Ultrafast fluorescence resonance energy transfer in a bile salt aggregate: Excitation wavelength dependence

Fluorescence resonance energy transfer (FRET) from Coumarin 153 (C153) to Rhodamine 6G (R6G) in a secondary aggregate of a bile salt (sodium deoxycholate, NaDC) is studied by femtosecond up-conversion. The emission spectrum of C153 in NaDC is analysed in terms of two spectra-one with emission maximum at 480 nm which corresponds to a non-polar and hydrophobic site and another with maximum at ∼530 nm which arises from a polar hydrophilic site. The time constants of FRET were obtained from the rise time of the emission of the acceptor (R6G). In the NaDC aggregate, FRET occurs in multiple time scales — 4 ps and 3700 ps. The 4 ps component is assigned to FRET from a donor (D) to an acceptor (A) held at a close distance (R _DA ∼ 17 ?) inside the bile salt aggregate. The 3700 ps component corresponds to a donor-acceptor distance ∼48 ?. The long (3700 ps) component may involve diffusion of the donor. With increase in the excitation wavelength (λ _ex) from 375 to 435 nm, the relative contribution of the ultrafast component of FRET (∼4 ps) increases from 3 to 40% with a concomitant decrease in the contribution of the ultraslow component (∼3700 ps) from 97 to 60%. The λ _ex dependence is attributed to the presence of donors at different locations. At a long λ _ex (435 nm) donors in the highly polar peripheral region are excited. A short λ _ex (375 nm) ‘selects’ donor at a hydrophobic location.     

Materials for fluorescence resonance energy transfer analysis: beyond traditional donor-acceptor combinations

The use of F?rster or fluorescence resonance energy transfer (FRET) as a spectroscopic technique has been in practice for over 50 years. A search of ISI Web of Science with just the acronym "FRET" returns more than 2300 citations from various areas such as structural elucidation of biological molecules and their interactions, in vitro assays, in vivo monitoring in cellular research, nucleic acid analysis, signal transduction, light harvesting and metallic nanomaterials. The advent of new classes of fluorophores including nanocrystals, nanoparticles, polymers, and genetically encoded proteins, in conjunction with ever more sophisticated equipment, has been vital in this development. This review gives a critical overview of the major classes of fluorophore materials that may act as donor, acceptor, or both in a FRET configuration. We focus in particular on the benefits and limitations of these materials and their combinations, as well as the available methods of bioconjugation.     

Benzoyl transfer reactivities of racemic 2,4-di-O-acyl-myo-inosityl 1,3,5-orthoesters in the solid state: molecular packing and intermolecular interactions correlate with the ease of the reaction

Racemic 2,4-di-O-acyl-myo-inosityl 1,3,5-orthoesters undergo transesterification catalyzed by sodium carbonate with varying ease of reaction in the solid state; reactions in solution and melt do not show such varied differences. An interesting crystal of a 1:1 molecular complex of highly reactive racemic 2,4-di-O-benzoyl-myo-inosityl 1,3,5-orthoformate and its orthoacetate analogue exhibited better reactivity than the latter component alone. Single-crystal X-ray structures of the reactants have been correlated with the observed differences in the acyl-transfer efficiencies in the solid state. Although each of the derivatives helically self-assembles around the crystallographic 2(1) axis linked through O-H...O hydrogen bonding, the pre-organization of the reactive groups (C=O [El] and OH [Nu]), C-H...O and the C-H...pi interactions are significantly more favourable for the reactive derivatives than the less reactive ones. Bond-length distributions also showed differences; the O-C bond of the axial benzoyl group, which gets cleaved during the reaction, is longer (1.345-1.361 A) relative to the chemically equivalent O-C bond of the equatorial benzoyl group (1.316-1.344 A) in the reactive derivatives. These bond-length differences are not significant in the less reactive derivatives. The overall molecular organization is different too; the strikingly discrete helices, which may be viewed as "reaction tunnels" and are held by interhelical interactions, are clearly evident in the reactive derivatives in comparison with the less reactive ones.     

