Single biomolecule imaging with frequency and force modulation in tapping-mode atomic force microscopy

A new intermittent-contact atomic force microscopy (AFM) mode (frequency and force modulation AFM, FFM-AFM) has been recently proposed to characterize soft samples. This method uses excitation force frequency and amplitude modulation to eliminate bistability and reduce the tip-sample forces. This letter describes theoretical modeling of FFM-AFM applied to a single bacteriorhodopsin molecule on a substrate, showing that its cross section can be measured without damage, in contrast to conventional tapping-mode AFM. Speculations are made regarding nonideal conditions and the ability of FFM-AFM to perform quantitative nanoelasticity measurements.     

Two-photon absorption in tetraphenylporphycenes: are porphycenes better candidates than porphyrins for providing optimal optical properties for two-photon photodynamic therapy?

Porphycenes are structural isomers of porphyrins that have many unique properties and features. In the present work, the resonant two-photon absorption of 2,7,12,17-tetraphenylporphycene (TPPo) and its palladium(II) complex (PdTPPo) has been investigated. The data obtained are compared to those from the isomeric compound, meso-tetraphenylporphyrin (TPP). Detection of phosphorescence from singlet molecular oxygen, O2(a(1)Delta(g)), produced upon irradiation of these compounds, was used to obtain two-photon excitation spectra and to quantify two-photon absorption cross sections, delta. In the spectral region of 750-850 nm, the two-photon absorption cross sections at the band maxima for both TPPo and PdTPPo, delta = 2280 and 1750 GM, respectively, are significantly larger than that for TPP. This difference is attributed to the phenomenon of so-called resonance enhancement; for the porphycenes, the two-photon transition is nearly resonant with a comparatively intense one-photon Q-band transition. The results of quantum mechanical calculations using density functional quadratic response theory are in excellent agreement with the experimental data and, as such, demonstrate that comparatively high-level quantum chemical methods can be used to interpret and predict nonlinear optical properties from such large molecular systems. One important point realized through these experiments and calculations is that one must exercise caution when using qualitative molecular-symmetry-derived arguments to predict the expected spectral relationship between allowed one- and two-photon transitions. From a practical perspective, this study establishes that, in comparison to porphyrins and other tetrapyrrolic macrocyclic systems, porphycenes exhibit many desirable attributes for use as sensitizers in two-photon initiated photodynamic therapy.     

Application of hydrocyanic acid vapor generation via focused microwave radiation to the preparation of industrial effluent samples prior to free and total cyanide determinations by spectrophotometric flow injection analysis

A sample preparation procedure for the quantitative determination of free and total cyanides in industrial effluents has been developed that involves hydrocyanic acid vapor generation via focused microwave radiation. Hydrocyanic acid vapor was generated from free cyanides using only 5 min of irradiation time (90 W power) and a purge time of 5 min. The HCN generated was absorbed into an accepting NaOH solution using very simple glassware apparatus that was appropriate for the microwave oven cavity. After that, the cyanide concentration was determined within 90 s using a well-known spectrophotometric flow injection analysis system. Total cyanide analysis required 15 min irradiation time (90 W power), as well as chemical conditions such as the presence of EDTA–acetate buffer solution or ascorbic acid, depending on the effluent to be analyzed (petroleum refinery or electroplating effluents, respectively). The detection limit was 0.018 mg CN l⁻¹ (quantification limit of 0.05 mg CN l⁻¹), and the measured RSD was better than 8% for ten independent analyses of effluent samples (1.4 mg l⁻¹ cyanide). The accuracy of the procedure was assessed via analyte spiking (with free and complex cyanides) and by performing an independent sample analysis based on the standard methodology recommended by the APHA for comparison. The sample preparation procedure takes only 10 min for free and 20 min for total cyanide, making this procedure much faster than traditional methodologies (conventional heating and distillation), which are time-consuming (they require at least 1 h). Samples from oil (sour and stripping tower bottom waters) and electroplating effluents were analyzed successfully.     

High-sensitivity analysis of specific peptides in complex samples by selected MS/MS ion monitoring and linear ion trap mass spectrometry: application to biological studies

Mass spectrometry (MS) is a technique of paramount importance in Proteomics, and developments in this field have been possible owing to novel MS instrumentation, experimental strategies, and bioinformatics tools. Today it is possible to identify and determine relative expression levels of thousands of proteins in a biological system by MS analysis of peptides produced by proteolytic digestion. In some situations, however, the precise characterization of a particular peptide species in a very complex peptide mixture is needed. While single-fragment ion-based scanning modes such as selected ion reaction monitoring (SIRM) or consecutive reaction monitoring (CRM) may be highly sensitive, they do not produce MS/MS information and their actual specificity must be determined in advance, a prerequisite that is not usually met in a basic research context. In such cases, the MS detector may be programmed to perform continuous MS/MS spectra on the peptide ion of interest in order to obtain structural information. This selected MS/MS ion monitoring (SMIM) mode has a number of advantages that are fully exploited by MS detectors that, like the linear ion trap, are characterized by high scanning speeds. In this work, we show some applications of this technique in the context of biological studies. These results were obtained by selecting an appropriate combination of scans according to the purpose of each one of these research scenarios. They include highly specific identification of proteins present in low amounts, characterization and relative quantification of post-translational modifications such as phosphorylation and S-nitrosylation and species-specific peptide identification.     

