Tertiary Motifs in RNA Structure and Folding

Specific tertiary structural motifs determine the complete architecture of RNA molecules (see picture for examples). Within the last few years a number of high-resolution crystal structures of complex RNAs have led to new insights into the mechanisms by which these complex folds are attained. In this review the structures of these tertiary motifs and how they influence the folding pathway of biological RNAs are discussed, as well as new developments in modeling RNA structure based upon these findings.     

Near threshold photoproduction of η mesons from 4 He

Photoproduction of - mesons from ⁴He has been measured for the first time. The experiment was performed at the Mainz Microtron (MAMI) using the TAPS photon spectrometer and the Glasgow/Mainz tagged photon facility. - mesons were identified in coincidence with recoil nucleons. Total and differential cross sections are presented in the photon energy range between threshold and 818 MeV. The exclusive data are used to determine the ratio of the elementary production cross sections on bound neutrons and protons, C_n/C_p = 0.68 - 0.02 - 0.09. In addition, upper limits for the total coherent cross section have been derived.     

Synthesis and Antimycobacterial Evaluation of N-(4-(Benzyloxy)benzyl)-4-aminoquinolines

Tuberculosis remains a global health problem that affects millions of people around the world. Despite recent efforts in drug development, new alternatives are required. Herein, a series of 27 N-(4-(benzyloxy)benzyl)-4-aminoquinolines were synthesized and evaluated for their ability to inhibit the M. tuberculosis H37Rv strain. Two of these compounds exhibited minimal inhibitory concentrations (MICs) similar to the first-line drug isoniazid. In addition, these hit compounds were selective for the bacillus with no significant change in viability of Vero and HepG2 cells. Finally, chemical stability, permeability and metabolic stability were also evaluated. The obtained data show that the molecular hits can be optimized aiming at the development of drug candidates for tuberculosis treatment.     

Potential of visible-near infrared spectroscopy combined with chemometrics for analysis of some constituents of coffee and banana residues

Banana (stalk, leaf, rhizome, rachis and stem) and coffee (leaf and husks) residues are promising feedstock for fuel and chemical production. In this work we show the potential of near-infrared spectroscopy (NIR) and multivariate analysis to replace reference methods in the characterization of some constituents of coffee and banana residues. The evaluated parameters were Klason lignin (KL), acid soluble lignin (ASL), total lignin (TL), extractives, moisture, ash and acid insoluble residue (AIR) contents of 104 banana residues (B) and102 coffee (C) residues from Brazil. PLS models were built for banana (B), coffee (C) and pooled samples (B + C). The precision of NIR methodology was better (p < 0.05) than the reference method for almost all the parameters, being worse for moisture. With the exception of ash (B and C) and ASL (C) content, which was predicted poorly (R² < 0.80), the models for all the analytes exhibited R² > 0.80. The range error ratios varied from 4.5 to 16.0. Based on the results of external validation, the statistical tests and figures of merit, NIR spectroscopy proved to be useful for chemical prediction of banana and coffee residues and can be used as a faster and more economical alternative to the standard methodologies.     

Thermal lens compensation by convex deformation of a flat mirror with variable annular force

An optical surface with convex parabolic shape over a large area has been created using a 12.7-mm-diameter annular pusher to deform a flat 25.4-mm-diameter mirror. The deformable mirror assembly has been modeled using finite element analysis software as well as analytical solutions. The measured parabolic surface deformation shows good agreement with those models. Mirror performance was studied using a Shack–Hartman wavefront sensor and the mirror has been applied to compensate thermal lensing in a Nd:YAG rod amplifier. PACS 41.85.Ct; 42.60.Da     

A hybrid OPCPA/Nd:phosphate glass multi-terawatt laser system for seeding of a petawatt laser

To enhance radiographic abilities on its Z-Accelerator, Sandia National Laboratories is incorporating a petawatt laser system into the existing Z-Backlighter laser facility. As part of this work, a short-pulse laser has been constructed to seed the larger Beamlet type Nd:phosphate glass slab amplifiers. This seed laser consists of an optical parametric chirped pulse amplification (OPCPA) system joined to a Nd:phosphate glass rod amplifier system in order to achieve multi-Joule sub-picosecond operation. The rod amplifier system has been modeled using the Miró code which shows good agreement with the experimental results. This system can achieve focal intensities up to 10¹⁸ W/cm² at a repetition rate of once every 20 min and has been applied to produce k-alpha X-rays in copper.     

Neutral and anionic guests and their effect on the formation of pseudorotaxanes by using a flexible tetracationic imidazolium macrocycle

The ability to control and direct molecular assembly has important implications in the design of environmentally responsive materials. Reported here is the use of competitive neutral- and anionic-guest recognition to control the formation, disruption, replacement-based construction and higher-order assembly properties of pseudorotaxane structures involving a large, cationic tetraimidazolium receptor. In particular, we showed that the chloride anion (as the tetrabutylammonium (TBA(+)) salt) serves to replace directly the 2,6-naphthalene dicarboxylate dianion from the preformed complex, involving this dianion. In contrast, the addition of the nitrate anion (as the TBA(+) salt) serves to effect displacement of a pre-bound 2,6-naphthalene dicarboxylate dianion in a stepwise manner allowing for stabilization of a so-called "outside"-binding mode under appropriate conditions. We have also found that by using biphenyl-3,4,3',4'-tetraamine as the guest, a 1D-donor-acceptor-donor coordination polymer can be stabilized, whereas the addition of 6-amino-naphthalene-2-sulfonate anion to the pre-formed complex between the tetraimidazolium receptor and the 2,6-naphthalene dicarboxylate dianion produces a new pseudorotaxane complex. This guest-based competition and subsequent molecular translocation is supported by solution-state NMR spectroscopic studies as well as solid-state single-crystal X-ray structural analyses. The results described herein provide initial evidence that guest competition can be used to control molecular "switching" and substrate binding within an appropriately designed anion receptor.     

