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Speech utterance clustering based on the maximization of within-cluster homogeneity of speaker voice characteristics.

This paper investigates the problem of how to partition unknown speech utterances into a set of clusters, such that each cluster consists of utterances from only one speaker, and the number of clusters reflects the unknown speaker population size. The proposed method begins by specifying a certain number of clusters, corresponding to one of the possible speaker population sizes, and then maximizes the level of overall within-cluster homogeneity of the speakers' voice characteristics. The within-cluster homogeneity is characterized by the likelihood probability that a cluster model, trained using all the utterances within a cluster, matches each of the within-cluster utterances. To attain the maximal sum of likelihood probabilities for all utterances, the proposed method applies a genetic algorithm to determine the cluster in which each utterance should be located. For greater computational efficiency, also proposed is a clustering criterion that approximates the likelihood probability with a divergence-based model similarity between a cluster and each of the within-cluster utterances. The clustering method then examines various legitimate numbers of clusters by adapting the Bayesian information criterion to determine the most likely speaker population size. The experimental results show the superiority of the proposed method over conventional methods based on hierarchical clustering.

Algorithms↗

Mixed-metal cluster chemistry. 19. Crystallographic, spectroscopic, electrochemical, spectroelectrochemical, and theoretical studies of systematically varied tetrahedral group 6-iridium clusters.

A systematically varied series of tetrahedral clusters involving ligand and core metal variation has been examined using crystallography, Raman spectroscopy, cyclic voltammetry, UV-vis-NIR and IR spectroelectrochemistry, and approximate density functional theory, to assess cluster rearrangement to accommodate steric crowding, the utility of metal-metal stretching vibrations in mixed-metal cluster characterization, and the possibility of tuning cluster electronic structure by systematic modification of composition, and to identify cluster species resultant upon electrochemical oxidation or reduction. The 60-electron tetrahedral clusters MIr(3)(CO)(11-x)(PMe(3))(x)(eta(5)-Cp) [M = Mo, x = 0, Cp = C(5)H(4)Me (5), C(5)HMe(4) (6), C(5)Me(5) (7); M = W, Cp = C(5)H(4)Me, x = 1 (13), x = 2 (14)] and M(2)Ir(2)(CO)(10-x)(PMe(3))(x)(eta(5)-Cp) [M = Mo, x = 0, Cp = C(5)H(4)Me (8), C(5)HMe(4) (9), C(5)Me(5) (10); M = W, Cp = C(5)H(4)Me, x = 1 (15), x = 2 (16)] have been prepared. Structural studies of 7, 10, and 13 have been undertaken; these clusters are among the most sterically encumbered, compensating by core bond lengthening and unsymmetrical carbonyl dispositions (semi-bridging, semi-face-capping). Raman spectra for 5, 8, WIr(3)(CO)(11)(eta(5)-C(5)H(4)Me) (11), and W(2)Ir(2)(CO)(10)(eta(5)-C(5)H(4)Me)(2) (12), together with the spectrum of Ir(4)(CO)(12), have been obtained, the first Raman spectra for mixed-metal clusters. Minimal mode-mixing permits correlation between A(1) frequencies and cluster core bond strength, frequencies for the A(1) breathing mode decreasing on progressive group 6 metal incorporation, and consistent with the trend in metal-metal distances [Ir-Ir < M-Ir < M-M]. Cyclic voltammetric scans for 5-15, MoIr(3)(CO)(11)(eta(5)-C(5)H(5)) (1), and Mo(2)Ir(2)(CO)(10)(eta(5)-C(5)H(5))(2) (3) have been collected. The [MIr(3)] clusters show irreversible one-electron reduction at potentials which become negative on cyclopentadienyl alkyl introduction, replacement of molybdenum by tungsten, and replacement of carbonyl by phosphine. These clusters show two irreversible one-electron oxidation processes, the easier of which tracks with the above structural modifications; a third irreversible oxidation process is accessible for the bis-phosphine cluster 14. The [M(2)Ir(2)] clusters show irreversible two-electron reduction processes; the tungsten-containing clusters and phosphine-containing clusters are again more difficult to reduce than their molybdenum-containing or carbonyl-containing analogues. These clusters show two one-electron oxidation processes, the easier of which is reversible/quasi-reversible, and the more difficult of which is irreversible; the former occur at potentials which increase on cyclopentadienyl alkyl removal, replacement of tungsten by molybdenum, and replacement of phosphine by carbonyl. The reversible one-electron oxidation of 12 has been probed by UV-vis-NIR and IR spectroelectrochemistry. The former reveals that 12(+) has a low-energy band at 8000 cm(-1), a spectrally transparent region for 12, and the latter reveals that 12(+) exists in solution with an all-terminal carbonyl geometry, in contrast to 12 for which an isomer with bridging carbonyls is apparent in solution. Approximate density functional calculations (including ZORA scalar relativistic corrections) have been undertaken on the various charge states of W(2)Ir(2)(CO)(10)(eta(5)-C(5)H(5))(2) (4). The calculations suggest that two-electron reduction is accompanied by W-W cleavage, whereas one-electron oxidation proceeds with retention of the tetrahedral core geometry. The calculations also suggest that the low-energy NIR band of 12(+) arises from a sigma(W-W) --> sigma*(W-W) transition.

