Folding Free Energy Determination of an RNA Three-Way Junction Using Fluctuation Theorems

Nonequilibrium work relations and fluctuation theorems permit us to extract equilibrium information from nonequilibrium measurements. They find application in single-molecule pulling experiments where molecular free energies can be determined from irreversible work measurements by using unidirectional (e.g., Jarzynski’s equality) and bidirectional (e.g., Crooks fluctuation theorem and Bennet’s acceptance ratio (BAR)) methods. However, irreversibility and the finite number of pulls limit their applicability: the higher the dissipation, the larger the number of pulls necessary to estimate ΔG within a few kBT. Here, we revisit pulling experiments on an RNA three-way junction (3WJ) that exhibits significant dissipation and work-distribution long tails upon mechanical unfolding. While bidirectional methods are more predictive, unidirectional methods are strongly biased. We also consider a cyclic protocol that combines the forward and reverse work values to increase the statistics of the measurements. For a fixed total experimental time, faster pulling rates permit us to efficiently sample rare events and reduce the bias, compensating for the increased dissipation. This analysis provides a more stringent test of the fluctuation theorem in the large irreversibility regime.     

Gap states at organic-metal interfaces: A combined spectroscopic and theoretical study

A systematic understanding and controlling of gap states formed at the organic-metal interfaces is a key factor for fabricating functional organic-metal systems, as in case of heterojunctions in semiconductor devices. We report here the characterization of gap states near the Fermi level of metal substrate by metastable atom electron spectroscopy and first-principles density functional calculations. The gap states in organic-metal systems are classified into two types, i.e., chemisorption-induced gap states (CIGSs) and complex-based gap states (CBGSs). CIGSs can be further classified whether the metal wave function tails a short distance into the chemisorbed species with the exponential decay (damping type) or is exposed sufficiently to the chemisorbed species by mixing with the organic orbitals (propagating type). CIGSs observed in alkanethiolate and C₆₀ on Pt(1 1 1) are their typical examples, respectively. As a consequence, alkanethiolate serves as a poor mediator of metal wave function, whereas C₆₀ acts as a good mediator, which is responsible for tunneling mechanism and eventually electric conductivity in the relevant metal-organic-metal junctions. CBGSs are identified in bathocuproine films deposited on K-covered Au, where the K atoms migrate into the film to form an organic-metal complex. The CBGSs are distributed over the multilayer film, in contrast to the case of CIGS. With increasing film thickness, the CBGSs exhibit incommensurate energy shifts with the valence band top of the film, indicating that the Schottky-Mott model breaks down as evaluating charge transport in organic-metal systems.     

Application of spectroscopic imaging in epilepsy

Functional and anatomical neuroimaging has had a dramatic effect on the evaluation of patients for seizure surgery. The demonstration by PET that the epileptogenic focus has interictal metabolic abnormalities has allowed a greater number of patients to come to seizure surgery, with fewer of these patients requiring intracranial electrode evaluations. Metabolic changes have also been demonstrated utilizing single voxel and whole brain ¹H and ³¹P MRS imaging techniques with the interictal focus characterized by increased Pi, pH, and decreased PME and NAA. These findings can be used to accurately lateralize temporal lobe as well as frontal lobe epilepsy. Furthermore, there is evidence that these findings can be used to localize the seizure focus with the changes specific for the epileptogenic region; although, more diffuse changes both ipsilaterally and contralaterally have been seen. In patients with anterior hippocampal seizure foci the pH is significantly alkaline only in the ipsilateral hippocampus, whereas the increased Pi and decreased PME can be seen throughout the ipsilateral temporal lobe. When compared to controls the contralateral hemisphere is acidotic. Decreased NAA concentrations as well as NAA/Cr ratios have been demonstrated in the epileptogenic region in temporal and frontal lobe epilepsy. The decreased NAA has been correlated with the severity of cell loss, and may be a more sensitive measure than qualitative or quantitative measures of the hippocampal atrophy; however, the NAA decrease is more widespread than just the epileptogenic focus but may be maximal at the site of seizure initiation. In preliminary work, NAA maps of deviation from normality have suggested the maximal change to coincide with the epileptogenic region. These results suggest that in focal epilepsy there is abnormal metabolic activity throughout the brain detectable by MRS, with patterns of metabolic asymmetry that are useful for seizure localization.     