Substituent effects on the structure and supramolecular assembly of bis(dioxaborole)s

Solid-state and solution analysis shows that dialkyl substituents on the central phenyl ring of bis(dioxaborole)s, such as , do not have an appreciable effect on the planarity but do significantly alter the supramolecular assembly of these compounds.     

Magnetochemical Properties and Reactions of Vanadium(III) Thiolate Complexes: Preparation of (NEt(4))(3)[V(3)Cl(6)(edt)(3)] and Mixed-Valence (NEt(4))[V(2)(edt)(4)] (edt = Ethane-1,2-dithiolate)

Reactions of the previously reported dinuclear vanadium(III) thiolate anion [V(2)(edt)(4)](2)(-) (edtH(2) = ethane-1,2-dithiol) are described. Treatment of (NEt(4))(2)[V(2)(edt)(4)] (1) in MeCN with equimolar (C(12)H(8)S(2))BF(4) (C(12)H(8)S(2)(+) = the thianthrenium radical cation) results in a one-electron oxidation and isolation of the V(III),V(IV) complex (NEt(4))[V(2)(edt)(4)] (2). The same product can also be obtained by controlled-potential electrolysis of 1 at -0.20 V vs Ag/AgCl. Treatment of 1 in CH(2)Cl(2) with py gives no reaction, but addition of Me(3)SiCl leads to formation of the known V(2)OCl(4)(py)(6) (3). The latter is also formed by the reduction of a 1:1 mixture of VOCl(3) and VCl(3)(THF)(3) in CH(2)Cl(2)/py and by the reaction in CH(2)Cl(2) of VCl(3)(THF)(3) and py with edt(2)(-). Treatment of 1 in MeCN with bpy (2,2'-bipyridine) gives no reaction, but addition of Me(3)SiCl results in formation and isolation of [V(2)OCl(2)(bpy)(4)]Cl(2) (4) identified by spectroscopic comparison with literature data. The reaction of 1 in MeCN with equimolar VCl(3)(THF)(3) and NEt(4)Cl gives (NEt(4))(3)[V(3)Cl(6)(edt)(3)] (5). A more convenient procedure to 5 is the reaction in MeCN of VCl(3)(THF)(3), Na(2)edt, and NEt(4)Cl in a 1:1:1 molar ratio. Complex 5.MeCN crystallizes in triclinic space group P&onemacr; with (at -154 degrees C) a = 14.918(3) ?, b = 17.142(5) ?, c = 11.276(3) ?, alpha = 106.78(1) degrees, beta = 95.03(1) degrees, gamma = 106.18(1) degrees, and Z = 2. The anion contains a near-linear V(3) unit with a face-sharing trioctahedral structure: the three edt(2)(-) groups provide the six bridging S atoms; two edt(2)(-) groups are in a &mgr;-eta(2):eta(2) mode (as in 1), but the third is in a &mgr;(3)-eta(1):eta(2):eta(1) mode. The V.V separations (>3.1 ?) preclude V-V bonding. Variable-temperature solid-state magnetic susceptibility studies have been performed on complexes 1, 2, and 5 in a 1.0 kG field and 5.00-300 K temperature range. For 1, the effective magnetic moment (&mgr;(eff)) gradually decreases from 1.09 &mgr;(B) at 300 K to 0.26 &mgr;(B) at 5.00 K. The data were fit to the Bleaney-Bowers equation, and the fitting parameters were J = -419(11) cm(-)(1) and g = 2.05. The singlet-triplet gap is thus 838 cm(-)(1). For 2, &mgr;(eff) is essentially temperature-independent, slowly decreasing from 1.90 &mgr;(B) at 300 K to 1.86 &mgr;(B) at 55 K and then to 1.63 &mgr;(B) at 5.00 K. The complex thus is S = (1)/(2) with no thermally accessible S = (3)/(2) state. The combined data on 1 and 2, together with the results of EHT calculations, show that 1 and 2 contain a V-V single bond tying up two of the d electrons and that the remaining two d electrons in 1 are antiferromagnetically coupled to give an S = 0 ground state and S = 1 excited state; for 2, the one remaining d electron gives an S = (1)/(2) state. For 5, &mgr;(eff) increases from 5.17 &mgr;(B) at 320 K to a maximum of 6.14 &mgr;(B) at 30.0 K and then decreases slightly to 6.08 &mgr;(B) at 5.00 K. The data were fit to the appropriate theoretical expression to give J = +42.5(6) cm(-)(1), J' = -1.8(5) cm(-)(1), and g = 1.77, where J and J' gauge the interactions between adjacent and terminal V(III) atoms, respectively. The complex has an S = 3 ground state and represents a very rare example of ferromagnetic coupling between V(III) centers.     

Hyperfine Interaction of Metamict Zircon Studied by PAC Spectroscopy

Zircon (ZrSiO₄) is a common accessory mineral found in igneous and metamorphic rocks and is generally in an amorphous state due to self-irradiation from radioactive impurities. The crystalline structure may be recovered by annealing. We have studied the annealing behavior of a nearly fully metamict zircon specimen by perturbed angular correlation spectroscopy and powder X-ray diffraction. Our results are consistent with accepted damage accumulation models and point to a two-stage recovery process for the transition from metamict to crystalline zircon. In all of our experiments PAC overestimates the amorphous fraction as compared to that determined by diffraction experiments, and we propose an explanation for this discrepancy. This revised version was published online in September 2006 with corrections to the Cover Date.