Pi-electron System Research Articles

Syntheses of ylidenbutenolide-modified derivatives of peridinin and their stereochemical and spectral characteristics

Peridinin is a light-harvesting carotenoid found in oceanic photosynthetic organisms. It possesses a unique gamma-ylidenbutenolide function and engages in energy transfer to chlorophyll a with very high (>90%) efficiency. In order to examine the relationship between the unique structure of peridinin and its facility in carrying out energy transfer, we have synthesized two different ylidenbutenolide-modified derivatives of peridinin. In this communication, the details of the syntheses are described as are the stereochemical and spectral characteristics of the derivatives; the novel ylidenbutenolide functional group stabilizes the molecule and maintains the conjugated pi-electron system in an all-trans configuration.

Rotationally Resolved Ground State Vibrational Levels of HC2S Studied by Two-Color Resonant Four-Wave Mixing

A high-resolution study of the X(2)Pi(3/2) ground state rovibronic energy levels of jet-cooled HC(2)S radical using the double-resonance two-color four-wave mixing technique (TC-RFWM) is reported. The rotational structure of the bands is observed by excitation of selected R-branch lines in the origin band of the A(2)Pi(3/2)-X(2)Pi(3/2) electronic system. The second laser frequency is scanned to transfer the population from the rotational level(s) of the upper state to selected vibronic levels of the ground state. Fourteen rotationally resolved vibrational bands have been recorded for energies up to 1800 cm(-1) above the v'' = 0 X(2)Pi(3/2) electronic ground state. Effective rotational constants and origins are determined for levels that involve fundamental and overtone combinations of the nu(3) (CS stretch), nu(4) (CCH bend), and nu(5) (CCS bend) vibrations. This illustrates the power and advantages of the TC-RFWM approach for the study of the ground state manifold of reactive intermediates produced in low concentrations with high resolution, good signal-to-noise and wide dynamic range.

Photoswitching Mechanism of Cyanine Dyes

Cyanine dyes have been shown to undergo reversible photoswitching, where the fluorophore can be switched between a fluorescent state and a dark state upon illumination at different wavelengths. The photochemical mechanism by which switching occurs has yet to be elucidated. In this study, we have determined the mechanism of photoswitching by characterizing the kinetics of dark state formation and the spectral and structural properties of the dark state. The rate of switching to the dark state depends on the concentration of the primary thiol in the solution and the solution pH in a manner quantitatively consistent with the formation of an encounter complex between the cyanine dye and ionized thiol prior to their conjugation. Mass spectrometry suggests that the photoconversion product is a thiol−cyanine adduct in which covalent attachment of the thiol to the polymethine bridge disrupts the original conjugated π-electron system of the dye.

Disentangling Eumelanin “Black Chromophore”: Visible Absorption Changes As Signatures of Oxidation State- and Aggregation-Dependent Dynamic Interactions in a Model Water-Soluble 5,6-Dihydroxyindole Polymer

A fundamental unsettled issue concerning eumelanins, the functional biopolymers of human skin and hair, is why they are black. The experimental difficulty lies in the virtual insolubility of these pigments, causing marked scattering effects and hindering characterization of the intrinsic absorption properties of the heterogeneous species produced by oxidative polymerization of 5,6-dihydroxyindole (DHI) and related monomer precursors. The synthesis of spectrally robust, water-soluble DHI polymers is therefore an important goal in the prospects of disentangling intrinsic absorption properties of eumelanin components by circumventing scattering effects. Reported herein is the first water-soluble DHI polymer produced by oxidation of ad hoc designed 5,6-dihydroxy-3-indolyl-1-thio-beta-D-galactopyranoside (1). The dark brown polymer exhibited a distinct band at 314 nm and a broad visible absorption, resembling that of natural eumelanins. Main isolable oligomer intermediates including 2,7'- and 2,4'-biindolyls 2 and 3, attest the close resemblance to the mode of coupling of the parent DHI. Sodium borohydride reduction caused decoloration and a marked absorbance decrease in the visible region around 550 nm, but did not affect the UV band at 314 nm. Measurements of absorbance variations with dilution indicated a linear response at 314 nm, but a significant deviation from linearity in the visible region, with the largest decrease around 500 nm. It is argued that eumelanin black color is not only intrinsically defined by the overlap of pi-electron conjugated chromophores within the individual polymer components, as commonly believed, but also by oxidation state- and aggregation-dependent interchromophoric interactions causing perturbations of the heterogeneous ensemble of pi-electron systems and overall spectral broadening.