Journal Article↗

Cluster size selectivity in the product distribution of ethene dehydrogenation on niobium clusters.

Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb8 and Nb10, for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb10, yielding either Nb(n)C2H2 or Nb(n)C2. Over the range Nb-Nb6, the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C2H4, C2H2, or C2. With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb(n) cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calculations of structures of Nb clusters up to Nb(6), and the reaction products Nb(n)C2H2 and Nb(n)C2 (n = 1...6) are presented. Investigation of the thermochemistry for the dehydrogenation of ethene to form molecular hydrogen, for the Nb atom and clusters up to Nb6, demonstrates that the exergonicity of the formation of Nb(n)C2 species increases with cluster size over this range, which supports the proposal that the extent of dehydrogenation is determined primarily by thermodynamic constraints. Analysis of the structural variations present in the cluster species studied shows an increase in C-H bond lengths with cluster size that closely correlates with the increased thermodynamic drive to full dehydrogenation. This correlation strongly suggests that all steps in the reaction are barrierless, and that weakening of the C-H bonds is directly reflected in the thermodynamics of the overall dehydrogenation process. It is also demonstrated that reaction exergonicity in the initial partial dehydrogenation step must be carried through as excess internal energy into the second dehydrogenation step.

Journal Article↗

Heterobimetallic Clusters of Copper(I) with Trithiotungstate and Trithiomolybdate. Synthesis and Characterization of the Octanuclear Clusters [Et(4)N](4)[M(4)Cu(4)S(12)O(4)] (M = Mo, W) and the Dodecanuclear Clusters [M(4)Cu(4)S(12)O(4)(CuTMEN)(4)] (M = Mo, W; TMEN = N,N,N',N'-Tetramethylethylenediamine).

Synthetic methods for [Et(4)N](4)[W(4)Cu(4)S(12)O(4)] (1), [Et(4)N](4)[Mo(4)Cu(4)S(12)O(4)] (2), [W(4)Cu(4)S(12)O(4)(CuTMEN)(4)] (3), and [Mo(4)Cu(4)S(12)O(4)(CuTMEN)(4)] (4) are described. [Et(4)N](2)[MS(4)], [Et(4)N](2)[MS(2)O(2)], Cu(NO(3))(2).3H(2)O, and KBH(4) (or Et(4)NBH(4)) were used as starting materials for the synthesis of 1 and 2. Compounds 3 and 4 were produced by reaction of [Et(4)N](2)[WOS(3)], Cu(NO(3))(2).3H(2)O, and TMEN and by reaction of [Me(4)N](2)[MO(2)O(2)S(8)], Cu(NO(3))(2).3H(2)O, and TMEN, respectively. Crystal structures of compounds 1-4 were determined. Compounds 1 and 2 crystallized in the monoclinic space group C2/c with a = 14.264(5) Å, b = 32.833(8) Å, c = 14.480(3) Å, beta = 118.66(2) degrees, V = 5950.8(5) Å(3), and Z = 4 for 1 and a = 14.288(5) Å, b = 32.937(10) Å, c = 14.490(3) Å, beta = 118.75(2) degrees, V = 5978.4(7) Å(3), and Z = 4 for 2. Compounds 3 and 4 crystallized in the trigonal space group P3(2)21 with a = 13.836(6) Å, c = 29.81(1) Å, V = 4942(4) Å(3), and Z = 3 for 3 and a = 13.756(9) Å, c = 29.80(2) Å, V = 4885(6) Å(3), and Z = 3 for 4. The cluster cores have approximate C(2v) symmetry. The anions of 1 and 2 may be viewed as consisting of two butterfly-type [CuMOS(3)Cu] fragments bridged by two [MOS(3)](2-) groups. Eight metal atoms in the anions are arranged in an approximate square configuration, with a Cu(4)M(4)S(12) ring structure. Compounds 3 and 4 can be considered to consist of one [M(4)Cu(4)S(12)O(4)](4-) (the anions of 1 and 2) unit capped by Cu(TMEN)(+) groups on each M atom; the Cu(TMEN)(+) groups extend alternately up and down around the Cu(4)M(4) square. The electronic spectra of the compounds are dominated by the internal transitions of the [MOS(3)](2-) moiety. (95)Mo NMR spectral data are investigated and compared with those of other compounds.

Journal Article↗

Re-evaluation of the classical Mycoplasma lipophilum cluster (Weisburg et al. 1989) and description of two new clusters in the hominis group based on 16S rDNA sequences.

