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Time-resolved spectroscopy provides the main tool for analyzing the dynamics of excitonic energy transfer in light-harvesting complexes. Inferring the time scales and effective coupling parameters from experimental data requires the development of numerically exact theoretical models. The finite duration of the laser--molecule interactions and the reorganization process during the exciton migration affect the location and strength of spectroscopic signals. We show that the nonperturbative hierarchical equations of motion method captures these processes in a model exciton system, including the charge-transfer state. [ABSTRACT FROM AUTHOR]

The noncovalently bound and structurallyidentical bacteriochlorophyll achromophores in theperipheral light-harvesting complexesLH2 (B800–850) and LH3 (B800–820) from photosyntheticpurple bacteria ensure the variability of the exciton spectra in thenear-infrared (820–850 nm) wavelength region. As a result,the spectroscopic properties of the antenna complexes, such as positionsof the maxima in the exciton absorption spectra, give rise to veryefficient excitation transfer toward the reaction center. In thiswork, we investigated the possible molecular origin of the excitonicallycoupled B820 bacteriochlorophylls in LH3 using femtosecond transientabsorption spectroscopy, deconvolution of steady-state absorptionspectra, and modeling of the electrostatic intermolecular interactionsusing a charge density coupling approach. Compared to LH2, the upperexcitonic level is red-shifted from 755 to 790 nm and is associatedwith an approximate 2-fold decrease of B820 intrapigment coupling.The absorption properties of LH3 cannot be reproduced by only changingthe B850 site energy but also require a different scaling factor tobe used to calculate interpigment couplings and a change of histidineprotonation state. Several protonation patterns for distinct aminoacid groups are presented, giving values of 162–173 cm–1at 100 K for the intradimer resonance interactionin the B820 ring. [ABSTRACT FROM AUTHOR]

Absorption and fluorescence spectral properties of J-aggregates of core-tetrasubstituted perylene bisimide (PBI) dyes have been investigated in the temperature range from 300 to 5 K. A special feature of the present PBI J-aggregates is that, in contrast to classical J-aggregates like that of pseudoisocyanine (PIC), the chromophores are held together not only by van-der-Waals interactions but also by hydrogen bonds. The temperature dependence of the spectral band widths and the Stokes shift for PBI 1aggregates are compared with those for 3,3′-bis-(3-sulfopropyl)-5,5′-dichloro-9-ethylthiacarbocyanine (THIATS) J-aggregates, which have been studied in detail previously (J. Phys. Chem. B2001, 105, 4636−4646). The assemblies of PBI 1possess very broad absorption bands compared to those of THIATS, even at low temperature (5 times broader). We interpret this observation as an indication for a very large level of disorder in the case of PBI 1assemblies. Possible sources of disorder in aggregates of PBI 1are discussed. Despite large quantitative differences, both aggregates show qualitatively the same temperature dependence of the Stokes shift calculated in units of fluorescence bandwidth. The observed temperature dependences are discussed in terms of exciton thermal population of different states of disordered aggregates. Unexpectedly low thermal activation energy of exciton migration is observed for PBI 1aggregates. [ABSTRACT FROM AUTHOR]

Signatures of chemical exchange and spectral diffusion in 2D photon-echo line shapes of molecular aggregates are studied using model calculations for a dimer whose Hamiltonian parameters are stochastically modulated. Cross peaks induced by chemical exchange and by exciton transport have different dynamics and distinguish two models which have the same absorption spectrum (a two-state jump bath modulation model of a dimer and a four-state jump bath model of a single chromophore). Slow Gaussian−Markovian spectral diffusion of a symmetric dimer induces new peaks which are damped as the dipole moment is equilibrated. These effects require an explicit treatment of the bath and may not be described by lower-level theories such as the Redfield equations, which eliminate the bath. [ABSTRACT FROM AUTHOR]

