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Ab initio DFT computations reveal that the essential structural and photophysical features of the conjugated π-electron system of retinal and carotenoids are dictated by "innocent" methyl substituents. These methyl groups shape the conformation and symmetry of the isoprenoid chromophores by causing a sigmoidal distortion of the polyene skeleton and increasing its flexibility, which facilitates fitting to their binding pockets in proteins. Comparison of in vacuo conformations of the chromophores with their native (protein-bound) conformations showed, surprisingly, that the peripheral groups and interactions with the protein environment are much less significant than the methyl side groups in tuning their structural features. The methyl side groups also contribute to a loss of symmetry elements specific to linear polyenes. In effect, the symmetry-imposed restrictions on the chromophore electronic properties are disabled, which is of tremendous relevance to their photophysics. This is evidenced by their non-negligible permanent dipole moments and by the simulated and experimentally measured circular dichroism spectra, which necessarily reflect the chirality of the conjugated π-electron system.

The aim of this work is the verification of symmetry effects on the electronic absorption spectra of carotenoids. The symmetry breaking in cis-β-carotenes and in carotenoids with nonlinear π-electron system is of virtually no effect on the dark transitions in these pigments, in spite of the loss of the inversion center and evident changes in their electronic structure. In the cis isomers, the S2 state couples with the higher excited states and the extent of this coupling depends on the position of the cis bend. A confrontation of symmetry properties of carotenoids with their electronic absorption and IR and Raman spectra shows that they belong to the C1 or C2 but not the C2h symmetry group, as commonly assumed. In these realistic symmetries all the electronic transitions are symmetry-allowed and the absence of some transitions, such as the dark S0 → S1 transition, must have another physical origin. Most likely it is a severe deformation of the carotenoid molecule in the S1 state, unachievable directly from the ground state, which means that the Franck-Condon factors for a vertical S0 → S1 transition are negligible because the final state is massively displaced along the vibrational coordinates. The implications of our findings have an impact on the understanding of the photophysics and functioning of carotenoids.

The chapter gives an overview about chlorophylls involved in oxygenic photosynthesis and summarizes the most recent findings about these key photosynthetic pigments. First, a general description of structural, stereochemical and photophysical features of chlorophylls is given, as this is relevant to their functioning. Next, the details of the electronic structure and the mechanisms contributing to fine tuning of chlorophylls in photosynthetic apparatus are discussed, including the roles of conservative structural elements of these molecules. Briefly, also the use and results of quantum chemical approaches are described. Further, the biosynthesis and biodegradation of chlorophylls is shortly reviewed, followed by a survey of the photosensitizing and photoprotective functions of chlorophylls, the commercial and therapeutic applications of the pigments and their impact on animal organisms.

In carotenoids, by analogy to polyenes, the symmetry of the π-electron system is often invoked to explain their peculiar electronic features, in particular the inactivity of the S 0 → S 1 transition in one-photon excitation. In this review, we verify whether the molecular symmetry of carotenoids and symmetry of their π-electron system are supported in experimental and computational studies. We focus on spectroscopic techniques which are sensitive to the electron density distribution, including the X-ray crystallography, electronic absorption, two-photon techniques, circular dichroism, nuclear magnetic resonance, Stark and vibrational spectroscopies, and on this basis we seek for the origin of inactivity of the S 1 state. We come across no experimental and computational evidence for the symmetry effects and the existence of symmetry restrictions on the electronic states of carotenoids. They do not possess an inversion centre and the C 2h symmetry approximation of carotenoid structure is by no means justified. In effect, the application of symmetry rules (and notification) to the electronic states of carotenoids in this symmetry group may lead to a wrong interpretation of experimental data. This conclusion together with the results summarized in the review allows us to advance a consistent model that explains the inactivity of the S 0 → S 1 transition. Within this model, S 1 is never accessible from S 0 due to the negative synergy of (i) the contributions of double excitations of very low probability, which elevate S 1 energy, and (ii) a non-verticality of the S 0 → S 1 transition, due to the breaking of Born–Oppenheimer approximation. Certainly, our simple model requires a further experimental and theoretical verification.

