Synthesis, Spectroscopic Characterization, and Structural Studies of Bis(&mgr;-sulfido)bis[{O,O-dialkyl (alkylene) dithiophosphato}oxomolybdenum(V)] Complexes. Crystal Structures of Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2), Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2).2NC(5)H(5), and Mo(2)O(3)[S(2)P(OPh)(2)](4)

A series of new complexes, Mo(2)O(2)S(2)[S(2)P(OR)(2)](2) (where R = Et, n-Pr, i-Pr) and Mo(2)O(2)S(2)[S(2)POGO](2) (where G = -CH(2)CMe(2)CH(2)-, -CMe(2)CMe(2)-) have been prepared by the dropwise addition of an ethanolic solution of the ammonium or sodium salt of the appropriate O,O-dialkyl or -alkylene dithiophosphoric acid, or the acid itself, to a hot aqueous solution of molybdenum(V) pentachloride. The complexes were also formed by heating solutions of Mo(2)O(3)[S(2)P(OR)(2)](4) or Mo(2)O(3)[S(2)POGO](4) species in glacial acetic acid. The Mo(2)O(2)S(2)[S(2)P(OR)(2)](2) and Mo(2)O(2)S(2)[S(2)POGO](2) compounds were characterized by elemental analyses, (1)H, (13)C, and (31)P NMR, and infrared and Raman spectroscopy, as were the 1:2 adducts formed on reaction with pyridine. The crystal structures of Mo(2)O(2)S(2)[S(2)P(OEt(2))](2), Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2).2NC(5)H(5), and Mo(2)O(3)[S(2)P(OPh)(2)](4) were determined. Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2) (1) crystallizes in space group C2/c, No. 15, with cell parameters a = 15.644(3) ?, b = 8.339(2) ?, c = 18.269(4) ?, beta = 103.70(2) degrees, V = 2315.4(8) ?(3), Z = 4, R = 0.0439, and R(w) = 0.0353. Mo(2)O(2)S(2)[S(2)P(OEt)(2)](2).2NC(5)H(5) (6) crystallizes in space group P&onemacr;, No. 2, with the cell parameters a = 12.663(4) ?,b = 14.291(5) ?, c = 9.349(3) ?, alpha = 100.04(3) degrees, beta = 100.67(3) degrees, gamma = 73.03(3) degrees V = 1557(1) ?(3), Z = 2, R = 0.0593, and R(w) = 0.0535. Mo(2)O(3)[S(2)P(OPh)(2)](4) (8) crystallizes in space group P2(1)/n, No. 14, with cell parameters a = 15.206(2)?, b = 10.655(3)?, c = 19.406(3)?, beta = 111.67(1) degrees, V = 2921(1)?(3), Z = 2, R = 0.0518, R(w) = 0.0425. The immediate environment about the molybdenum atoms in 1 is essentially square pyramidal if the Mo-Mo interaction is ignored. The vacant positions in the square pyramids are occupied by two pyridine molecules in 6, resulting in an octahedral environment with very long Mo-N bonds. The terminal oxygen atoms in both 1 and 6 are in the syn conformation. In 8, which also has a distorted octahedral environment about molybdenum, two of the dithiophosphate groups are bidentate as in 1 and 6, but the two others have one normal Mo-S bond and one unusually long Mo-S bond.     

Extraction of kinetic information from single-molecule experiments.

We discuss two possible approaches for extracting kinetic information from single-molecule experiments. The first approach is based on computing correlation functions from measured fluorescence signals, and the second on studying the statistics of on and off times of the same fluorescence signal. We show that in both cases it is possible to extract kinetic information about the nature of intramolecular fluctuations of the single molecule. We show that for single-molecule kinetics the intramolecular fluctuations produce stochastic memory effects which lead to new dynamic features that do not exist in traditional chemical kinetics. In particular, we investigate a new type of chemical oscillations in correlation functions observed experimentally by Edman and Rigler (Proc. Natl. Acad. Sci. USA 2000, 97, 8266).     

