Chain-length effects on molecular conformation in and chirality of self-assembled monolayers of alkoxylated benzo[c]cinnoline derivatives on highly oriented pyrolytic graphite

Self-assembled structures of alkoxylated benzo[c]cinnoline derivatives prepared on highly oriented pyrolytic graphite at room temperature from their solutions in solvents such as 1-phenyloctane, toluene, and 1-octanol were studied by scanning tunneling microscopy. The alkoxy chain length markedly affected the molecular conformations in 2-dimensional assemblies of these derivatives. Long-chain derivatives adopted the trans conformations more often than cis, whereas short-chain derivatives took exclusively the cis conformations in the self-assembled monolayers (SAMs). For the derivatives of intermediate chain lengths, polymorphism existed, with four molecular conformations identified experimentally. Experimental evidence substantiated the formation of chiral SAM structures at the surface, which can be explained by the conformations of the molecules. The chirality was also affected by the chain length of the molecules. A simple method analyzing the angles between different domains in the SAMs was used to identify the molecular conformations and to predict their relative structures.     

Light-activated reassembly of split green fluorescent protein

Truncated green fluorescent protein (GFP) with the 11th β-strand removed is potentially interesting for bioconjugation, imaging, and the preparation of semisynthetic proteins with novel spectroscopic or functional properties. Surprisingly, the truncated GFP generated by removing the 11th strand, once refolded, does not reassemble with a synthetic peptide corresponding to strand 11 but does reassemble following light activation. The mechanism of this process has been studied in detail by absorption, fluorescence, and Raman spectroscopy. The chromophore in this refolded truncated GFP is found to be in the trans configuration. Upon exposure to light a photostationary state is formed between the trans and cis conformations of the chromophore, and only truncated GFP with the cis configuration of the chromophore binds the peptide. A kinetic model describing the light-activated reassembly of this split GFP is discussed. This unique light-driven reassembly is potentially useful for controlling protein-protein interactions.     

PHOTOREACTION OF THE ACIDIFIED FORM OF BACTERIORHODOPSIN AND ITS 9-CIS DERIVATIVE IN PURPLE MEMBRANE AT LOW TEMPERATURES

Abstract— The photoreaction of the acidified form of bacteriorhodopsin and its 9-cis derivative was studied by low temperature spectroscopy.
A short exposure of the acidified form of bacteriorhodopsin, which was prepared by adding 2 m M HC1 to purple membrane suspension in 67% glycerol at 0°C, to red light at – 72°C resulted in the blue-shift of the spectrum. The feature of the shift was very similar to that accompanied by the formation of stable 9- cis acidified form of bacteriorhodopsin at 0°C, but only 13- cis - and all- trans -retinals were found in the extract from this product. No blue-shifted product was found on irradiation at – 190°C.
Irradiation of the 9- cis form of acidified bacteriorhodopsin at -72°C with blue light caused the isomerization of its 9- cis -retinylidene chromophore to 13- cis and all- trans forms without a significant spectral change. It became greater only after the sample was warmed above – 24°C. These results indicate the presence of the light-induced product which has trans configuration on the 9-10 double bond and exhibits the 9- cis type spectrum.     

Bidirectional photocontrol of peptide conformation with a bridged azobenzene derivative

It goes both ways: A thiol-reactive cross-linker based on a bridged azobenzene derivative permits photoreversible control of peptide conformation on irradiation with violet (407?nm) and green (500-550?nm) light (see picture) through isomerization of the cross-linker. The large separation of the absorbance bands of the cis (yellow) and trans (red) isomers enables complete bidirectional photoswitching.     