Physico-Chemical Evaluation of Rationally Designed Melanins as Novel Nature-Inspired Radioprotectors

BackgroundMelanin, a high-molecular weight pigment that is ubiquitous in nature, protects melanized microorganisms against high doses of ionizing radiation. However, the physics of melanin interaction with ionizing radiation is unknown.Methodology/Principal FindingsWe rationally designed melanins from either 5-S-cysteinyl-DOPA, L-cysteine/L-DOPA, or L-DOPA with diverse structures as shown by elemental analysis and HPLC. Sulfur-containing melanins had higher predicted attenuation coefficients than non-sulfur-containing melanins. All synthetic melanins displayed strong electron paramagnetic resonance (2.14·1018, 7.09·1018, and 9.05·1017 spins/g, respectively), with sulfur-containing melanins demonstrating more complex spectra and higher numbers of stable free radicals. There was no change in the quality or quantity of the stable free radicals after high-dose (30,000 cGy), high-energy (137Cs, 661.6 keV) irradiation, indicating a high degree of radical stability as well as a robust resistance to the ionizing effects of gamma irradiation. The rationally designed melanins protected mammalian cells against ionizing radiation of different energies.Conclusions/SignificanceWe propose that due to melanin's numerous aromatic oligomers containing multiple π-electron system, a generated Compton recoil electron gradually loses energy while passing through the pigment, until its energy is sufficiently low that it can be trapped by stable free radicals present in the pigment. Controlled dissipation of high-energy recoil electrons by melanin prevents secondary ionizations and the generation of damaging free radical species.

Kinetic Study of the Prooxidant Effect of α‐Tocopherol. Hydrogen Abstraction from Lipids by α‐Tocopheroxyl Radical

A kinetic study of the prooxidant effect of alpha-tocopherol was performed. The rates of allylic hydrogen abstraction from various unsaturated fatty acid esters (ethyl stearate 1, ethyl oleate 2, ethyl linoleate 3, ethyl linolenate 4, and ethyl arachidonate 5) by alpha-tocopheroxyl radical in toluene were determined, using a double-mixing stopped-flow spectrophotometer. The second-order rate constants (k (p)) obtained are <1 x 10(-2) M(-1 )s(-1) for 1, 1.90 x 10(-2) M(-1 )s(-1) for 2, 8.33 x 10(-2 )M(-1 )s(-1) for 3, 1.92 x 10(-1) M(-1 )s(-1) for 4, and 2.43 x 10(-1 )M(-1 )s(-1) for 5 at 25.0 degrees C. Fatty acid esters 3, 4, and 5 contain two, four, and six -CH(2)- hydrogen atoms activated by two pi-electron systems (-C=C-CH(2)-C=C-). On the other hand, fatty acid ester 2 has four -CH(2)- hydrogen atoms activated by a single pi-electron system (-CH(2)-C=C-CH(2)-). Thus, the rate constants, k (abstr)/H, given on an available hydrogen basis are k (p)/4 = 4.75 x 10(-3 )M(-1 )s(-1) for 2, k (p)/2 = 4.16 x 10(-2) M(-1 )s(-1) for 3, k (p)/4 = 4.79 x 10(-2 )M(-1 )s(-1) for 4, and k (p)/6 = 4.05 x 10(-2 )M(-1 )s(-1) for 5. The k (abstr)/H values obtained for 3, 4, and 5 are similar to each other, and are by about one order of magnitude higher than that for 2. From these results, it is suggested that the prooxidant effect of alpha-tocopherol in edible oils, fats, and low-density lipoproteins may be induced by the above hydrogen abstraction reaction.

Tuning the Thermodynamics of Association of Transmembrane Helices

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 degrees<0). 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.

Synthesis and hybridization of oligonucleotides attached to a redox reporter via ethenyl linker at 5-position of pyrimidine base

We describe a new ferrocene-based redox-reporter that electronically couples to the DNA Pi-electron system.

π-Conjugated Phosphasilenes Stabilized by Fused-Ring Bulky Groups

Pi-conjugated phosphasilenes with a variety of aryl substituents on the silicon atom have been synthesized by the use of a 1,1,3,3,5,5,7,7-octaethyl-s-hydrindacen-4-yl (Eind) group. X-ray structural analysis shows the highly coplanar pi-framework stabilized by the perpendicularly fixed Eind groups. The strong pi-pi* absorptions have been observed, demonstrating the extension of pi-conjugation over the skeleton. The DFT calculations indicate that the LUMO involves the substantial contribution of the 3p(pi)*(Si-P)-2p(pi)*(carbon pi-electron system) conjugation. The electrochemical properties of the phosphasilens are also presented.

