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Michael B Hall

Publications and source records attributed to Michael B Hall.

At least 19 recordsLinked to original sources
PubMed2025

Genome size estimation from long read overlaps.

MOTIVATION: Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existing tools are primarily optimized for short-read data. RESULTS: We present LRGE, a novel tool that uses read-to-read overlap information to estimate genome size in a reference-free manner. LRGE calculates per-read genome size estimates by analysing the expected number of overlaps for each read, considering read lengths and a minimum overlap threshold. The final size is taken as the median of these estimates, ensuring robustness to outliers such as reads with no overlaps. Additionally, LRGE provides an expected confidence range for the estimate. We validate LRGE on a large, diverse bacterial dataset and confirm it generalizes to eukaryotic datasets. On bacterial genomes, LRGE outperforms k-mer-based methods in both accuracy and computational efficiency and produces genome size estimates comparable to those from assembly-based approaches, like Raven, while using significantly less computational resources. AVAILABILITY AND IMPLEMENTATION: Our method, LRGE (Long Read-based Genome size Estimation from overlaps), is implemented in Rust and is available as a precompiled binary for most architectures, a Bioconda package, a prebuilt container image, and a crates.io package as a binary (lrge) or library (liblrge). The source code is available at https://github.com/mbhall88/lrge and an archive at https://doi.org/10.5281/zenodo.17183812 under an MIT license.

Genome Size↗
PubMed2006

Synthesis, reactivity, and DFT studies of tantalum complexes incorporating diamido-N-heterocyclic carbene ligands. Facile endocyclic C-H bond activation.

The syntheses of tantalum derivatives with the potentially tridentate diamido-N-heterocyclic carbene (NHC) ligand are described. Aminolysis and alkane elimination reactions with the diamine-NHC ligands, (Ar)[NCN]H(2) (where (Ar)[NCN]H(2) = (ArNHCH(2)CH(2))(2)(C(3)N(2)); Ar = Mes, p-Tol), provided complexes with a bidentate amide-amine donor configuration. Attempts to promote coordination of the remaining pendent amine donor were unsuccessful. Metathesis reactions with the dilithiated diamido-NHC ligand ((Ar)[NCN]Li(2)) and various Cl(x)Ta(NR'(2))(5-)(x) precursors were successful and generated the desired octahedral (Ar)[NCN]TaCl(x)(NR'(2))(3-)(x) complexes. Attempts to prepare trialkyl tantalum complexes by this methodology resulted in the formation of an unusual metallaaziridine derivative. DFT calculations on model complexes show that the strained metallaaziridine ring forms because it allows the remaining substituents to adopt preferable bonding positions. The calculations predict that the lowest energy pathway involves a tantalum alkylidene intermediate, which undergoes C-H bond activation alpha to the amido to form the metallaaziridine moiety. This mechanism was confirmed by examining the distribution of deuterium atoms in an experiment between (Mes)[NCN]Li(2) and Cl(2)Ta(CD(2)Ph)(3). The single-crystal X-ray structures of (p)(-Tol)[NCNH]Ta(NMe(2))(4) (3), (Mes)[NCNH]Ta=CHPh(CH(2)Ph)(2) (4), (p)(-Tol)[NCN]Ta(NMe(2))(3) (7), (Mes)[NCCN]Ta(CH(2)(t)Bu)(2) (11), and (Mes)[NCCN]TaCl(CH(2)(t)Bu) (14) are included.

Journal Article↗
PubMed2006

Mechanistic investigation of the oxygen-atom-transfer reactivity of dioxo-molybdenum(VI) complexes.

