The photophysics of flavins: What makes the difference between gas phase and aqueous solution?

The ground and low-lying excited electronic states of isoalloxazine, 10-methylisoallox-azine and lumiflavin, three flavin-related compounds, were investigated by means of quantum chemical methods. Minimum structures were determined employing (time-dependent) Kohn–Sham density functional theory. Spectral properties were computed utilizing a combined density functional and multi-reference configuration interaction (DFT/MRCI) method. Solvent effects were mimicked by a conductor like screening model and micro-hydration with four explicit water molecules. At selected points along a linearly interpolated path connecting the Franck–Condon region and the S₁minimum, spin–orbit interaction was computed employing a nonempirical mean-field Hamiltonian. For isoalloxazine, intersystem crossing (ISC) rate constants were computed, taking both direct and vibronic spin–orbit coupling into account.On the basis of these calculations we suggest the following photo relaxation model. In the vacuum, efficient ISC takes place between the primarily excited state (S₁) and the lowest state (T₂). The energetic proximity of the state (S₂) enhances the nonradiative relaxation of S₁ by internal conversion (IC). In aqueous solution these ISC and IC channels are energetically not accessible due to the blue shift of the states. The high triplet quantum yield observed in experiment [J.T.M. Kennis, S. Crosson, M. Gauden, I.H.M. van Stokkum, K. Moffat, R. van Grondelle, Biochemistry 42 (2003) 3385–3392] is explained by the intersection between the state (S₁) potential energy hypersurface (PEH) and the second (T₂) PEH along the relaxation pathway and the strong enhancement of their spin–orbit coupling by vibronic interactions. The calculated ISC rate for this channel is in good agreement with experimental results. According to our model, lack of an efficient IC channel leads to an increased fluorescence quantum yield in aqueous solution.     

Comparison of the reactivity of β-thiolactones and β-lactones toward ring-opening by thiols and amines

An investigation into the comparative reactivity of simple β-lactones and β-thiolactones toward a thiol and a primary amine is reported. A simple 3-mercaptomethyl-2-oxetanone is found to undergo rearrangement in the presence of aqueous base to give the corresponding thietane-3-carboxylic acid rather than the 3-hydroxymethyl-2-thietanone. Implications for the use of β-thiolactones in bioorganic and medicinal chemistry are discussed.     

Low-temperature dynamics in amorphous polymers and low-molecular-weight glasses--what is the difference?

Numerous experiments have shown that the low-temperature dynamics of a wide variety of disordered solids is qualitatively universal. However, most of these results were obtained with ensemble-averaging techniques which hide the local parameters of the dynamic processes. We used single-molecule (SM) spectroscopy for direct observation of the dynamic processes in disordered solids with different internal structure and chemical composition. The surprising result is that the dynamics of low-molecular-weight glasses and short-chain polymers does not follow, on a microscopic level, the current concept of low-temperature glass dynamics. An extra contribution to the dynamics was detected causing irreproducible jumps and drifts of the SM spectra on timescales between milliseconds and minutes. In most matrices consisting of small molecules and oligomers, the spectral dynamics was so fast that SM spectra could hardly or not at all be recorded and only irregular fluorescence flares were observed. These results provide new mechanistic insight into the behavior of glasses in general: At low temperatures, the local dynamics of disordered solids is not universal but depends on the structure and chemical composition of the material.     

NR transfer reactivity of azo-compound I of P450. How does the nitrogen substituent tune the reactivity of the species toward C-H and C=C activation?

We studied electronic structures and reactivity patterns of azo-compound I species (RN-Cpd I) by comparison to O-Cpd I of, e.g., cytochrome P450. The study shows that the RN-Cpd I species are capable of C=C aziridination and C-H amidation, in a two-state mechanism similar to that of O-Cpd I. However, unlike O-Cpd I, here the nitrogen substituent (R) exerts a major impact on structure and reactivity. Thus, it is demonstrated that Fe=NR bonds of RN-Cpd I will generally be substantially longer than Fe=O bonds; electron-withdrawing R groups will generate a very long Fe=N bond, whereas electron-releasing R groups should have the opposite effect and hence a shorter Fe=N bond. The R substituent controls also the reactivity of RN-Cpd I toward C=C and C-H bonds by exerting steric and electronic effects. Our analysis shows that an electron-releasing substituent will lower the barriers for both bond activation reactions, since the electronic factor makes the reactions highly exothermic, while an electron-withdrawing one should raise both barriers. The steric bulk of the substituent is predicted to inhibit more strongly the aziridination reactions. It is predicted that electron-releasing substituents with small bulk will create powerful aziridination reagents, whereas electron-withdrawing substituents like MeSO(2) will prefer C-H bond activation with preference that increases with steric bulk. Finally, the study predicts (i) that the reactions of RN-Cpd I will be less stereospecific than those of O-Cpd I and (ii) that aziridination will be more stereoselective than amidation.     