Prediction of the Intrinsic Hydrogen Bond Acceptor Strength of Chemical Substances from Molecular Structure

Hydrogen bonding affects the partitioning of organic compounds between environmental and biological compartments as well as the three-dimensional shape of macromolecules. Using the semiempirical quantum chemical AM1 level of calculation, we have developed a model to predict the site-specific hydrogen bond (HB) acceptor strength from ground-state properties of the individual compounds. At present, the model parametrization is confined to compounds with one HB acceptor site of the following atom types: N, O, S, F, Cl, and Br that act as lone-pair HB acceptors, and pi-electron (aromatic or conjugated) systems with the associated C atoms as particularly weak HB acceptors. The HB acceptor strength is expressed in terms of the Abraham parameter B and calculated from local molecular parameters, taking into account electrostatic, polarizability, and charge transfer contributions according to the Morokuma concept. For a data set of 383 compounds, the squared correlation coefficient r2 is 0.97 when electrostatic potential (ESP) derived net atomic charges are employed, and the root-mean-square (rms) error is 0.04 that is in the range of experimental uncertainty. The model is validated using an extended leave-50%-out approach, and its performance is comparatively analyzed with the ones of earlier introduced ab initio (HF/6-31G**) and density functional theory (B3LYP/6-31G**) models as well as of two increment methods with respect to the total compound set as well as HB acceptor type subsets. The discussion includes an explorative model application to amides and organophosphates that demonstrates the robustness of the approach, and further opportunities for model extensions.

A B−B Bond-Containing Polycyclic π-Electron System: Dithieno-1,2-dihydro-1,2-diborin and Its Dianion

As a B-B bond-containing polycyclic pi-electron system, a dithieno[3,2-c:2',3'-e](1,2-dihydro-1,2-diborin) derivative and its dianion salts were successfully prepared, and their structures were determined by X-ray crystallography. The neutral dithieno-1,2-dihydro-1,2-diborin has a twisted diborin ring in which both the sigma-pi and p-pi* orbital interactions between the bithiophene pi framework and the B-B bond moiety effectively take place, giving rise to an absorption that is significantly red-shifted compared with that of the parent bithiophene. Upon a two-electron reduction, the dithienodiborin pi framework becomes planar and has a characteristic peripheral pi conjugation through the B-B bond with 14 pi electrons. Furthermore, the dianion salts show an intriguing countercation effect on their photophysical properties, indicative of possible electronic tuning by the countercations.

A multiconfigurational molecular orbital study of N-methyl oxatriazole

A multiconfigurational molecular orbital analysis has been carried out for a representative of a class of compounds found to have hypotensive activity in biological systems. N-methyl oxatriazole is a mesoionic compound isoelectronic with N-methyl sydnone and is found to be a highly polar, delocalized heterocyclic pi-electron system. A pair-excitation multiconfiguration self-consistent field (PEMCSCF) treatment of the three lowest states indicates substantial mixing of the lowest unoccupied orbital with the ground state. Orthonormal resonance analysis shows how the orbital mixing improves the description of the dipole moment in the ground state. The PEMCSCF calculation was carried out using a minimum basis of Slater–Transform–Preuss functions fitted by six Cartesian Gaussian orbitals (STP-6G) which were previously optimized on smaller molecules to yield energies below 4–31G values. This PEMCSCF calculation is one of the first applications of ab initio MCSCF techniques to a molecule of 10 atoms and represents development of practical methods for PEMCSCF treatment of up to 15 atoms.

