构,晶体属于三斜晶系,空间群P1,晶胞参数a=0.73796(15)nm,b=0.90136(18)nm,c=1.6644(3)nm,α=86.87(3)°,β=78.25(3)°,γ=89.94(3)°,V=1.0822(4)nm3,Dc=1.272g/cm3,Z=2,F(000)=436,μ=0.077mm-1,R1=0.0459,wR2=0.1303.研究了四种化合物的紫外与荧光性质,发现官能团硝基与苄基的引入,对其吸收峰和发射峰均有不同程度的影响:在紫外光谱中两种官能团均使吸收峰蓝移;在荧光光谱中苄基使发射峰蓝移而硝基使发射峰红移.测定了2a和2c在不同溶剂中的荧光寿命,其中2a在DMSO中寿命最长,为3.18ns.这些光谱性质为研究其双光子吸收、双光子荧光和非线性光学性质奠定了理论和实验基础.     

Beyond green with synthetic chlorophylls – Connecting structural features with spectral properties

The distinct features of chlorophylls in photosynthesis have led to the formation of numerous derivatives for applications encompassing solar energy conversion, molecular photonics, photodynamic therapy, and molecular imaging. Synthetic chlorins created de novo and bearing a geminal dimethyl group in the reduced ring have proved invaluable for fundamental studies. Four decades of research have led to accumulation of tabulated spectra for > 400 such synthetic chlorins with distinct structural frameworks (17-oxochlorins, 13¹-oxophorbines, chlorinimides) and substituents (alkyl, aryl, ethynyl, phenylethynyl, acetyl, formyl) located at specific (meso, β) positions. In this review, spectral traces (324 absorption, 247 fluorescence) are assembled along with photophysical data including the molar absorption coefficient (ε), fluorescence quantum yield (Φ_f) and singlet excited-state lifetime (τ_s). The review uses the accumulated spectral data derived from chlorins all containing a uniform molecular scaffold to (1) highlight the effects of molecular structure on spectral features, and (2) identify trends including how ε, Φ_f and τ_s vary with wavelength and other features. Use of a common geminal-dimethyl-substituted chlorin scaffold – beginning with no substituents, to one substituent at designated sites, and to 2 or more substituents – provides a systematic Aufbau approach for understanding the absorption spectra of chlorins on a path to and beyond the native chlorophylls. The review provides insights concerning the rational design of potent analogues of Nature’s preeminent red-region absorbers for potential utilization in diverse applications and is aimed at multiple audiences: those interested in spectral properties, tetrapyrrole photophysics, and the molecular design of new chromophores.