The Mycoplasma lipophilum cluster (Weisburg et al. 1989) in the hominis group of the mollicutes is re-evaluated in this work to update the phylogenetic framework for classification of species within the genus Mycoplasma. Therefore, sequences of the 16S rRNA gene were determined from previously described species, and 11 were found to be closely related to the M. lipophilum cluster. A selection of members of the other hitherto defined clusters of the hominis group was included for phylogenetic analysis, revealing that the classical M. lipophilum cluster could be re-organized into two clusters, namely the M. lipophilum cluster and the Mycoplasma bovis cluster. The former was found to contain two species, while the latter contained 20 species. The two clusters were closely related, sharing an ancestral branch with the Mycoplasma synoviae cluster. Furthermore, the M. bovis cluster could be divided into subclusters. Interestingly, two species, Mycoplasma equigenitalium and Mycoplasma elephantis, formed a distinct and early branch of the M. lipophilum, M. bovis and M. synoviae clusters. This entity was termed the M. equigenitalium cluster. The clusters and subclusters could be verified by using neighbour-joining and maximum-likelihood analyses on a variety of data sets, bootstrap calculations, secondary structure analysis and signature nucleotides. Therefore, the new 16S rDNA data presented in this work were used to re-evaluate the M. lipophilum cluster, leading to the definition of two additional clusters. At present, the mollicutes belonging to the hominis group can be classified into ten evolutionary lineages.

Bacterial Typing Techniques↗

On the distributions of ion/neutral molecule clusters in electrospray and laser spray -- a cluster division model for the electrospray process.

The clustering of a medium-sized, involatile, neutral molecule, octyl beta-D-glucopyranoside (OG), with Na(+), Ca(2+), and Yb(3+) (M(z+)) ions in electrospray (ESI) was investigated using laser spray (LSI). Extensive distributions of [(M(z+))(i) (OG)(a)](n+)-clusters, extending beyond 50 kDa, were observed. The distributions were highly stable and reproducible and changed only marginally when concentrations of electrolyte or neutral compound were varied by orders of magnitude. Compared with ESI, laser spray yielded superior intensities, particularly of the larger clusters. The cluster distributions demonstrated a range of remarkable features. In particular, the Yb(3+)/OG cluster distribution was unusual. For example, no clusters with 35-52 or with 110-116 OG molecules were observed. The distribution pattern revealed that the clusters were formed as a result of cluster dissociations, such as [(Yb(3+))(3)(OG) ( approximately 110)W](9+) --> [(Yb(3+))(2)(OG)( approximately 90)W](6+) + [(Yb(3+))(1)(OG) ( approximately 20)W](3+), where W represents the water content at the time of dissociation. Based on this study, a cluster division model for electrospray of aqueous solutions of strongly solvated ions is proposed: the Rayleigh droplet disintegration process, which is well-established for the initial stages of electrospray, maintains its general character as it proceeds through a final regime of multiply charged cluster dissociations to the singly and multiply charged ions in mass spectrometry. In the dissociation of multiply charged clusters, the size of each daughter cluster is roughly proportional to the square of the cluster charge. Observed cluster distributions are consistent with a mixture of symmetric and asymmetric cluster dissociations.

Journal Article↗

Observed intra-cluster correlation coefficients in a cluster survey sample of patient encounters in general practice in Australia.

BACKGROUND: Cluster sample study designs are cost effective, however cluster samples violate the simple random sample assumption of independence of observations. Failure to account for the intra-cluster correlation of observations when sampling through clusters may lead to an under-powered study. Researchers therefore need estimates of intra-cluster correlation for a range of outcomes to calculate sample size. We report intra-cluster correlation coefficients observed within a large-scale cross-sectional study of general practice in Australia, where the general practitioner (GP) was the primary sampling unit and the patient encounter was the unit of inference. METHODS: Each year the Bettering the Evaluation and Care of Health (BEACH) study recruits a random sample of approximately 1,000 GPs across Australia. Each GP completes details of 100 consecutive patient encounters. Intra-cluster correlation coefficients were estimated for patient demographics, morbidity managed and treatments received. Intra-cluster correlation coefficients were estimated for descriptive outcomes and for associations between outcomes and predictors and were compared across two independent samples of GPs drawn three years apart. RESULTS: Between April 1999 and March 2000, a random sample of 1,047 Australian general practitioners recorded details of 104,700 patient encounters. Intra-cluster correlation coefficients for patient demographics ranged from 0.055 for patient sex to 0.451 for language spoken at home. Intra-cluster correlations for morbidity variables ranged from 0.005 for the management of eye problems to 0.059 for management of psychological problems. Intra-cluster correlation for the association between two variables was smaller than the descriptive intra-cluster correlation of each variable. When compared with the April 2002 to March 2003 sample (1,008 GPs) the estimated intra-cluster correlation coefficients were found to be consistent across samples. CONCLUSIONS: The demonstrated precision and reliability of the estimated intra-cluster correlations indicate that these coefficients will be useful for calculating sample sizes in future general practice surveys that use the GP as the primary sampling unit.

Australia↗

Biotin synthase contains two distinct iron-sulfur cluster binding sites: chemical and spectroelectrochemical analysis of iron-sulfur cluster interconversions.