The oxygen-atom-transfer (OAT) reactivity of [LiPrMoO2(OPh)] (1, LiPr=hydrotris(3-isopropylpyrazol-1-yl)borate) with the tertiary phosphines PEt3 and PPh2Me in acetonitrile was investigated. The first step, [LiPrMoO2(OPh)]+PR3-->[LiPrMoO(OPh)(OPR3)], follows a second-order rate law with an associative transition state (PEt3, DeltaH not equal=48.4 (+/-1.9) kJ mol-1, DeltaS not equal=-149.2 (+/-6.4) J mol-1 K-1, DeltaG not equal=92.9 kJ mol-1; PPh2Me, DeltaH not equal=73.4 (+/-3.7) kJ mol-1, DeltaS not equal=-71.9 (+/-2.3) J mol-1 K-1, DeltaG not equal=94.8 kJ mol-1). With PMe3 as a model substrate, the geometry and the free energy of the transition state (TS) for the formation of the phosphine oxide-coordinated intermediate were calculated. The latter, 95 kJ mol-1, is in good agreement with the experimental values. An unexpectedly large O-P-C angle calculated for the TS suggests that there is significant O-nucleophilic attack on the P--C sigma* in addition to the expected nucleophilic attack of the P on the Mo==O pi*. The second step of the reaction, that is, the exchange of the coordinated phosphine oxide with acetonitrile, [LiPrMoO(OPh)(OPR3)]+MeCN-->[LiPrMoO(OPh)(MeCN)]+OPR3, follows a first-order rate law in MeCN. A dissociative interchange (Id) mechanism, with activation parameters of DeltaH not equal=93.5 (+/-0.9) kJ mol-1, DeltaS not equal=18.2 (+/-3.3) J mol-1 K-1, DeltaG not equal=88.1 kJ mol-1 and DeltaH not equal=97.9 (+/-3.4) kJ mol-1, DeltaS not equal=47.3 (+/-11.8) J mol-1 K-1, DeltaG not equal=83.8 kJ mol-1, for [LiPrMoO(OPh)(OPEt3)] (2 a) and [LiPrMoO(OPh)(OPPh2Me)] (2 b), respectively, is consistent with the experimental data. Although gas-phase calculations indicate that the Mo--OPMe3 bond is stronger than the Mo--NCMe bond, solvation provides the driving force for the release of the phosphine oxide and formation of [LiPrMoO(OPh)(MeCN)] (3).

Chemical Phenomena↗
PubMed2006

Density functional study of the catalytic cycle of nickel-iron [NiFe] hydrogenases and the involvement of high-spin nickel(II).

In light of recent experiments suggesting high-spin (HS) Ni(II) species in the catalytic cycle of [NiFe] hydrogenase, a series of models of the Ni(II) forms Ni-SI(I,II), SI-CO and Ni-R(I,II,III) were examined in their high-spin states via density functional calculations. Because of its importance in the catalytic cycle, the Ni-C form was also included in this study. Unlike the Ni(II) forms in previous studies, in which a low-spin (LS) state was assumed and a square-planar structure found, the optimized geometries of these HS Ni(II) forms resemble those observed in the crystal structures: a distorted tetrahedral to distorted pyramidal coordination for the NiS4. This resemblance is particularly significant because the LS state is 20-30 kcal/mol less stable than the HS state for the geometry of the crystal structure. If these Ni(II) forms in the enzyme are not high spin, a large change in geometry at the active site is required during the catalytic cycle. Furthermore, only the HS state for the CO-inhibited form SI-CO has CO stretching frequencies that match the experimental results. As in the previous work, these new results show that the heterolytic cleavage reaction of dihydrogen (where H2 is cleaved with the metal acting as a hydride acceptor and a cysteine as the proton acceptor) has a lower energy barrier and is more exothermic when the active site is oxidized to Ni(III). The enzyme models described here are supported by a calibrated correlation of the calculated and measured CO stretching frequencies of the forms of the enzyme. The correlation coefficient for the final set of models of the forms of [NiFe] hydrogenase is 0.8.

Catalysis↗
PubMed2006

De novo design of synthetic di-iron(I) complexes as structural models of the reduced form of iron-iron hydrogenase.