High pressure in combination with optical spectroscopy was used to gain insights into the interactions between Mg(2+), Zn(2+), and Ni(2+) ions and macrocyclic ligands of porphyrinoid type. In parallel, the central metal ion-macrocycle bonding was investigated using theoretical approaches. The symmetry properties of the orbitals participating in this bonding were analyzed, and pigment geometries and pressure/ligation effects were computed within DFT. Bacteriopheophytin a was applied as both a model chelator and a highly specific spectroscopic probe. The analysis of solvent and pressure effects on the spectral properties of the model Mg(2+), Zn(2+), and Ni(2+) complexes with bacteriopheophytin a shows that various chemical bonds are formed in the central pocket, depending on the valence configuration of the central metal ion. In addition, the character of this bonding depends on symmetry of the macrocyclic system. Since in most cases it is not coordinative bonding, these results challenge the conventional view of metal ion bonding in such complexes. In (labile) complexes with the main group metals, the metal ion-macrocycle interaction is mostly electrostatic. Significantly, water molecules are not preferred as a second axial ligand in such complexes, mainly due to the entropic constraints. The metal ions with a closed d shell may form (stable) complexes with the macrocycle via classical coordination bonds, engaging their p and s orbitals. Transition metals, due to the unfilled d shell, do form much more stable complexes, because of strong bonding via both coordination and covalent interactions. These conclusions are confirmed by DFT computations and theoretical considerations, which altogether provide the basis to propose a consistent and general mechanism of how the central metal ion and its interactions with the core nitrogens govern the physicochemical properties of metalloporphyrinoids.

In the Ni-substituted chlorophylls, an ultrafast (

Modular photosynthetic LH1 complex is applied as a model system to investigate the thermodynamics of a self-assembling membrane protein and the effects of cosolvents and cofactor (carotenoid) on the process. Native chromophores of LH1, bacteriochlorophyll, and carotenoid are excellent intrinsic spectroscopic reporter molecules. Their presence allows us to follow the association of transmembrane helices of LH1, without the use of any external markers, by electronic absorption/emission and circular dichroism. Furthermore, the assembly correctness can be monitored by the intracomplex energy transfer. Both the cosolvent and carotenoid markedly affect DeltaH degrees and DeltaS degrees associated with the complex formation in detergent, but the driving force of the process remains almost constant due to an efficient enthalpy-entropy compensation in the system. In the absence of cosolvent and cofactor, the energy of interactions between transmembrane helices in LH1 equals -580 kJ/mol. DeltaH degrees drastically increases upon the addition of acetone (-1160 kJ/mol) and carotenoid (-1900 kJ/mol), whereas DeltaS degrees lowers from +1.5 kJ/mol.K to -0.4 kJ/mol.K and to -2.6 kJ/mol.K, respectively. The stabilization of the ensemble by cofactor seems to be due to the pi-pi stacking of aromatic residues of LH1 polypeptides with the carotenoid pi-electron system. The cosolvent, lowering the medium permittivity and thus enhancing helix-helix interactions, has an ordering effect on the system (DeltaS degrees0). This effect of cosolvent on DeltaH degrees and DeltaS degrees of association of transmembrane helices is relevant for crystallization of membrane proteins, as it explains in thermodynamic terms the action of amphiphiles used for crystallization of membrane proteins in the micellar phase.

