Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.     

罗丹明B内酯单晶的生长及晶体结构

从含有罗丹明B的溶胶-凝胶中首次水热合成了罗丹明B内酯的单晶,并测定了其晶体结构。每个不对称单位含有两个独立分子。     

香豆素衍生物的荧光发射能计算及XC泛函的合理选择

采用含时密度泛函理论(TDDFT)与单激发组态相互作用(CIS)处理相结合的计算方案对香豆素系列15种已知荧光化合物的发射能进行了系统考察. 结果表明, 发射能与吸收能一样, 其计算值主要取决于交换-相关(XC)泛函的选择. 只要泛函选用得当, 在使用较小基组的TDDFT/6-31G(d)//CIS/3-21G(d)理论水平上即可使绝大部分化合物的实验发射能在精度达0.16 eV以内得以重现. 与吸收能计算不同的是, 无法选用单一的一种泛函来对全系列化合物的发射能作出满意的理论预测. 激发态无明显电荷转移的、7位上有氨(或胺)基取代或有氮原子相连的化合物, 其适用泛函为不含Hartree-Fock(HF)交换能的纯泛函OLYP和BLYP. 而激发态发生较大程度电荷转移的、3 位上有共轭取代基的衍生物, 其适用泛函则为含20%的HF交换成分的混合泛函B3LYP. 因此, 发射能计算中的XC泛函选择, 应同时考虑取代基团效应以及激发态的电子结构特征. 其中, 发射能计算值受XC泛函中HF交换能比例的影响十分敏感. 文中还对激发能计算中的溶剂效应校正方案和激发态几何优化精度的影响进行了讨论.     

Proper Choice of XC Functionals and Calculations of Fluorescence-Emitting Energies for Coumarin Derivatives

A scheme of time-dependent density functional theory (TDDFT) combined with single-excitation configuration interaction (CIS) approach was employed to make a detailed investigation of the emitting energy for fifteen well-known coumarin derivatives. The results showed that the predicted emitting energies as well as the absorption ones were dominated mainly by the exchange-correlation (XC) functional to be used. So long as a functional is properly chosen, the experimental emitting energy of most derivatives can be accurately reproduced within 0.16 eV by a calculation at the TDDFT/6-31G(d)//CIS/3-21G(d) theoretical level. It was found that, nevertheless, the hybrid functional, B3LYP, well predicted the absorption energies for all the fifteen coumarin derivatives but none of the functionals could work equally well for the emitting energy calculations. Two pure functionals, OLYP and BLYP, yield good emitting energies for the 7-aminocoumarins or derivatives with a N atom connected to 7-position, which exhibit inconspicuous charge transfer (CT) in their excited states, whereas the B3LYP hybrid functional, with 20% Hartree-Fock (HF) exchange energy, performs significantly better than OLYP and BLYP for those 3-substituted coumarins with larger CT in excited states. Thus, in comparison with the absorption energies, the selection of proper functionals for the emitting energy calculations becomes more complex. In all probability, it is effective and doable to choose an XC-functional with alterable fraction of HF exchange energy according to the composition and structure characteristics of molecule.     

Quantitative assessment of rhodamine spectra

With the development of single-molecule detection and super-resolution fluorescence imaging, rhodamine dyes gain new life. Through the modification of the N-substituents and the replacement of the oxygen atom in xanthene, the wavelength and brightness can be effectively changed. However, the spectra of rhodamine, especially due to the balance between ring-closed non-fluorescent lactone and ring-opened fluorescent zwitterion/cation, are sensitive to interference from various environmental factors. In this way, the spectral data of various rhodamines reported by different research groups under different test conditions lacked comparability, sometimes even lacked accuracy. In order to meet the requirements for the accuracy and uniformity of spectral data in the research of single molecule imaging and dye structure-fluorescence relationship study, we have tested the spectra of fifteen rhodamine dyes that cover the visible and near-infrared regions under exactly the same conditions. By studying the dependence of the spectra on dye concentrations, it was confirmed that 1 μmol/L was ideal for detection less from the interference of dye molecule aggregation. We provide comprehensive and reliable spectral data of these fifteen dyes, which are expected to be used as references for future research. And the direct comparison of different rhodamine spectra would help to understand the structure-fluorescence relationship of rhodamines.     

