Gas-phase structures and mass spectra of binary pentafluorides

Most known non-radioactive pentafluorides have been examined by molecular-beam mass spectrometry and by the deflection of molecular beams in inhomogeneous electric fields. Extensive association of the vapors occurs for all but the lighter pentafluorides and the interhalogens. The interhalogen pentafluorides are strongly polar, consistent with the accepted C_4v symmetry. The transition-metal and Group V pentafluorides are all non-polar, except VF₅ and CrF₅ for which temperature-dependent polarity is observed. However, uncertainty exists as to whether these observations are applicable to monomeric pentafluorides in all cases. Mass-spectral cracking patterns are presented for all species.     

Reversible aggregation/deaggregation of gold nanoparticles induced by a cleavable dithiol linker

Aqueous solutions of Au colloids (12 +/- 4 nm size) when treated with a blend of mono- and dithiols aggregate forming stable clusters, as evidenced by the shift of their surface plasmon (SP) band from 512 to ca. 600 nm. The presence of carboxylate ester functions on the dithiol allows its cleavage by addition of a cleaving agent, such as hydrazine. The cleavage process results in the breaking down of the clusters of nanoparticles and the shift of the SP band back to lower wavelengths. Further addition of dithiol causes the formation of the clusters again. The aggregation/deaggregation process may be monitored visually by following the color change from pink-red to purple and vice versa in the forward and backward steps, respectively.     

Accurate intermolecular ground state potential of the Ne-N2 van der Waals complex

Ab initio ground state potential energy surfaces are obtained from interaction energies calculated with the coupled cluster singles and doubles model including connected triples corrections [CCSD(T)] and the aug-cc-pVXZ (X=5,Q,T,D) basis sets augmented with two different sets of midbond functions (denoted 33221 and 33211). The aug-cc-pV5Z-33221 surface is characterized by a T-shaped 49.5 cm(-1) minimum at Re=3.38 Angstroms and a linear saddle point at 3.95 Angstroms with De=36.6 cm(-1). These results agree well with the values provided by the accurate semiempirical potentials available. The rovibronic spectroscopic properties are determined and compared to the available experimental data and previous theoretical results. We study the basis set convergence of the intermolecular potentials and the rotational frequencies. The aug-cc-pVTZ basis sets provide reasonable binding parameters, but seem not to be converged enough for the evaluation of the microwave spectra. The aug-cc-pVQZ basis sets considerably improve the triple zeta results. The differences between the results obtained with the aug-cc-pVTZ-33221 basis set surface and those with the aug-cc-pVQZ-33221 are smaller than those of the corresponding bases with the set of 33211 midbond functions. The aug-cc-pVQZ surfaces are close to the aug-cc-pV5Z, that are expected to be close to convergence. With our best surfaces the errors in the frequencies with respect to the accurate experimental results go down to 0.6%.     

Feasibility of atmospheric pressure desorption/ionization on silicon mass spectrometry in analysis of drugs

The feasibility of atmospheric pressure desorption/ionization on silicon mass spectrometry (AP-DIOS-MS) for drug analysis was investigated. It was observed that only compounds with relative high proton affinity are efficiently ionized under AP-DIOS conditions. The limits of detection (LODs) achieved in MS mode with midazolam, propranolol, and angiotensin II were 80 fmol, 20 pmol, and 1 pmol, respectively. In MS/MS mode the LODs for midazolam and propranolol were 10 fmol and 5 pmol, respectively. The good linearity (r(2) > 0.991), linear dynamic range of 3 orders of magnitude, and reasonable repeatability showed that the method is suitable for quantitative analysis.     

Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases

The biological function of the aspartic protease from HIV-1 has recently been related to the conformational flexibility of its structural scaffold. Here, we use a multistep strategy to investigate whether the same mechanism affects the functionality in the pepsin-like fold. (i) We identify the set of conserved residues by using sequence-alignment techniques. These residues cluster in three distinct regions: near the cleavage-site cavity, in the four beta-sheets cross-linking the two lobes, and in a solvent-exposed region below the long beta-hairpin in the N-terminal lobe. (ii) We elucidate the role played by the conserved residues for the enzymatic functionality of one representative member of the fold family, the human beta-secretase, by means of classical molecular dynamics (MD). The conserved regions exhibit little overall mobility and yet are involved into the most important modes of structural fluctuations. These modes influence the substrate-catalytic aspartates distance through a relative rotation of the N- and C-terminal lobes. (iii) We investigate the effects of this modulation by estimating the reaction free energy at different representative substrate/enzyme conformations. The activation free energy is strongly affected by large-scale protein motions, similarly to what has been observed in the HIV-1 enzyme. (iv) We extend our findings to all other members of the two eukaryotic and retroviral fold families by recurring to a simple, topology-based, energy functional. This analysis reveals a sophisticated mechanism of enzymatic activity modulation common to all aspartic proteases. We suggest that aspartic proteases have been evolutionarily selected to possess similar functional motions despite the observed fold variations.     

Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment

Near-UV irradiation of structurally characterized [Re(I)(CO)3(1,10-phenanthroline)(Q107H)](W48F/Y72F/H83Q/Y108W)AzM(II) [Az = Pseudomonas aeruginosa azurin, M = Cu, Zn]/[Co(NH3)5Cl]Cl2 produces a tryptophan radical (W108*) with unprecedented kinetic stability. After rapid formation (k = 2.8 x 106 s-1), the radical persists for more than 5 h at room temperature in the folded ReAzM(II) structure. The absorption spectrum of ReAz(W108*)M(II) exhibits maxima at 512 and 536 nm. Oxidation of K4[Mo(CN)8] by ReAz(W108*)Zn(II) places the W108*/W108 reduction potential in the protein above 0.8 V vs NHE.     