Simple synthetic di-iron dithiolate complexes provide good models of the composition of the active site of the iron-iron hydrogenase enzymes. However, the formally Fe(I)Fe(I) complexes synthesized to date fail to reproduce the precise orientation of the diatomic ligands about the iron centers that is observed in the molecular structure of the reduced form of the enzyme active site. This structural difference is often used to explain the fact that the synthetic di-iron complexes are generally poor catalysts when compared to the enzyme. Herein, density functional theory computations are used for the rational design of synthetic complexes as structural models of the reduced form of the enzyme active site. These computations suggest several possible synthetic targets. The synthesis of complexes containing five-atom S-to-S linkers of the form S(CH2)2X(CH2)2S (X = CH2, NH, or O) or pendant functionalities attached to the three-carbon framework is one method. Another approach is the synthesis of asymmetrically substituted complexes, in which one iron center has strongly electron donating ligands and the adjacent iron center has strongly electron accepting ligands. The combination of a sterically demanding S-to-S linker and asymmetric substitution of the CO ligands is predicted to be a particularly effective synthetic target.

Hydrogenase↗
PubMed2006

Do B3LYP and CCSDT predict different hydrosilylation mechanisms? Influences of theoretical methods and basis sets on relative energies in ruthenium-silylene-catalyzed ethylene hydrosilylation.

A series of density functional theory (DFT) and wave function theory (WFT) methods were used in conjunction with a series of basis sets to investigate the influence of the computational methodology on the relative energies of key intermediates and transition states in potential reaction pathways in ruthenium-silylene-catalyzed hydrosilylation reactions. A variety of DFT methods in a modest basis set and B3LYP calculations in a variety of basis sets calculated the key transition in the Glaser-Tilley (GT) pathway to be energetically favored. In contrast, with the smaller basis sets, the CCSD(T) method calculated the Chalk-Harrod (CH) pathway to be favored; however, CCSD(T) results extrapolated to larger basis sets favored the GT pathway.

Journal Article↗
PubMed2006

Hydrogen-substituted osmium silylene complexes: effect of charge localization on catalytic hydrosilation.

Addition of bulky primary silanes to the osmium benzyl compound, Cp*(iPr3P)OsCH2Ph, afforded two neutral hydrogen-substituted silylene complexes via activation of two Si-H bonds. These species have been structurally characterized, and their reactivity has been examined experimentally and computationally. Comparison of these neutral silylene complexes with their cationic analogue highlights the dramatic influence of charge distribution on the reaction chemistry of metal silylene complexes.

Journal Article↗
PubMed2006

Correlation between computed gas-phase and experimentally determined solution-phase infrared spectra: models of the iron-iron hydrogenase enzyme active site.

Gas-phase density functional theory calculations (B3LYP, double zeta plus polarization basis sets) are used to predict the solution-phase infrared spectra for a series of CO- and CN-containing iron complexes. It is shown that simple linear scaling of the computed C--O and C--N stretching frequencies yields accurate predictions of the the experimentally determined nu(CO) and nu(CN) values for a variety of complexes of different charges and in solvents of varying polarity. As examples of the technique, the resulting correlation is used to assign structures to spectroscopically observed but structurally ambiguous species in two different systems. For the (mu-SCH2CH2CH2S)[Fe(CO)3]2 complex in tetrahydrofuran solution, our calculations show that the initial electrochemical reduction process leads to a simple one-electron reduced product with a structure very similar to the (mu-SCH2CH2CH2S)[Fe(CO)3]2 parent complex. For the iron-iron hydrogenase enzyme active site, our computations show that the absence or presence of a water molecule near the distal iron center (the iron center further from the [4Fe4S] cluster and protein backbone) has very little effect on the predicted infrared spectra.

Binding Sites↗
PubMed2005

Mechanistic insights into iridium-catalyzed asymmetric hydrogenation of dienes.