The excited-state behavior of synthetic DNA dumbbells possessing stilbenedicarboxamide (Sa) linkers separated by short A-tracts or alternating A−T base-pair sequences has been investigated by means of fluorescence and transient absorption spectroscopy. Electronic excitation of the Sa chromophores results in conversion of a locally excited state to a charge-separated state in which one Sa is reduced and the other is oxidized. This symmetry-breaking process occurs exclusively via a multistep mechanismhole injection followed by hole transport and hole trappingeven at short distances. Rate constants for charge separation are strongly distance-dependent at short distances but become less so at longer distances. Disruption of the A-tract by inversion of a single A−T base pair results in a pronounced decrease in both the rate constant and efficiency of charge separation. Hole trapping by Sa is highly reversible, resulting in rapid charge recombination that occurs via the reverse of the charge separation process:  hole detrapping, hole transport, and charge return to regenerate the locally excited Sa singlet state. These results differ in several significant respects from those previously reported for guanine or stilbenediether as hole traps. Neither charge separation nor charge recombination occur via a single-step superexchange mechanism, and hole trapping is slower and detrapping faster when Sa serves as the electron donor. Both the occurrence of symmetry breaking and reversible hole trapping by a shallow trap in a DNA-based system are without precedent. [ABSTRACT FROM AUTHOR]

We present the results of time-dependent density functional theory calculations of the optical absorption spectra of synthetic nucleobases and of their hydrogen-bonded and stacked base pairs. We focus on size-expanded analogues of the natural nucleobases obtained through the insertion of a benzene ring bonded to the planar heterocycles (x-bases), according to the protocol designed and realized by the group of Eric Kool (e.g., see:  Gao, J.; Liu, H.; Kool, E.T. Angew. Chem., Int. Ed.2005, 44, 3118, and references therein). We find that the modifications of the frontier electron orbitals with respect to natural bases, which are induced by the presence of the aromatic ring, also affect the optical response. In particular, the absorption onset is pinned by the benzene component of the HOMO of each x-base (xA, xG, xT, xC). In addition, the main trait of the H-bonding interbase coupling is a conspicuous red shift of spectral peaks in the low-energy range. Finally, the hypochromicity, a well-known fingerprint of stacking, is more pronounced in stacked xG−C and xA−T pairs than that in stacked G−C and A−T pairs, an index of enhanced stacking. [ABSTRACT FROM AUTHOR]

A method of simulating two-dimensional infrared spectra accounting for nonadiabatic effects is presented. The method is applied to the amide I modes of a dipeptide. The information necessary to construct the time-dependent Hamiltonian for the system is extracted from molecular dynamics simulations using a recently published ab initio-based model. It is shown that the linear absorption spectrum agrees with experiment only if the nonadiabatic effects are accounted for. The two-dimensional infrared spectrum is predicted for a range of mixing times. It is shown that population transfer between the amide I site vibrations affects the anisotropy at longer mixing times. It is also demonstrated that the population transfer can, to a good approximation, be extracted from the simulated spectra using a procedure that should also be applicable to experimental spectra. [ABSTRACT FROM AUTHOR]

It was recently suggested that liquid water primarily comprises hydrogen-bonded rings and chains, as opposed to the traditionally accepted locally tetrahedral structure (Wernet et al. Science2004, 304, 995). This controversial conclusion was primarily based on comparison between experimental and calculated X-ray absorption spectra (XAS) using computer-generated ice-like 11-molecule clusters. Here we present calculations which conclusively show that when hydrogen-bonding configurations are chosen randomly, the calculated XAS does not reproduce the experimental XAS regardless of the bonding model employed (i.e., rings and chains vs tetrahedral). Furthermore, we also present an analysis of a recently introduced asymmetric water potential (Soper, A. K. J. Phys.:  Condens. Matter2005, 17, S3273), which is representative of the rings and chains structure, and make comparisons with the standard SPC/E potential, which represents the locally tetrahedral structure. We find that the calculated XAS from both potentials is inconsistent with the experimental XAS. However, we also show the calculated electric field distribution from the rings and chains structure is strongly bimodal and highly inconsistent with the experimental Raman spectrum, thus casting serious doubt on the validity of the rings and chains model for liquid water. [ABSTRACT FROM AUTHOR]