ISOMERIZATION OF THE RETINYLIDENE CHROMOPHORE OF BACTERIORHODOPSIN IN LIGHT ADAPTATION: INTRINSIC ISOMERIZATION OF THE CHROMOPHORE AND ITS CONTROL BY THE APO-PROTEIN

Abstract— The dependence of the isomeric configuration of the retinylidene chromophore of bacteriorhodopsin on the pH value and on the wavelength of irradiation (in a photostationary state) were examined by high performance liquid chromatographic analyses of extracted retinal. The process of isomerization of the chromophore during light adaptation was also traced. More than 93% of all- trans and less than 5% of 13- cis retinal were extracted in the photostationary state for irradiation at 560 nm in the pH region of5–9 as well as for irradiation in the wavelength region of 400–650 nm at pH 7. Comparison of the above photostationary state composition with that of protonated n -butylamine Schiff base of retinal indicates that strong constraint is applied to the chromophore by the apo-protein. The constraint can be changed at low or high pH by a partial denaturation or transition of the apo-protein, which results in the generation of 11- cis retinal in the extract. At higher photon density, the isomerization process of the chromophore during light adaptation at pH 7 was characterized, as extracted isomeric retinal, by (1) the initial decrease in 13- cis and increase in all- trans , (2) a subsequent, transient toward the above photostationary state composition. The results are discussed in terms of both the photoisomerization pattern inherent in the retinylidene chromophore and the control by the apo-protein.     

Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611

An important class of red fluorescent proteins (RFPs) feature a 2-iminomethyl-5-(4-hydroxybenzylidene)imidazolinone chromophore. Among these proteins, eqFP611 has the chromophore in a coplanar trans orientation, whereas the cis isomer is preferred by other RFPs such as DsRed and its variants. In the photoactivatable protein asFP595, the chromophore can even be switched from the nonfluorescent trans to the fluorescent cis state by light. By using X-ray crystallography, we have determined the structure of dimeric eqFP611 at high resolution (up to 1.1 A). In the far-red emitting eqFP611 variant d2RFP630, which carries an additional Asn143Ser mutation, the chromophore resides predominantly (approximately 80%) in the cis isomeric state, and in RFP639, which has Asn143Ser and Ser158Cys mutations, the chromophore is found completely in the cis form. The pronounced red shift of excitation and emission maxima of RFP639 can thus unambiguously be assigned to trans-cis isomerization of the chromophore. Among RFPs, eqFP611 is thus unique because its chromophore is highly fluorescent in both the cis and trans isomeric forms.     

Correlation between the molecular structure and photoresponse in aliphatic self-assembled monolayers with azobenzene tailgroups

We have compared the structural and photoisomerization properties of self-assembled monolayers (SAMs) comprising either the trans or cis isomers of azobenzene terminated dithiolane with in-chain amide unit, viz., 4-(phenyldiazenyl)phenyl-4-(1,2-dithiolane-3-yl)-butylcarboxamide ( 1). These films were prepared on Au(111) from solutions of both isomers. Structure and composition of the SAMs were studied by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The photoresponse of the films was monitored in real time by ellipsometry. SAMs fabricated from the trans isomer were found to be densely packed and highly ordered. These films did not show any discernible photoresponse upon irradiation with UV light, which, under favorable conditions, triggers the trans- cis isomerization. In contrast, films prepared from solutions containing predominantly the cis isomer were loosely packed and mostly disordered but exhibited reversible photoreactivity. The results confirm that steric effects, i.e., available free volume, play a dominant role for the photoresponse of aliphatic SAMs bearing the photoactive azobenzene group. The crystal structure of 1 ( trans isomer) exhibits a row-like aggregation of neighboring molecules by weak hydrogen bonds and can be taken as a model for the arrangement of 1 in the monolayer films. Further, in addition to the surface coordination behavior, we have also mimicked the chemisorption of the 1,2-dithiolane moiety onto the gold substrate in molecular coordination chemistry in oxidative addition reactions with the zero-valent platinum complex [Pt(PPh 3) 4].     

SPECTROSCOPIC BEHAVIOUR OF RETINYL POLYENES IN SOLID FILMS

Abstract— The absorption spectroscopic study of retinyl polyenes, i.e. all- trans retinal, 9- cis retinal, 13- cis retinal, all- trans retinol, 13- cis retinol and all- trans retinyl acetate in solid films is discussed. The spectra of the films with low surface coverages obtained from dilute solutions are red shifted relative to their solution spectra. This shift is interpreted as due to the weak interaction between the surface and polyene molecules. With increased surface coverages, i.e. the films obtained from concentrated solutions, the retinals show a large red shift whereas a blue shift is observed with the retinols. Chromophore–chromophore interactions in addition to the surface effects are believed to be responsible for such observations. Effect of surface causing permanent changes in molecule is also discussed.     

