Gas-phase reactions between O−. and C6H5F: On the acidity of fluorobenzene and 1,4-difluorobenzene

The gas-phase reactions of negative ions (O^-., NH ₂ ^? , C₂H₅NH^?, (CH₃)₂N^?, C₆H ₅ ^t- , and CH₃SCH ₂ ^? ) with fluorobenzene and 1,4-difluorobenzene have been studied with Fourier transform ion cyclotron resonance mass spectrometry. The O^?. ion reacts predominantly by (1) proton abstraction, (2) formal H ₂ ^+. abstraction, and (3) attack on an unsubstituted carbon atom. In addition to these processes, attack on a fluorine bearing carbon atom yielding F^? and C₆H₄FO^? ions occurs with 1,4-difluorobenzene. Site-specific deuterium labeling reveals the occurrence of competing 1,2-, 1,3-, and 1,4-H ₂ ^+. abstractions in the reaction of O^?. with fluorobenzene. Attack of the O^?. ion on the 3- and 4-positions in fluorobenzene with formation of the 3- and 4-fluorophenoxide ions, respectively, is preferred to reaction at the 2-position, as indicated by the relative extent of loss of a hydrogen and a deuterium atom in the reactions with labeled fluorobenzenes. The NH ₂ ^? , C₂H₅NH^?, (CH₃)₂N^?, C₆H ₅ ^? , and CH₃SCH ₂ ^? anions react with fluoroberuene and 1,4-difluorobenzene only by proton abstraction. The relative importance of H⁺ and D⁺ abstraction in the reaction of these anions with labeled fluorobenzenes indicates that the 2-position in fluorobenzene is more acidic than the 3- and 4-positions, suggesting that the literature value of the gas-phase acidity of this compound (ΔH _acid ^o = 1620 ± 8 kJ mol^?1) refers to the former site. Based on the occurrence of reversible proton transfer between the CH₃O^? ion and 1,4-difluorobenzene, the ΔH _acid ^o of this compound is redetermined to be 1592 ± 8 kJ mol^?1.     

6,6′-Dimethoxygossypol: molecular structure,crystal polymorphism,and solvate formation

6,6′-Dimethoxygossypol (DMG) is a naturally occurring derivative of gossypol that is found in relatively high concentration in some Gossypium barbadense cotton varieties. Like gossypol, DMG forms an equimolar solvate with acetic acid, but it was not known if, like gossypol, the compound would also form clathrates with other molecules. To test for this, the compound was crystallized from different solvents. Four new structures of DMG were found that include two polymorphic and two solvated forms. The polymorphs include two monoclinic structures with P2₁/c and C2/c space groups (P1 and P2, respectively). Packing of the DMG molecules P1 is similar to packing of the gossypol molecules in the P1 polymorphic form of gossypol. The DMG molecules in P2 pack in a highly ordered arrangement that has not been previously observed among gossypol structures. DMG forms equimolar solvates with water (S1) and cyclohexanone (S2). Both structures are triclinic with P [`1]P \bar {1} space groups. The DMG molecules in S2 assemble in a manner that is similar to the gossypol molecules of gossypol–cyclohexanone (1:1), and the DMG molecules in S1 pack in a manner that is similar to the DMG molecules in DMG–acetic acid (1:1) as well as the gossypol molecules in gossypol–acetic acid (1:1). Although DMG is not as versatile a host compound as gossypol, it still forms solvates under many crystallization conditions. Consequently, some care is needed to be sure that one understands exactly which form is recovered when the compound is isolated.     

Ring-enlargement reactions of donor-acceptor-substituted cyclopropanes: which combinations are most efficient?

A detailed theoretical study of ring-enlargement reactions of 72 differently substituted donor-acceptor-substituted cyclopropanes is presented. Transition states, activation barriers, and, for representative examples, the behavior in solution were additionally determined using the B3LYP/6-311G(d) level of theory.     

Gas-phase fragmentation of the Ag+—phenylalanine complex: Cation—π interactions and radical cation formation

Collision-induced dissociation experiments on the Ag+-phenylalanine complex using several collision energies were shown to yield ten different fragment ions. Unambiguous assignment of these fragment ions were made by careful analysis of deuterium labeling experiments. The losses of H2O, CO, CO2, and AgH were commonly observed; also encountered were the losses of H2, Ag, and H. Deuterium labeling experiments and density functional calculations have been employed to probe fragmentation mechanisms that account for all experimental results.     