A(15)Tl(27) (A = Rb, Cs): A Structural Type Containing Both Isolated Clusters and Condensed Layers Based on the Tl(11) Fragment. Syntheses, Structure, Properties, and Band Structure

The isomorphous title compounds (and the ordered substitutional Rb(14)CsTl(27)) are obtained directly from reactions of the elements in sealed Ta below approximately 330 degrees C. Refinements of single-crystal data for the three established a structure with alternate layers of isolated pentacapped trigonal prismatic Tl(11)(7)(-) (D(3)(h)()) ions and condensed [Tl(16)(8-)] networks that are separated by cations. The condensed layer consists of Tl(11) units that share prismatic edges and are interbridged through waist-capping atoms (Tl(6/2)Tl(3)Tl(2)). (Rb(15)Tl(27): P&sixmacr;2m, Z = 1, a = 10.3248(6) ?, c = 17.558(2) ?.) The rubidium phase is a poor metal (rho(293) approximately 34 &mgr;Omega.cm) and is Pauli-paramagnetic. Extended Hückel band calculations indicate partially filled bands and a non-zero DOS at E(F), consistent with the observed metallic behavior, although appropriate cation tuning or modest anion doping should provide a Zintl phase. The band structure and COOP curves are also used to rationalize the distortion of the Tl(11) unit on condensation and the critical role of the interfragment bonds between waist-capping atoms in stabilizing the layer.     

Detection of chlorinated quinones using interdigitated electrodes coupled with capillary electrophoresis

An array of eight interdigitated microband gold electrodes (IDEs) has been developed together with electrophoretic separation for analysis of chlorinated hydroquinones (ClHQs) and benzoquinones (ClBQs). The IDE chip positioned very close to the separation capillary outlet served as an amplification/detection system without the requirement for frequent "capillary-electrode" alignment. ClHQs, electrophoretically migrating to the IDE surface, were oxidized at +1.1 V by seven electrodes of the array and then detected by the remaining electrode, poised at -0.1 V. Conversely, ClBQs were detected at +1.1 V by the detecting electrode after having been reduced at the 7 adjacent electrodes poised at -0.1 V. There was an amplification effect on both the detecting electrode as well as the adjacent electrodes because of the recycle between ClHQs and ClBQs. The detecting "amplification" current response was dependent on the potentials applied, the position of the detecting electrode on the array, the number of adjacent electrodes being used for recycling and the distance between the oxidative and reductive electrodes. Micellar electrokinetic chromatography (MEKC) separation of the analytes was achieved using 30 mM sodium dodecyl sulfate (SDS) with a detection limit in the range of 2-20 micro M. In addition to a facile "capillary-electrode" alignment, the important aspect described here was the capability of detecting through recycling a reduced compound (in the case of ClHQs) at a negative potential to circumvent fouling and electroactive interferences. An appealing feature was also the concurrent oxidation/reduction detection for each compound to ascertain peak assignment, as interfering compounds are less likely to exhibit the same oxidative/reductive characteristics and electrophoretic mobilities as the target analytes.     

Collision-Induced dissociations of deprotonated peptides. Dipeptides containing aspartic or glutamic acids

Deprotonated dipeptides, on collisional activation, fragment by the characteristic process NH₂CH(R¹) CONHCH(R²)CO₂^? → NH₂^?C(R¹)CONHCH(R²)CO₂H → ^?NHCH(R²)CO₂H + NH₂C(R¹)?C?O, when R¹ and R² = H or alkyl. However, when one of the constituent amino acids is either aspartic acid or glutamic acid, the standard cleavage becomes minor in comparison with fragmentation through the α-side-chain of Asp or Glu. For example, [Asp-Leu - H]^? and [Leu-Asp - H]^? both fragment principally by loss of water, a fragmentation not normally noted for peptides. In addition, [Leu-Asp - H]^? loses CO₂ and also forms HO₂CCH?CHCO₂^?˙. These fragmentations establish that Asp is the C-terminal amino acid. In contrast, isomeric Glu dipeptides, e.g. [Glu-Ala - H]^? and [Ala-Glu - H]^? undergo similar fragmentation, both competitively losing H₂O and CO₂. Both spectra also contain a product ion at m/z 128, identified as the pyroglutamate anion. Product ion and deuterium-labelling studies have been used in an attempt to elucidate the complex fragmentation mechanisms in these systems.     