Biotin synthase is an iron-sulfur protein that utilizes AdoMet to catalyze the presumed radical-mediated insertion of a sulfur atom between the saturated C6 and C9 carbons of dethiobiotin. Biotin synthase (BioB) is aerobically purified as a dimer that contains [2Fe-2S](2+) clusters and is inactive in the absence of additional iron and reductants, and anaerobic reduction of BioB with sodium dithionite results in conversion to enzyme containing [4Fe-4S](2+) and/or [4Fe-4S](+) clusters. To establish the predominant cluster forms present in biotin synthase in anaerobic assays, and by inference in Escherichia coli, we have accurately determined the extinction coefficient and cluster content of the enzyme under oxidized and reduced conditions and have examined the equilibrium reduction potentials at which cluster reductions and conversions occur as monitored by UV/visible and EPR spectroscopy. In contrast to previous reports, we find that aerobically purified BioB contains ca. 1.2-1.5 [2Fe-2S](2+) clusters per monomer with epsilon(452) = 8400 M(-)(1) cm(-)(1) per monomer. Upon reduction, the [2Fe-2S](2+) clusters are converted to [4Fe-4S] clusters with two widely separate reduction potentials of -140 and -430 mV. BioB reconstituted with excess iron and sulfide in 60% ethylene glycol was found to contain two [4Fe-4S](2+) clusters per monomer with epsilon(400) = 30 000 M(-)(1) cm(-)(1) per monomer and is reduced with lower midpoint potentials of -440 and -505 mV, respectively. Finally, as predicted by the measured redox potentials, enzyme incubated under typical anaerobic assay conditions is repurified containing one [2Fe-2S](2+) cluster and one [4Fe-4S](2+) cluster per monomer. These results indicate that the dominant stable cluster state for biotin synthase is a dimer containing two [2Fe-2S](2+) and two [4Fe-4S](2+) clusters.

Aerobiosis↗

Iron-sulfur cluster biosynthesis. A comparative kinetic analysis of native and Cys-substituted ISA-mediated [2Fe-2S]2+ cluster transfer to an apoferredoxin target.

ISA type proteins mediate cluster transfer to apoprotein targets. Rate constants have been determined for cluster transfer from Schizosaccharomyces pombe ISA to apo Fd. Substitution of the cysteine residues of ISA produced derivative proteins (C72A, C136A, and C138A) that were found to be at least as active in cluster transfer reactions as the native form at 25 degrees C (k(2) approximately 170 M(-1) min(-1) for native, k(2) approximately 169 M(-1) min(-1) for C72A, k(2) approximately 206 M(-1) min(-1) for C136A, and k(2) approximately 242 M(-1) min(-1) for C138A), although the yield of cluster transfer was found to be lower as a consequence of the enhanced lability of clusters in the derivative proteins. Minor variations in rate constant for the ISA Cys derivatives do not reflect any change in the affinity of binding to the apo Fd since k(2) was found to be independent of the concentration of apo Fd over the range of 1-25 microM. The pH dependence of cluster transfer rates was found to be similar for native and C136A ISA, with an observed pK(a) of 7.8 determined from the pH profiles for cluster transfer activity of each protein. The temperature dependence of the rate constant defining the cluster transfer reaction for the wild type versus this C136A ISA derivative is distinct (DeltaH* approximately 6.3 kcal mol(-1) and DeltaS* approximately -27.3 cal K(-1) mol(-1) for native and DeltaH* approximately 2.7 kcal mol(-1) and DeltaS* approximately -38.9 cal K(-1) mol(-1) for C136A ISA). Instability of the protein-bound cluster precluded a comparison with data from pH and temperature dependencies for the two other Cys derivatives. Experiments to determine the dependence of reaction rate constants on viscosity indicate cluster transfer is rate-limiting. A comparison of cross-species rate constants for cluster transfer to apo Fd targets from Homo sapiens and S. pombe demonstrated that the identity of the Fd is less critical for promoting cluster transfer from Sp ISA (at 25 degrees C, k(2) approximately 170 M(-1) min(-1) for Sp Fd and k(2) approximately 169 M(-1) min(-1) for Hs Fd). This contrasts with an earlier observation for ISU-mediated cluster assembly [Wu, S., et al. (2002) Biochemistry 41, 8876-8885], where the rates differed for Hs and Sp target Fd's, suggesting distinct binding sites for binding of holo ISA and ISU to apo Fd.

Amino Acid Substitution↗

Metal-Metal Bonding in Pentanuclear Bow-Tie Metal Sulfido Clusters. Synthetic and Structural Studies on the Cationic Pentanuclear Clusters [(CpIr)(2)(&mgr;(3)-S)(2)M(&mgr;(3)-S)(2)(IrCp)(2)](n)()(+) (M = Fe, Co, Ni; n = 1, 2).

