Design and characterization of a functional library for NMR screening against novel protein targets

In the past few years, NMR has been extensively utilized as a screening tool for drug discovery using various types of compound libraries. The designs of NMR specific chemical libraries that utilize a fragment-based approach based on drug-like characteristics have been previously reported. In this article, a new type of compound library will be described that focuses on aiding in the functional annotation of novel proteins that have been identified from various ongoing genomics efforts. The NMR functional chemical library is comprised of small molecules with known biological activity such as: co-factors, inhibitors, metabolites and substrates. This functional library was developed through an extensive manual effort of mining several databases based on known ligand interactions with protein systems. In order to increase the efficiency of screening the NMR functional library, the compounds are screened as mixtures of 3-4 compounds that avoids the need to deconvolute positive hits by maintaining a unique NMR resonance and function for each compound in the mixture. The functional library has been used in the identification of general biological function of hypothetical proteins identified from the Protein Structure Initiative.     

A low-Mach number model for time-harmonic acoustics in arbitrary flows

This paper concerns the finite element simulation of the diffraction of a time-harmonic acoustic wave in the presence of an arbitrary mean flow. Considering the equation for the perturbation of displacement (due to Galbrun), we derive a low-Mach number formulation of the problem which is proved to be of Fredholm type and is therefore well suited for discretization by classical Lagrange finite elements. Numerical experiments are done in the case of a potential flow for which an exact approach is available, and a good agreement is observed.     

Influence of spectral phase on cross-polarized wave generation with short femtosecond pulses

In this paper we present the first comprehensive study of the role of spectral phase on cross-polarized wave (XPW) generation using sub-30 femtosecond (fs) laser pulses. XPW generation improves the temporal contrast and shortens the pulse duration of fs chirped pulse amplification (CPA) lasers. For Ti:Sa lasers, compression below 30?fs is non-trivial and therefore never perfect. We therefore systematically analyze the effect of an arbitrary input spectral phase on the output spectrum and efficiency of the XPW process, both theoretically and experimentally. We derive the maximum acceptable value of residual phase for a given initial pulse duration in order to efficiently drive the XPW process for pulse shortening and contrast improvement.     

Group 6 Oxyfluoro-Anion Salts of [XeF5]+ and [Xe2F11]+: Syntheses and Structures of [XeF5][M2O2F9] (M=Mo,W), [Xe2F11][M′OF5] (M′=Cr,Mo, W), [XeF5][HF2]⋅CrOF4, and [XeF5][WOF5]⋅XeOF4

The reactions of the fluoride-ion donor, XeF₆, with the fluoride-ion acceptors, M′OF₄ (M′=Cr, Mo, W), yield [XeF₅]⁺ and [Xe₂F₁₁]⁺ salts of [M′OF₅]⁻ and [M₂O₂F₉]⁻ (M=Mo, W). Xenon hexafluoride and MOF₄ react in anhydrous hydrogen fluoride (aHF) to give equilibrium mixtures of [Xe₂F₁₁]⁺, [XeF₅]⁺, [(HF)_nF]⁻, [MOF₅]⁻, and [M₂O₂F₉]⁻ from which the title salts were crystallized. The [XeF₅][CrOF₅] and [Xe₂F₁₁][CrOF₅] salts could not be formed from mixtures of CrOF₄ and XeF₆ in aHF at low temperature (LT) owing to the low fluoride-ion affinity of CrOF₄, but yielded [XeF₅][HF₂]⋅CrOF₄ instead. In contrast, MoOF₄ and WOF₄ are sufficiently Lewis acidic to abstract F⁻ ion from [(HF)_nF]⁻ in aHF to give the [MOF₅]⁻ and [M₂O₂F₉]⁻ salts of [XeF₅]⁺ and [Xe₂F₁₁]⁺. To circumvent [(HF)_nF]⁻ formation, [Xe₂F₁₁][CrOF₅] was synthesized at LT in CF₂ClCF₂Cl solvent. The salts were characterized by LT Raman spectroscopy and LT single-crystal X-ray diffraction, which provided the first X-ray crystal structure of the [CrOF₅]⁻ anion and high-precision geometric parameters for [MOF₅]⁻ and [M₂O₂F₉]⁻. Hydrolysis of [Xe₂F₁₁][WOF₅] by water contaminant in HF solvent yielded [XeF₅][WOF₅]⋅XeOF₄. Quantum-chemical calculations were carried out for M′OF₄, [M′OF₅]⁻, [M′₂O₂F₉]⁻, {[Xe₂F₁₁][CrOF₅]}₂, [Xe₂F₁₁][MOF₅], and {[XeF₅][M₂O₂F₉]}₂ to obtain their gas-phase geometries and vibrational frequencies to aid in their vibrational mode assignments and to assess chemical bonding.     