A Schiff base expanded porphyrin macrocycle that acts as a versatile binucleating ligand for late first-row transition metals

The coordination chemistry of the Schiff base polypyrrolic octaaza macrocycle 1 toward late first-row transition metals was investigated. Binuclear complexes with the divalent cations Ni(II), Cu(II), and Zn(II) and with the monovalent cation Cu(I) were prepared and characterized. Air oxidation of the Cu(I) ions in the latter complex to their divalent oxidation state resulted in a change in the coordination mode relative to the macrocycle.     

Non-trivial behavior of palladium(II) acetate

Reaction of activated palladium metal with a HNO3/acetic acid mixture produces both orange Pd3(OAc)6, 1, and purple Pd3(OAc)5(NO2), 2. Compound has a trinuclear structure derived from that of the well-known triangular complex 1 in which one acetate group has been replaced by a nitrite group which is bonded to one palladium atom by the nitrogen atom and to another Pd atom using one of the oxygen atoms. Highly pure 1 can be made by continuous removal of the nitric oxides from the reaction mixture using a flow of N2. 1H NMR spectra of solutions of 1 in CDCl3 and C6D6 show several signals of various intensities when a small amount of water is present in the deuterated solvents but only one signal when the solvents are thoroughly dried. These results are consistent with the occurrence of one or more hydrolysis processes when the solvents contain water and suggest that hypotheses about various [Pd(OAc)2]n aggregates that have previously been brought forward in the literature to explain the complexity of the spectrum of 1 are unnecessary, especially for nonpolar solvents. Compound 2 does not hydrolyze, and in wet or dried solvents shows a 1H NMR spectrum that consists of five equal-intensity signals due to the five nonequivalent acetate groups.     

An automated method for the analysis of stable isotope labeling data in proteomics

An algorithm is presented for the generation of a reliable peptide component peak table from liquid chromatography-mass spectrometry (LC-MS) and subsequent quantitative analysis of stable isotope coded peptide samples. The method uses chemical noise filtering, charge state fitting, and deisotoping toward improved analysis of complex peptide samples. Overlapping peptide signals in mass spectra were deconvoluted by correlation with modeled peptide isotopic peak profiles. Isotopic peak profiles for peptides were generated in silico from a protein database producing reference model distributions. Doublets of heavy and light labeled peak clusters were identified and compared to provide differential quantification of pairs of stable isotope coded peptides. Algorithms were evaluated using peptides from digests of a single protein and a seven-protein mixture that had been differentially coded with stable isotope labeling agents and mixed in known ratios. The experimental results correlated well with known mixing ratios.     

Adaptation of a fast Fourier transform-based docking algorithm for protein design

Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to approximately 70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 A C(alpha) RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.     

Two-particle dynamics on an electrode in ac electric fields

The relative motion between pairs of negatively charged latex particles 9.7 microm in diameter and deposited on an electrode was measured by optical microscopy and image analysis. At an rms field of approximately 30 V cm(-1), the two particles moved toward each other at frequencies below 500 Hz, but they separated at 1000 Hz. In the cases of aggregation, there are several interesting characteristics. First, when the center-to-center separation of a pair was initially 6 particle radii or more apart, a transient 'incubation' period of tens of seconds was observed before the particles began to move toward each other. Second, the two particles never came into contact, rather at long times the pair maintained a stationary gap between them equal to approximately one-half the particle radius. This stationary gap between particles was also observed for the aggregation of clusters of three or more particles. Finally, the rate of approach for a pair of particles decreased as the frequency increased. Larger fields are required to move particles together in ac compared to dc fields; at 30 Hz the ac field must be 130 times greater than the dc field to achieve the same rate of approach. Taking advantage of the qualitative and quantitative differences of the cooperative motion of particles in dc vs. ac fields, one should be able to re-position particles by alternating between these two modes. We demonstrated that the same pair of particles can be brought together at low frequency (100 or 200 Hz) and then separated at high frequency (1000 Hz).