Reactions of [CpMCl(&mgr;(2)-SH)(2)MCpCl] (1, M = Ir; 2, M = Rh; Cp = eta(5)-C(5)Me(5)) with excess FeCl(2).4H(2)O in THF gave the paramagnetic trinuclear clusters [(CpM)(2)(&mgr;(3)-S)(2)FeCl(2)] (3, M = Ir; 4, M = Rh), which were further converted into the dicationic 78e(-) pentanuclear bow-tie cluster [(CpIr)(2)(&mgr;(3)-S)(2)Fe(&mgr;(3)-S)(2)(IrCp)(2)](2+) (5) by treatment with NaBPh(4). When complex 1 was allowed to react with CoCl(2) and NiCl(2).6H(2)O or Ni(cod)(2) (cod = cyclooctadiene), the related pentanuclear 79e(-) and 80e(-) bow-tie clusters [(CpIr)(2)(&mgr;(3)-S)(2)M(&mgr;(3)-S)(2)(IrCp)(2)](2+) (6, M = Co; 7, M = Ni) were obtained directly, respectively. Cyclic voltammograms of 5[BPh(4)](2), 6[BPh(4)](2), and 7[BPh(4)](2) showed two reversible reduction waves at -0.25 to -0.43 V and -1.04 to -1.34 V. In both redox couples, the redox potential was in the order Fe < Co < Ni. One-electron reduction of clusters 5[BPh(4)](2), 6[BPh(4)](2), and 7[BPh(4)](2) with Co(eta(5)-C(5)H(5))(2) gave the corresponding monocationic pentanuclear 79-81e(-) bow-tie clusters [(CpIr)(2)(&mgr;(3)-S)(2)M(&mgr;(3)-S)(2)(IrCp)(2)](+) (8, M = Fe; 9, M = Co; 10, M = Ni). The molecular structures of 3, 4, 5[BPh(4)](2).CH(2)Cl(2), 6[CoCl(3)(NCMe)](2), 7[NiCl(4)].CH(2)Cl(2), 8[BPh(4)], 9[BPh(4)], and 10[BPh(4)] were unambiguously determined by X-ray diffraction study. The structures of the pentanuclear bow-tie cluster cores remarkably changed stepwise as the core electrons increased from 78 to 81. Two of the M-Ir (M = Fe, Co) bonds in the 79e(-) clusters 6 and 8 show significant elongation in comparison with the Fe-Ir bonds in the 78e(-) cluster 5. Two different types of the bow-tie structures were observed for the 80e(-) clusters 7 and 9. Cluster 7 has a Z-shaped metal core with only two Ni-Ir bonds, while in cluster 9, the six metal-metal bonds in the bow-tie structure are retained with slight elongation of the Co-Ir bonds in comparison with the corresponding dication 6. The 81e(-) cluster 10 has two normal Ni-Ir bonds and one long Ni-Ir bonding interaction with the fourth nonbonding Ni-Ir contact. This structural variation is interpreted in terms of the total electron counts and molecular orbital calculations of the clusters.

Journal Article↗

Synthesis of a molecular Mo2Fe6S9 cluster with the topology of the PN cluster of nitrogenase by rearrangement of an edge-bridged Mo2Fe6S8 double cubane.

The structures of the P cluster and cofactor cluster of nitrogenase are well-defined crystallographically. They have been obtained only by biosynthesis; their chemical synthesis remains a challenge. Synthetic routes are sought to the P cluster in the P(N) state in which two cuboidal Fe(3)S(3) units are connected by a mu(6)-S atom and two Fe-(mu(2)-S(Cys))-Fe bridges. A reaction scheme affording a Mo(2)Fe(6)S(9) cluster in molecular form having the topology of the P(N) cluster has been devised. Reaction of the single cubane [(Tp)MoFe(3)S(4)Cl(3)](1)(-) with PEt(3) gives [(Tp)MoFe(3)S(4)(PEt(3))(3)](1+) (2), which upon reduction with BH(4)(-) affords the edge-bridged all-ferrous double cubane [(Tp)(2)Mo(2)Fe(6)S(8)(PEt(3))(4)] (4) (Tp = tris(pyrazolylhydroborate(1-)). Treatment of 4 with 3 equiv of HS(-) produces [(Tp)(2)Mo(2)Fe(6)S(9)(SH)(2)](3)(-) (7) as the Et(4)N(+) salt in 86% yield. The structure of 7 is built of two (Tp)MoFe(3)(mu(3)-S)(3) cuboidal fragments bridged by two mu(2)-S atoms and one mu(6)-S atom in an arrangement of idealized C(2) symmetry. The cluster undergoes three one-electron oxidation reactions and is oxidatively cleaved by p-tolylthiol to [(Tp)MoFe(3)S(4)(S-p-tol)(3)](2)(-) and by weak acids to [(Tp)MoFe(3)S(4)(SH)(3)](2-). The cluster core of 7 has the bridging pattern [Mo(2)Fe(6)(mu(2)-S)(2)(mu(3)-S)(6)(mu(6)-S)](1+) with the probable charge distribution [Mo(3+)(2)Fe(2+)(5)Fe(3+)S(9)](1+). Cluster 7 is a topological analogue of the P(N) cluster but differs in having two heteroatoms and two Fe-(mu(2)-S)-Fe instead of two Fe-(mu(2)-S(Cys))-Fe bridges. A best-fit superposition of the two cluster cores affords a weighted rms deviation in atom positions of 0.38 A. Cluster 7 is the first molecular topological analogue of the P(N) cluster. This structure had been prepared previously only as a fragment of complex high-nuclearity Mo-Fe-S clusters.