Thermal behavior of rhodamine 6G-TiO2 microspherical particles

An aerosol procedure was used for the preparation at room temperature of rhodamine 6G-doped TiO₂ spherical particles. The luminescence properties and in particular the lifetime of the trapped rhodamine 6G were studied by analysis of fluorescence decay kinetics which yields information about the entrapping medium. Lifetimes were resolved using variable-frequency (0.01–120 MHz) phase and modulation data. This information is important to understand the identity of the different rhodamine 6G emitting species, and the mechanism of interaction of the molecules with the surface. The evolution of the excitation and fluorescence spectra of rhodamine 6G-doped particles with thermal treatment at 70°C, and drying time was also evaluated.     

A Highly Photostable Near‐Infrared Labeling Agent Based on a Phospha‐rhodamine for Long‐Term and Deep Imaging

Various fluorescence microscopy techniques require bright NIR‐emitting fluorophores with high chemical and photostability. Now, the significant performance improvement of phosphorus‐substituted rhodamine dyes (PORs) upon substitution at the 9‐position with a 2,6‐dimethoxyphenyl group is reported. The thus obtained dye PREX 710 was used to stain mitochondria in living cells, which allowed long‐term and three‐color imaging in the vis‐NIR range. Moreover, the high fluorescence longevity of PREX 710 allows tracking a dye‐labeled biomolecule by single‐molecule microscopy under physiological conditions. Deep imaging of blood vessels in mice brain has also been achieved using the bright NIR‐emitting PREX 710‐dextran conjugate.     

Structural conversions of rhodamines in solution

A study has been made of the acidic ionization, structural conversions, and prototropic tautomerism of rhodamine chromogens in methanol and dimethyl sulfoxide, using IR, ¹³ C NMR, and electronic spectroscopy. The lactone structure has been established for the colorless form of rhodamines in DMSO. For rhodamine B in mixtures of water with DMSO, the lactone/zwitterion ratio has been estimated.V. I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences, Moscow 117975. Khar'kov State University, Khar'kov 310077. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 3, pp. 512–521, March, 1992.     

Ab initio study of the reaction of H2 with an AuPt3 cluster

The study of the interaction of a pyramidal tetramer of AuPt3 with H2 is carried out by means of Hartree-Fock self-consistent field (SCF) calculations using relativistic effective core potentials and multiconfigurational SCF plus multireference variational and perturbational on second-order Moller-Plesset configuration interaction calculations. The AuPt3-H2 interaction was carried out in C(s) symmetry. The three lowest electronic states X 2A", A 2A', and a 4A' of the bare cluster were considered in order to study this interaction. The AuPt3+H2 reaction by a Pt vertex shows that AuPt3 cluster in the three lowest-lying electronic states can spontaneously capture and dissociate the H2 molecule. While, by the AuPt2 face side, the AuPt3 cluster only in the A 2A' electronic state can capture and dissociate the H2 molecule after surmounting a small energy barrier. For the Au vertex, this cluster in the three electronic states can also spontaneously capture and dissociate the H2 molecule. On the other hand, by the Pt3 face side, the AuPt3 cluster is able to capture and dissociate the H2 molecule after surmounting energy barriers, where the AuPt3 (X 2A" and 4A'-H2 adsorption are slightly activated.     

Long-range interaction and the dynamics of nonadiabatic transitions in collisions of the I2(E) molecule with inert gas atoms

A special form of perturbation theory based on intermolecular interaction was used to analyze the contributions to the interaction energy between a homonuclear diatomic molecule with dipole-coupled electronic states n and n′ and a neutral particle A. At large distances, the energy of the system in both states n and n′ is determined by the induction contribution similar to the induction interaction of particle A and a polar molecule. The presence of a constant electric moment of particle A gives an electrostatic contribution to the matrix element of the nonadiabatic coupling of the states n and n′. The equations obtained were specialized to describe the interaction of the iodine molecule excited to ion-pair states with an inert gas atom and used as corrections to the potential energy surfaces of this system constructed within the diatomics-in-molecule approximation. The dynamics of transitions between the ion-pair states of the I₂ molecule induced by collisions with the Ar and He atoms was calculated. The results demonstrate the importance of correctly including long-range interaction.     

