Origin of the absorption maxima of the photoactive yellow protein resolved via ab initio multiconfigurational methods

We discuss the role of the protein in controlling the absorption spectra of photoactive yellow protein (PYP), the archetype xanthopsin photoreceptor, using quantum mechanics/molecular mechanics (QM/MM) methods based on ab initio multireference perturbation theory, combined with molecular dynamics (MD) simulations. It is shown that in order to get results in agreement with the experimental data, it is necessary to use a model that allows for a proper relaxation of the whole system and treats the states involved in the electronic spectrum in a balanced way, avoiding biased results due to the effect of nonrepresentative electrostatic interactions on the chromophore.     

Conformational Distributions of N‐Acetyl‐L‐cysteine in Aqueous Solutions: A Combined Implicit and Explicit Solvation Treatment of VA and VCD Spectra

The conformational distributions of N‐acetyl‐L ‐cysteine (NALC) in aqueous solutions at several representative pH values are investigated using vibrational absorption (VA), UV/Vis, and vibrational circular dichroism (VCD) spectroscopy, together with DFT and molecular dynamics (MD) simulations. The experimental VA and UV/Vis spectra of NALC in water are obtained under strongly acid, neutral, and strongly basic conditions, as well as the VCD spectrum at pH 7 in D₂O. Extensive searches are carried out to locate the most stable conformers of the protonated, neutral, deprotonated, and doubly deprotonated NALC species at the B3LYP/6‐311++G(d,p) level. The inclusion of the polarizable continuum model (PCM) modifies the geometries and the relative stabilities of the conformers noticeably. The simulated PCM VA spectra show significantly better agreement with the experimental data than the gas‐phase ones, thus allowing assignment of the conformational distributions and dominant species under each experimental condition. To further properly account for the discrepancies noted between the experimental and simulated VCD spectra, PCM and the explicit solvent model are utilized. MD simulations are used to aid the modelling of the NALC–(water)_N clusters. The geometry optimization, harmonic frequency calculations, and VA and VCD intensities are computed for the NALC–(water)_3,4 clusters at the B3LYP/6‐311++G(d,p) level without and with the PCM. The inclusion of both explicit and implicit solvation models at the same time provides a decisively better agreement between theory and experiment and therefore conclusive information about the conformational distributions of NALC in water and hydrogen‐bonding interactions between NALC and water molecules.     

Modeling of phytochrome absorption spectra

Phytochromes constitute one of the six well‐characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high‐resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV‐vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes. © 2013 Wiley Periodicals, Inc.     

Effect of molecular vibrations on the MD/QC‐simulated absorption spectra

Effect of molecular vibrations on the absorption spectra simulated via a sequential approach combining molecular dynamics (MD) with quantum‐chemical calculations has been investigated. Simulated spectra have been obtained from the time‐dependent density functional theory results averaged over series of molecular geometries retrieved from Born–Oppenheimer MD trajectories. Distributions of bond lengths have been analyzed and related to the features of calculated spectra. For NVE simulations of small systems, absorption spectra exhibit bimodal bandshape as a result of classical treatment of vibrations. For NVE trajectories of larger systems or simulations in the NVT ensemble calculated absorption bands are symmetric, however, they may not agree with the results of Franck–Condon analysis. These results are practical manifestations of effects predicted theoretically from general principles. Consequences for the modeling of absorption spectra have been discussed. © 2013 Wiley Periodicals, Inc.     

IR,Raman, and UV/Vis Spectra of Corannulene for Use in Possible Interstellar Identification

The spectroscopic characterization of corannulene (C₂₀H₁₀) is carried out by several techniques. The high purity of the material synthesized for this study was confirmed by gas chromatography‐mass spectrometry (GC‐MS). During a high‐performance liquid chromatography (HPLC) process, the absorption spectrum of corannulene in the ultraviolet (UV) and visible (vis) ranges is obtained. The infrared (IR) absorption spectrum is measured in CsI pellets, and the Raman scattering spectrum is recorded for pure crystal grains. In addition to room temperature measurements, absorption spectroscopy in an argon matrix at 12 K is also performed in the IR and UV/Vis ranges. The experimental spectra are compared with theoretical Raman and IR spectra and with calculated electronic transitions. All calculations are based on the density functional theory (DFT), either normal or time‐dependent (TDDFT). Our results are discussed in view of their possible application in the search for corannulene in the interstellar medium.     

BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study

Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (“W_in”/“W_out”), structure determination (X‐ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in W_in position. Using snapshots from MD and time‐dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red‐shifted and thermally broadened for all calculated π → π* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach. © 2012 Wiley Periodicals, Inc.     

Matrix isolation spectroscopy and molecular dynamics simulations for 2,7,12,17-tetra-tert-butylporphycene in argon and xenon

Electronic absorption spectra of 2,7,12,17-tetra-tert-butylporphycene (TTPC) have been recorded in low-temperature argon and xenon matrices for various deposition conditions. In the region of the S(0)-S(1) electronic transition, the spectra of TTPC in argon reveal a rich site structure, characterized by a series of more than 30 absorption peaks. Studies of the temperature dependence of the electronic spectra in solid argon demonstrated remarkable spectral changes, resulting in the broadening of all bands with increasing temperature. These temperature-induced spectral changes are, to a large degree, reversible, so lowering of temperature is accompanied by the recovery of the original fine-line spectrum. The absorption spectra in xenon reveal broad bands, on which a rich pattern of lines becomes superimposed at low temperatures. Trapping site distribution and the structure of the microenvironment around the TTPC chromophore, embedded in argon and xenon hosts, have been analyzed using molecular dynamics (MD) simulations. The MD results show that the trapping of TTPC in rare-gas solids is influenced by favorable embedding of the bulky tert-butyl groups inside the matrix cage. The crucial role of the tert-butyl groups for the thermodynamics and kinetics of matrix deposition is demonstrated by comparing the results with those obtained for the parent, unsubstituted porphycene.     

Synthesis and Characterization of Azobenzene–Porphyrins

A new series of novel covalently connected meso‐tetrakis(3‐azophenyl‐4‐hydroxy‐5‐methoxyphenyl)porphyrins were synthesized by linking azobenzene unit at the meta‐position of the meso‐phenyl group. These are characterized by UV–vis, IR, ¹H‐NMR, CHN, and FABMS spectroscopic techniques. All the porphyrin compounds showed a typical high energy Soret band at around 435 nm and azobenzene absorption at around 350 nm in UV–vis spectra. Fluorescence intensity of meso‐tetrakis(3‐(4‐methoxyazophenyl)‐4‐hydroxy‐5‐methoxyphenyl)porphyrin ( 2c ) has been observed to be maximum compared with other azobenzene porphyrins.     

Influence of Surface Structure,Pigmentation and Particulate Matter on Plant Reflectance and Fluorescence

Optical properties of plant leaves are relevant to evaluate their physiological state and stress effect. The main objective of this work was to study how variegation, pigment composition or reflective features modifies leaves' photophysical behavior. For this purpose, green leaves (Ficus benjamina), purple leaves (Tradescantia pallida), green leaves covered by white trichomes (Cineraria maritima) and variegated leaves (Codiaeum aucubifolium) were analyzed. Firstly, foliar surface morphology was evaluated by scanning electron microscopy. UV‐vis and near‐IR reflectance and transmittance spectra were obtained to calculate absorption (k) and scattering (s) coefficients. The theoretical approaches of Pile of Plates and Kubelka–Munk's theory resulted still valid for nonstandard leaves with differing surface conditions. However, frequently used spectral indices were not reliable for predicting water content, when leaves differed from conventional ones. The proportionality between the absorption factor and chromophore/pigment concentration was also lost for hairy leaves. A simplified model to describe these facts was presented here. Fluorescence spectra were recorded and corrected, due to light re‐absorption. Water‐optical parameter connection and pigment‐optical parameter connection were thoroughly discussed. Leaf surface morphology and pigmentation have not only influenced the optical features of leaves but also played a role in the effect that particulate matter could cause on leaf photosynthesis.     