Biomimetic Materials↗

Cluster phase chemistry: gas-phase reactions of anionic sodium salts of dicarboxylic acid clusters with water molecules.

A homologous series of anionic gas-phase clusters of dicarboxylic acids (oxalic acid, malonic acid, succinic acid, glutaric acid, and adipic acid) generated via electrospray ionization (ESI) are investigated using collision-induced dissociation (CID). Sodiated clusters with the composition (Na(+))(2)(n+1)(dicarboxylate(2-)(n+1) for singly charged anionic clusters, where n = 1-4, are observed as major gas-phase species. Isolation of the clusters followed by CID results mainly in sequential loss of disodium dicarboxylate moieties for the clusters of succinic acid, glutaric acid, and adipic acid (C4-C6). However, all oxalate (C2) and malonate (C3) clusters and dimers (n = 1) of succinate (C4) and glutarate (C5) exhibit more complex chemistry initiated by collision of the activated cluster with water molecules. For example, with water addition, malonate clusters dissociate to yield sodium acetate, carbon dioxide, and sodium hydroxide. More generally, water molecules serve as proton donors for reacting dicarboxylate anions in the cluster and introduce energetically favorable dissociation pathways not otherwise available. Density functional theory (DFT) calculations of the binding energy of the cluster correlate well with the cluster phase reactions of oxalate and malonate clusters. Clusters of larger dicarboxylate ions (C4-C6) are more weakly bound, facilitating the sequential loss of disodium dicarboxylate moieties. The more strongly bound small dicarboxylate anions (oxalate and malonate) preferentially react with water molecules rather than dissociate to lose disodium dicarboxylate monomers when collisionally activated. Implications of these results for the atmospheric aerosol chemistry of dicarboxylic acids are discussed.

Anions↗

Electron and nuclear dynamics of molecular clusters in ultraintense laser fields. III. Coulomb explosion of deuterium clusters.

In this paper we present a theoretical and computational study of the energetics and temporal dynamics of Coulomb explosion of molecular clusters of deuterium (D2)n/2 (n = 480 - 7.6 x 10(4), cluster radius R0 = 13.1 - 70 A) in ultraintense laser fields (laser peak intensity I = 10(15) - 10(20)W cm(-2)). The energetics of Coulomb explosion was inferred from the dependence of the maximal energy EM and the average energy Eav of the product D+ ions on the laser intensity, the laser pulse shape, the cluster radius, and the laser frequency. Electron dynamics of outer cluster ionization and nuclear dynamics of Coulomb explosion were investigated by molecular dynamics simulations. Several distinct laser pulse shape envelopes, involving a rectangular field, a Gaussian field, and a truncated Gaussian field, were employed to determine the validity range of the cluster vertical ionization (CVI) approximation. The CVI predicts that Eav, EM proportional to R0(2) and that the energy distribution is P(E) proportional to E1/2. For a rectangular laser pulse the CVI conditions are satisfied when complete outer ionization is obtained, with the outer ionization time toi being shorter than both the pulse width and the cluster radius doubling time tau2. By increasing toi, due to the increase of R0 or the decrease of I, we have shown that the deviation of Eav from the corresponding CVI value (Eav(CVI)) is (Eav(CVI) - Eav)/Eav(CVI) approximately (toi/2.91tau2)2. The Gaussian pulses trigger outer ionization induced by adiabatic following of the laser field and of the cluster size, providing a pseudo-CVI behavior at sufficiently large laser fields. The energetics manifest the existence of a finite range of CVI size dependence, with the validity range for the applicability of the CVI being R0 < or = (R0)I, with (R0)I representing an intensity dependent boundary radius. Relating electron dynamics of outer ionization to nuclear dynamics for Coulomb explosion induced by a Gaussian pulse, the boundary radius (R0)I and the corresponding ion average energy (Eav)I were inferred from simulations and described in terms of an electrostatic model. Two independent estimates of (R0)I, which involve the cluster size where the CVI relation breaks down and the cluster size for the attainment of complete outer ionization, are in good agreement with each other, as well as with the electrostatic model for cluster barrier suppression. The relation (Eav)I proportional to (R0)I(2) provides the validity range of the pseudo-CVI domain for the cluster sizes and laser intensities, where the energetics of D+ ions produced by Coulomb explosion of (D)n clusters is optimized. The currently available experimental data [Madison et al., Phys. Plasmas 11, 1 (2004)] for the energetics of Coulomb explosion of (D)n clusters (Eav = 5 - 7 keV at I = 2 x 10(18) W cm(-2)), together with our simulation data, lead to the estimates of R0 = 51 - 60 A, which exceed the experimental estimate of R0 = 45 A. The predicted anisotropy of the D+ ion energies in the Coulomb explosion at I = 10(18) W cm(-2) is in accord with experiment. We also explored the laser frequency dependence of the energetics of Coulomb explosion in the range nu = 0.1 - 2.1 fs(-1) (lambda = 3000 - 140 nm), which can be rationalized in terms of the electrostatic model.

