FLUORESCENCE AND CIRCULAR DICHROISM STUDIES ON THE PHYCOERYTHROCYANINS FROM THE CYANOBACTERIUM

Two phycoerythrocyanin (PEC) fractions have been obtained from the phycobilisomes of the cyanobac-terium Westiellopsis prolifica ARM 365. They have been characterized by absorption, fluorescence and circular dichroism spectroscopy. One of them is spectroscopically similar to a PEC trimer known from other organisms. Whereas efficient energy transfer from its violin (α-84) to the cyanin (β-84, 155) chromophores is efficient in the trimer (αβ it is impeded after dissociation to the monomer (α,β). A second fraction of PEC which we earlier termed PEC(X) (Maruthi Sai et al., Photochem. Photobiol. 55 ,119–124, 1992), exhibited the spectral properties similar to that of the α-subunit of PEC from Mastigocladus laminosus. With this highly photoactive fraction, the circular dichroism spectra of the violobilin chromophore in both photoreversible states were obtained.     

Circular dichroism, optical rotation and absolute configuration of 2-cyclohexenone-cis-diol type phenol metabolites: redefining the role of substituents and 2-cyclohexenone conformation in electronic circular dichroism spectra

The absolute configurations of 2-cyclohexenone cis-diol metabolites resulting from the biotransformation of the corresponding phenols have been determined by comparison of their experimental and calculated circular dichroism spectra (TDDFT at the PCM/B2LYP/Aug-cc-pVTZ level), optical rotations (calculated at the PCM/B3LYP/Aug-cc-pVTZ level) and by stereochemical correlation. It is found that circular dichroism spectra and optical rotations of 2-cyclohexenone derivatives are strongly dependent on the ring conformation (M or P sofa S(5) or half-chair), enone non-planarity and the nature and positions of the hydroxy and alkyl substituents. The effect of non-planarity of the enone chromophore, including the distortion of the C=C bond, is determined for the model structures by TDDFT calculations at the PCM/B2LYP/6-311++G(2d,2p) level. Non-planarity of the C=C bond in the enone chromophore is commonly encountered in 2-cyclohexenone derivatives and it is a source of significant rotatory strength contribution to the electronic circular dichroism spectra. It is shown that the two lowest-energy transitions in acrolein and 2-cyclohexenone and its derivatives are n(C=O)-π(C=O)* and π(C=C)-π(C=O)*, as expected, while the shorter-wavelength (below 200 nm) transitions are of more complex nature. In 2-cyclohexenone and its alkyl derivatives it is predominantly a mixture of π(C=C)-π(C=C)* and π(C=C)-σ* transitions, whereas the presence of hydroxy substituent results in a dominant contribution due to the n(OH)-π(C=O)* transition. A generalized model for correlation of the CD spectra of 2-cyclohexenones with their structures is presented.     

Circular dichroism spectra and absolute configuration of some aryl methyl sulfoxides

The absorption and circular dichroism (CD) spectra of three aryl sulfoxides, i.e. (-)-(S)-1-naphthyl methyl sulfoxide, (S)-1, (-)-(S)-1-(2-methyl)naphthyl methyl sulfoxide, (S)-2 and (-)-(S)-9-phenanthryl methyl sulfoxide, (S)-3, have been interpreted by means of the coupled oscillator model formulated by DeVoe. Theoretical spectra have been calculated starting from input geometries provided by molecular mechanics (MMX) calculations and by employing standard spectroscopic parameters to describe the allowed transitions of the aromatic and the sulfoxide chromophores. The satisfactory agreement between the predicted and experimental spectra allows us to confirm the configurational assignment of these compounds as (-)/(S). The analysis of CD spectra, affording the right assignment of the absolute configuration (AC) of the alkyl aryl sulfoxides, then offers a practical alternative to the more complex vibrational circular dichroism spectroscopy and ab initio optical rotation calculation techniques that have been used very recently to assign the AC of (-)-2 and (-)-3.     