On the efficiency of exchange in parallel tempering monte carlo simulations

We introduce the concept of effective fraction, defined as the expected probability that a configuration from the lowest index replica successfully reaches the highest index replica during a replica exchange Monte Carlo simulation. We then argue that the effective fraction represents an adequate measure of the quality of the sampling technique, as far as swapping is concerned. Under the hypothesis that the correlation between successive exchanges is negligible, we propose a technique for the computation of the effective fraction, a technique that relies solely on the values of the acceptance probabilities obtained at the end of the simulation. The effective fraction is then utilized for the study of the efficiency of a popular swapping scheme in the context of parallel tempering in the canonical ensemble. For large dimensional oscillators, we show that the swapping probability that minimizes the computational effort is 38.74%. By studying the parallel tempering swapping efficiency for a 13-atom Lennard-Jones cluster, we argue that the value of 38.74% remains roughly the optimal probability for most systems with continuous distributions that are likely to be encountered in practice.     

Dichloro and alkylchloro gallium derivatives of dichalcogenoimidodiphosphinate ligands: isolation of a spirogallium cation

Dichloro and chloromethyl Ga(III) complexes of general formulae [XClGa-eta2-{R2P(E)NP(E'R'2-E,E'}](X = Cl, R, R'= Ph, E, E'= O (1), S (2), Se (3); R = Ph, R'= OEt, E = O, E'= S (4); R = Me, R'= Ph, E, E'= S (5) and X = Me, E, E'= O (6), S (7), Se (8)) were synthesised by either metathesis reactions between GaCl3 and the potassium salt of the ligand (X = Cl) or by methane eliminations from in situ prepared GaMe2Cl and the protonated ligands LH (X = Me). Redistribution reaction of (3) in either CDCl3 or THF afforded the solvent-free tetracoordinate gallium spirocycle cation [Ga-{eta2-{Ph2P(Se)NP(Se)Ph2-Se,Se'})2]+ (9+). The molecular structures of complexes 2, 4, 5, 7 and 9(+) show non-planar gallacycle rings.     

HPLC monitored synthesis of R2NCH2 substituted benzene derivatives used as (C,N)-ligands for organometallic compounds

2-(Diethylaminomethyl)phenyl bromide and 1,3-bis(dimethylaminomethyl)-benzene, useful ligands for the synthesis of hypervalent organometallic compounds, were prepared and characterized by NMR (¹H, ¹³C, 2D experiments) spectroscopy. Their synthesis was monitored by the HPLC method. The compounds were eluted on a Nucleosil 120 Si column (5 μm, 25×0.4 cm) with n-hexane at room temperature using a 1.0 ml/min flow-rate. The maximum values of absorbance for the studied compounds, excepting the diethylamine, were located in a narrow range around 212 nm, the wavelength used for their UV detection. The diethylamine was detected at 190 nm. The calibration curves are straight lines with correlation factors r>0.995. The HPLC data are in good agreement with those provided by NMR spectroscopy.     

Synthesis and structure of the incomplete cuboidal clusters [W3Se4H3(dmpe)3]+, [W3Se4H(3-x)(OH)x(dmpe)3]+ and [W3Se4(OH)3(dmpe)3]+, and the mechanism of the acid-assisted substitution of the coordinated hydrides

The novel incomplete cuboidal cluster [W3Se4H3(dmpe)3](PF6), [1](PF6), has been prepared by reduction of [W3Se4Br3(dmpe)3](PF6) with LiBH4 in THF solution. The trihydroxo complex [W3Se4(OH)3(dmpe)3](PF6), [2](PF6), was obtained by reacting [W3Se4Br3(dmpe)3](PF6) with NaOH in MeCN-H2O solution. The complexes [1](PF6) and [2](PF6) were converted to their BPh4- salts by treatment with NaBPh4. Recrystallisation of [1](BPh4) in the presence of traces of water affords the mixed dihydride hydroxo complex [W3Se4H2(OH)(dmpe)3](BPh4). The crystal structures of [1](BPh4), [2](BPh4) and [W3Se4H2(OH)(dmpe)3](BPh4) have been resolved. Although the [1]+ trihydride does not react with an excess of halide salts, reaction with HX leads to [W3Se4X3(dmpe)3]+ (X = Cl, Br). The kinetics of this reaction has been studied at 25 degrees C in MeCN-H2O solution (1:1, v/v) and found to occur with two consecutive kinetic steps. The first step is independent of the nature and concentration of the X(-) anion but shows a first order dependence on the concentration of acid (k1 = 12.0 mol(-1) dm(3) s(-1)), whereas the second one is independent of the nature and concentration of both the acid and added salts (k2 = 0.024 s(-1)). In contrast, the reaction of [2]+ with acids occurs in a single step with kobs = 0.63 s(-1)(HCl) and 0.17 s(-1)(HBr). These kinetic results are discussed on the basis of the mechanism previously proposed for the reactions of the analogous [W3S4H3(dmpe)3]+ cluster, with special emphasis on the effects caused by the change of S by Se on the rate constants for the different processes involved.