Journal Article↗

d2_cluster: a validated method for clustering EST and full-length cDNAsequences.

Several efforts are under way to condense single-read expressed sequence tags (ESTs) and full-length transcript data on a large scale by means of clustering or assembly. One goal of these projects is the construction of gene indices where transcripts are partitioned into index classes (or clusters) such that they are put into the same index class if and only if they represent the same gene. Accurate gene indexing facilitates gene expression studies and inexpensive and early partial gene sequence discovery through the assembly of ESTs that are derived from genes that have yet to be positionally cloned or obtained directly through genomic sequencing. We describe d2_cluster, an agglomerative algorithm for rapidly and accurately partitioning transcript databases into index classes by clustering sequences according to minimal linkage or "transitive closure" rules. We then evaluate the relative efficiency of d2_cluster with respect to other clustering tools. UniGene is chosen for comparison because of its high quality and wide acceptance. It is shown that although d2_cluster and UniGene produce results that are between 83% and 90% identical, the joining rate of d2_cluster is between 8% and 20% greater than UniGene. Finally, we present the first published rigorous evaluation of under and over clustering (in other words, of type I and type II errors) of a sequence clustering algorithm, although the existence of highly identical gene paralogs means that care must be taken in the interpretation of the type II error. Upper bounds for these d2_cluster error rates are estimated at 0.4% and 0.8%, respectively. In other words, the sensitivity and selectivity of d2_cluster are estimated to be >99.6% and 99.2%.

Algorithms↗

Clustering and re-clustering for pattern discovery in gene expression data.

The combined interpretation of gene expression data and gene sequences is important for the investigation of the intricate relationships of gene expression at the transcription level. The expression data produced by microarray hybridization experiments can lead to the identification of clusters of co-expressed genes that are likely co-regulated by the same regulatory mechanisms. By analyzing the promoter regions of co-expressed genes, the common regulatory patterns characterized by transcription factor binding sites can be revealed. Many clustering algorithms have been used to uncover inherent clusters in gene expression data. In this paper, based on experiments using simulated and real data, we show that the performance of these algorithms could be further improved. For the clustering of expression data typically characterized by a lot of noise, we propose to use a two-phase clustering algorithm consisting of an initial clustering phase and a second re-clustering phase. The proposed algorithm has several desirable features: (i) it utilizes both local and global information by computing both a "local" pairwise distance between two gene expression profiles in Phase 1 and a "global" probabilistic measure of interestingness of cluster patterns in Phase 2, (ii) it distinguishes between relevant and irrelevant expression values when performing re-clustering, and (iii) it makes explicit the patterns discovered in each cluster for possible interpretations. Experimental results show that the proposed algorithm can be an effective algorithm for discovering clusters in the presence of very noisy data. The patterns that are discovered in each cluster are found to be meaningful and statistically significant, and cannot otherwise be easily discovered. Based on these discovered patterns, genes co-expressed under the same experimental conditions and range of expression levels have been identified and evaluated. When identifying regulatory patterns at the promoter regions of the co-expressed genes, we also discovered well-known transcription factor binding sites in them. These binding sites can provide explanations for the co-expressed patterns.

Algorithms↗

IscU as a scaffold for iron-sulfur cluster biosynthesis: sequential assembly of [2Fe-2S] and [4Fe-4S] clusters in IscU.

Iron-sulfur cluster biosynthesis in both prokaryotic and eukaryotic cells is known to be mediated by two highly conserved proteins, termed IscS and IscU in prokaryotes. The homodimeric IscS protein has been shown to be a cysteine desulfurase that catalyzes the reductive conversion of cysteine to alanine and sulfide. In this work, the time course of IscS-mediated Fe-S cluster assembly in IscU was monitored via anaerobic anion exchange chromatography. The nature and properties of the clusters assembled in discrete fractions were assessed via analytical studies together with absorption, resonance Raman, and Mössbauer investigations. The results show sequential cluster assembly with the initial IscU product containing one [2Fe-2S](2+) cluster per dimer converting first to a form containing two [2Fe-2S](2+) clusters per dimer and finally to a form that contains one [4Fe-4S](2+) cluster per dimer. Both the [2Fe-2S](2+) and [4Fe-4S](2+) clusters in IscU are reductively labile and are degraded within minutes upon being exposed to air. On the basis of sequence considerations and spectroscopic studies, the [2Fe-2S](2+) clusters in IscU are shown to have incomplete cysteinyl ligation. In addition, the resonance Raman spectrum of the [4Fe-4S](2+) cluster in IscU is best interpreted in terms of noncysteinyl ligation at a unique Fe site. The ability to assemble both [2Fe-2S](2+) and [4Fe-4S](2+) clusters in IscU supports the proposal that this ubiquitous protein provides a scaffold for IscS-mediated assembly of clusters that are subsequently used for maturation of apo Fe-S proteins.