Effects of solute structure on local solvation and solvent interactions: results from UV/vis spectroscopy and molecular dynamics simulations

Solvation of heterocyclic amines in CO(2)-expanded methanol (MeOH) has been explored with UV/vis spectroscopy and molecular dynamics (MD) simulations. A synergistic study of experiments and simulations allows exploration of solute and solvent effects on solvation and the molecular interactions that affect absorption. MeOH-nitrogen hydrogen bonds hinder the n-pi* transition; however, CO(2) addition causes a blue shift relative to MeOH because of Lewis acid/base interactions with nitrogen. Effects of solute structure are considered, and very different absorption spectra are obtained as nitrogen positions change. MD simulations provide detailed solvent clustering behavior around the solute molecules and show that the local solvent environment and ultimately the spectra are sensitive to the solute structure. This work demonstrates the importance of atomic-level information in determining the structure-property relationships between solute structure, local salvation, and solvatochromism.     

Polymerizable benzophenone derivatives for labeling vinyl acetate‐butylacrylate latex particles

We describe the synthesis and characterization of three new polymerizable benzophenone derivatives [2‐acryloxy‐5‐methyl benzophenone ( 8 ), 4′‐dimethylamino‐2‐acryloxy‐5‐methyl benzophenone ( 9 ), and 4′‐dimethylamino‐2‐(β‐acryloxyethyl)oxy‐5‐methyl benzophenone ( 10 )]. We show that these monomers can successfully be incorporated into vinyl acetate (VAc) copolymer latex particles. These particles were prepared by semicontinuous emulsion polymerization and mini‐emulsion polymerization of VAc with butylacrylate (BA) for VAc/BA = 4/1 by weight. The two monomers 9 and 10 bearing the 4′‐dimethylamino group satisfy the important spectroscopic criteria required of a dye to serve as an acceptor chromophore for nonradiative energy transfer from phenanthrene (Phe) as the donor. Their UV absorption spectra suggest significant overlap with the emission spectrum of Phe, which can be incorporated into P(VAc‐co‐BA) latex through copolymerization with 9‐acryloxymethyl Phe ( 2 ). In addition, these chromophores provide a window in their absorption spectra for excitation of the Phe chromophore at 300 nm. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 3001–3011, 2002     

UV‐Light‐Induced Hydrogen Transfer in Guanosine–Guanosine Aggregates

Aggregates of a lipophilic guanine (G) derivative have been studied in n‐hexane by femtosecond‐to‐microsecond UV‐visible broadband transient absorption, stationary infrared and UV‐visible spectroscopy and by quantum chemical calculations. We report the first time‐resolved spectroscopic detection of hydrogen transfer in GG aggregates, which leads to (G?H) ^. radicals by means of G⁺G^? charge transfer followed by proton transfer. These radicals show a characteristic electronic spectrum in the range 300–550 nm. The calculated superimposed spectrum of the species that result from NH???N proton transfer agrees best with the experimental spectrum.     

Synthesis of soluble electron‐donating polymers containing vinylogous TTF by oxidative dimerization of 1,4‐bisdithiafulvenyl‐2,5‐dialkoxybenzene

A new electron‐donating polymer composed of a vinylogous tetrathiafulvalene (TTF) unit was prepared by the oxidative dimerization of 1,4‐bisdithiafulvenyl‐2,5‐didodecyloxybenzene using iodine. The polymer was soluble in common organic solvents such as CHCl₃ and toluene. The number‐average molecular weight of the polymer with dodecyloxy group was 24,900 determined from GPC. The UV–vis spectrum of the polymer showed the absorption maxima at 587, 712, and 803 nm, which are due to a cation radical of the vinylogous TTF unit in the polymer. The reduction of the polymer to its neutral state was performed using sodium hydrogen sulfite. The structure of the polymer was confirmed by ¹H NMR and UV–vis spectra compared with that of a dimer model compound prepared by oxidation of 1‐dithiafulvenyl‐2,5‐didodecyloxybenzene using iodine. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4600–4608, 2005     

