Gas phase photo-formation and vacuum UV photofragmentation spectroscopy of tryptophan and tyrosine radical-containing peptides

Tryptophan (Trp(?)) and tyrosyl (Tyr(?)) radical containing peptides were produced by UV laser-induced electron detachment from a suitable precursor. Vacuum ultraviolet (VUV) action spectra of these radical peptides were recorded with synchrotron radiation in the 4.5-16 eV range, from which fragmentation pathways and yields are measured as a function of the VUV photon energy. An enhancement in photofragmentation yields of radical species by 1 order of magnitude with respect to nonradical peptides is demonstrated here for the first time. Photofragmentation spectra are compared with absorption spectra for model chromophores calculated in the frame of the time-dependent density functional theory (TDDFT). A qualitative agreement in the position of bands in the 6-8 eV region is observed between experimental photofragmentation and calculated absorption spectra. Photofragmentation spectra of peptide radicals can be useful to better assess the complex deactivation pathways that occur following the absorption of a VUV photon in biomolecular radical anions.     

Analysis of charge-transfer absorption and emission spectra on an absolute scale: evaluation of free energies, matrix elements, and reorganization energies

The relationship between the absorption and emission spectra of the charge-transfer complexes formed between a series of methyl-substituted benzene donors with 1,2,4,5-tetracyanobenzene as acceptor in 1,2-dichloroethane was examined in detail. The association constants for charge-transfer complex formation and the emission quantum yields for these complexes were used to place the experimental absorption and emission spectra on absolute scales. The simultaneous analysis of these spectra is valid only when the Mulliken two-state model is justified. For several of the complexes included in this study the electron-transfer parameters, including the electronic coupling matrix elements, obtained from the analysis of the individual absorption and emission spectra are in close agreement. The simultaneous analysis of the combined absorption and emission spectra leads to a well-defined set of electron-transfer parameters for these complexes. In other complexes, where the two-state model does not apply because of the influence of localized excited states on the absorption spectrum, analysis of the absorption and emission spectra led to significantly different sets of electron-transfer parameters. It is demonstrated that the electronic coupling matrix elements are a very sensitive indicator of the influence of localized excited states on these spectra.     

Ground and excited states calculations of 7-phenylamino-substituted coumarins

A theoretical calculation of the ground and first excited states of two 7-phenylamino-substituted coumarin compounds are performed. In order to study the effect of phenyl substituted in amino group and fluorine atoms substituted in methyl group, 7-amino-4-methyl coumarin (C120) and 7-amino-4-(trifluoromethyl) coumarin (C151) were also studied. The geometries of the ground state and the first ground state were optimized using density function theory and configuration interaction singles levels of theory. Molecular orbitals (MO) of the ground and first excited states of the four coumarin compounds were obtained to explain the change of the structures. ZINDO and TD-DFT methods with different basis sets were applied to predict the UV absorption spectra. The solvent effect had also been taken into account using self-consistent isodensity polarized continuum model. The predicted spectra are in agreement with the experimental data.     

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.     

Density Functional Theory Study on Organic Dye Sensitizers Containing Bis-dimethylfluorenyl Amino Benzofuran

The geometries, electronic structures, polarizabilities and hyperpolarizabilities, as well as the UV-Vis spectra of the two organic dye sensitizers containing bis-dimethylfluorenyl amino benzofuran were studied via density functional theory （DFT） and time-dependent DFT. The features of electronic absorption spectra were assigned on account of the agreement between the experiment and the calculations. The absorption bands in visible region are related to photoinduced electron transfer processes, and the dimethylfluorenyl amino benzo[b]furan groups are major chromophore that contributed to the sensitization of photo-to-current conversion. The role of vinylene group in geometry, electronic structure and spectra property is analyzed according to the comparative study of the dyes.     

Symmetry forbidden vibronic spectra and internal conversion in benzene

The spectra of symmetry-forbidden transitions and internal conversion were investigated in the present work. Temperature dependence was taken into account for the spectra simulation. The vibronic coupling, essential in the two processes, was calculated based on the Herzberg-Teller theory within the Born-Oppenheimer approximation. The approach was employed for the symmetry-forbidden absorption/fluorescence, and internal conversion between 1(1)A(1g) and 1(1)B(2u) states in benzene. Vibrational frequencies, normal coordinates, electronic transition dipole moments, and non-adiabatic coupling matrix elements were obtained by ab initio quantum chemical methods. The main peaks, along with the weak peaks, were in good agreement with the observed ones. The rate constant of the 1(1)A(1g)← 1(1)B(2u) internal conversion was estimated within the order of 10(3) s(-1). This could be regarded as the lower limit (about 4.8 × 10(3) s(-1)) of the internal conversion. It is stressed that the distortion effect was taken into account both in the symmetry-forbidden absorption/fluorescence, and the rate constants of internal conversion in the present work. The distortion effects complicate the spectra and increase the rate constants of internal conversion.     