Synthesis and Surface-Active Properties of New Photosensitive Surfactants Containing the Azobenzene Group

Several water-soluble cationic surfactants, 4-alkylazobenzene-4'-(oxy-2-hydroxypropyl)trimethylammonium methylsulfate (AZMS) (AZMS-0, AZMS-1, AZMS-2, AZMS-4, and AZMS-8), containing alkylglycidylether and azoarene have been synthesized with high yields of 63-78% and their surface-active properties have been investigated upon irradiation with UV/vis light. All of the trans-AZMS surfactants are isomerized to cis-trans mixtures containing 92.5% cis isomer by UV light irradiation at 350 nm. The cis isomers in the mixtures are reverted to trans isomers by visible light irradiation (lambda>445 nm). Such photoisomerization induces changes in the surface activity of each surfactant. The critical micelle concentration (cmc) of the trans form of AZMS-8 surfactant is about 1.28x10(-4) mol/l. At the photostationary state, 92.5% of the trans form is changed to the cis form which exhibits a slightly higher cmc (3.41x10(-4) mol/l). The new cmc of AZMS surfactants upon photoisomerization is similar to that of the ideal mixed micellar system. In particular, the ratio of cmc(cis) to cmc(trans) of AZMS derivatives is about 1.87-2.85 which increases proportionally with the chain length of alkyl group. The minimum average area per molecule (A(min)(a/w)) for the trans and cis isomers of AZMS-8 is 0.60 and 0.74 nm(2), respectively. The difference in the A(min)(a/w) may originate from the structural differences in the two isomers. These values are quite different as compared to those of the conventional azobenzene surfactants. Copyright 2000 Academic Press.     

Azobenzene photoswitching without ultraviolet light

Most azobenzene-based photoswitches use UV light for photoisomerization. This can limit their application in biological systems, where UV light can trigger unwanted responses, including cellular apoptosis. We have found that substitution of all four ortho positions with methoxy groups in an amidoazobenzene derivative leads to a substantial (~35 nm) red shift of the n-π* band of the trans isomer, separating it from the cis n-π* transition. This red shift makes trans-to-cis photoswitching possible using green light (530-560 nm). The cis state is thermally stable with a half-life of ~2.4 days in the dark in aqueous solution. Reverse (cis-to-trans) photoswitching can be accomplished with blue light (460 nm), so bidirectional photoswitching between thermally stable isomers is possible without using UV light at all.     

Polymerization of diacetylenes by hydrogen bond templated adlayer formation

Adlayers were formed on self-assembled monolayers (SAMs) formed by alkanethiols on gold. Base SAMs exposing amide functional groups at the SAM surface were formed with 12-mercaptododecanamide. Adlayers of diacetylene-containing monomers were then formed via amide hydrogen bonding in decalin and decalin/toluene mixtures. Grazing angle FTIR, contact angle measurements, and ellipsometry suggest that these adlayer films exhibit ordering and packing similar to that of SAMs on gold. Resonance Raman spectroscopy showed that these diacetylene adlayers could be readily polymerized by exposure to UV light.     

FACILE CHARACTERIZATION OF THE SPECTRA OF cis AND trans PHOTOISOMERS IN A MIXTURE OF ACYL-ENZYMES BY RAMAN DIFFERENCE SPECTROSCOPY

Abstract Raman difference spectroscopy is used to provide the spectra of both the cis and trans forms of acryloyl-based acyl enzymes from a mixture without resorting to purification. A mixture of cis and trans , about the-C=C-C(=O) ethylenic linkage, is generated photochemically and by subtracting the Raman spectrum of the mixture from the spectrum of the pure trans form prior to photochemical irradiation, Raman peaks of the trans acyl-enzyme appear as "negative" features and of the cis form appear as "positive" features. No operator intervention is required to scale the spectra for subtraction, and thus information on the relative Raman scattering efficiencies of the cis and trans isomers can be obtained immediately from the data. Results for 5-methylthienylacryloyl chymotrypsin confirm earlier data for the purified cis and trans forms and data for cis indoleacryloyl chymotrypsin are presented for the first time.     