β-榄香烯振动光谱的量子化学从头计算

利用G98及GAMESS从头计算程序的RHF／6－31方法,对β－榄香烯的全部振动基频作了计算,并与实测红外光谱做了对比,归属了它们的振动模式,讨论了它们的特征基频,并对理论计算的振动频率进行了标度校正。     

Non-Invasive Detection of Anti-Inflammatory Bioactivity and Key Chemical Indicators of the Commercial Lanqin Oral Solution by Near Infrared Spectroscopy

Quality control methods of current traditional Chinese medicine (TCM) preparation is time-consuming and difficult to assess in terms of overall efficiency of the drug. A non-destructive rapid near-infrared spectroscopy detection system for key chemical components and biological activity of Lanqin oral solution (LOS), one of the best-selling TCM formulations, was established for comprehensive quality evaluation. Near infrared spectral scanning was carried out on 101 batches of commercial LOS under the penetrated vial state and traditional state. RAW 264.7 cells were cultured to detect the anti-inflammatory ability of LOS, and the reference concentrations of epigoitrin, geniposide, and baicalin were obtained by HPLC. The quantitative models were optimized by three kinds of variable selection methods. The correlation coefficients of prediction value of the models were greater than 0.94. The system also passed the external validation. The performance of the non-invasive models was similar to the traditional models. The established non-destructive system can be applied to the rapid quality inspection of LOS to avoid unqualified drugs from entering the market and ensure drug effectiveness. The biological activity index of LOS was introduced and predicted by NIRs for the first time, which provides a new idea about the quality control of TCM formulations.     

Ein Vergleich zwischen radioaktiver Markierung und Indikator-Aktivierungsanalyse bei der Messung von Verweilzeitspektren

An VK-Z-Rohren zur Herstellung von Polyamid wurden Verweilzeitspektren mit der Methode der radioaktiven Markierung und der Methode der Indikatoraktivierungsanalyse gemessen. Die nach den beiden Methoden ermittelten Verweilzeitspektren werden miteinander verglichen. Die Übereinstimmung der Verweilzeitspektren wird durch Gegenüberstellung der statistischen Momente und durch einen Test nach Kolmogoroff-Smirnov geprüft. Es wird der experimentelle Aufwand beider Verfahren diskutiert und eine Fehlerabschätzung durchgeführt.     

Ageing of AgCl/Cd nuclear track detectors monitored by luminescence spectroscopy

Abstract

Solid-state nuclear track detectors, made of Cd doped AgCl crystals, are commonly prepared by rolling into the form of thin foils. Subsequent long-term relaxation is however needed to obtain good quality tracks. The present communication shows for the first time that this detector “ageing” is reflected in lowtemperature (77 K) luminescence spectra. Maximum of the emission band shows a slow (lasting for ～ 100 hours) blue shift, the magnitude of which (as much as 25 nm) depends on the compression ratio caused by the rolling. The shift is believed to be due to the rearrangement of Cd⁺⁺ ions around freshly introduced dislocations. This finding opens the possibility of monitoring non-destructively the process of detector ageing and to determine the minimum time required for saturation.     

Doping profiles from the capacity-voltage (C–V) characteristics of the [111] Si(p) single crystals doped by the In+ -ion-implantation

The ²³⁵U(n, f) cross-section has been measured after the installation of a liquid nitrogen cooled methane moderator at GELINA. The results are compared with previous data, and the influence of the cross section shape on the Westcott gf-factor is discussed.     

Sulfur Ligands. from β-Lactam Antibiotics to Contrast Agents for MRI

Abstract

NMR, IR and semi empirical Molecular Orbital PM3 studies on selected β-lactam antibiotics are reported. The role of sulfur in β-lactam antibiotics is discussed.     

1H, 13C and 15N NMR spectral analysis of substituted 1,2,3,4‐tetrahydro‐pyrido[1,2‐a]pyrimidines

The NMR spectroscopic data of a series of thirty‐four 3‐acylpyrido[1,2‐a]pyrimidinium salts are analyzed, which were prepared as either perchlorates or chlorides. Methyl group substituted 3‐aroyltetrahydropyrido[1,2‐a]pyrimidines with the methyl substituent in positions 6, 8 and 9 as well as both in positions 6 and 8 were investigated bearing various aroyl substituents. Unequivocal assignment of all resonances was achieved via two‐dimensional ¹H,¹H‐COSY measurements, ¹H,¹³C and ¹H,¹⁵N HSQC as well as HMBC experiments, and important diagnostic CH and NH couplings in the heteroaromatic ring system are evaluated. The influence of the methyl substituents was analyzed on the proton, carbon and nitrogen shifts. A significant effect of the counter ion on some chemical shifts of the nuclei under discussion of the pyridopyrimidines is found, allowing the indirect detection of the anion, which is confirmed by direct measurement of the ³⁵Cl nucleus of the perchlorates. Copyright © 2013 John Wiley & Sons, Ltd.