The electronic structure of the low-energy states of 1,4,5,8-naphthalenetetracarboxy diimide ( 1 ) is investigated in terms of CASSCF method. At this level of approximation the Franck–Condon (FC) parameters were evaluated for the 13 totally symmetric modes of ( 1 ) molecule in its dipole-allowed low-energy 1 1 B 2 u and 1 1 B 3 u electronic states. These parameters are then employed to simulate the vibrational structures of absorption and fluorescence spectra of N , N ′ -dibutyl ( 2 ) and N , N ′ -bis-hydroxypropyl ( 3 ) derivatives of naphthyl diimides measured in the region corresponding to the low-energy 1 1 A g → 1 1 B 2 u and 1 1 A g → 1 1 B 3 u overlapping transitions.

The absorption and circular dichroism (CD) spectra of (-)-2,2'-dimethyl-4,5-(1-naphthyl)-1,3-dioxolane (DND) were studied in the energy region 30,000 cm(-1) to 50,000 cm(-1). The DND ketal is treated as a naphthalene dimer and its spectra are interpreted in terms of a vibronic dimer model which includes the (1)L(a) and (1)B(b) states of the naphthalene chromophore. To fix the most stable conformation of DND molecule, the MNDO/AM1, RHF/6-31G, and SVWN5, BPW91 methods are employed with 6-31G and 6-31G(d',p') basis sets. All the methods are shown to yield the DND geometry that is entirely consistent with the CD and absorption spectra studied.

The absorption and circular dichroism spectra of PCP (peridinin–chlorophyll a protein) light-harvesting complexes from Glenodiniumsp. and Gonyaulaxpolyedra are studied in terms of vibronic coupling theory. Analysis based on a tetramer model allows the determination of the relative positions of peridinin molecules in the PCP complexes studied. The tetrameric arrangementof four peridinins around the chlorophyll a is suggested to favour the efficient transfer of energy from the peridinin to thechlorophyll. The simple arguments presented suggest that the energy transfer from peridin to chlorophyll might occur from theΨ1± states of the peridinin tetramer to the Bx, and By states of the chlorophyll a.

Theoretical analysis of the vibrational magnetic moments for the four T 1u fundamental vibrational states of the C 60 fullerene molecule is reported. An attempt to determine these moments is made in terms of a theory which includes both mechanical and vibronic contributions. At this level the theory leads to magnetic moments which are consistent in sign and relative magnitude with those measured for ν 3 =1183 cm −1 and ν 4 =1430 cm −1 vibrations of C 60 using magnetic vibrational circular dichroism. Predictions for the lower energy vibrations at ν 1 =528 cm −1 and ν 2 =577 cm −1 are also provided. The moments of these latter transitions appear to arise almost totally from the mechanical (ground state) terms in the theory while those of higher energy modes have both vibronic and mechanical contributions. For the ν 4 vibration the absolute magnitude of the combined vibronic and nuclear contributions was found to be larger than found in MVCD experiment. This may be due to the severe approximations implicit in the SCFPPP-CI method used.

The theoretical of magnetic vibrational circular dichroism (MVCD) A terms is reported for the degenerate ν9 and ν10 vibrations of sym-C6H3X3 (X=D, Cl, Br) molecules. An attempt to determine the A1/D0 ratios for A′1→E′(ν9) and A′1→E′(ν10) fundamentals is made in terms of a theory which includes both mechanical and vibronic contributions to MVCD and absorption spectra.

A vibronic theory which includes multimode and multistate effects is developed to study magnetic vibrational circular dichroism (MVCD) and absorption spectra for molecular systems with fourfold symmetry. The MVCD and absorption spectra of the e fundamental transition and its combinations with infrared inactive modes are discussed in some detail to demonstrate the importance of electric and magnetic anharmonicity arising from vibronic coupling. The theory is applied to experimental MVCD spectra for the CuTPP molecule.