Ground state isomerism in betacarboline hydrogen bond complexes: The charge transfer nature of its large Stokes shifted emission

The hydrogen bonding and excited state proton transfer reactions between betacarboline, 9H-pyrido[3,4-b]indole, BC, and 1,1,1,3,3,3-hexafluoropropan-2-ol, HFIP, have been studied in the aprotic solvents cyclohexane and toluene by absorption, steady state and time resolved fluorescence measurements. On the basis of these results and those of previous works (Refs. [A. Sánchez-Coronilla, C. Carmona, M.A. Muñoz, M. Balón, Chem. Phys., 327 (2006) 70] and [A. Sánchez-Coronilla, M. Balón, M.A. Muñoz, C. Carmona, Chem. Phys. 344 (2008) 72]) two main fundamental conclusions can be drawn on the photophysical behaviour of BC. Thus, it is shown, for the first time, that the non-cyclic double hydrogen bond complexes formed through both nitrogen atoms of BC, DHB, can suffer, in their ground state, an isomerisation process. These adducts acquire a quinoid structure in cyclohexane, but maintain a dipolar zwitterionic structure in toluene. Moreover, it is concluded that the observed large Stokes shifted emission, around 520 nm, is not due, as it has been so far generally accepted, to the emission of a BC zwitterionic phototautomer, but to the intramolecular charge transfer, ICT, excited state emissions of the DHB hydrogen bond adducts.     

Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system

The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.     

固相萃取-高效液相色谱-串联质谱法检测香辛料中罗丹明B

建立了香辛料中罗丹明B的固相萃取-高效液相色谱-串联质谱分析方法。样品经乙腈提取后离心,在提取液中加入10 mL 1%三氯乙酸溶液后,用Bond Elut Plexa PCX强阳离子固相萃取柱净化、富集,Pursuit C18色谱柱(100 mm×2.0 mm, 3 μm)分离,以0.1%甲酸水和甲醇为流动相梯度洗脱,电喷雾电离正离子模式下多反应监测(MRM)模式进行定性、定量检测。结果表明,在0.6～6 μg/L范围内的线性相关系数R2＞0.99;方法的定量限为1.2 μg/kg;添加量分别为1.197、2.992及5.985 μg/L时的加标回收率为80%～121%,相对标准偏差＜15%。同时对流动相的洗脱梯度、提取溶剂、固相萃取柱等条件进行了优化。该方法的专属性较强,基质效应较小,可用于固体香辛料产品中罗丹明B的定性、定量分析。     

Ultrafast dynamics in a nanocage of enzymes: solvation and fluorescence resonance energy transfer in reverse micelles

In this contribution we report studies of the nature of solvation and resonance energy transfer processes in a reverse micelle (RM) upon encapsulation of a digestive enzyme, alpha-chymotrypsin (CHT). We have used one donor, Coumarin 500 (C500), and three acceptors Rhodamine 123 (R123, cationic), ethidium bromide (EtBr, cationic), and Merocyanine 540 (MC540, anionic). By selectively exciting the donor at the surface of the RM with a proper excitation wavelength we have examined solvation dynamics in the microenvironment. The solvation correlation function in the RM without CHT exhibits single-exponential decay with time constant approximately 660 ps, which is similar to that of the CHT-included RM. However, in the case of CHT-included RM (w(0)=10), the time-resolved anisotropy and spectral linewidth analysis of the surface-bound donor reveal the existence of an annular aqueous channel of thickness approximately 2.5 A between the enzyme surface and the inner surface of the RM. The aqueous channel is a potential host for the water-soluble substrate and also is involved in maintaining the proper functionality of RM encapsulated CHT. The studies use both steady-state and time-resolved fluorescence resonance energy transfer (FRET) techniques to measure donor-acceptor distances in the RM and also emphasize the danger of using steady-state fluorescence quenching as a method in careful estimation of the distances. The local geometrical restriction on the donor and acceptor molecules was estimated from time-resolved polarization (anisotropy) measurements. The time-resolved anisotropy of the donor and acceptor molecules also revealed significant randomization of the relative orientation of transition dipoles of the donor and acceptor, justifying the use of 2/3 as the value of the orientation factor kappa2. These studies attempt to elucidate the excellence of the RM as a nanohost of biological macromolecules.     