Aggregation-induced emission enhancement (AIEE)-active mechanofluorochromic tetraphenylethene derivative bearing a rhodamine unit

A novel tetraphenylethene derivative with a rhodamine unit was successfully synthesized via high-efficiency Suzuki coupling reaction. The highly solid-state emissive target fluorescent molecule exhibited significative aggregation-induced emission enhancement (AIEE) feature. Furthermore, the luminogen showed reversible mechanochromic luminescence behavior involving color change from orange to red. In addition, the powder X-ray diffraction (XRD) test results verified that the mechanofluorochromic phenomenon of luminogen 1 was attributed to a morphological transformation between the crystalline and amorphous states.     

Restriction of Molecular Twisting on a Gold Nanoparticle Surface

To understand the photophysical properties of intramolecular charge transfer (ICT) and twisted intramolecular charge transfer (TICT) states on a gold nanoparticle (Au NP) surface, we have designed and synthesized a new coumarin molecule (C3) that exists both as ICT and TICT states in its excited state in a polar environment. On a Au NP surface, an excited C3 molecule only exists as an ICT state owing to restricted molecular rotation of a diethylamino group; as a result, no conversion from the ICT to TICT state was observed. Selection of the preferential state of a molecule with dual emitting states can be helpful for selected biological applications.     

Ground and valence excited states of BI: a MR-CISD+Q study

Ab initio calculations on the valence electronic states of the BI molecule have been performed by using the entirely uncontracted all-electronic aug-cc-pVQZ (for the B atom) and Sadlej-pVTZ (for the I atom) basis sets and the internally contracted multireference singles and doubles configuration interaction method with Davidson size-extensively correction and Douglas-Kroll scalar relativistic correction. The potential energy curves of all valence states and the spectroscopic constants of bound states are fitted. It is the first time that the 12 Lambda-S states of BI molecule and all of the 23 Omega states generated from the former are studied in a theoretical way. Calculation results reproduce well most of the experimental data. The effects of the spin-orbit coupling and the avoided crossing rule between Omega states of the same symmetry are analyzed. The transition properties of the A3Pi0+, B3Pi1, and C1Pi1 states to the ground-state transitions are predicted, including the transition dipole moments, the Franck-Condon factors, and the radiative lifetimes. The radiative lifetime of the C1Pi1 state of BI molecule is less than 1 micros, while that of the A3Pi0+ and B3Pi1 states are the order of 1 ms.     

Intramolecular energy transfer in rhodamine–phthalocyanine conjugates

Conjugates of tetrasulphosubstituted zinc phthalocyanine with rhodamine 6G or rhodamine B have been synthesized and characterized to have four rhodamine 6G or average two rhodamine B residues per phthalocyanine molecule. The ionized conjugates (positive charge on the rhodamine part) are non-soluble in water. Photochemical and photophysical measurements, carried out in dimethylsulphoxide, have shown that the main result of conjugation is efficient intramolecular energy transfer from rhodamine to phthalocyanine part of molecular system. The conjugation results in about twofold decrease of quantum yields for photodegradation, fluorescence and singlet oxygen photogeneration.     

Total synthesis of novel D-ring-modified triptolide analogues: structure-cytotoxic activity relationship studies on the D-ring of triptolide

The total synthesis of a trans-position butenolide analogue of triptolide 3 and the semi-synthesis of analogue 4, with a furan ring, and compound 5, without a planar D-ring, are described. Studies into the antitumor activity of these compounds suggest that the five-membered unsaturated lactone ring (D-ring) of triptolide is essential to its potent anticancer activity and the C18 carbonyl group may exert an important influence on the interaction between triptolide and the target molecule(s) responsible for initiating their cytotoxic effects.     

Rhodamine B as ligand for affinity chromatography. Fixation studies onto cellulose by a curing method

Rhodamine B was post-grafted onto cellulose in order to be lately used for affinity chromatography as a biomimetic ligand. A curing method has been developed to bound rhodamine onto cellulose via esterification, by heating an intimate mixture of both, at different temperatures above 180 °C. The lactone form of rhodamine B has been proposed as the effective reactant generated in situ during the experimental conditions. Pursuing further improvements of the amount of rhodamine bound onto cellulose, identical experiments were carried out in the presence of catalytic amounts of zinc chloride and sodium hypophosphite. The grafted materials obtained were quantitatively and qualitatively characterized using SEM, tlc, GPC, EA, FT-IR and Vis spectroscopy.     