How homogeneous are the trehalose, maltose, and sucrose water solutions? An insight from molecular dynamics simulations

The structural properties resulting from the reciprocal influence between water and three well-known homologous disaccharides, namely, trehalose, maltose, and sucrose, in aqueous solutions have been investigated in the 4-66 wt % concentration range by means of molecular dynamics computer simulations. Hydration numbers clearly show that trehalose binds to a larger number of water molecules than do maltose or sucrose, thus affecting the water structure to a deeper extent. Two-dimensional radial distribution functions of trehalose solutions definitely reveal that water is preferentially localized at the hydration sites found in the trehalose dihydrate crystal, this tendency being enhanced when increasing trehalose concentration. Over a rather wide concentration range (4-49 wt %), the fluctuations of the radius of gyration and of the glycosidic dihedral angles of trehalose indicate a higher flexibility with respect to maltose and sucrose. At sugar concentrations between 33 and 66 wt %, the mean sugar cluster size and the number of sugar-sugar hydrogen bonds formed within sugar clusters reveal that trehalose is able to form larger clusters than sucrose but smaller than maltose. These features suggest that trehalose-water mixtures would be more homogeneous than the two others, thus reducing both desiccation stresses and ice formation.     

What are the enthalpy of formation and the stabilization energy of acrolein?

Acrolein (propenal) is a ubiquitous compound in the global environment with diverse deleterious ramifications for human health. Despite its importance, its measured enthalpy of formation is still contentious. Using high level quantum chemical calculations, we recommend a consensus value of ?65 ± 3 kJ mol^?1 for the gas phase species. Comparison is made with the other “acrylo” species, acrylonitrile and acrylic acid, and to other conjugated species such as butadiene and crotonaldehyde.     

Adsorption of gases in carbon nanotubes: are defect interstitial sites important?

Molecular simulations are used to shed light on an ongoing controversy over where gases adsorb on single walled carbon nanotube bundles. We have performed simulations using models of carbon nanotube bundles composed of tubes of all the same diameter (homogeneous) and tubes of different diameters (heterogeneous). Simulation data are compared with experimental data in an effort to identify the best model for describing experimental data. Adsorption isotherms, isosteric heats of adsorption, and specific surface areas have been computed for Ar, CH 4, and Xe on closed, open, and partially opened homogeneous and heterogeneous nanotube bundles. Experimental data from nanotubes prepared from two different methods, electric arc and HiPco, were examined. Experimental adsorption isotherms and isosteric heats for nanotubes prepared by the electric arc method are in best agreement with simulations for heterogeneous bundles of closed nanotubes. Models including adsorption in defect interstitial channels are required to achieve good agreement with experiments. Experimental isosteric heats and specific surface areas on HiPco nanotubes are best described by a model consisting of heterogeneous bundles with approximately 11% of the nanotubes opened.     

Chalcogen–mercury bond formation and disruption in model Rabenstein's reactions: A computational analysis

Methylmercury is a highly toxic compound and human exposure is mainly related to consumption of polluted fish and seafood. The inactivation of thiol-based enzymes, promoted by the strong affinity binding of electrophilic mercuric ions to thiol and selenol groups of proteins, is likely an important factor explaining its toxicity. A key role is played by the chemistry and reactivity of the mercury–chalcogens bond, particularly Hg S and Hg Se, which is the focus of this computational work (level of theory: (COSMO)-ZORA-BLYP-D3(BJ)/TZ2P). We analyze nine ligand-exchange model reactions (the so-called Rabenstein's reactions) involving an entering ligand (methylchalcogenolate) and a substrate (methylchalcogenolatemethylmercury). Trends in reaction and activation energies are discussed and a change in mechanism is reported for all cases when going from gas phase to water, that is, from a single-well potential energy surface (PES) to a canonical S_N2-like mechanism. The reasons accounting for the biochemically challenging and desired displacement of methylmercury from a seleno/thiol protein can be found already in these model reactions, as can be seen from the similarities of the ligand exchange reactions in solution in thermodynamics and kinetics.     

