π Acceptor Abilities of Anionic Ligands: Comparisons Involving Anionic Ligands Incorporated into Linear d10 [(NH3)Pd(A)]-, Square Planar d8 [(NN2)Ru(A)]-, and Octahedral d6 [(AsN4)Tc(A)]- Complexes.

Extended transition state-natural orbitals for chemical valence (ETS-NOCV)] data were used to rank electron acceptor capacities for several potentially synergistic anionic ligands incorporated into linear d10 [(NH3)Pd(A)]-, square planar d8 [(NN2)Ru(A)]-, and octahedral d6 [(AsN4)Tc(A)]- complexes [A = anionic ligand, NN2 = HN(CH2CH2CH2NH2)2, and AsN4 = [As(CH2CH2CH2NH2)4]-]. It was possible to differentiate between the best acceptors, among them BI2- and B(CF3)2-, and the poorest ones. A sizable fraction of the anionic ligands studied exhibit similar acceptor capacities (backbonding), mostly regardless of d electron count. A number of trends were discerned, including the fact that acceptor capacity decreases down families and across rows but increases down families of the peripheral substituents. The latter appears tied to the ability of the peripheral ligands to compete with the metal in donating electrons to the ligand-binding atom.

Additivity of Diene Substituent Gibbs Free Energy Contributions for Diels-Alder Reactions between Me2C=CMe2 and Substituted Cyclopentadienes.

Systematic computational studies of pericyclic Diels-Alder reactions between (H3C)2C=C(CH3)2, 1, and all permutations of substituted cyclopentadienes c-C5R1R2R3R4R5aR5b (R = H, CH3, CF3, F) allowed isolation of substitutional effects on Gibbs free energy barrier heights and reaction Gibbs free energies. "Average Substitution Gibbs Free Energy Correction" ΔG ASC# ‡/ΔG ASC# values for each substituent in each position appeared to be additive. Substituent effects on barriers showed interesting contrasts. Methyl substitution at positions 5a and 5b increased barriers significantly, while substitution at all other positions had essentially no impact. In contrast, fluoro substitution at positions 5a and 5b lowered barriers more than substitution at other positions. Trifluoromethyl substitution mixed these effects, in that substitution at positions 5a and 5b increased barriers, but substitution at other positions lowered them. Despite the variances, ΔG ASC# ‡/ΔG ASC# values allowed reliable prediction of barriers and exergonicities for reactions between 1 and highly substituted cyclopentadienes, and between 1 and cyclopentadienes with random mixtures of CH3/CF3/F substituents. ΔG ASC# ‡/ΔG ASC# values were correlated with steric considerations and quantum theory of atoms in molecules (QTAIM) calculations. Overall, the ASC values provide a resource for predicting which Diels-Alder reactions of this type should occur at rapid rates and/or give stable bicyclic products.

Synthesis, characterization, X-ray and electronic structures of diethyl ether and 1,2-dimethoxyethane adducts of molybdenum(IV) chloride and tungsten(IV) chloride.

The bis(diethyl ether) and 1,2-dimethoxyethane (dme) adducts of molybdenum(IV) chloride and tungsten(IV) chloride are valuable starting materials for a variety of synthetic inorganic and organometallic reactions. Despite the broad utility and extensive use of these 6-coordinate complexes, their syntheses remain unoptimized, and their characterization incomplete after more than three decades. While exploring the ligand exchange behaviour of trans-MoCl4(OEt2)2, we obtained single crystals of this red-orange complex and subsequently compared its structural parameters with those of the recently reported trans-WCl4(OEt2)2. Significantly improved procedures for both MoCl4(dme) and WCl4(dme) were developed, and X-ray diffraction data were obtained and analysed. The magnetic properties of the dme adducts were probed, both with Gouy and SQUID magnetometry measurements. The magnetic moment of WCl4(dme) was smaller than that of MoCl4(dme), an observation that we attribute to the greater spin-orbit coupling of tungsten. Electronic structure studies were also conducted to probe the preferential trans configuration of the diethyl ether adducts and to assign the UV-Vis spectra of the dme adducts.

"MoCl3(dme)" Revisited: Improved Synthesis, Characterization, and X-ray and Electronic Structures.