Detailed analysis of the vibronic structure in the electronic absorption spectrum of Cs2NaYbF6at temperatures between 10 and 300 K enables the crystal field energy level diagram of Yb3in this cubic host to be deduced. Ultraviolet and visible laser excitation of Cs2NaYbF6, Cs2NaY0.9Yb0.1F6, and Cs2NaHo0.99Yb0.01F6give spectral features mainly due to Yb3being situated at a range of defect sites. The 4f13crystal field analyses of octahedral YbX63-(X F, Cl, Br) systems show the expected trends in parameter values, but the energy level fits are poor. Inclusion of the interaction with the charge-transfer configuration 4f14np5provides an exact fitting of energy levels for YbX63-, and a smooth variation of ff and fp crystal field parameters for Cs2NaLnCl6(Ln Er, Tm, Yb) is observed. [ABSTRACT FROM AUTHOR]

A full multiple theoretical model (MXAN) is applied to fit picosecond difference X-ray absorption spectra at the ruthenium L3edge upon photoexcitation of aqueous RuII(bpy)32. We show that fitting difference spectra allows an increase in sensitivity, such that slight structural changes can be retrieved, which are not detected in fitting full spectra. The Ru−N bond distances of the excited complex in the 3MLCT state are in good agreement with recently published values. The implementation of the present approach to L-edge spectra and its high sensitivity opens opportunities for its extension to a large class of experiments where difference X-ray absorption spectra are recorded. [ABSTRACT FROM AUTHOR]

In this work, a novel expression for nonequilibrium free energy is introduced within the framework of the continuum model. A simple and analytical model for the solvent effect of absorption spectrum of an interfacial molecule is deduced. This model overcomes some lacks existing in the previous theoretical treatments. Associated with the experimental data of N,N-diethyl-p-nitroaniline and 4-(2,4,6-triphenylpyridinium)-2,6-diphenylphenoxide, the present model gives reasonable predication of orientational angles for different interfaces. [ABSTRACT FROM AUTHOR]

A bilayer composite of single walled carbon nanotubes (SWNTs) deposited onto Nafion exhibits substantial mechanical motion upon exposure to visible or near-infrared light. The magnitude of the actuation parallels the absorption spectrum of the SWNTs in the near-infrared, but the actuation diminishes in the visible and disappears in the UV portions of the spectrum. In the near-infrared region, the photoactuation is linear with respect to the light intensity. The photoactuation also appears to be associated with a photocurrent across the nanotube/Nafion interface. The proposed mechanism for the actuation is that band bending of the semiconducting SWNTs induces polarization of mobile hydrogen ions at the Nafion interface, which then causes swelling of the polymer. [ABSTRACT FROM AUTHOR]

The self-assembed chitosan CdSe quantum dots (QDs) and chitosan CdSe−ZnS core−shell QDs films have been prepared by using layer-by-layer electrostatic technique. The well-ordered nanostructure and the layer-by-layer deposition of the QDs are revealed by AFM and exciton absorption spectra, respectively. The optical nonlinearity of the composite films were studied by using Z-scan technique with femtosecond pulses at the wavelength of 790 nm, the value of third-order susceptibility of core−shell QDs are measured to be about 1.1 × 10-8 esu, which is about 200% larger than that of CdSe QDs of 5.3 × 10-9 esu. This has potential applications in all-optical switches in optical information processing. [ABSTRACT FROM AUTHOR]

We have applied time-dependent density functional theory (TDDFT) to study the valence &pgr;−&pgr;* excited states of the tryptophan chromophore in the environment of the proteins barnase and human serum albumin. The chromophore is represented by indole. Due to the approximate nature of TDDFT, in the gas phase the calculated vertical transition energies to the 1L valence states are reordered with respect to experiment. The 1La state responds more than the 1Lb state to the local environment, described fully at the TDDFT level, and to bulk environment, described by a set of point charges. Nevertheless, the vertical transitions are readily identified. For human serum albumin, our calculations predict distinct spectral characteristics between structures with different tryptophan side chain torsion angles. The computational tractability of TDDFT relative to more accurate ab initio methods allows a large part of the surrounding protein environment (up to 100 atoms) to be explicitly included in the TDDFT calculations. [ABSTRACT FROM AUTHOR]