Dimeric palladium complexes with bridging aryl groups: when are they stable?

Stable dimeric palladium(II) complexes of general formula [Pd(2)(mu-R)(2)(eta(3)-allyl)(2)] (R=haloaryl, mesityl) have been prepared. Their X-ray crystal structures, determined for some of the complexes, show that the two coordination square planes are usually coplanar. The haloaryl complexes are fluxional in solution, showing exchange between cis and trans isomers (relative to the orientation of the two allyl groups in the dimer) through solvent-assisted associative bridge splitting. A number of other ancillary ligands (O,O, S,S, or C,N donors) failed to stabilize the bridging situation. Also, bridging phenyls were unstable. The reasons for this behavior and the formation of alternative compounds in attempts at synthesizing them are fully analyzed and explained. Stable aryl bridges seem to be favored by a combination of factors: the use of ancillary ligands of small size and lacking electron lone pairs, and the use of aryl ligands reluctant to homo and hetero C--C coupling. These seem to be more important factors in the stabilization of bridging aryl complexes than the strength of the bridges themselves.     

Concerted proton-electron transfer reactions in water. are the driving force and rate constant depending on pH when water acts as proton donor or acceptor?

The competition between stepwise and concerted (CPET) pathways in proton-coupled electron-transfer reactions in water is discussed on thermodynamic and kinetic bases. In the case where water is the proton acceptor, the CPET pathway may compete favorably with the stepwise pathway. The main parameter of the competition is pK of the oxidized form of the substrate being smaller or larger than 0. The driving force of the forward reaction is however independent of pH, despite the equilibrium redox potential of the proton-electron system being a function of pH. At high pH values, CPET reactions involving OH- as proton acceptor may likewise compete favorably with stepwise pathways. The overall reaction rate constant is an increasing function of pH, not because the driving force depends on pH but because OH- is a reactant. In buffered media, association of the substrate with the basic components of the buffer offers an alternative CPET route; the driving force comes closer to that offered by the pH-dependent equilibrium redox potential.     

Electrophilicity of α-oxo gold carbene intermediates: halogen abstractions from halogenated solvents leading to the formation of chloro/bromomethyl ketones

α-Oxo gold carbenes generated via intermolecular oxidation of terminal alkynes are shown to be highly electrophilic and can effectively abstract halogen from halogenated solvents such as 1,2-dichloroethane or 1,2-dibromoethane. Chloro/bromomethyl ketones are prepared in moderate efficiencies in one step using Ph(3)PAuNTf(2) as the catalyst and 8-methylquinoline N-oxide as the oxidant.     

Theoretical and computational studies of organometallic reactions: successful or not?

Theoretical and computational methods are powerful in studying transition metal complexes. Our theoretical studies of C–H σ‐bond activation of benzene by Pd(II)–formate complex and that of methane by Ti(IV)‐imido complex successfully disclosed that these reactions are understood to undergo heterolytic σ‐bond activation and the driving force is the formation of strong O–H and N–H bonds in the former and the latter, respectively. Orbital interactions are considerably different from those of σ‐bond activation by oxidative addition. The transmetallation, which is a key process in the cross‐coupling reaction, is understood to be heterolytic σ‐bond activation. Our theoretical study clarified how to accelerate this transmetallation. Also, we wish to discuss weak points in theoretical and computational studies of large systems including transition metal elements, such as the necessity to incorporate solvation effect and to present quantitatively correct numerical results. The importance of solvation effects is discussed in the oxidative addition of methyliodide to Pt(II) complex which occurs in a way similar to an S_N2 substitution. To apply the CCSD(T) (coupled cluster singles and doubles with perturbative triples correction) method, which is the gold standard of electronic structure theory, to large system, we need to reduce the size of the system by employing a small model. But, such modeling induces neglects of electronic and steric effects of substitutents which are replaced in the small model. Frontier‐orbital‐consistent quantum‐capping potential (FOC‐QCP) was recently proposed by our group to incorporate the electronic effects of the substituents neglected in the modeling. The CCSD(T) calculation with the FOC‐QCP was successfully applied to large systems including transition metal elements. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 000–000; 2010: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.200900019     

The quest for affinity chromatography ligands: are the molecular libraries the right source?