Structural Basis of Enhanced Photoconversion Yield in Green Fluorescent Protein-like Protein Dendra2

Dendra2 is an engineered, monomeric GFP-like protein that belongs to a subclass of fluorescent proteins undergoing irreversible photoconversion from a green- to a red-emitting state upon exposure to purple-blue light. This photoinduced process occurs only in the neutral state of the chromophore and is known to result from backbone cleavage accompanied by an extension of the delocalized pi-electron system. We have measured the X-ray structure of the green species of Dendra2 and performed a comprehensive characterization of the optical absorption and fluorescence properties of the protein in both its green and red forms. The structure, which is very similar to those reported for the closely related proteins EosFP and Kaede, revealed a local structural change involving mainly Arg66 and a water molecule W4, which are part of a charged and hydrogen-bonded cluster of amino acids and water molecules next to the chromophore. Unlike in EosFP and Kaede, Arg66 of Dendra2 does not contribute to negative charge stabilization on the imidazolinone ring by hydrogen bonding to the imidazolinone carbonyl. This structural change may explain the blue shift of the absorption and emission bands, as well as the markedly higher pKs of the hydroxyphenyl moiety of the chromophore, which were determined as 7.1 and 7.5 for the green and red species, respectively. The action spectrum of photoconversion coincides with the absorption band of the neutral species. Consequently, its 20-fold enhancement in Dendra2 at physiological pH accounts for the higher photoconversion yield of this protein as compared to EosFP.

Experimental and density functional studies on 4-(2,3-dichlorobenzylideneamino)antipyrine and 4-(2,5-dichlorobenzylideneamino)antipyrine

Two antipyrine derivates, both with formula C 18H 15Cl 2N 3O, are structurally similar Schiff bases derived from the condensation of 2,3-dichlorobenzaldehyde or 2,5-dichlorbenzaldehyde with 4-aminoantipyrine in methanol solution. The compounds were characterized by elemental analysis, FT-IR, FT-Raman, UV–vis and X-ray single crystal diffraction techniques. As expected, both compounds adopt trans configurations about the Schiff base imine C N bonds. Density functional calculations were performed to further optimize and characterize them. The results indicate that the theoretical values show good agreement with experimental ones. The thermodynamic functions (standard heat capacities, standard entropies and standard enthalpy changes) and their correlations with temperatures have been obtained from their theoretical harmonic frequencies of the optimized structures. The intramolecular electronic transfer and nonlinear optical properties of the compounds can be explained clearly by the molecular frontier orbitals and pi-electron systems.

Derivatives of Spiropentadiene Dication: New Species with Planar Tetracoordinate Carbon (ptC) atom

In this work, nine tetrasubstituted derivatives [NH(2), OCH(3), Li, Na, Si(CH(3))(3)/SiH(2)CH(3,) P(CH(3))(2), Cl, F, and CN] of the spiropentadiene dication were analyzed within the framework of QTAIM. In the studied series, the electron-withdrawing substituents destabilize the ptC-containing spiropentadiene dication. On the other hand, stabilization of this dication is possible for electron-donating substituents only through sigma bonds, such as Li and Na. In all studied systems, according to QTAIM, the pi-electron system does not participate in the stabilization of the ptC atom in the spiropentadiene dication. sigma-electron-donating groups stabilize the spiropentadiene dication system by increasing the charge density of C(ext)-ptC bonds, whereas electron-withdrawing groups remove the charge density from C(ext)-ptC bonds.

Synthesis and Photophysics of Benzotexaphyrin: A Near-Infrared Emitter and Photosensitizer

Texaphyrins are pentaazadentate macrocycles with interesting photophysical properties and potential applications as nonlinear optical (NLO) materials, photosensitizers, magnetic resonance imaging (MRI) contrasting reagents, and radiation sensitizers, etc. To further red-shift the Q-like band of the texaphyrins, a benzotexaphyrin with an extensively delocalized pi-electron system was synthesized for the first time. Its photophysical characteristics were systematically investigated. Due to the extended pi-conjugation, the Q(0,0) band of benzotexaphyrin bathochromically shifts to 810 nm, and it emits at 825 nm with a singlet excited-state lifetime of 895 ps. Its triplet excited-state energy is estimated to be 119 kJ/mol. The triplet excited-state lifetime is approximately 2.2 micros, and the quantum yield of the triplet excited-state formation is 0.78. It also exhibits a triplet-triplet transient absorption in the region 505-590 nm. In addition, benzotexaphyrin exhibits high efficiency in generating singlet oxygen in methanol (Phi(Delta) = 0.65). Therefore, benzotexaphyrin could potentially be a NIR photosensitizer and emitter for photodynamic therapy and bioimaging applications.