Development of a fluorescence model for the determination of constants associated with binding,quenching, and Förster resonance energy transfer efficiency

Determining accurate dissociation constants for equilibrium processes involving a fluorescent mechanism can prove to be quite challenging. Typically, titration curves and nonlinear least squares fitting of the data using computer programs are employed to obtain such constants. However, these approaches only consider the total fluorescence signal and often ignore other energy transfer processes within the system. The current model considers the impact on fluorescence from equilibrium binding (viz., metal-ligand, ligand-substrate, etc.), quenching, and resonance energy transfer. This model should provide more accurate binding constant as well as insights into other photonic processes. The equations developed for this model are discussed and are applied to experimental data from titrimetric experiments. Since the experimental data are generally in excess of the number of parameters that are needed to define the system, fitting is operated in an overdetermined mode and employs error minimization (either absolute or relative) to define goodness of fit. Examples of how changes in certain parameters affect the shape of the titrimetric curve are also presented. The current model does not consider chelation-enhanced fluorescence.     

Inequivalence of substitution pairs in hydroxynaphthaldehyde: A theoretical measurement by intramolecular hydrogen bond strength,aromaticity, and excited‐state intramolecular proton transfer reaction

The inequivalence of substitution pair positions of naphthalene ring has been investigated by a theoretical measurement of hydrogen bond strength, aromaticity, and excited state intramolecular proton transfer (ESIPT) reaction as the tools in three substituted naphthalene compounds viz 1‐hydroxy‐2‐naphthaldehyde (HN12), 2‐hydroxy‐1‐naphthaldehyde (HN21), and 2‐hydroxy‐3‐naphthaldehyde (HN23). The difference in intramolecular hydrogen bond (IMHB) strength clearly reflects the inequivalence of substitution pairs where the calculated IMHB strength is found to be greater for HN12 and HN21 than HN23. The H‐bonding interactions have been explored by calculation of electron density ρ(r) and Laplacian ?²ρ(r) at the bond critical point using atoms in molecule method and by calculation of interaction between σ* of OH with lone pair of carbonyl oxygen atom using NBO analysis. The ground and excited state potential energy surfaces (PESs) for the proton transfer reaction at HF (6‐31G**) and DFT (B3LYP/6‐31G**) levels are similar for HN12, HN21 and different for HN23. The computed aromaticity of the two rings of naphthalene moiety at B3LYP/6‐31G** method also predicts similarity between HN12 and HN21, but different for HN23. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Directional hydrogen bonding in the MM3 force field: II

Extensive calculations on hydrogen bonded systems were carried out using the improved MM3 directional hydrogen bond potential. The resulting total function was reoptimized. Comparisons of the hydrogen bonding potential function from ab initio calculations (MP2/6-31G**); the original MM3(89); and the reoptimized MM3 force field MM3(96), for a variety of C, N, O, and Cl systems including the formamide dimer and formamide–water complex, are described herein. Hydrogen bonding is shown to be a far more complicated and ubiquitous phenomenon than is generally recognized. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1001–1016, 1998     

Structural motifs in secondary ammonium halides: ring-stacking and ring-laddering in the organic solid state

The ring-stacking and ring-laddering concepts of structural inorganic chemistry may be applied to rationalize motifs observed for secondary ammonium halides R(2)NH(2)X (X = Cl, Br) in the organic solid state. General examination of the directional preferences of N(+)...X(-) contacts in 166 crystal structures confirms that the shortest contacts (3.0-3.2 and 3.2-3.4 A, X = Cl, Br) are N(+)-H...X(-) hydrogen bonds lying approximately along the directions of the N(+)-H bond vectors. The next shortest N(+)...X(-) contacts display two preferred directions of approach: i) contacts in the distance range 3.2-3.5 (X = Cl) and 3.2-3.9 A (X = Br) lie close to the H-N(+)-H plane, along the direction of the bisector of the H-N(+)-H angle; ii) contacts in the distance range 4.0-4.2 (X = Cl) and 4.0-4.4 A (X = Br) lie close to the H-N(+)-H plane, along the direction of an axis extending to the rear of one of the N(+)-H bonds. Both directions of approach lead frequently to association of R(2)NH(2) (+)X(-) ion pairs into laddered motifs. Stacking association is also observed, giving rise in one case to discrete cubanes and in several other cases to extended stacked-cube arrangements. In each case, the distribution of N(+)...X(-) contacts reflects a balance between the directional properties of the N(+)-H...X(-) hydrogen bonds and (primarily steric) interactions between the R groups of the organic moieties. The ladder and stack motifs of the organic ammonium halides are in many cases directly comparable to those in alkali metal amides, [R(2)NM](n), and information derived from the extensive organic sample provides insight into the motifs adopted by the inorganic complexes.     