Affinity chromatography separations of proteins call for highly specific ligands. Antibodies are the most obvious approach; however, except for specific situations, technical and economic reasons are arguments against this choice especially for preparative purposes. With this in mind, the rationale is to select the most appropriate ligands from collections of pre‐established molecules. To reach the objective of having a large structural coverage, combinatorial libraries have been proposed. These are classified according to their nature and origin. This review presents and discusses the most common affinity ligand libraries along with the most appropriate screening methods for the identification of the right affinity chromatography selective structure according to the type of library; a side‐by‐side comparison is also presented.     

Euclidean chemical spaces from molecular fingerprints: Hamming distance and Hempel’s ravens

Journal of Computer-Aided Molecular Design - Molecules are often characterized by sparse binary fingerprints, where 1s represent the presence of substructures and 0s represent their absence....     

Cyclopropanespiro-β-lactones derived from 4-[(Z)-ethylidene]-3-methyloxetan-2-one: diastereoselective formation and rearrangement reactions

The metal catalysed reaction of monosubstituted diazo esters and ketones with 4-[(Z)-ethylidene]-3-methyloxetan-2-one results in the formation of cyclopropanespiro-β-lactones. In contrast to most alkene cyclopropanations, including those involving diketene, the reaction occurs diastereoselectively. A computational model of the reaction has been developed that accounts for the observed stereochemistry. The metal promoted thermal rearrangement of these spiro compounds is also unusual in that it affords pyranones, rather than the decarboxylation products characteristic of β-lactones in general, or the furanones formed from diketene derived cyclopropanespiro-β-lactones.     

Polypeptoids: A perfect match for molecular definition and macromolecular engineering?

Precision synthesis of polymers has been a hot topic in recent years. While this is notoriously difficult to address for polymers with a C? C backbone, Merrifield has discovered a way many decades ago for polypeptides. Using a similar approach, N‐substituted polypeptides, so‐called polypeptoids have been synthesized and studied for about 20 years. In contrast, the living ring‐opening polymerization (ROP) of N‐substituted N‐carboxyanhydrides was among the first living polymerizations to be discovered. More recently, a surge in new synthetic approaches led to the efficient synthesis of cyclic or linear multiblock copolypeptoids. Thus, polypeptoids can be synthesized either by solid phase synthesis to yield complex and exactly defined oligo‐ and small polymers or by ROP of appropriately N‐substituted N‐carboxyanhydrides (NNCA) to give linear, cyclic, or star‐like polymers. Together with an excellent biocompatibility, this polymer family may have a bright future ahead as biomaterials. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2731–2752     

Comparative selectivities of two copper-based catalysts: Mixed Cu?Cr and Cu?Al oxides for allylic alcohol reactions in the presence of molecular hydrogen

In the presence of mixed copper-chromium (aluminium) oxide, allylic alcohols react with molecular hydrogen and lead to several primary products. This is due to the simultaneous presence of two active sites in the mixed oxides. Copper species (Cu⁺) are responsible for hydrogenation (HYD) and the chromium (Cr³⁺) (aluminium [Al³⁺]) species for the isomerization (I) and the hydrodeoxygenation (HDO) reactions. However, the stronger acidic character of Al³⁺, compared with Cr³⁺, entails some differences evidenced by the HYD/(I+HDO) and HDO/I ratios.

---

- () , . . (Cu⁺ (), (Cr³⁺) ( Al³⁺) (), (). , Al³⁺ Cr³⁺ , /(+) /.

     

Iron/copper promoted fragmentation reactions of α-alkoxy hydroperoxides: Regio- and stereocontrolled formation of olefin-containing macrolides

Several new examples of iron/copper mediated fragmentation reactions of hydroperoxides are reported. The regio- and stereochemistry of olefin formation is in accord with a model that takes into account the preferred conformations of the radical intermediate and potential olefin products. In combination with group selective peroxyketalization reactions, several stereocontrolled syntheses of olefin containing macrolides have been achieved.