Inherent chirality dominates the visible/near-ultraviolet CD spectrum of rhodopsin

The visible (alpha) and near-UV (beta) CD bands of rhodopsin have been studied extensively, but their source(s) have never been definitively established. Do they result from the intrinsic chirality of the polyene chromophore of the protonated Schiff base of retinal (retPSB) or from the coupling of the transitions of this chromophore with those of protein groups? We have calculated the contributions of these two mechanisms to the CD of rhodopsin. The intrinsic CD of the retPSB chromophore was calculated using time-dependent density functional theory (TDDFT) and, for comparison, the semiempirical ZINDO method. First-order perturbation theory was used to calculate the effects of coupling of the retPSB transitions with the pi pi* transitions of the aromatic chromophores and the pi pi* and n pi* transitions of the peptide groups in rhodopsin. Calculations were performed for eight structures based upon the two molecules in the asymmetric unit of four crystal structures. The most reliable results were obtained from TDDFT calculations on the structure of Okada et al. (J. Mol. Biol. 2004, 342, 571), PDB 1U19. Averaging over the two molecules in the asymmetric unit, the intrinsic rotational strengths are 0.62 +/- 0.00 DBM (Debye-Bohr magneton) and 0.90 +/- 0.03 DBM for the alpha- and beta-bands, respectively. The contributions from coupling with protein groups are, respectively, -0.32 +/- 0.05 and -0.01 +/- 0.03 DBM. Our results show that the visible/near-UV CD bands of rhodopsin are determined by the intrinsic chirality of the retPSB chromophore and that the contributions of coupling with the protein are significantly smaller for the alpha-band and negligible for the beta-band.     

Self-assembly of oligothiophene chromophores by m-calix[3]amide scaffold

m-Calix[3]amides carrying the bithiophene chromophore (BTC3A) and terthiophene chromophore (TTC3A) were synthesized by the cyclic trimerization of m-aminobenzoic acid esters for the purpose of the control and understanding of the self-assembly of oligothiophene chromophores. Polymers and model compounds were also prepared for comparison. From the (1)H NMR experiments, cyclic trimer BTC3A showed the syn/anti equilibrium in solution, and the syn/anti conformer ratio (76/24 in CDCl(3)) was influenced by the solvent character. Namely, the population of the syn conformer was lowest (70%) in THF-d(8) and was highest (86%) in CDCl(3)/CD(3)OD (1/1 in volume). On the other hand, the population of the syn conformer of cyclic trimer TTC3A was high (84%) even in CDCl(3). In a CHCl(3) solution of cyclic trimer BTC3A, the absorption maximum (342 nm) blue-shifted and the emission maximum (448 nm) red-shifted compared with those of polymer BTPA and model compound BTM. The solvent character also had an impact on the optical properties of cyclic trimer BTC3A. The red-shifted emission maximum (481 nm) of cyclic trimer BTC3A in CH(3)OH indicated the interaction between three bithiophene chromophores. The emission maxima of cyclic trimer TTC3A (486 nm) demonstrated a small red-shift from model compound TTM (477 nm), and no solvent dependency was observed, unlike cyclic trimer BTC3A.     

First-principles simulation of amide and aromatic side chain ultraviolet spectroscopy of a cyclic dipeptide

By combining time-dependent density functional theory (TDDFT) and molecular dynamics (MD) simulations, we calculate the ultraviolet absorption and circular dichroism (CD) of a cyclic dipeptide, cyclo(L-Pro-D-Tyr), in the 185-300 nm region. The absorption is dominated by the phenol chromophore of tyrosine. The CD spectrum shows both phenol and amide units transitions. A crude coherent two-dimensional ultraviolet spectrum (2DUV) calculated by neglecting the two-excitation states shows a cross-peak between two transitions of the phenol in the tyrosine side chain. Additional cross-peaks between the side chain and the backbone are observed when using a chirality-induced pulse polarization configuration.     

Excited-state absorption and circular dichroism of ruthenium(II) tris(phenanthroline) in the ultraviolet region

Excitation of ruthenium(II) tris(phenanthroline) in the visible region results in the tranfer of an electron from the central atom toward one of the ligands. To probe this excited state, we have performed pump-induced absorption and circular dichroism in the ultraviolet wavelengths, in the intraligand pi-pi* transition region. On top of the bleaching of the ground state transitions, new structures appear in the absorption and CD spectra. Thanks to a classical calculation based on the polarizability theory, we can interpret these features as the result of a strong reduction of the excitonic coupling due to a blue shift of the pi-pi* transition in the reduced ligand accompanied by the onset of new excited-state transitions.     