Evidences for the relationship between surface structure and reactivity of goethite nanoparticles based on advanced molecular-probe methods

Surface properties of two goethites have been studied in order to compare the amount of acid surface sites and their distribution over the various surface domains. For this purpose, ammonia, pyridine and nitrogen were used as basic molecular probes. Calorimetry measurements of ammonia adsorption provided the image of the average surface acidity being moderate. This conclusion was supported by the moderate resistance of the adsorbed pyridine molecules to degassing conditions. Adsorption and desorption of pyridine prior to gaseous nitrogen adsorption resulting in masking/unmasking of acid surface sites on the goethite surface allowed confirmation of the acid character of the specific adsorption sites characterized by the high-energy adsorption of electron-donating molecular nitrogen. The amount of acid sites probed by nitrogen and ammonia were of the same order of magnitude but systematically higher for ammonia. The subsequent analysis of the argon and nitrogen derivatives of first-layer adsorption isotherm led to determine the distribution of {101} and {121} crystallographic faces and discuss the location of acid sites on these surface domains.     

Is there a difference between leads and drugs? A historical perspective

To be considered for further development, lead structures should display the following properties: (1) simple chemical features, amenable for chemistry optimization; (2) membership to an established SAR series; (3) favorable patent situation; and (4) good absorption, distribution, metabolism, and excretion (ADME) properties. There are two distinct categories of leads: those that lack any therapeutic use (i.e., "pure" leads), and those that are marketed drugs themselves but have been altered to yield novel drugs. We have previously analyzed the design of leadlike combinatorial libraries starting from 18 lead and drug pairs of structures (S. J. Teague et al. Angew. Chem., Int. Ed. Engl. 1999, 38, 3743-3748). Here, we report results based on an extended dataset of 96 lead-drug pairs, of which 62 are lead structures that are not marketed as drugs, and 75 are drugs that are not presumably used as leads. We examined the following properties: MW (molecular weight), CMR (the calculated molecular refractivity), RNG (the number of rings), RTB (the number of rotatable bonds), the number of hydrogen bond donors (HDO) and acceptors (HAC), the calculated logarithm of the n-octanol/water partition (CLogP), the calculated logarithm of the distribution coefficient at pH 7.4 (LogD(74)), the Daylight-fingerprint druglike score (DFPS), and the property and pharmacophore features score (PPFS). The following differences were observed between the medians of drugs and leads: DeltaMW = 69; DeltaCMR = 1.8; DeltaRNG = DeltaHAC =1; DeltaRTB = 2; DeltaCLogP = 0.43; DeltaLogD(74) = 0.97; DeltaHDO = 0; DeltaDFPS = 0.15; DeltaPPFS = 0.12. Lead structures exhibit, on the average, less molecular complexity (less MW, less number of rings and rotatable bonds), are less hydrophobic (lower CLogP and LogD(74)), and less druglike (lower druglike scores). These findings indicate that the process of optimizing a lead into a drug results in more complex structures. This information should be used in the design of novel combinatorial libraries that are aimed at lead discovery.     

On the predictions and limitations of the Becker-Döring model for reaction kinetics in micellar surfactant solutions

We investigate the breakdown of a system of micellar aggregates in a surfactant solution following an order-one dilution. We derive a mathematical model based on the Becker-D?ring system of equations, using realistic expressions for the reaction constants fit to results from Molecular Dynamics simulations. We exploit the largeness of typical aggregation numbers to derive a continuum model, substituting a large system of ordinary differential equations for a partial differential equation in two independent variables: time and aggregate size. Numerical solutions demonstrate that re-equilibration occurs in two distinct stages over well-separated timescales, in agreement with experiment and with previous theories. We conclude by exposing a limitation in the Becker-D?ring theory for re-equilibration of surfactant solutions.     

Selective bromination of the aromatic ring in ω-phenylpolyoxaalkanes and alkanols in micelles

The regioselectivity of bromination of ω -phenylpolyoxaalkanes and alkanols by bromine in aqueous solution of dodecyl sulfate (SDS) and aqueous solution of cetyltrimethylammonium bromide (CTAB) are shown to be related to the average orientation of substrate as indicated by ¹H NMR studies. Thus ortho-bromination is promoted at higher concentrations of the surfactant relative to pure water. In contrast, at an equal ratio of the surfactant and substrate para-bromination is promoted. The results are discussed with respect to the average orientation of substrate in a micellar microenvironment and the formation of an ether-bromine comples as possible bromination agent.     

The acid—base equilibria of dimethylphenols in the ground and the first excited singlet states

Measurements of the acidity constants in the ground (pK_a(S₀)) and the lowest excited singlet (pK_a(S₁)) states for 2,3-, 2,4-, 2,5-, 2,6-, 3,4- and 3,5-dimethylphenols in aqueous solution have been carried out spectrophotometrically at 25°C. The pK_a values in S₀ have been derived from the absorption spectra and the pK_a values in S₁ were estimated by means of the Forster cycle. It is found that the hydroxy group is more acidic in the first excited singlet than in the ground state.     