Hydrogenation of 2,3-diphenylbutadiene (1) with the chiral carbene-oxazoline-iridium complex C has been studied by means of a combined experimental and computational approach. A detailed kinetic profile of the reaction was obtained with respect to consumption of the substrate and formation of the intermediate half-reduction products, 2,3-diphenylbut-1-ene (2) and the final product, 2,3-diphenylbutane (3). The data generated from these analyses, and from NMR experiments, revealed several facets of the reaction. After a brief induction period (presumably involving reduction of the cyclooctadiene ligand on C), the diene concentration declines in a zero-order process primarily to give monoene intermediates. When all the diene is consumed, the reaction accelerates and compound 3 begins to accumulate. Interestingly, the prevalent enantiomer of the monoene intermediate 2 is converted mostly to meso-3 so the enantioselectivity of the reaction appears to reverse. The reaction seems to be first-order with respect to the catalyst when the catalyst concentration is less than 0.0075 M; diffusion of hydrogen across the gas-liquid interface complicates the analysis at higher catalyst concentrations. Similarly, these diffusion effects complicated measurements of reaction rate versus applied pressure of dihydrogen; other factors like stir speed and flask geometry come into play under some, but not all, the conditions examined. Density functional theory (DFT) calculations, using the PBE method, were used to probe the reaction. These studies indicate a transoid-eta(4)-diene-dihydride complex forms in the first stages of the catalytic cycle. Further reaction requires dissociation of one alkene ligand to give a eta(2)-diene-dihydride-dihydrogen intermediate. A catalytic cycle that features Ir(3+)/Ir(5+) seems to be involved thereafter.

Journal Article↗
PubMed2005

Electronic and steric effects on molecular dihydrogen activation in [CpOsH4(L)]+ (L = PPh3, AsPh3, and PCy3).

Single-crystal neutron diffraction, inelastic neutron scattering, and density functional calculations provide experimental and theoretical analyses of the nature of the osmium-bound, "elongated" dihydrogen ligands in [Cp*OsH(4)(L)][BF(4)] complexes (L = PPh(3), AsPh(3), or PCy(3)). The PPh(3) and AsPh(3) complexes clearly contain one dihydrogen ligand and two terminal hydrides; the H(2) ligand is transoid to the Lewis base, and the H-H vector connecting the central two hydrogen atoms lies parallel to the Ct-Os-L plane (Ct = centroid of Cp* ring). In contrast, in the PCy(3) complex the H-H vector is perpendicular to the Ct-Os-L plane. Not only the orientation of the central two hydrogen atoms but also the H-H bond length between them depends significantly on the nature of L: the H...H distance determined from neutron diffraction is 1.01(1) and 1.08(1) A for L = PPh(3) and AsPh(3), respectively, but 1.31(3) A for L = PCy(3). Density functional calculations show that there is a delicate balance of electronic and steric influences created by the L ligand that change the molecular geometry (steric interactions between the Cp* and L groups most importantly change the Ct-Os-L angle), changing the relative energy of the Os 5d orbitals, which in turn govern the H-H distance, preferred H-H orientation, and rotational dynamics of the elongated dihydrogen ligand. The geometry of the dihydrogen ligand is further tuned by interactions with the BF(4)(-) counterion. The rotational barrier of the bound H(2) ligand in [Cp*OsH(4)(PPh(3))](+), determined experimentally (3.1 kcal mol(-)(1)) from inelastic neutron scattering experiments, is in reasonable agreement with the B3LYP calculated H(2) rotational barrier (2.5 kcal mol(-)(1)).

Journal Article↗
PubMed2005

Urea decomposition facilitated by a urease model complex: a theoretical investigation.

Density functional theory calculations were used to examine the role of the urease model complex [Ni2(bdptz)(micro-OH)(micro-H2O)(H2O)2](OTs)3(bdptz=1,4-bis(2,2'-dipyridylmethyl)-phthalazine; OTs=tosylate) in the degradation of urea. An elimination mechanism that converts urea to ammonium cyanate was investigated in detail. The lowest energy pathway involves urea coordination through the oxygen atom to a Ni center followed by protonation of a urea NH2 group by the bridging water ligand. Subsequent rotation of the protonated urea, followed by deprotonation of the NH2 by a bridging OH ligand generates the bound, disproportionated urea substrate, HNCONH3, from which ammonium cyanate was produced.

Journal Article↗
PubMed2005

Dual electron uptake by simultaneous iron and ligand reduction in an N-heterocyclic carbene substituted [FeFe] hydrogenase model compound.