Towards a correlation of absolute configuration and chiroptical properties of alkyl aryl sulfoxides: a coupled-oscillator foundation of the empirical Mislow rule?

The absorption and circular dichroism (CD) data for a series of alkyl aryl sulfoxides 1-16 of known S configuration have been analyzed. The strong bathochromic effect exerted by the nitro group in the para position of the phenyl sulfoxides indicates that the sulfur atom acts as an electron donor moiety towards the phenyl ring. Such behavior requires a significant 2p(C)-3sp3(S) overlap, and therefore the phenyl (and p-substituted phenyl) sulfoxides 1-12, as well as the 2-naphthyl sulfoxides 15 and 16, must assume a conformation which permits such orbital overlap. The steric effect of the peri hydrogen in 1-naphthyl-substituted compounds 13 and 14 does not allow a conformation of this type, and in these compounds the above-mentioned 2p(C) and 3sp3(S) orbitals are positioned in almost orthogonal planes. This conformational difference is clearly shown by the absorption spectra: compounds 1-12, 15, and 16 show the lowest energy sigma --> sigma* transition of the sulfoxide chromophore at approximately 250 nm, indicating the existence of a conjugated S=O chromophore. In contrast, the corresponding absorption in 13 and 14 occurs at about 200 nm, indicating the presence of an isolated S=O chromophore. The CD spectra of 13 and 14 show a negative, couplet-like feature between 250 and 200 nm. This spectral feature can be interpreted in terms of exciton coupling between the allowed sigma --> sigma* transition of the isolated S=O chromophore at 200 nm and the 1B transition of the naphthalene chromophore. In fact, the Harada-Nakanishi rule predicts a negative CD couplet for an S-configured sulfoxide in the conformation found by UV analysis, as found experimentally. The CD spectrum of 13 is quantitatively reproduced by DeVoe coupled-oscillator calculations, strongly implying that a coupled-oscillator mechanism is operative in determining the optical activity of 13 and 14. This approach has also tentatively been extended to the conjugated sulfoxides 1-12, taking into account the coupling of the benzene chromophore 1La transition with the sigma --> sigma* transition of the S=O chromophore. In this case the Harada-Nakanishi rule also predicts a negative CD couplet for the S-configured sulfoxides, as found experimentally.     

Planar‐Chiral Through‐Space Conjugated Oligomers: Synthesis and Characterization of Chiroptical Properties

Optically active through‐space conjugated oligomers, namely, a dimer, trimer, tetramer, and cyclic trimer, consisting of a planar‐chiral [2.2]paracyclophane skeleton were synthesized. In the ground state, observed similarities in the chiroptical properties of the oligomers were attributed to the equivalent orientations of two adjacent chromophores. In the excited state, the oligomers were folded into a form analogous to a one‐handed helix by photoexcitation. All the compounds in dispersed solution exhibited intense circularly polarized luminescence with relatively large anisotropy factors on the order of 10^?3.     

Enantiopure, monodisperse alleno-acetylenic cyclooligomers: effect of symmetry and conformational flexibility on the chiroptical properties of carbon-rich compounds

A series of enantiopure, monodisperse alleno-acetylenic cyclooligomers were synthesized. The single-crystal X-ray structures of the cyclic trimer and hexamer were resolved, providing insights into the symmetry of these molecules. Electronic circular dichroism (ECD), optical rotatory dispersion (ORD), Raman spectroscopy, and vibrational circular dichroism (VCD) data were analyzed with the aid of theoretical calculations. This multidimensional approach ultimately provided general guidelines that are useful for designing carbon-rich compounds with intense chiroptical properties.     

Synchrotron radiation circular dichroism spectroscopy of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides.