"MoCl3(dme)" (dme = 1,2-dimethoxyethane) is an important precursor for midvalent molybdenum chemistry, particularly for triply Mo-Mo bonded compounds of the type Mo2X6 (X = bulky anionic ligand). However, its exact structural identity has been obscure for more than 50 years. In search of a convenient, large-scale synthesis, we have found that trans-MoCl4(Et2O)2 dissolved in dme can be cleanly reduced with dimethylphenylsilane, Me2PhSiH, to provide khaki Mo2Cl6(dme)2 in ∼90% yield. If the reduction is performed on a small scale, single crystals suitable for X-ray crystallography can be obtained. Two different crystal morphologies were identified, each belonging to the P21/n space group, but with slightly different unit cell constants. The refined structure of each form is an edge-shared bioctahedron with overall Ci symmetry and metal-metal separations on the order of 2.8 Å. The bulk material is diamagnetic as determined by both the Gouy method and SQUID magnetometry. Density functional theory calculations suggest a σ2π2δ*2 ground state for the dimer with the diamagnetism arising from a singlet diradical "broken symmetry" electronic configuration. In addition to a definitive structural assignment for "MoCl3(dme)", this work highlights the utility of organosilanes as easy to handle, alternative reductants for inorganic synthesis.

Additivity of Diene Substituent Gibbs Free Energy Contributions for Diels-Alder Reactions between (F3C)2B = NMe2 and Substituted Cyclopentadienes.

Systematic computational studies of pericyclic Diels-Alder-type reactions between aminoborane (F3C)2B = N(CH3)2, 1, and all permutations of substituted cyclopentadienes c-C5R1R2R3R4R5aR5b (R = H, CH3, CF3, F) allow isolation of substitutional effects on Gibbs free energy barrier heights and reaction Gibbs free energies. The effects appear to be additive in all cases. Substitution at positions 5a and 5b always increases barriers and reaction energies, an effect explained by steric interactions between substituents and the aminoborane moiety. For cases R = CH3, regioselectivities differ from those expected from canonical organic chemistry predictions. Frontier molecular orbital calculations suggest this arises from the extreme polarization of the π interaction in 1. For cases R = CF3, the 2/3-substitution comparison accords with canon, but the 1/4-substitution comparison does not. This appears to arise from a combination of electronic and steric issues. For cases R = F, many of the reactions are exergonic, in contrast to the cases R = CH3, CF3. Additionally, fluorine substitution at positions 2 and 4 has a barrier-lowering effect. Frontier molecular orbital calculations support an orbital-based preference for formation of 2- and 4-substituted "meta" products rather than "ortho/para" products.

Computational Study of the Ene/Rearrangement Reaction between (F3C)2B═NMe2, 1, and Acetonitrile: Reactant-Catalyzed Mechanism of the Ketenimine-Nitrile-Like Rearrangement.

The reaction between (F3C)2B═NMe2, 1, and acetonitrile at low temperature in pentane yields a bora-acetonitrile rather than the expected coordination complex. This appears to arise from the two undergoing an ene reaction followed by a rearrangement analogous to a ketenimine-nitrile rearrangement. Computational studies indicate that mechanistic steps suggested for the latter require energies too large for the reaction to take place under the experimental conditions. Instead, a mechanism in which the ene reaction product is attacked by a second molecule of 1, followed by hydrogen transfer and decomposition, exhibits barriers lower than that for the ene reaction. The mechanism implies that the fragment of 1 in the observed product is not the one that underwent the ene reaction. The ene reaction barrier is rate-determining, and it is low enough to conform to the experimental conditions.

Computational studies of ene reactions between aminoborane (F3C)2B[double bond, length as m-dash]N(CH3)2 and substituted propenes: additive effects on barriers and reaction energies.

Systematic computational studies of concerted pericyclic ene-type reactions between aminoborane (F3C)2B[double bond, length as m-dash]N(CH3)2, 1, and substituted propenes (R1a)(R1e)C[double bond, length as m-dash]C(R2)-C(R3a)(R3e)H (R = Me, CF3, F; a = axial position in transition state, e = equatorial position in transition state) show that in all cases but one the reactions are exothermic. The reactions proceed through six-membered cyclic envelope-like transition states except in the case of 1 + C3H(CF3)5. The data allow isolation of substitutional effects on barrier heights; the effects appear to be additive in all cases. Substitution at positions 1a, 1e, and 3a increases barriers, while substitution at positions 2 and 3e has variable impacts. The former observation is ascribed to steric crowding in the transition states, and is particularly prevalent for substitution at positions 1a and 1e. Substitution at position 2 lowers barriers for R = Me, F, possibly due to electronic demands, while raising them for R = CF3 because of 1,3-diaxial repulsions between boron- and carbon-bound CF3 groups. Substitution at position 3e has little impact on the barriers for R = Me, CF3, but significantly raises them for R = F. This seems to arise from charge effects on the position of the transition states.