An N-heterocyclic carbene containing [FeFe]H(2)ase model complex, whose X-ray structure displays an apical carbene, shows an unexpected two-electron reduction to be involved in its electrocatalytic dihydrogen production. Density functional calculations show, in addition to a one-electron Fe-Fe reduction, that the aryl-substituted N-heterocyclic carbene can accept a second electron more readily than the Fe-Fe manifold. The juxtaposition of these two one-electron reductions resembles the [FeFe]H(2)ase active site with an FeFe di-iron unit joined to the electroactive 4Fe4S cluster.

Binding Sites↗
PubMed2005

Rhodium boryl complexes in the catalytic, terminal functionalization of alkanes.

A series of studies have been conducted by experimental and theoretical methods on the synthesis, structures, and reactions of CpRh boryl complexes that are likely intermediates in the rhodium-catalyzed regioselective, terminal functionalization of alkanes. The photochemical reaction of CpRh(eta(6)-C(6)Me(6)) with pinacolborane (HBpin) generates the bisboryl complex CpRh(H)(2)(Bpin)(2) (2), which reacts with neat HBpin to generate CpRh(H)(Bpin)(3) (3). X-ray diffraction, density functional theory (DFT) calculations, and NMR spectroscopy suggest a weak, but measurable, B-H bonding interaction. Both 2 and 3 dissociate HBpin and coordinate PEt(3) or P(p-Tol)(3) to generate the conventional rhodium(III) species CpRh(PEt(3))(H)(Bpin) (4) and CpRh[P(p-tol)(3)](Bpin)(2) (5). Compounds 2 and 3 also react with alkanes and arenes to form alkyl- and arylboronate esters at temperatures similar to or below those of the catalytic borylation of alkanes and arenes. Further, these compounds were observed directly in catalytic reactions. The enthalpies and free energies for generation of the 16-electron intermediate and for the C-H bond cleavage and B-C bond formation have been calculated with DFT. These results strongly suggest that the C-H bond cleavage process occurs by a metal-assisted sigma-bond metathesis mechanism to generate a borane complex that isomerizes if necessary to place the alkyl group cis to the boryl group. This complex with cis boryl and alkyl groups then undergoes B-C bond formation by a second sigma-bond metathesis to generate the final functionalized product.

Journal Article↗
PubMed2005

High nuclearity iridium-platinum clusters: synthesis, structures, bonding, and reactivity.

The reaction of Ir4(CO)12 with an excess of Pt(PBu(t)3)2 at room temperature yielded the bis-Pt(PBu(t)3) adduct Ir4(CO)12[Pt(PBu(t)3)]2 (9), which contains two Pt(PBu(t)3) groups bridging opposite edges of a central Ir4 pseudotetrahedron. The same reaction at 110 degrees C yielded two new higher nuclearity complexes, Ir8(CO)12[Pt(PBu(t)3)]4 (10) and Ir6(CO)10[Pt(PBu(t)3)]4 (11). Compound 10 consists of a central Ir4(CO)4 tetrahedron with four edge-bridging Ir(CO)2 groups and four Pt(PBu(t)3) groups that are each bonded to Ir3 triangles of the Ir4 tetrahedron and two of the Ir(CO)2 groups. Compound 11 consists of a central Ir4(CO)4 pseudotetrahedron with two edge-bridging Ir(CO)2 groups and four Pt(PBu(t)3) groups; one Pt(PBu(t)3) group is bonded to five iridium atoms as found in 10; two are bonded to four iridium atoms, and one is bonded to one of the outer Ir2Pt triangles. Compound 11 reacted with hydrogen at 97 degrees C to give the new tetrahydrido complex Ir6(CO)8[Pt(PBu(t)3)]4(mu-H)4 (12). Compound 12 is formed by the loss of the two bridging carbonyl ligands from 11 and the addition of four hydrido ligands. All four new compounds were characterized by both 1H and 31P NMR and by single-crystal X-ray diffraction analyses. The bonding in 9 was studied by Fenske-Hall molecular orbital calculations, which in this case provides a delocalized bonding description for the Ir-Ir and Ir-Pt bonding, where the attachment of the 0 e- fragments of Pt(PR3) use Ir-Ir bonding orbitals of the Ir4(CO)12 cluster to form multicenter Pt-Ir bonds.