The decay from the dark npi* excited state in uracil: an integrated CASPT2/CASSCF and PCM/TD-DFT study in the gas phase and in water

By integrating the results of MS-CASPT2/CASSCF and TD-PBE0 calculations, we propose a mechanism for the decay of the excited dark state in pyrimidine, fully consistent with all the available experimental results. An effective conical intersection (CI-npi) exists between the spectroscopic pi/pi* excited state (Spi) and a dark n/pi* state (Sn), and a fraction of the population decays to the minimum of Sn (Sn-min). The conical intersection between Sn and the ground-state is not involved in the decay mechanism, because of its high energy gap with respect to Sn-min. On the other hand, especially in hydrogen bonding solvents, the energy gap between Sn-min and CI-npi is rather small. After thermalization in Sn-min, the system can thus recross CI-npi and then quickly proceed on the Spi barrierless path toward the conical intersection with the ground state.     

Fluorescence and phosphorescence properties of the low temperature forms of the MAl2Si2O8:Eu (M=Ca, Sr, Ba) compounds

The fluorescence and phosphorescence properties of Europium-doped MAl₂Si₂O₈ (M=Ca, Sr, Ba) are reinvestigated and discussed on the basis of the propensity of an activator to agglomerate with an oxygen vacancy. Due to a stronger attraction of the anion vacancy towards Eu²⁺ cations going from BaAl₂Si₂O₈ to SrAl₂Si₂O₈ and CaAl₂Si₂O₈ host lattices, the interpretation of the fluorescence spectra turns out to be less trivial in the Ca and Sr host lattices than in the Ba one and requests the account for Eu²⁺ cations lying at alkaline-earth sites with or without vacancy in their neighborhood. Phosphorescence in these compounds is highlighted.     

F5SN(H)Xe+; a rare example of xenon bonded to sp3-hybridized nitrogen; synthesis and structural characterization of [F5SN(H)Xe][AsF6

The salt [F5SN(H)Xe][AsF6] has been synthesized by the reaction of [F5SNH3][AsF6] with XeF2 in anhydrous HF (aHF) and BrF5 solvents and by solvolysis of [F3S triple bond NXeF][AsF6] in aHF. Both F5SN(H)Xe(+) and F5SNH3(+) have been characterized by (129)Xe, (19)F, and (1)H NMR spectroscopy in aHF (-20 degrees C) and BrF5 (supercooled to -70 degrees C). The yellow [F5SN(H)Xe][AsF6] salt was crystallized from aHF at -20 degrees C and characterized by Raman spectroscopy at -45 degrees C and by single-crystal X-ray diffraction at -173 degrees C. The Xe-N bond length (2.069(4) A) of the F5SN(H)Xe(+) cation is among the shortest Xe-N bonds presently known. The cation interacts with the AsF6(-) anion by means of a Xe---F-As bridge in which the Xe---F distance (2.634(3) A) is significantly less than the sum of the Xe and F van der Waals radii (3.63 A) and the AsF6(-) anion is significantly distorted from Oh symmetry. The (19)F and (129)Xe NMR spectra established that the [F5SN(H)Xe][AsF6] ion pair is dissociated in aHF and BrF5 solvents. The F5SN(H)Xe(+) cation decomposes by HF solvolysis to F5SNH3(+) and XeF2, followed by solvolysis of F5SNH3(+) to SF6 and NH4(+). A minor decomposition channel leads to small quantities of F5SNF2. The colorless salt, [F5SNH3][AsF6], was synthesized by the HF solvolysis of F3S triple bond NAsF5 and was crystallized from aHF at -35 degrees C. The salt was characterized by Raman spectroscopy at -160 degrees C, and its unit cell parameters were determined by low-temperature X-ray diffraction. Electronic structure calculations using MP2 and DFT methods were used to calculate the gas-phase geometries, charges, bond orders, and valencies as well as the vibrational frequencies of F 5SNH3(+) and F5SN(H)Xe(+) and to aid in the assignment of their experimental vibrational frequencies. In addition to F5TeN(H)Xe(+), the F5SN(H)Xe(+) cation provides the only other example of xenon bonded to an sp (3)-hybridized nitrogen center that has been synthesized and structurally characterized. These cations represent the strongest Xe-N bonds that are presently known.     

A Random Shock Model with Mixed Effect,Including Competing Soft and Sudden Failures,and Dependence

A system is considered, which is subject to external and possibly fatal shocks, with dependence between the fatality of a shock and the system age. Apart from these shocks, the system suffers from competing soft and sudden failures, where soft failures refer to the reaching of a given threshold for the degradation level, and sudden failures to accidental failures, characterized by a failure rate. A non-fatal shock increases both degradation level and failure rate of a random amount, with possible dependence between the two increments. The system reliability is calculated by four different methods. Conditions under which the system lifetime is New Better than Used are proposed. The influence of various parameters of the shocks environment on the system lifetime is studied.