Evidence for the Cation−π Interaction between Cu2+and Tryptophan

The cation-pi interaction, a noncovalent interaction of electrostatic nature between a cation and an electron-rich pi system, is increasingly recognized as an important force that influences the structures and functions of molecules including proteins. Unlike other metal cations, the transition metal cation Cu2+ is not regarded to take part in a cation-pi interaction because Cu2+ tends to oxidize the pi electron system, in particular that of Trp, and to introduce covalency in the metal-pi electron interaction. This paper reports the first spectral evidence for the cation-pi interaction between Cu2+ and Trp. The Cu2+ ion bound to the amino N-terminal Cu2+/Ni2+ binding motif composed of three amino acid residues interacts with the indole ring of the fourth Trp residue in a noncovalent manner. The Cu2+-Trp interaction produces a distinct negative band at 223 nm in circular dichroism (CD), which disappears upon mutation or depletion of the Trp residue or upon replacement of the Cu2+ ion by Ni2+. In UV absorption, a pair of negative/positive intensity changes is generated at 222/231 nm by the Cu2+-Trp interaction, being consistent with the previous observations on the indole ring interacting with K+ or a cationic His imidazole ring. The negative CD band around 223 nm is characteristic of the Cu2+-Trp pair and may be useful as a marker of the Cu2+-Trp cation-pi interaction. Coordination of negatively charged ligands to Cu2+ is suggested to be important for the cation to be involved in a cation-pi interaction.

Structural Characterization of a Thiazoline-Containing Chromophore in an Orange Fluorescent Protein, Monomeric Kusabira Orange

Monomeric Kusabira Orange (mKO) is a green fluorescent protein (GFP)-like protein that emits orange light at a peak of 559 nm. We analyzed its X-ray structure at 1.65 A and found a novel three-ring chromophore that developed autocatalytically from a Cys65-Tyr66-Glu67 tripeptide in which the side chain of Cys65 formed the third 2-hydroxy-3-thiazoline ring. As a result, the chromophore contained the CNCOH group at the 2-position of the imidazolinone moiety such that the conjugated pi-electron system of the chromophore was more extended than that of GFP but less extended than that of the Discosoma sp. red fluorescent protein (DsRed). Since a sulfur atom has potent nucleophilic character, the third 3-thiazoline ring is rapidly and completely cyclized. Furthermore, our structure reveals the presence of a pi-pi stacking interaction between His197 and the chromophore as well as a pi-cation interaction between Arg69 and the chromophore. These structural findings are sufficient to account for the orange emission, pH tolerance, and photostability of mKO.

グアイアズレニル基とチエニル基とを有する新しい拡張π電子系の合成: 生成物の分子構造，スペクトル，電気化学的および化学的特性

グアイアズレニル基とチエニル基とを有する新しい拡張π電子系の合成: 生成物の分子構造，スペクトル，電気化学的および化学的特性

Modeling Photoabsorption of the asFP595 Chromophore

The fluorescent protein asFP595 is a promising photoswitchable biomarker for studying processes in living cells. We present the results of a high level theoretical study of photoabsorption properties of the model asFP595 chromophore molecule in biologically relevant protonation states: anionic, zwitterionic, and neutral. Ground state equilibrium geometry parameters are optimized in the PBE0/(aug)-cc-pVDZ density functional theory approximation. An augmented version of multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) following the state-averaged CASSCF/(aug)-cc-pVDZ calculations is used to estimate the vertical S0-S1 excitation energies for all chromophore species. An accuracy of this approach is validated by comparing the computed estimates of the S0-S1 absorption maximum of the closely related chromophore from the DsRed protein to the known experimental value in the gas phase. An influence of the CASSCF active space on the aug-MCQDPT2 excitation energies is analyzed. The zwitterionic form of the asFP595 chromophore is found to be the most sensitive to a particular choice and amount of active orbitals. This observation is explained by the charge-transfer type of the S0-S1 transition involving the entire conjugated pi-electron system for the zwitterionic protonation state. According to the calculation results, the anionic form in the trans conformation is found to possess the most red-shifted absorption band with the maximum located at 543 nm. The bands of the zwitterionic and neutral forms are considerably blue-shifted compared to those of the anionic form. These conclusions are at variance with the results obtained in the TDDFT approximation for the asFP595 chromophore. The absorption wavelengths computed in the aug-MCQDPT2/CASSCF theory are as follows: 543 (535), 470 (476), and 415 (417) nm for the anionic, zwitterionic, and neutral forms of the trans and cis (in parentheses) isomers of the asFP595 chromophore. These data can be used as a reference for further theoretical studies of the asFP595 chromophore in different media and for modeling photoabsorption properties of the asFP595 fluorescent protein.