trans-cis Photoisomerization of a photoactive yellow protein model chromophore in crystalline phase

We have studied the photoinduced trans/cis isomerization of the protonated form of p-hydroxycinnamic thiophenyl ester, a model chromophore of the photoactive yellow protein (PYP), in crystalline phase, by both fluorescence and infrared spectroscopies. The conversion from trans to cis configuration is revealed by a shift of the fluorescence peak and by inspection of the infrared maker bands. The crystal packing apparently stabilizes the cis photoproduct, suggesting different environmental effects from the solvent molecules for this model chromophore in liquid solutions or from the amino acid residues for the PYP chromophore.     

AN IMPROVED HPLC METHOD FOR THE SEPARATION OF RETINALDEHYDE ISOMERS FROM VISUAL PIGMENTS

Abstract— A method for the analytical separation of retinal isomers such as 13- cis , 11- cis , 9- cis and all- trans retinal, dissolved in aqueous solutions of detergents, is described. The retinals are extracted by means of a non-isomerizing procedure and separated by HPLC on an octadecyl silane column used in normal phase. This column retains detergents without deteriorating and gives a satisfactory separation of retinal isomers with a resolution comparable with that obtained with silica gel column. The reliability of the method is verified by analysing the chromophore of visual pigment rhodopsin in digitonin solution, before and after irradiation with white light.     

Controlling Radical Formation in the Photoactive Yellow Protein Chromophore

To understand how photoactive proteins function, it is necessary to understand the photoresponse of the chromophore. Photoactive yellow protein (PYP) is a prototypical signaling protein. Blue light triggers trans–cis isomerization of the chromophore covalently bound within PYP as the first step in a photocycle that results in the host bacterium moving away from potentially harmful light. At higher energies, photoabsorption has the potential to create radicals and free electrons; however, this process is largely unexplored. Here, we use photoelectron spectroscopy and quantum chemistry calculations to show that the molecular structure and conformation of the isolated PYP chromophore can be exploited to control the competition between trans–cis isomerization and radical formation. We also find evidence to suggest that one of the roles of the protein is to impede radical formation in PYP by preventing torsional motion in the electronic ground state of the chromophore.     

8-hydroxyquinoline monomer, water adducts, and dimer. Environmental influences on structure, spectroscopic properties, and relative stability of cis and trans conformers

The low fluorescence quantum yield of 8-hydroxyquinoline cannot be correctly interpreted without knowing the form that such a compound assumes in different environments. The commonly accepted emission-quenching excited-state proton transfer can follow different reaction paths if 8-hydroxyquinoline is dimeric or monomeric or if it exists in the form of cis and trans conformers; in this light, the knowledge of the compound form in a particular environment is basic. We have performed a spectroscopic and computational investigation aimed at the determination of the form of 8-hydroxyquinoline in different solvents. UV-vis, fluorescence, and IR spectral features have been assigned by ab initio computations based on the density functional theory and time-dependent density functional theory; the density functional theory and MP2 computations have been applied to the determination of the relative stability of the dimeric and monomeric cis and trans forms of 8-hydroxyquinoline in different solvents. Molecular dynamics computations have been used to determine the compound behavior in water solutions. According to our results, 8-hydroxyquinoline shows a clear preference for the cis conformation (as dimer or monomer), but, in water solutions, a small fraction of the trans conformation is also present.     

Light-driven molecular hinge: a new molecular machine showing a light-intensity-dependent photoresponse that utilizes the trans-cis isomerization of azobenzene

[reaction: see text] A new class of molecular machine exhibits a hingelike motion upon photoirradiation. The motion (close and open) can be operated by alternate irradiation with UV and visible light. The trans/trans and cis/cis isomers are thermally stable at 40 degrees C, and the photochemical closure reaction (from trans/trans to cis/cis isomer) is dependent on the intensity of the light used because of the short-lived intermediate (trans/cis isomer).     