Role of Ligand in the Selective Production of Hydrogen from Formic Acid Catalysed by the Mononuclear Cationic Zinc Complexes [(L)Zn(H)]+ (L=tpy, phen, and bpy).

A series of zinc-based catalysts was evaluated for their efficiency in decomposing formic acid into molecular hydrogen and carbon dioxide in the gas phase using quadrupole ion trap mass spectrometry experiments. The effectiveness of the catalysts in the series [(L)Zn(H)]+ , where L=2,2':6',2''-terpyridine (tpy), 1,10-phenanthroline (phen) or 2,2'-bipyrydine (bpy), was found to depend on the ligand used, which turned out to be fundamental in tuning the catalytic properties of the zinc complex. Specifically, [(tpy)Zn(H)]+ displayed the fastest reaction with formic acid proceeding by dehydrogenation to produce the zinc formate complex [(tpy)Zn(O2 CH)]+ and H2 . The catalysts [(L)Zn(H)]+ are reformed by decarboxylating the zinc formate complexes [(L)Zn(O2 CH)]+ by collision-induced dissociation, which is the only reaction channel for each of the ligands used. The decarboxylation reaction was found to be reversible, since the zinc hydride complexes [(L)Zn(H)]+ react with carbon dioxide yielding the zinc formate complex. This reaction was again substantially faster for L=tpy than L=phen or bpy. The energetics and mechanisms of these processes were modelled using several levels of density functional theory (DFT) calculations. Experimental results are fully supported by the computational predictions.

Gas-phase functionalized carbon-carbon coupling reactions catalyzed by Ni (II) complexes.

Gas-phase C-C coupling reactions mediated by Ni (II) complexes were studied using a linear quadrupole ion trap mass spectrometer. Ternary nickel cationic carboxylate complexes, [(phen)Ni (OOCR1 )]+ (where phen = 1,10-phenanthroline), were formed by electrospray ionization. Upon collision-induced dissociation (CID), they extrude CO2 forming the organometallic cation [(phen)Ni(R1 )]+ , which undergoes gas-phase ion-molecule reactions (IMR) with acetate esters CH3 COOR2 to yield the acetate complex [(phen)Ni (OOCCH3 )]+ and a C-C coupling product R1 -R2 . These Ni(II)/phenanthroline-mediated coupling reactions can be performed with a variety of carbon substituents R1 and R2 (sp3 , sp2 , or aromatic), some of them functionalized. Reaction rates do not seem to be strongly dependent on the nature of the substituents, as sp3 -sp3 or sp2 -sp2 coupling reactions proceed rapidly. Experimental results are supported by density functional theory calculations, which provide insights into the energetics associated with the C-C bond coupling step.

Chiral Brønsted Acid-Catalyzed Metal-Free Asymmetric Direct Reductive Amination Using 1-Hydrosilatrane.

The asymmetric direct reductive amination of prochiral ketones with aryl amines using 1-hydrosilatrane with a chiral Brønsted acid catalyst is reported. This is the first known example of chiral Brønsted acid-catalyzed asymmetric reductive amination using a silane as the hydride source. The reaction features a highly practical reducing reagent and proceeds efficiently at room temperature without a specialized reaction setup or equipment to exclude air or moisture. This method provides high conversion and enantiomeric excess up to 84% of the desired chiral secondary amines with minimal side products.

Computational Studies of Relative Stabilities of Low-Spin d6 cis- and trans-[M(en)2X2]+ Complexes (M = Co, Rh, Ir): Steric and Electronic Effects in the Context of the Structural Trans Influence.

Computational studies of low spin d6 cis- and trans-[M(en)2X2]+ complexes (M = Co, Rh, Ir) employing multiple model chemistries find that isomer preferences fall into three categories. Complexes where X is largely a σ-donor (H-, CH3-, CF3-) prefer cis geometries, in keeping with predictions associated with the trans influence series. Complexes where this donor characteristic is augmented by π acceptor behavior (B(CF3)2-, BCl2-, SiCl3-) evince even greater preference for cis geometries. QTAIM charge data suggest this is marked by lower positive charge on the metal in cis complexes. In contrast, complexes where X is a π donor and low in the trans influence series (X = OH-, F-, Cl-, I-) prefer trans geometries to varying degrees. QTAIM calculations indicate that this arises because the cis complexes are destabilized by distortions of the electron density in the M-X bonds. This can be viewed conceptually as resulting from repulsions between lone pair electrons on the ligands. Complexes where the X ligands are moderately trans-influencing and can interact conjugatively (CN-, NC-, NO2-, C≡CH-) prefer trans geometries because they combine destabilization of cis geometries with enhanced stabilization of trans geometries resulting from conjugation.