Excited state intramolecular proton transfer in 5-hydroxy flavone: A DFT study

Potential energy surfaces (PES) for the ground and excited state intramolecular proton transfer (ESIPT) processes in 5-hydroxy-flavone (5HF) were studied using DFT-B3LYP/6-31G(d) and TD-DFT/6-31G(d) level of theory, respectively. Our calculations suggest the non-viability of ground state intramolecular proton transfer (GSIPT) in 5HF. Excited states PES calculations support the existence of ESIPT process in 5HF. ESIPT in 5HF has been explained in terms of HOMO, LUMO electron density of the enol and keto tautomer of 5HF. PES scan by phenyl group rotation suggests that the twisted form, i.e., phenyl group rotated by 18.7° out of benzo-γ-pyrone ring plane is the most stable conformer of 5HF.     

Single-molecule transistors: Electron transfer in the solid state

Single-molecule transistors (SMTs) incorporating individual small molecules are unique tools for examining the fundamental physics and chemistry of electronic transport in molecular systems at the single nanometer scale. We describe the fabrication and characterization of such devices, and the synthesis and surface attachment chemistry of novel transition metal complexes that have been incorporated into such SMTs. We present gate-modulated inelastic electron tunneling vibrational spectroscopy of single molecules, strong Kondo physics (T_K ∼ 75 K) as evidence of excellent molecule/electrode electronic coupling, and a demonstration that covalent attachment chemistry can produce SMTs that survive repeated thermal cycling to room temperature. We conclude with a look ahead at the prospects for these nanoscale systems.     

Synthesis and characterization of anthracene-clustering dendrimers: observation of fluorescence resonance energy transfer in the multichromophoric system

A series of anthracene-clustering dendrimers bearing various aliphatic substituents at the terminal positions were synthesized using a direct coupling strategy. A remarkable effect of the side chains was imparted to chemical properties of the dendrimers such as drastically increased solubility. Although the multibranched anthracene arrays in the dendritic architectures exhibited no cooperativity in terms of the absorption feature and behaved as single chromophoric systems, investigations focusing on fluorescence properties revealed that a type of cooperativity was present as expressed in the reduced quantum yields of fluorescence. An alternative approach utilizing time-resolved fluorescence decay measurements clearly demonstrated that the most reasonable mechanism of the cooperative action should involve two discernible channels of intramolecular fluorescence resonance energy transfer (FRET) occurring from one chromophore to the others within and across junctions of the branching units.     

Fluorescence resonance energy transfer (FRET) in chemistry and biology: Non-F?rster distance dependence of the FRET rate

Fluorescence resonance energy transfer (FRET) is a popular tool to study equilibrium and dynamical properties of polymers and biopolymers in condensed phases and is now widely used in conjunction with single molecule spectroscopy. In the data analysis, one usually employs the F?rster expression which predicts (l/R ⁶) distance dependence of the energy transfer rate. However, critical analysis shows that this e_xpression can be of rather limited validity in many cases. We demonstrate this by explicitly considering a donor-acceptor system, polyfluorene (PF₆)-tetraphenylporphyrin (TPP), where the size of both donor and acceptor is comparable to the distance separating them. In such cases, one may expect much weaker distance (as l/R ² or even weaker) dependence. We have also considered the case of energy transfer from a dye to a nanoparticle. Here we find l/R ⁴ distance dependence at large separations, completely different from F?rster. We also discuss recent application of FRET to study polymer conformational dynamics. Dedicated to Prof J Gopalakrishnan on his 62nd birthday.     

Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors

The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.     

An analytic potential energy function for the amide–amide and amide–water intermolecular hydrogen bonds in peptides

An analytic potential energy function is proposed and applied to evaluate the amide–amide and amide–water hydrogen‐bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen‐bonded training dimers. The analytic potential energy function is then employed to calculate the N? H…O?C, C? H…O?C, N? H…OH₂, and C?O…HOH hydrogen‐bonding interaction energies in amide–amide and amide–water dimers containing N‐methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N‐methylformamide, N‐methylpropanamide, N‐ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O…H) and the hydrogen‐bonding energies. The function is also applied to calculate the binding energies in models of β‐sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen‐bonding interaction energies in peptides quickly and accurately. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009