Azotobacter vinelandii↗

Structural conversions of molybdenum-iron-sulfur edge-bridged double cubanes and P(n)-type clusters topologically related to the nitrogenase P-cluster.

Edge-bridged Mo-Fe-S double cubanes are versatile precursors for the synthesis of other clusters of the same nuclearity. Thus, the double cubane [(Tp)(2)Mo(2)Fe(6)S(8)(PEt(3))(4)] sustains terminal ligand substitution with retention of the Mo(2)Fe(6)(micro(3)-S)(6)(micro(4)-S)(2) core structure and rearrangement to the Mo(2)Fe(6)(micro(2)-S)(2)(micro(3)-S)(6)(micro(6)-S) topology of the nitrogenase P(N) cluster upon reaction with certain nucleophiles. Four distinct processes for the conversion of double cubanes to P(N)-type clusters are documented, affording the products [(Tp)(2)Mo(2)Fe(6)S(9)(SR)(2)](3)(-), [(Tp)(2)Mo(2)Fe(6)S(8)(OMe)(3)](3)(-), and [(Tp)(2)Mo(2)Fe(6)S(7)(OMe)(4)](2)(-). In the latter clusters, two methoxides are terminal ligands and one or two are micro(2)-bridging ligands. The reverse transformation of a P(N)-type cluster to an edge-bridged double cubane has been demonstrated by the reaction of [(Tp)(2)Mo(2)Fe(6)S(8)(OMe)(3)](3)(-) with Me(3)SiX to afford [(Tp)(2)Mo(2)Fe(6)S(8)X(4)](2)(-) (X = Cl(-), Br(-)). Edge-bridged double cubanes have been obtained in the oxidation states [Mo(2)Fe(6)S(8)](2+,3+,4+). The stable oxidation state of P(N)-type clusters is [Mo(2)Fe(6)S(9)](+). Structures of five double cubanes and four P(N)-type clusters are reported. The P(N)-type clusters are synthetic representations of the biologically unique topology of the native P(N) cluster. Best-fit superpositions of the native and synthetic cluster cores gives weighted rms deviations in atom positions of 0.20-0.38 A. This study and an earlier investigation (Zhang, Y.; Holm, R. H. J. Am. Chem. Soc. 2003, 125, 3910-3920) provide a comprehensive account of the synthesis of structural analogues of the native P(N) cluster and provide the basis for continuing investigation of the synthesis of weak-field Mo-Fe-S clusters related to nitrogenase. (Tp = tris(pyrazolyl)hydroborate(1-).)

Crystallography, X-Ray↗

Redox control of light-induced charge separation in a transition metal cluster: photochemistry of a methyl viologen-substituted [Os3(CO)10(alpha-diimine)] cluster.

(Sub)picosecond transient absorption (TA) and time-resolved infrared (TRIR) spectra of the cluster [Os3(CO)10-(AcPy-MV)]2+ (the dication AcPy-MV = AcPy-MV2+ = [2-pyridylacetimine-N-(2-(1'-methyl-4,4'-bipyridine-1,1'-diium-1-yl)ethyl)](PF6)2) (1(2+)) reveal that photoinduced electron transfer to the electron-accepting 4,4'-bipyridine-1,1'-diium (MV2+) moiety competes with the fast relaxation of the initially populated sigmapi excited state of the cluster to the ground state and/or cleavage of an Os-Os bond. The TA spectra of cluster 1(2+) in acetone, obtained by irradiation into its lowest-energy absorption band, show the characteristic absorptions of the one-electron-reduced MV*+ unit at 400 and 615 nm, in accordance with population of a charge-separated (CS) state in which a cluster-core electron has been transferred to the lowest pi orbital of the remote MV2+ unit. This assignment is confirmed by picosecond TRIR spectra that show a large shift of the pilot highest-frequency nu(CO) band of 1(2+) by ca. +40 cm(-1), reflecting the photooxidation of the cluster core. The CS state is populated via fast (4.2 x 10(11) s(-1)) and efficient (88%) oxidative quenching of the optically populated sigmapi excited state and decays biexponentially with lifetimes of 38 and 166 ps (1.2:1 ratio) with a complete regeneration of the parent cluster. About 12% of the cluster molecules in the sigmapi excited state form long-lived open-core biradicals. In strongly coordinating acetonitrile, however, the cluster core-to-MV2+ electron transfer in cluster 1(2+) results in the irreversible formation of secondary photoproducts with a photooxidized cluster core. The photochemical behavior of the [Os3(CO)10(alpha-diimine-MV)]2+ (donor-acceptor) dyad can be controlled by an externally applied electronic bias. Electrochemical one-electron reduction of the MV2+ moiety prior to the irradiation reduces its electron-accepting character to such an extent that the photoinduced electron transfer to MV(*+) is no longer feasible. Instead, the irradiation of reduced cluster 1(*+) results in the reversible formation of an open-core zwitterion, the ultimate photoproduct also observed upon irradiation of related nonsubstituted clusters [Os3(CO)10(alpha-diimine)] in strongly coordinating solvents such as acetonitrile.

Journal Article↗