Computational Study of Ways by Which exo-Silatranes Might Be Prepared.

exo-Silatranes involve cage structures where the nitrogen lone pair points away from the cage rather than into it. This distinguishes them from the well-established endo-silatranes. exo-Silatranes have not been observed experimentally, consistent with a significant benefit to silicon-nitrogen interactions inside the cages as suggested for endo-silatranes. Identifying examples of exo-silatranes would prove useful in understanding Si-N interactions, as they would represent the "no interaction" extreme of the spectrum. We have found four means by which exo-silatranes might be synthesized: (1) employing smaller cages; (2) employing constrained rings to stiffen the cage backbones; (3) employing steric interactions to enhance preference for the less crowded exo-geometry around nitrogen; (4) modifying the Lewis acidity and basicity of the silicon and nitrogen so significantly as to remove their desire to interact. The preference for exo geometries is established using the parameter Δ, representing the distance between the nitrogen atom and the least-squares plane containing the adjacent carbon atoms. In some cases, Δ values for exo-silatranes are greater than 0.3 Å. In others, they are near zero, indicating a nearly planar nitrogen atom. There are no obvious structural markers besides Δ that distinguish between exo- and endo-silatranes.

Estimating Ring Strain Energies of Highly Substituted Cyclohexanes with the Semi-homodesmotic Approach: Why Substantial Ring Strain Exists for Nominally Tetrahedral Ring Carbon Atoms.

Estimation of ring strain energies (RSEs) of substituted cyclohexanes c-C6H(x)R(12-x) (R = F, Cl, Me; x = 0, 2, 4, 8, 10, 12) using homodesmotic reaction methods gives implausible results for highly substituted cases, particularly, c-C6R12. Prior work suggests that this stems from poorly canceled interactions between substituents on the acyclic reference molecules. We apply here our semi-homodesmotic approach that minimizes use of acyclic references and ensures cancellation of intramolecular substituent interactions. The approach provides RSEs that are more consistent with chemical intuition, although they are higher than expected for "strain-free" cyclohexanes. The RSE for c-C6Me12 is predicted to be 11.9 kcal mol(-1). RSEs for halogenated rings rise significantly from 8-9 kcal mol(-1) for c-1,1,2,2-C6H8R4 to 44-50 kcal mol(-1) for c-C6R12 (R = F, Cl). The increase, and accompanying observation of larger RSEs for "adjacent CR2" systems, can be tied to increased bond distances in the rings upon progressive substitution. The sizable RSE for perchlorocyclohexane suggests that it may be susceptible to ring-opening reactions, a facet of its chemistry that is currently unexplored.

Application of a semi-homodesmotic approach in estimating ring strain energies (RSEs) of highly substituted cyclobutanes: RSEs for c-C4R8 that make sense.

A semi-homodesmotic method for estimating of ring strain energies (RSEs) of substituted cyclopropanes is applied to substituted cyclobutanes c-C4HxR8-x (R = F, Cl, Me; x = 0, 2, 4). Whereas (hyper)homodesmotic reaction methods predict implausible results, particularly for c-C4R8, the semi-homodesmotic approach provides RSEs consistent with thermodynamic and independent computational data regardless of the degree of substitution. The method requires employing homodesmotic group equivalent reactions only for disubstituted cyclobutanes, relying solely on absolute energy calculations for more substituted rings. We find that, consistent with QTAIM data, RSEs increase with substitution regardless of the electronic nature of R, although the increase is more dramatic when R is electron-withdrawing. Overall, the semi-homodesmotic method is simpler than hyperhomodesmotic approaches and gives more trustworthy results.

A semi-homodesmotic approach for estimating ring strain energies (RSEs) of highly substituted cyclopropanes that minimizes use of acyclic references and cancels steric interactions: RSEs for c-C3R6 that make sense.