On the reactivity of metal and organometallic halides toward R3Sn?O?SnR3 systems

Interaction of metallic salts (M = Hg, Sb, and Te) with bis(triorganotin)oxide, (R₃Sn)₂O, where (R = C₆H₅, p‐CH₃C₆H₄, and cyclo‐C₆H₁₁) at room temperature proceeded with the simultaneous cleavage of the Sn C and Sn O bonds, invariably yielding R₂SnO along with other products. Thus the treatment of HgX₂ (X = Cl, CN, SCN) with (R₃Sn)₂O resulted in the formation of polymeric diorganotin oxide R₂SnO along with R₃SnX and RHgX derivatives. The reaction of SbCl₃ with (R₃Sn)₂O was found to give R₂SnO, R₃SnCl, and RSbCl₂, whereas interaction with SbCl₅ provided R₂SnO, R₂SnCl₂, and R₂SbCl₃. Treatment of TeCl₄ with (R₃Sn)₂O provided R₂SnO, R₃SnCl, and RTeCl₃ at room temperature. At reflux temperature, reaction of PhTeCl₃ with (R₃Sn)₂O yielded R₂SnO, R₃SnCl, and mixed diorganotellurium dichloride, RPhTeCl₂. The course of reaction indicated the instability of Sn O Sn system proceeding via a four‐centered mechanism, providing organometallic compounds in profitable yield. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:278–283, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20547     

Mercury in fish products: what’s the best for consumers between bluefin tuna and yellowfin tuna?

A total of 205 bluefin and yellowfin tuna samples were examined for mercury detection in order to verify possible differences and have a detailed risk assessment of the two tuna species. The results showed significant higher mercury concentration in muscle tissue of bluefin tuna respect yellowfin tuna (p < 0.001) with mean concentration of 0.84 mg/kg and maximum value of 1.94 mg/kg. These differences can be due the different biological and ecological aspects of the two tuna species and to different oceanographic aspects between Atlantic Ocean and Mediterranean sea. The results obtained in this study suggest an advisable containment of the sources of pollution and further studies on the closed-loop farming of bluefin tuna, in order to ensure the product safety.     

Does the concept of Clar's aromatic sextet work for dicationic forms of polycyclic aromatic hydrocarbons?--testing the model against charged systems in singlet and triplet states

The concept of Clar's π-electron aromatic sextet was tested against a set of polycyclic aromatic hydrocarbons in neutral and doubly charged forms. Systems containing different types of rings (in the context of Clar's concept) were chosen, including benzene, naphthalene, anthracene, phenanthrene and triphenylene. In the case of dicationic structures both singlet and triplet states were considered. It was found that for singlet state dicationic structures the concept of aromatic sextet could be applied and the local aromaticity could be discussed in the context of that model, whereas in the case of triplet state dicationic structures Clar's model rather failed. Different aromaticity indices based on various properties of molecular systems were applied for the purpose of the studies. The discussion about the interdependence between the values of different aromaticity indices applied to neutral and charged systems in singlet and triplet states is also included.     

What Is the Trait d’Union between Retroactivity and Molecular Communication Performance Limits?

Information exchange is a critical process in all communication systems, including biological ones. Retroactivity describes the load that downstream modules apply to their upstream systems in biological circuits. The motivation behind this work is that of integrating retroactivity, a concept proper of biochemical circuits, with the metrics defined in Information Theory and Digital Communications. This paper focuses on studying the impact of retroactivity on different biological signaling system models, which present analogies with well-known telecommunication systems. The mathematical analysis is performed both in the high and low molecular counts regime, by mean of the Chemical Master Equation and the Linear Noise Approximation, respectively. The main goal of this work is to provide analytical tools to maximize the reliable information exchange across different biomolecular circuit models. Results highlight how, in general, retroactivity harms communication performance. This negative effect can be mitigated by adding to the signaling circuit an independent upstream system that connects with the same pool of downstream circuits.     

Effective interactions between charged nanoparticles in water: What is left from the DLVO theory?

The keystone of the modelling of complex systems is the potential of mean force (PMF) between particles. This review focuses on recent numerical simulation studies that concern the computation of the PMF between charged nanoparticles in solution. Such simulations explicitly sample the configurations of the microions or water molecules over which the potential is averaged out. The studies rely on different levels of modelling and permit to quantify the relative amplitude of the different factors governing the interaction, such as the structure of the nanoparticle, the polarisability of microions, or hydrophobic interactions. We discuss the conditions in which the potential of mean force can safely be expressed as a DLVO potential, and why in some cases such a simple analytical expression cannot be used.     

Is the ring conformation the most critical parameter in lipase-catalysed acylation of cycloalkanols?

CAL-B catalysed the resolution of several five and six-membered cyclic beta-hydroxy esters efficiently with the exception of the cis-cyclohexanol (+/-)-4. When employing molecular modelling techniques the conformation turned out to be the most important determinant for their reactivity towards O-acetylation. In all cases, the R enantiomers reacted faster than the S enantiomers since the reactive intermediates of the former can adopt more favourable ring conformations and thus experience less steric hindrance in the active site. Furthermore, the minimised structure for the main conformer of R-4 showed that the axial hydrogens in the 3 and 5-positions with respect to the hydroxyl group prevent the enzymatic reaction.