High-resolution terahertz spectroscopy of crystalline trialanine: extreme sensitivity to beta-sheet structure and cocrystallized water

High-resolution terahertz absorption spectra (0.06-3 THz) have been obtained at 4.2 K for three crystalline forms of trialanine [H2+-(Ala)3-O-]. The crystal structures differ in their beta-sheet forms (parallel vs antiparallel) and in their water composition (hydrated vs dehydrated antiparallel beta-sheet). The spectra are nearly vibrationally resolved, with little absorption below 1 THz. In sharp contrast to observations made in the mid-IR region, the spectral patterns of all three forms are qualitatively different, illustrating the extreme sensitivity to changes in the intermolecular hydrogen-bonding networks that stabilize peptide crystals. Predictions obtained from a classical force field model (CHARMM) and density functional theory (DFT/PW91) for periodic solids are compared with the X-ray structural data and the terahertz absorption spectra. In general, the results for the parallel beta-sheet are in better agreement with experiment than those for the antiparallel beta-sheet. For all three structures, however, most hydrogen bond distances are underestimated at both levels of theory, and the predicted absorption features are significantly red-shifted for the two antiparallel beta-sheet structures. Moreover, the nuclear motions predicted at the two levels of theory are qualitatively different. These results indicate that the PW91 functional is not sufficient to treat the weak intersheet hydrogen bonding present in the different beta-sheet forms and strongly suggest the need for improved force field models that include three-atom hydrogen-bonding terms for periodic solids.     

Effect of substituents on the absorption properties of three pyridylindolizine derivatives: A DFT and TDDFT study

Ground state properties and the UV–Vis absorption spectra of three recently synthesized pyridylindolizine derivatives have been studied by using density functional theory (DFT) and its time-dependent counterpart TDDFT. Performances of the two widely used hybrid functionals, B3LYP and PBE0, and of four different basis sets have been compared. The two functionals yield absorption spectra which have very similar shapes and characteristics but the excitations calculated with PBE0 are obtained at slightly shorter wavelengths. Basis sets affect the appearances of the calculated absorption spectra only little. Independent of the solvent polarity, simulation of the solvent effects by COSMO induces only slight changes into the ground state properties compared to those calculated in the gas-phase and into the absorption spectra.     

Terahertz spectroscopy of enantiopure and racemic polycrystalline valine

Experimental and computational THz (or far-infrared) spectra of polycrystalline valine samples are reported. The experimental spectra have been measured using THz time-domain spectroscopy. Spectra of the pure enantiomers, both D and L, as well as the dl racemate have been taken at room temperature and low temperature (78 K). The spectra of the pure D and L enantiomers are essentially identical, and they are markedly different from the DL racemate. In addition, a temperature-dependent study of L-valine was undertaken in which the absorption maxima were found to red shift as a function of increasing temperature. The vibrational absorption spectra (frequencies and intensities) were calculated using the harmonic approximation with the Perdew-Burke-Ernzerhof (PBE) functional, localized atomic orbital basis sets, and periodic boundary conditions. The calculated and experimental spectra are in good qualitative agreement. A general method of quantifying the degree to which a calculated mode is intermolecular versus intramolecular is demonstrated, with the intermolecular motions further separated into translational versus rotational/librational motion. This allows straightforward comparison of spectra calculated using different basis sets or other constraints.     

Fluorescence properties of organic dyes: quantum chemical studies on the green/blue neutral and protonated DMA-DPH emitters in polymer matrices

The absorption and fluorescence spectra of the green emitter DMA-DPH {1-[4-(dimethylamino)phenyl]-6-phenylhexa-1,3,5-triene} and its protonated blue-emitter form have been studied theoretically through time-dependent density functional theory (TD-DFT) and resolution-of-identity 2nd order perturbative coupled cluster (RI-CC2) calculations with basis sets up to augmented triple-ζ quality, in the gas phase and in solvents of different polarity. These systems dispersed in a polymer matrix are of interest for applications in organic light emitting diode devices (OLEDs). Calculations show that the observed absorption and emission spectra correspond to transitions between the S(0) and S(1) states, in both systems. The nature and characteristics of these transitions are discussed. Excellent agreement with experimental data is obtained, both for absorption and emission, provided that the state-specific polarized continuum model (SS-PCM) method is employed for the inclusion of the solvent.     