Estimation of ring strain energies (RSEs) of substituted cyclopropanes c-C(3)H(x)R(6-x) (R = F, Cl, Me; x = 0, 2, 4) using homodesmotic reaction methods has been plagued by implausible results. Prior work suggests that this stems from poorly canceled interactions between substituents on the acyclic reference molecules. We report a semi-homodesmotic approach that minimizes use of acyclic references, focusing instead on canceling substituent interactions. The method requires employing homodesmotic group equivalent reactions only for disubstituted cyclopropanes and relies solely on absolute energy calculations for more substituted rings. This provides RSEs consistent with chemical intuition regardless of the degree of substitution. We find that RSEs increase with substitution regardless of the electronic nature of R, although the increase is more dramatic when R is electron-withdrawing. The RSEs determined are consistent with QTAIM data, which show that progressive substitution always increases critical path angles. Overall, the semi-homodesmotic approach is simpler than hyperhomodesmotic reaction methods, and gives more trustworthy results.

Computational studies of lewis acidity and basicity in frustrated lewis pairs.

Computational studies that characterize the effects of Lewis acidity/basicity on FLP formation and reactivity are reviewed. Formation of the FLP encounter complex "cage" depends on Lewis acidities and basicities of substituent "external" atoms, and their abilities to interact intramolecularly. Computations indicate that these interactions are worth 9-18 kcal mol⁻¹ for partly fluorinated FLPs such as (F5C6)3B···P(t-Bu)3, and less for less fluorinated species such as (H5C6)3B···P(t-Bu)3. Reactivity within the cage depends on the "classical" Lewis acidities/basicities of the internal atoms. Energetics here fall into the range of 5-50 kcal mol⁻¹; the larger the value, the greater the ability of the FLP to capture or split a substrate. In several cases the computationally predicted reaction barriers differ little with internal Lewis acidity/basicity, indicating that the rate-determining step involves the substrate entering the cage rather than attack by the Lewis acid/base atoms. In others, barriers vary sizably with Lewis acidity/basicity, indicating the opposite. In one case it was shown that these effects cancel, such that the three component barriers are identical for a range of substituted Lewis acid FLP components.

Erratum to: Axial imidazole binding strengths in porphyrinoid cobalt(III) complexes as studied by tandem mass spectrometry.

The Co(II) complexes of twelve meso-tetraaryl-porphyrins, -chlorins, and chlorin analogues containing non-pyrrolic heterocycles were synthesized and converted in situ to the corresponding Co(III) complexes coordinated to one or two imidazoles. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) in conjunction with the energy-variable collision-induced dissociation (CID) technique was used to compare the relative gas-phase binding strength of the axially coordinated imidazoles to the octahedral and square planar Co(III) porphyrinoid complex ions. The observed binding energies of these ligands were rationalized in terms of the effects of porphyrinoid core structure and meso-substitution on the electron density on the central Co(III) centers. Some of these trends were supported by DFT-based computational studies. The study highlights to which extend porphyrins vary from chlorins and chlorin analogues in their coordination abilities and to which extraordinary degree meso-thienyl-substituents influence the electronic structure of porphyrins. The study also defines further the scope and limits CID experiments can be used to interrogate the electronic structures of metalloporphyrin complexes.

Improving the performance of true single molecule sequencing for ancient DNA.

BACKGROUND: Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase. RESULTS: We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted. CONCLUSIONS: We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targeted.

Axial imidazole binding strengths in porphyrinoid cobalt(III) complexes as studied by tandem mass spectrometry.

The Co(II) complexes of twelve meso-tetraaryl-porphyrins, -chlorins, and chlorin analogues containing non-pyrrolic heterocycles were synthesized and converted in situ to the corresponding Co(III) complexes coordinated to one or two imidazoles. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) in conjunction with the energy-variable collision-induced dissociation (CID) technique was used to compare the relative gas-phase binding strength of the axially coordinated imidazoles to the octahedral and square planar Co(III) porphyrinoid complex ions. The observed binding energies of these ligands were rationalized in terms of the effects of porphyrinoid core structure and meso-substitution on the electron density on the central Co(III) centers. Some of these trends were supported by DFT-based computational studies. The study highlights to which extend porphyrins vary from chlorins and chlorin analogues in their coordination abilities and to which extraordinary degree meso-thienyl-substituents influence the electronic structure of porphyrins. The study also defines further the scope and limits CID experiments can be used to interrogate the electronic structures of metalloporphyrin complexes.