Surface modification of functional self-assembled monolayers on 316L stainless steel via lipase catalysis

Lipase catalyzed esterification of therapeutic drugs to functional self-assembled monolayers (SAMs) on 316L stainless steel (SS) after assembly has been demonstrated. SAMs of 16-mercaptohexadecanoic acid (-COOH SAM) and 11-mercapto-1-undecanol (-OH SAM) were formed on 316L SS, and lipase catalysis was used to attach therapeutic drugs, perphenazine and ibuprofen, respectively, on these SAMs. The reaction was carried out in toluene at 60 degrees C for 5 h using Novozyme-435 as the biocatalyst. The FTIR spectra after surface modification of -OH SAMs showed the presence of the C=O stretching bands at 1745 cm(-1), which was absent in the FTIR spectra of -OH SAMs. Similarly, the FTIR spectra after the reaction of the -COOH SAM with perphenazine showed two peaks in the carbonyl region, a peak at 1764 cm(-1), which is the representative peak for the C=O stretching for esters. The second peak at 1681 cm(-1) is assigned to the C=O stretching of the remaining unreacted terminal COOH. XPS spectra after lipase catalysis with ibuprofen showed a photoelectron peak evolving at 288.5 eV which arises from the carbon (C=O) of the carboxylic acid of the drug (ibuprofen). Similarly for -COOH SAMs, after esterifiation we see a small, photoelectron peak evolving at 286.5 eV which corresponds to the C in the methylene groups adjacent to the oxygen (C-O), which should evolve only after the esterification of perphenazine with the -COOH SAM. Thus, lipase catalysis provides an alternate synthetic methodology for surface modification of functional SAMs after assembly.     

PHOTOCHEMISTRY OF RETINOCHROME

Abstract— Retinochrome is a photopigment found in the visual cells of cephalopods. It has been considered to act as a supplier of the 11- cis -retinal required for synthesis of rhodopsin, because its all-trans chromophore is isomerized to 11- cis form in the light. Light and thermal reactions of squid retinochrome were investigated by low-temperature spectrophotometry.
On irradiation with green light at liquid-nitrogen temperature, retinochrome (λ_max 496 nm, – 190°C) is converted mainly to an intermediate lumiretinochrome (λ_max 475 nm, – 190°C), its chromophore being changed to 11- cis -retinal. On irradiation with blue light at - 190°C, retinochrome is changed to a photosteady–state mixture (λ_max 487 nm, – 190°C) composed mainly of retinochrome and lumiretinochrome, since lumiretinochrome is partially regenerated back to retinochrome. Similarly, irradiation of lumiretinochrome with blue light also results in the same photosteady-state mixture, which can be completely reverted to lumiretinochrome on re-irradiation with green light.
Lumiretinochrome is stable at a wide range of temperatures from – 190°C to about – 20°C. Above – 20°C, it is further converted, thermally, into metaretinochrome (λ_max 470 nm), which is the same bleached product as has been observed on irradiation of retinochrome at room temperatures. Thus, the light-bleaching process of retinochrome is rather simple compared with that of rhodopsin.     

Photochemical patterning of a self-assembled monolayer of 7-diazomethylcarbonyl-2,4,9-trithiaadmantane on gold films via Wolff rearrangement

Photolithographic attachment of functional organic molecules via ester or amide linkages to self-assembled monolayers (SAMs) on gold thin films was achieved by employing a novel photoreactive surface anchor, 7-diazomethylcarbonyl-2,4,9-trithiaadmantane. The photoreactive SAM was prepared by the spontaneous physical adsorption of the photoreactive surface anchor onto gold surfaces. The alpha-diazo ketone moiety of the SAM was found to display the classical Wolff rearrangement reactivity to produce a ketene intermediate on the exposed area. Organic molecules such as alcohols and amines can thus be attached to the gold surfaces selectively by the facile in situ formation of ester or amide linkages. The structure and reactivity of the photoreactive surface anchor were characterized by real-time FT-IR, fluorescence, and polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS). The Wolff rearrangement reactivity of the SAM suggested that a "surface-isolated" carbonylcarbene may be generated when the SAM was exposed to 255-nm irradiation.