New insight into the gas-phase bimolecular self-reaction of the HOO radical

The singlet and triplet potential energy surfaces (PESs) for the gas-phase bimolecular self-reaction of HOO*, a key reaction in atmospheric environments, have been investigated by means of quantum-mechanical electronic structure methods (CASSCF and CASPT2). All the reaction pathways on both PESs consist of a first step involving the barrierless formation of a prereactive doubly hydrogen-bonded complex, which is a diradical species lying about 8 kcal/mol below the energy of the reactants at 0 K. The lowest energy reaction pathway on both PESs is the degenerate double hydrogen exchange between the HOO* moieties of the prereactive complex via a double proton transfer mechanism involving an energy barrier of only 1.1 kcal/mol for the singlet and 3.3 kcal/mol for the triplet at 0 K. The single H-atom transfer between the two HOO* moieties of the prereactive complex (yielding HOOH + O2) through a pathway keeping a planar arrangement of the six atoms involves a conical intersection between either two singlet or two triplet states of A' and A" symmetries. Thus, the lowest energy reaction pathway occurs via a nonplanar cisoid transition structure with an energy barrier of 5.8 kcal/mol for the triplet and 17.5 kcal/mol for the singlet at 0 K. The simple addition between the terminal oxygen atoms of the two HOO* moieties of the prereactive complex, leading to the straight chain H2O4 intermediate on the singlet PES, involves an energy barrier of 7.3 kcal/mol at 0 K. Because the decomposition of such an intermediate into HOOH + O2 entails an energy barrier of 45.2 kcal/mol at 0 K, it is concluded that the single H-atom transfer on the triplet PES is the dominant pathway leading to HOOH + O2. Finally, the strong negative temperature dependence of the rate constant observed for this reaction is attributed to the reversible formation of the prereactive complex in the entrance channel rather than to a short-lived tetraoxide intermediate.     

Electrochemical behavior of copper complexes with substituted polypyridinic ligands: an experimental and theoretical study

Experimental redox potentials of the couples [Cu(R-L ( n ))(CH 3CN)] (2+,+), where L (1) is bis-(pyridine-2-ylmethyl)-benzylamine, L (2) is (pyridine-2-ylethyl)(pyridine-2-ylmethyl)-benzylamine, and R is H, Me, or CF 3, were determined in dichloromethane solution. The compounds exhibited one simple quasi-reversible wave over the measured potential range of -500 to +1200 mV, and the E 1/2 values varied from +200 to +850 mV versus SCE. These experimental values were correlated with redox potentials calculated using density functional theory. The optimized geometries and the predicted redox potentials were obtained using the BP86 functional and a combination of the basis sets LACV3P** (for Cu) and cc-pVTZ(-f) (for light atoms). A distortion analysis of all of the optimized geometries for both oxidation states was performed using the generalized interconversion coordinate phi. A linear relation was obtained between this parameter and the redox potentials. However, the [Cu(CF 3-L (1))(CH 3CN)] (+) complex showed the largest deviation, which was explained by the more-rigid structure of the ligand.     

Magnetic structure of the large-spin Mn10 and Mn19 complexes: a theoretical complement to an experimental milestone

High-spin molecules have been proposed as candidates for the storage of information at the molecular level. The electronic structure of two complex magnetic molecular systems, Mn 10 and Mn 19, is characterized by means of a computational study based on density functional theory. All the exchange interactions in the recently reported Mn 19 complex with the highest known spin value of 83/2, and in its highly symmetric Mn 10 parent compound, are ferromagnetic. In these complexes, there are two kinds of ferromagnetic coupling: the first one corresponds to Mn (II)-Mn (III) interactions through a double mu 2-alkoxo-mu 4-oxo bridge where the high coordination number of the Mn (II) cations results in long Mn (II)-O bond distances, while the second one involves Mn (III)-Mn (III) interactions through mu 2-alkoxo-mu 3-eta (1):eta (1):eta (1) azido bridging ligands with long Mn (III)-N distances due to a Jahn-Teller effect.     

Use of fluorescence spectroscopy to study polymeric materials with porous structure based on imprinting by self-assembled fibrillar networks

Different polymeric materials have been prepared from the organogels formed by a polymerizable methacrylic mixture (methyl methacrylate/ethylene glycol dimethacrylate, 1:1, w/w) and the macrocyclic pseudopeptide 1. The use of (2,4,6-trimethylbenzoyl)diphenylphosphine oxide as a very efficient radical initiator allows polymeric materials in which the structure of the fibrils formed by self-assembly of the organogelator 1 is truly preserved to be obtained. Removal of the pseudopeptidic molecule provides materials with a porous structure reflecting that of the original self-assembled fibrils. The use of fluorescent probes such as rhodamine B and pyrene greatly facilitate the study of the porous structures formed and, accordingly, that of the morphology of the original fibrils. Those studies reveal the presence of a permanent porosity and the organization of the substructures as a porous network. This confirms the existence of a nucleation and growth mechanism for the generation of the fibrils, giving rise to the formation of spherulitic structures. Those spherulites are additionally linked by connections of variable size. A series of diffusion experiments allowed establishment of a direct dependence of the inner porosity of the materials on the amount of self-organizing template used for their preparation.     

Aldol reactions between L-erythrulose derivatives and chiral alpha-amino and alpha-fluoro aldehydes: competition between Felkin-Anh and Cornforth transition states

Both matched and mismatched diastereoselection have been observed in aldol reactions of a boron enolate of a protected L-erythrulose derivative with several chiral alpha-fluoro and alpha-amino aldehydes. Strict adherence to the Felkin-Anh model for the respective transition structures does not account satisfactorily for all the observed results, as previously observed in the case of alpha-oxygenated aldehydes. In some cases, only the Cornforth model provides a good explanation. The factors that influence this dichotomy are discussed and a general mechanistic model is proposed for aldol reactions with alpha-heteroatom-substituted aldehydes. Additional support for the model was obtained from density functional calculations.