Synchrotron radiation circular dichroism (SRCD) spectra of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides and cyclic derivatives were measured in the vacuum ultraviolet region (down to 168 nm for sugars and 175 nm for adenine derivatives) and at different pH values (3, 6-7, 9-10) and temperatures (between 5 and 45 degrees C). The information content in the VUV region is important since the CD bands strongly depend on the chemical structure of the sugar, the presence and orientation of a phosphate group and the protonation state of adenine. On the other hand, single or double deprotonation of the phosphoric acid group has no influence on the spectra. We assign the vacuum ultraviolet (VUV) CD bands of the nucleoside and nucleotides to be due mainly to n-->pi* transitions in the adenine nucleobase based on a comparison with the absorption spectra. The CD bands of the sugars are due to n(O -->sigma*) transitions and are much smaller than the CD signal from the nucleotides in the VUV region. Bands are assigned to both pyranose and open-chain forms.     

Direct quantum chemical calculation of rotatory strengths of methylpyrrolidones : Model compounds containing a peptide group

CNDO/S method is used to compute the rotatory strengths of L-5-methylpyrrolid-2-one and S-3-methylpyrrolid-2-one, cyclic compounds containing a peptide group. The observed circular dichroism (CD) bands in the regions of 185 and 220 nm corresponded to π → π^* and n → π^* transitions, respectively. The computed rotatory strengths indicate that nonplanarity of pyrrolidone ring makes a substantial contribution to the CD of compounds under consideration. The comparison of computed and experimental rotatory strengths suggests that both compounds have a nonplanar ring conformation.     

Studies of the circular dichroism spectra of dissymmetric Schiff-bases by means of the exciton chirality method

The circular dichroism spectra of some dissymmetrical Schiff-bases derived from condensation of 2 mol salicylaldehyde with 1 mol of a chiral diamine are analyzed in terms of a simple conformational model taking the angle between the aromatic chromophores as a variable. The rotatory strengths of the π→π* transitions are calculated with AM1 molecular orbitals in combination with the dipole-coupling approximation. Calculated CD curves are found to be in reasonable agreement with the experimental CD spectra. Differences in the CD spectra of the Schiff-bases are discussed in relation to variation of the theoretical CD curve of ethylenebis(salicylideneimine) as a function of conformation.     

The optical activity of β,γ-enones in ground and excited states using circular dichroism and circularly polarized luminescence

The circularly polarized luminescence (CPL) and electronic circular dichroism (CD) spectroscopic parameters corresponding to the n←π* and n→π* transitions, respectively, have been calculated for selected β,γ-enones using density functional theory. For the smallest β,γ-enone, (1R,4R)-bicyclo[2.2.1]hept-5-en-2-one (norbornenone), coupled-cluster calculations have also been carried out. The excited-state potential energy surface for three of the five enones studied reveals two minima with different C[double bond, length as m-dash]OC[double bond, length as m-dash]C dihedral angles, and with rotatory strengths of opposite sign. The relative energies of the minima determine the sign of the CPL intensity, which may be the same or opposite as in the CD spectrum, in agreement with experimental data. The results obtained in this first computational study of CPL demonstrate its usefulness as an indicator of excited-state structures of chiral species.     

Excitation and circular dichroism spectra of (-)-(3aS, 7aS)-2-chalcogena-trans-hydrindans(Ch = S, Se, Te): SAC and SAC-CI calculations

The ground and several electronic excited states of (3aS,7aS)-2-chalcogena-trans-hydrindans were calculated by the symmetry adapted cluster (SAC) and SAC-configuration interaction (SAC-CI) methods. Theoretical electronic excitation spectra and natural circular dichroism (CD) spectra were obtained for these compounds, and the calculated spectra showed good agreement with the experimental ones reported by Laur (Proceedings of the Third International Symposium on Organic Selenium and Tellurium compounds, Metz, France, 1979, pp. 219-299). For all the chalcogen compounds, the first singlet excited states are assigned to n-sigma* and the other states are assigned to n-Rydberg in our calculations. It indicates that the spectra for the sulfide, selenide, and telluride are almost regarded as the analogues except for the red shifts of the band positions from the sulfide to the telluride. For the telluride, however, the experimental spectra have shapes that cannot be interpreted by the singlet excitations solely. Our calculations predict the triplet states that account for the spectral shapes, indicating importance of the spin-orbit interaction effects for the accurate reproduction of the experimental spectra of the telluride.     