Optical absorption of methoxy and carboethoxy derivatives of 1,3-diphenyl-1H-pyrazolo[3,4-b]quinoline

Paper deals with experimental investigations and quantum chemical calculations of the optical absorption spectra of methoxy and carboethoxy 1,3-diphenyl derivatives of the pyrazoloquinoline ([PQ]): 6-methoxy-1,3-dyphenil-[PQ], 6-methoxy-1,3-(p-methoxyphenyl)-[PQ], 6-methoxy-1-(p-methoxyphenyl)-[PQ] and 6-carboethoxy-1,3-diphenyl-[PQ]. The quantum chemical calculations are performed by means of the semiempirical quantum chemical methods (AM1 or PM3) applied to: (a) the equilibrium molecular conformation in vacuo (T=0 K); (b) the molecular dynamic (MD) trajectory (T=300 K) which includes the dynamics of a certain molecular fragment (moiety) only (fragmental MD simulations); or (c) the MD trajectory obtained for most general case within the total MD simulations at T=300 K. The results of these calculations are compared with the measured spectra of the optical absorption. The quantum chemical simulations show that the dynamics of the methoxy or carboethoxy groups practically does not influence the absorption spectrum whereas the strongest its modification (300相似文献   

Band gap tuning of narrow‐polydispersity two‐dimensional conductive polymers with electroactive side‐chains

A series of two‐dimensional donor–acceptor–donor (D1–A(D2)) type of conducting polymers (CPs) all with electroactive bulky side chain structure has been designed, synthesized, and investigated by introducing the donor–acceptor (D1–A) thiophene–quinoxaline moiety in the main chain alongside and additional donor and hole transporting units in the side chain. All the UV‐vis spectra of the 2D polymers, PTPQT, PFPQT, and PCPQT, each with triphenylamine, fluorene, and carbazole units as the D2 side chain, possess strong intramolecular charge transfer absorption, thus resulting in better light harvesting. Their optical and electronic properties were thoroughly explored experimentally and computationally. The effect of molecular weight of the narrow polydispersity polymers on their optoelectronic property was studied in detail. In summary, the 2‐D CPs show potential for use as an active material in optoelectronic devices. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 1217–1227     

Identification of Intermediates in Zeolite‐Catalyzed Reactions by In Situ UV/Vis Microspectroscopy and a Complementary Set of Molecular Simulations

The optical absorption properties of (poly)aromatic hydrocarbons occluded in a nanoporous environment were investigated by theoretical and experimental methods. The carbonaceous species are an essential part of a working catalyst for the methanol‐to‐olefins (MTO) process. In situ UV/Vis microscopy measurements on methanol conversion over the acidic solid catalysts H‐SAPO‐34 and H‐SSZ‐13 revealed the growth of various broad absorption bands around 400, 480, and 580 nm. The cationic nature of the involved species was determined by interaction of ammonia with the methanol‐treated samples. To determine which organic species contribute to the various bands, a systematic series of aromatics was analyzed by means of time‐dependent density functional theory (TDDFT) calculations. Static gas‐phase simulations revealed the influence of structurally different hydrocarbons on the absorption spectra, whereas the influence of the zeolitic framework was examined by using supramolecular models within a quantum mechanics/molecular mechanics framework. To fully understand the origin of the main absorption peaks, a molecular dynamics (MD) study on the organic species trapped in the inorganic host was essential. During such simulation the flexibility is fully taken into account and the effect on the UV/Vis spectra is determined by performing TDDFT calculations on various snapshots of the MD run. This procedure allows an energy absorption scale to be provided and the various absorption bands determined from in situ UV/Vis spectra to be assigned to structurally different species.