Differentiation between Shallow and Deep Charge Trap States on Single Poly(3‐hexylthiophene) Chains through Fluorescence Photon Statistics

Blinking of the photoluminescence (PL) emitted from individual conjugated polymer chains is one of the central observations made by single‐molecule spectroscopy (SMS). Important information, for example regarding excitation energy transfer, can be extracted by evaluating dynamic quenching. However, the nature of trap states, which are responsible for PL quenching, often remains obscured. We present a detailed investigation of the photon statistics of single poly(3‐hexylthiophene) (P3HT) chains obtained by SMS. The photon statistics provide a measure of the number and brightness of independently emitting areas on a single chain. These observables can be followed during blinking. A decrease in PL intensity is shown to be correlated with either 1) a decrease in the average brightness of the emitting sites; or 2) a decrease in the number of emitting regions. We attribute these phenomena to the formation of 1) shallow charge traps, which can weakly affect all emitting areas of a single chain at once; and 2) deep traps, which have a strong effect on small regions within the single chains.     

Synthesis and stability of small molecule probes for Pseudomonas aeruginosa quorum sensing modulation

The human pathogen Pseudomonas aeruginosa uses N-butyryl-L-homoserine lactone (BHL) and N-(3-oxododecanyl)-L-homoserine lactone (OdDHL) as small molecule intercellular signals in a phenomenon known as quorum sensing (QS). QS modulators are effective at attenuating P. aeruginosa virulence; therefore, they are a potential new class of antibacterial agent. The lactone in BHL and OdDHL is hydrolysed under physiological conditions. The hydrolysis proceeds at a rate faster than racemisation of the alpha-chiral centre. Non-hydrolysable, non-racemic analogues (small molecule probes) were designed and synthesised, replacing the lactone with a ketone. OdDHL analogues were found to be relatively unstable to decomposition unless they were difluorinated between the beta-keto amide. Stability studies on a non-hydrolysable, cyclohexanone analogue indicated that racemisation of the alpha-chiral centre was relatively slow. This analogue was assayed to show that the L-isomer is likely to be responsible for the QS autoinducing activity in P. aeruginosa and Serratia strain ATCC39006.     

A new Cu~(2+)-induced color reaction of a rhodamine derivative N-(3-carboxy)acryloyl rhodamine B hydrazide

A new rhodamine derivative,N-(3-carboxy)acryloyl rhodamine B hydrazide(CARB),has been synthesized,and its unusual spectroscopic reaction with Cu2+ has been investigated.The derivative exhibits a rapid and reversible non-fluorescent absorption upon coordination to Cu2+,which is a rather unusual phenomenon for rhodamine B derivatives.Stoichiometric measurements using the Job's method and the molar ratio method reveal that one CARB molecule combines two Cu2+ ions,and the two Cu2+ ions play different roles:one ...     

Substituent effect on exo stereoselectivity in the 1,3-Dipolar cycloaddition reaction of tulipalin A with nitrile ylides

1,3-Dipolar cycloaddition reactions of dihydro-3-methylene-2(3H)-furanone (tulipalin A) with various benzonitrile(p-X-benzylide) ylides prefer formation of exo-cycloadducts in the extent corresponding to an increasing electron donor character of the substituent X in the para-position of the benzylide phenyl ring of the 1,3-dipolar reagent. The substituent effect on diastereoselectivity of the 1,3-DC reaction is rationalized in terms of CH/pi interaction between the dipole and the dipolarophile in an exo-transition state. The determining role of such an interaction is demonstrated by the correlation of the observed diastereoselectivities with substituent Hammett sigma constants, which shows a small negative rho value. A certain contribution of CO/pi interaction between the lactone carbonyl and the substituted phenyl ring to mediation of the substituent effect is also discussed. The energy profiles of both reaction pathways were analyzed using DFT and RI-MP2 theoretical approaches. Calculated energy and structural differences between located transition states are consistent with reaction diastereoselectivities.