Pyrazoloquinolines are highly fluorescent, both in liquid solutions and in the solid state, which makes them good candidates for various optical devices. The aim of the current work is to understand the photochemical behavior of pyrazolo[3,4-b]quinoline (PQ), which is quite complicated since in n-alkane solvents PQ tends to form strong complexes with protic solvent constituents (often present as minor impurities), as well as dimers. Both types of H-bond complexes were studied systematically by temperature-dependent conventional absorption and fluorescence spectroscopy; the effect of protic solvent constituents was mimicked by varying the ethanol concentration in n-octane in the range from 0.0 to 0.8%. At room temperature the PQ:ethanol association constant was estimated at 80 M-1 and the dimerization constant at 2 x 103 M-1. Dimer formation is enhanced upon lowering the temperature in pure n-alkane down to 220 K, and the fluorescence is strongly reduced since the dimer is nonfluorescent. Surprisingly, when irradiating a frozen sample for several minutes at very low temperatures (

A method of subtraction and normalization of IR spectra (MSN-IR) was developed and successfully applied to extract mathematically the pure paint spectrum from the spectrum of paint coat on different bases, both acquired by the Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) technique. The method consists of several stages encompassing several normalization and subtraction processes. The similarity of the spectrum obtained with the reference spectrum was estimated by means of the normalized Manhattan distance. The utility and performance of the method proposed were tested by examination of five different paints sprayed on plastic (polyester) foil and on fabric materials (cotton). It was found that the numerical algorithm applied is able – in contrast to other mathematical approaches conventionally used for the same aim – to reconstruct a pure paint IR spectrum effectively without a loss of chemical information provided. The approach allows the physical separation of a paint from a base to be avoided, hence a time and work-load of analysis to be considerably reduced. The results obtained prove that the method can be considered as a useful tool which can be applied to forensic purposes.

The vibronic dimer model is formulated in order to study the absorption and circular dichroism (CD) spectra of (1 R ,2 R )-1,2-bis-( N ′ -cyclohexyl-1 ′ ,4 ′ ,5 ′ ,8 ′ -naphthalenetetracarboxydiimido) cyclohexane (NTD) molecule treated as a dimer with the 1,4,5,8-naphthalenetetracarboxydiimide chromophores. To find out the most stable conformation of the NTD molecule the RHF/STO-3G and the density functional B3LYP/3-21G methods are employed. The results of conformational analysis are shown to be entirely consistent with the experiment. In particular it is shown that the CD and absorption spectra of the NTD dimer observed in the excitation region 25,000–35,000 cm −1 are correctly reproduced by the vibronic dimer model applied with the model parameters directly obtained from CASSCF/5π4n5π * computations. In the debatable region the CD of the NTD dimer results from the 1 1 A g →1 1 B 2 u and 1 1 A g →1 1 B 3 u overlapping transitions in the chromophore. Since that later transition is hidden in the vibronic manifold of the former, the effect of the hidden state on the chiroptical properties of the NTD molecule is discussed in some details.

Chiral properties of peridinin-chlorophyll-protein (PCP) light-harvesting complexes are studied in terms of vibronic dimer theory previously applied to study certain structural aspects of α-crustacyanin pigments. On the base of CD spectra it is shown that the peridinin dimer acts as a chiral group in PCP complexes and its geometrical structure is such that the peridinin monomers cannot be coplanar. Certain observations concerning the energy transfer process in PCP complexes in vivo are also made.

In order to gain control over the assembly and functioning of photosynthetic antenna, we have developed methods to manipulate pigment composition of bacterial LH1 complexes via their reconstitution with modi ed bacteriochlorophylls or carotenoids, major photoactive cofactors of these antennae. In the present work we show how the reconstitution and pigment exchange approach is applied to control structural and functional parameters of LH1 and its subunits. The size of the subunits and the energy of the rst excited singlet state can be controlled via the use of detergent while the thermodynamics of LH1 formation can be modi ed using carotenoids and/or a co-solvent. Carotenoids a ect the e ciency of the intracomplex energy transfer, while the replacement of native bacteriochlorophyll a with its Ni-substituted analog allows one to control the excited state properties of LH1. These results show that LH1 is a very promising model system applicable for the design of bio-inspired device performing solar energy conversion.