Journal Article↗
PubMed2004

Electronic effects steer the mechanism of asymmetric hydrogenations of unfunctionalized aryl-substituted alkenes.

Density functional theory (PBE and B3LYP) was used to study asymmetric hydrogenations of alkenes catalyzed by an iridium imidazolylidine oxazoline complex. The calculation predicts that the alkene preferentially coordinates to the site trans to the carbene. The coordinated alkene then reacts first with the H2 ligand, then with the hydride to form alkane. Finally, the alkane is released by equilibrating with extrinsic H2 and alkene. Enantioface selectivities for hydrogenations of trisubstituted alkenes seem to be driven primarily by steric interactions with the adamantyl part of the ligand; only the smallest substituents can adopt a site close to it. Application of this theoretical model leads to correct predictions regarding the experimentally observed sense and magnitude of the enantioselectivities.

Journal Article↗
PubMed2004

Superloading of tin ligands into rhodium and iridium carbonyl cluster complexes.

The reactions of Rh4(CO)12 and Ir4(CO)12 with Ph3SnH have yielded the new Rh-Sn and Ir-Sn cluster complexes M3(CO)6(mu-SnPh2)3(SnPh3)3, 1 (M=Rh) and 2 (M=Ir). Both compounds contain triangular M3 clusters with three bridging SnPh2 and three terminal SnPh3 ligands. The M-M bonds are unusually long. Molecular orbital calculations indicate that this is due to the importance of M-Sn bonding and weak direct M-M interactions. Reaction of 1 with Ph3SnH at reflux in 1,2-dichlorobenzene solvent yielded the complex Rh3(CO)3(SnPh3)3(mu-SnPh2)3(mu3-SnPh)2, 3, which contains eight tin ligands: three terminal SnPh3, three edge-bridging SnPh2, and two triply bridging SnPh ligands.

Journal Article↗
PubMed2004

Reaction products of W(CO)(6) with formamidines; electronic structure of a W(2)(mu-CO)(2) core with unsymmetric bridging carbonyls.

Reactions of W(CO)(6) with formamidines contrast with those of Mo(CO)(6) and Cr(CO)(6) in that the former do not yield quadruply bonded dimetal species. From the reaction of W(CO)(6) with HDAniF (HDAniF = N,N'-di-p-anisylformamidine), several new ditungsten carbonyl compounds (W(2)(mu-CO)(2)(mu-DAniF)(2)(eta(2)-DAniF)(2) (1), W(2)(mu-CO)(2)(mu-DAniF)(2)(eta(2)-DAniF)(eta(2)-CH(2)DAniF) (2), and W(2)(mu-CO)(mu-CNC(6)H(4)OCH(3))(mu-DAniF)(2)(eta(2)-DAniF)(2) (3)) have been isolated and fully characterized. In 2, CH(2)DAniF represents a DAniF ligand in which a methylene group has been added to one of the nitrogen atoms. This ligand binds to the tungsten atom using a nitrogen and a carbon atom. Compound 1 has a tungsten-tungsten bond distance of 2.476(1) A and a planar W(2)(mu-CO)(2) core structure which has C(2)(h)() symmetry with short and long W-C bond distances (1.99(1) and 2.28(1) A, respectively). DFT calculations on a model of 1 indicate that (a) the C(2)(h)() instead of D(2)(h)() symmetry of the ditungsten core may be attributed to W --> CO pi back-bonding interactions and (b) the bond between the tungsten atoms may be formulated as a double bond. The new tetragonal paddlewheel compound W(2)(DAniF)(4) (4) and the edge-sharing bioctahedron W(2)(mu-O)(mu-NC(6)H(3)Cl(2))(mu-D(Cl)PhF)(2)(eta(2)-D(Cl)PhF)(2) (5) (D(Cl)PhF = N,N'-di-(3,5-dichlorophenyl)formamidinate) have also been prepared.

Amidines↗