Unsaturated surface in CO saturation

In this paper, density functional theory calculations are used to address the puzzle of CO saturation on Fe(100). Through a comprehensive modeling of possible local configurations, we would be able to figure out a structural model for the CO‐saturated Fe(100). The structural model is featured by forming a local structural motif of coupled on‐top and hollow CO molecules. In this model, the on‐top‐bonded CO molecules pertain to critical couplings in the next neighbor spacing, which exclude all couplings below and above the next neighbor spacing. Rather than forming tilted on‐top CO on the surface, the critical couplings align the on‐top CO molecules in the perpendicular orientation. The new model with the coverage of 0.5 ML yields even better X‐ray emission and absorption spectra calculated by using density functional theory and shows consistent agreement with all previous experiments. Copyright © 2017 John Wiley & Sons, Ltd.     

N-K near-edge x-ray-absorption fine structures of acetonitrile in gas phase

The dynamic processes of N(1s) core-hole excitation in gas-phase CH3CN molecule have been studied at both Hartree-Fock and hybrid density-functional theory levels. The vibrational structure is analyzed for fully optimized core-excited states. Frank-Condon factors are obtained using the linear coupling model for various potential surfaces. It is found that the vibrational profile of the N-K absorption can be largely described by a summation of two vibrational progressions: a structure-rich profile of nu(CN) stretching mode and a large envelope of congestioned vibrational levels related to the strong (-C-CN) terminal bending bond. Excellent agreement between theoretical and experimental spectra is obtained.     

SPECTROSCOPY OF CHLOROPHYLL IN BIOLOGICAL AND SYNTHETIC SYSTEMS*

Abstract. –This review discusses recent spectroscopic studies aimed at discovering the structure, orientation, and function of chlorophyll in vivo. In plant membranes there appear to be at least two distinct types of chlorophyll a. The greater part, over 99%, is antenna chlorophyll which absorbs and transfers radiant energy to a few specialized chlorophyll molecules in a reaction center where the actual charge separation occurs. A dimer-oligomer model for antenna chlorophyll has been proposed on the basis of comparative studies of the absorption spectra of chlorophyll in various dry solvents and in vivo. Unfortunately a similarity between essentially structureless broad spectra is very weak evidence for their original identity. Also the requirement of an anhydrous environment for most of the chlorophyll in biological material is an unlikely postulate. A cross-linked, linear polymer model of chlorophyll in vivo has also been proposed. Recent Resonance Raman spectroscopic results appear to rule out, in large part, either polymer model and once again suggest that it is the various attachments of chlorophyll to proteins which determine its function as antenna pigment in vivo. Circular dichroism measurements of chlorophyll in various plant materials have also led to the conclusion that antenna chlorophyll has strong interaction with protein. However, some doubt still exists as to the interpretation of these CD results. New studies of fluorescence, polarized fluorescence and Resonance Raman spectroscopy of various plant species corroborate the original proposition, based upon deconvolution of absorption spectra, that antenna chlorophyll occurs in vivo in at least five discrete pools, and that each pool is likely to be located in the same environment in different plants. A new model-systems approach to simulating chlorophyll in vivo has come through the use of lipid bilayers and liposomes. Charge transfer has been observed between chlorophyll in a lipid phase and phycobiliproteins or cytochrome c. The most promising, newly synthesized model for the reaction center, P700, is a covalently bound dimeric derivative of pyrochlorophyllide a. Its properties are similar to P700 in several respects except for reversible photooxidation which has not yet been observed. By detergent treatments chlorophyll-protein complexes having about 20–40 chlorophyll a molecules for every P700 have been isolated from different plants, and their spectroscopic properties are under investigation in several laboratories. The several hypotheses to explain the shape of the oxidized minus reduced absorption difference spectrum of P700 have not yet been reconciled. The nature of the photosystem II reaction center chlorophyll, P680, is also a subject of active investigation. Its absorption difference spectrum appears to have two kinetic components.     

A DFT/TDDFT study of the structural and spectroscopic properties of Al(III) complexes with 4-nitrocatechol in acidic aqueous solution

The complexation of 4-nitrocatechol in aqueous solution at pH 5 has been studied by molecular spectroscopy combined with quantum chemical calculations. In these physico-chemical conditions, the formation of the two complexes [4ncatAl(H₂O)₄]⁺ and [(4ncat)₂Al(H₂O)₂]⁻ has been highlighted. The electronic absorption spectra of the 1:1 and 1:2 complexes of Al(III) with 4-nitrocatechol have been computed using the time-dependent density functional theory and the polarizable continuum model. It turns out that the 6-311+G(d,p) basis set provides a good agreement between experimental and theoretical absorption spectra. This good agreement has allowed the determination of the preferential conformation of the 1:2 complex in aqueous solution. A complete assignment of the UV–Vis absorption and Raman spectra of the complexes has been proposed.     