The time dependent density functional theory (TDDFT) has been employed to calculate the X-ray absorption spectra of the alkaline-earth oxides at the metal K and L and oxygen K edges. Cluster models to mimic the bulk are considered, embedded within an array of point charges to simulate the Madelung potential. Comparison with experimental data allows a precise assessment of the performances of the method, which appears competitive and suitable to reproduce the measurements. The configuration mixing explicitly included in the TDDFT scheme appears mandatory for a correct reproduction of the oscillator strength distribution in the metal 2p spectra. The origin of the theoretical spectral features is investigated with the help of the partial density of the virtual states (PDOS) calculated for each core hole considered. The trends of the spectral features along the series are discussed in terms of the nature of the virtual final states and related to the presence of the empty nd orbitals of the metal cations. The trend of the below-edge features in the O1s excitation spectra is discussed in terms of the metal-oxygen bonding interaction. [ABSTRACT FROM AUTHOR]

The spectral properties of composite materials based on small particles under 1D, 2D, and 3D size confinement are described using a combination of dispersive internal field and effective media theory approaches. Calculations performed for a number of crystalline materials have shown that the peak position and intensity of the vibrational band of the material under conditions of 1D, 2D, and 3D size confinement are changed, whereas the bandwidth of the band remains the same. In the case of 3D confinement, the peak position of the spectrum of isolated “mesoparticles” ([inline equation] ) appears to be very close to the intrinsic frequency of the lattice vibrations, calculated from the elastic constants of this crystal, as well as to the Fröhlich's frequency. The largest shift (Δν) of the peak frequency, νmax, from the bulk value is obtained in the case of 1D confinement when the peak position is practically coincident with the frequency of the longitudinal optical phonon (νLO). These shifts are the result of intermolecular interactions, including both resonant and induced resonant dipole-dipole interactions. [ABSTRACT FROM AUTHOR]

Two-photon absorption spectra (2PA) of a series of conjugated dimers and the corresponding monomer were studied in the near-IR region. All of the dimers show very large peak cross section values, &sgr;2 = (3−10) × 103 GM (1 GM = 1 × 10-50 cm4 s photon-1), which is several hundred times larger than that obtained for the corresponding monomer in the same region. We explain such dramatic cooperative enhancement by a combination of several factors, such as strong enhancement of the lowest one-photon Q-transition, better resonance conditions in the three-level system, dramatic enhancement of the excited-state singlet−singlet transition, and parallel arrangement of consecutive transitions in dimers, as compared to perpendicular arrangement in the monomer. We show that the absolute values of the 2PA cross section in these molecules are quantitatively described by a quantum-mechanical expression, derived for the three-level model. We also demonstrate the possibility of singlet oxygen generation upon one- and two-photon excitation of these dimers, which makes them particularly attractive for photodynamic therapy. [ABSTRACT FROM AUTHOR]

Various end-substituted distyrylbenzenes have been synthesized to serve as guest molecules in inclusion compounds to promote efficient energy transport along one-dimensional channels. Their optical and photophysical properties have been characterized at both experimental and theoretical levels. All molecules display a large transition dipole moment between the ground state and lowest excited state and hence a short radiative lifetime (on the order of 1−2 ns). They also exhibit a large spectral overlap between the emission and absorption spectra, which enables efficient energy transport between molecules arranged in a head-to-tail configuration in nanochannels. Hopping rates on the order of 1012 s-1 are calculated at a full quantum-chemical level; this is much larger than the radiative lifetimes and opens the way for energy migration over large distances. Changes in the nature of the terminal substituents are found to modulate the optical properties weakly but to impact significantly the energy transfer rates. [ABSTRACT FROM AUTHOR]