THE ATTACHMENTS OF PHYCOBILINS TO CYSTEINYL RESIDUES

The attachments of phycobilins to cysteinyl residues have been worked out through the reactions of phycoerytbrobilin dimethyl ester and phycocyanobilin dimethyl ester with cysteine methyl ester and reduced glutathione dimethyl ester respectively. A series of model compounds which carry the same conjugative skeletons as the chromophores in phycobillproteins have been purified anti identified. These compounds are characterized with strong fluorescence emission and circular dichroism effects which appeared weaker for the common bilinoid chromophores. Analyses of the circular dichroism effects of these compounds indicated that the major reaction products of phycobilins with cysteine methyl ester and reduced glutathione dimethyl ester carried the same stereochemical configuration as the chromophores in phvcobilinoroteins     

Computational modeling of the optical rotation of amino acids: a new look at an old rule for pH dependence of optical rotation

The molar rotation of a solution of a natural alpha amino acid is changed in the positive direction by addition of a strong acid. Three decades ago, an attempt to rationalize this old rule, named for Clough, Lutz, and Jirgensons (CLJ), was made by assigning circular dichroism octants for overlapping carbonyl n to pi* transitions. Modern quantum chemical methods allow us to take a new look at this phenomenon. Time-dependent density functional theory was used to model the electronic structure and transitions responsible for CLJ. We show that sector rules originally developed for circular dichroism (CD) can be applied to the optical rotation in this case, but with some restrictions, and with great caution, due to the change of the overall charge of the acids upon protonation and the distortion of the COO- chromophore in the zwitterions. We have prepared sector maps based on first-principles computations to study the correspondence between CD and optical rotation for zwitterionic and protonated l-amino acid chromophores. The CLJ effect is correctly obtained from the computations for all 12 amino acids studied in this work.     

Frenkel‐exciton decomposition analysis of circular dichroism and circularly polarized luminescence for multichromophoric systems

Recently, a method to calculate the absorption and circular dichroism (CD) spectra based on the exciton coupling has been developed. In this work, the method was utilized for the decomposition of the CD and circularly polarized luminescence (CPL) spectra of a multichromophoric system into chromophore contributions for recently developed through‐space conjugated oligomers. The method which has been implemented using rotatory strength in the velocity form and therefore it is gauge‐invariant, enables us to evaluate the contribution from each chromophoric unit and locally excited state to the CD and CPL spectra of the total system. The excitonic calculations suitably reproduce the full calculations of the system, as well as the experimental results. We demonstrate that the interactions between electric transition dipole moments of adjacent chromophoric units are crucial in the CD and CPL spectra of the multichromophoric systems, while the interactions between electric and magnetic transition dipole moments are not negligible. © 2018 Wiley Periodicals, Inc.     

DNA molecular photonics

Synthetic DNA conjugates in which one or both ends of a short duplex is capped by a stilbene chromophore have been prepared and characterized crystallographically. Selective excitation of the chromophore can be used to initiate electron transfer processes in which a nucleobase serves as either an electron donor or an electron acceptor. These processes include hole- and electron injection and hole migration. The dynamics of these processes and its dependence on distance, driving force, and base sequence have been investigated by means of femtosecond time-resolved spectroscopy. Duplexes with identical chromophores at both ends have been used to study both the dynamics of electron transfer processes and exciton coupling between the two chromophores by means of circular dichroism spectroscopy. Duplexes with different chromophores can also be used to study distance dependence of both electron transfer and exciton coupling.     

Circularly Polarized Light Probes Excited-State Delocalization in Rectangular Ladder-type Pentaphenyl Helices

Ladder-type pentaphenyl chromophores have a rigid, planar π-system and show bright fluorescence featuring pronounced vibrational structure. Such moieties are ideal for studying interchromophoric interactions and delocalization of electronic excitations. We report the synthesis of helical polymers with a rigid square structure based on spiro-linked ladder-type pentaphenyl units. The variation of circular dichroism with increasing chain length provides direct evidence for delocalization of electronic excitations over at least 10 monomeric units. The change in the degree of circular polarization of the fluorescence across the vibronic side bands shows that vibrational motion can localize the excitation dynamically to almost one single unit through breakdown of the Born-Oppenheimer approximation. The dynamic conversion between delocalized and localized excited states provides a new paradigm for interpreting circular dichroism in helical polymers such as proteins and polynucleic acids.