Experimental and theoretical study of two new pyrazoline derivatives based on dibenzofuran

Two novel pyrazoline derivatives, named 2,8-bis(1,3-diphenyl-pyrazoline-5-yl)dibenzofuran (A) and 2,8-bis(1-(4-bromophenyl)-3-phenyl-pyrazoline-5-yl)dibenzofuran (B), were synthesized and characterized by elemental analysis, NMR, MS and thermogravimetric analysis. The absorption and emission spectra of them were determined by experimental methods in different polar solvents and were computed using the density functional theory (DFT) and the time-dependent density functional theory (TDDFT) at the same time. The calculated absorption and emission wavelengths are in good agreement with the experimental data. The fluorescence quantum yields and fluorescence lifetimes of them in different polar solvents were studied by means of steady state and time resolved fluorescence. The calculated reorganization energy for hole and electron indicates that the two compounds are in favor of hole transport than electron transport. The results show the two compounds present high fluorescence quantum yields and excellent thermal stability. It makes them of great interest as novel fluorescent probes and optoelectronic materials.     

High level ab initio study of the structure and vibrational spectra of HO(2)NO(2)

A high-level ab initio study has been performed on the conformational structure and vibrational spectra of HO(2)NO(2). Calculations carried out with coupled-cluster methods using a series of Pople and Dunning basis sets reveal that there is a significant basis set dependence on the predicted ab initio structure. Higher angular momentum basis sets are shown to be necessary in order to bring the calculated structure into agreement with experimental rotational constants. Harmonic vibrational frequencies of HO(2)NO(2) are computed at the CCSD(T)/aug-cc-pVTZ level of theory while the corresponding vibrational anharmonicities are calculated at the MP2/cc-pVTZ level. In addition, the absorption cross sections of OH stretching overtones in HO(2)NO(2) are calculated using a dipole function computed at the QCISD level of theory and found to be in good agreement with the available experimental data.     

Jet-cooled laser spectroscopy of the cyclohexoxy radical

The laser-induced fluorescence and laser-excited dispersed fluorescence spectra of the cyclohexoxy radical has been observed under two sets of free-jet-cooling conditions, characterized by rotational temperatures of approximately 1 and 100 K. Although five conformers of cyclohexoxy are possible, it appears that all presently observed spectral bands can be accounted for by a single one. All cold spectral bands are assigned to the B-X electronic transition of the cyclohexoxy radical. Transitions to both a' and a" B state vibrational levels are observed and allowed due to a substantial pseudo-Jahn-Teller effect in the X state. Hot bands are also observed, which we attributed to transitions to the B state from the low-lying A electronic state. Analysis of the spectra yields vibrational frequencies for the X, A, and B states as well as the energy separations of their vibrationless levels.     

Interactions between frenkel excitons. I. Formalism and preliminary results

For the tightest-bound Frenkel excitons a many-particle hamiltonian is adopted which includes terms representing interactions between the excitons. The parameters of the model are the excitation energy of an isolated localized excitation, the excitation-transfer matrix elements, and the interaction energies. Several special cases, involving particular relations between the latter two sets of parameters, are treated qualitatively. Equations are translated into the language of spin-$\text{1}\text{2}$ lattices, so that use may be made of the results of that theory. Favorable conditions for observation of polyexcitons and of phase transition to a liquid of excitons are discussed. A standard formalism for the determination of absorption and emission spectra and of their moments is adapted to the present problem. Possible generalizations of the model are briefly discussed.     

PHOTOPHYSICAL BEHAVIOUR OF 5-METHOXYPSORALEN IN DIOXANE-WATER MIXTURES

Abstract— Triplet-triplet absorption spectra, intersystem crossing quantum yields, fluorescence lifetimes, and fluorescence quantum yields of 5-methoxypsoralen (5MOP) in dioxane-water mixtures are reported. The fluorescence and triplet formation quantum yields depend strongly on the water content in the mixtures, increasing up to maximum values which are, respectively, twentyfold and fivefold larger than in dioxane and then decreasing. This behaviour is essentially due to the variation of the internal conversion rate constant. With these solvent mixtures it is possible to emulate the dielectric response of 5MOP photophysical parameters in other media, such as in biological model systems and in human blood lipoproteins. The biological importance of these results is discussed.