Unusual behavior of indolenine and hydroxyphenyl squaraines has been observed in solution capillary layers and adsorbed films. The confined solutions showed anomalous aggregation of squaraine molecules in contrast to their monomer behavior in the bulk solutions of the same concentration, along with formation of a macroscopic cell-like structure in the confined solution layer, with the diameter of cells being 3-5 μm. The aggregate structure, as observed through electronic absorption spectra, was strongly dependent on the chemical structure of squaraine used and solvent used, and it also was different from squaraine aggregates observed in aqueous solutions and films prepared by vacuum evaporation. It has been found that indolenine squaraine is capable of forming H-aggregates in confined dimethylformamide solutions and hydroxyphenyl squaraine is capable of forming J-aggregates in confined dimethylformamide solutions and adsorbed films. The results were compared with pseudoisocyanine, which forms J-aggregates in aqueous bulk solutions readily; however, no J-aggregates have been found in their capillary layers. The interplay of dye-dye, dye-surface, and dye-solvent interactions resulting in the above effects is discussed. [ABSTRACT FROM AUTHOR]

Low-temperature emission and polarized absorption spectra have been recorded for U3+ ions diluted in Cs3Lu2Cl9 and Cs3Y2I9 host crystals. The experimental crystal-field levels were fitted to 13 parameters of a semiempirical Hamiltonian representing the combined atomic, one-electron crystal field (CF) as well as two-particle correlation crystal-field (CCF) operators. The red shift of the first f−d transitions from ~14 800 cm-1 in the spectrum of U3+:Cs3Lu2Cl9 to as low as 11 790 cm-1 in that of U3+:Cs3Y2I9 has been attributed to an increase in the covalence of the U3+−X- bonds. Comparison of the differences in the Coulomb repulsion strength between U3+ and Er3+ ions in Cs3Lu2Cl9 and Cs3Y2I9 crystals suggests that the 5f electrons of U3+ ions are more 3d-like than 4f. The CF splitting of the 2H9/2 and 4F5/2 multiplets is unexpectedly larger for U3+:Cs3Y2I9 than for U3+:Cs3Lu2Cl9, which may be viewed as a result of the proximity of f−d states. For a correct description of the energy level structure of the 2H9/2 and 4F5/2 multiplets, the inclusion of CCF terms in the parametric Hamiltonian has proved to be essential. The larger f−f transition intensities for U3+:Cs3Y2I9 were also considered to be a consequence of the red shift of the first f−d states. The inadequacy in determination of the minor atomic parameters (other than parameters for Coulomb and spin−orbit interactions) and the insufficient inclusion of the influence of excited configuration in the applied CF Hamiltonian are assumed to be the main deficiencies preventing a better agreement between the experimental and calculated energies of CF levels. [ABSTRACT FROM AUTHOR]

Hybrid density functional calculations have been carried out on cluster models of the pristine and oxidized hydrogen-terminated Si(100)-2×1 surface to investigate the changes in the surface infrared absorption spectrum upon incorporation of oxygen. Due to a combination of geometric and electronic effects, a dramatic increase in the ν(Si-H) band intensity is found for the oxidized surface. An increase in infrared intensity of up to 62% is predicted for multiply oxidized sites. The results presented here may prompt the reinterpretation of infrared studies examining silicon surface chemistry using the ν(Si-H) region to probe changes in surface structure and coverage. [ABSTRACT FROM AUTHOR]

The electronic structure of a monolayer-protected gold cluster, [Au13(SCH3)8]3+, has been investigated by performing density functional calculations. The cluster has a characteristic structure with Oh molecular symmetry, and eight (111) facets of a centered cuboctahedral Au13 core cluster are fully passivated by eight methanethiolates. The bond distance between two neighboring gold atoms (3.673 Å) is much larger than that of the bare Au13 cluster (2.929 Å), whereas the Au-S bond distance is 2.403 Å. This atomic rearrangement means that the methanethiolates stabilize the enlarged bare Au13 cluster by bonding to the (111) hollow sites of the bare cluster. The absorption spectrum of the [Au13(SCH3)8]3+ cluster is simulated within time-dependent density functional theory. The spectrum shows clear absorption peaks and each peak is assigned to specific excitation processes. [ABSTRACT FROM AUTHOR]

The differences among radial distribution functions (RDFs) of monoclinic ZrO2, tetragonal ZrO2, and mixed-phase ZrO2 have been discussed. A much decreased Zr−Zr peak was found in the RDF of mixed-phase ZrO2. The result was explained by Lu Kunquan's equation very well. [ABSTRACT FROM AUTHOR]