Liquid ammonia as a dipolar aprotic solvent for aliphatic nucleophilic substitution reactions

The rate constants for the reactions of a variety of nucleophiles reacting with substituted benzyl chlorides in liquid ammonia (LNH(3)) have been determined. To fully interpret the associated linear free-energy relationships, the ionization constants of phenols ions in liquid ammonia were obtained using UV spectra. These equilibrium constants are the product of those for ion-pair formation and dissociation to the free ions, which can be separated by evaluating the effect of added ammonium ions. There is a linear relationship between the pK(a) of phenols in liquid ammonia and those in water of slope 1.68. Aminium ions exist in their unprotonated free base form in liquid ammonia and their ionization constants could not be determined by NMR. The rates of solvolysis of substituted benzyl chlorides in liquid ammonia at 25 °C show a Hammett ρ of zero, having little or no dependence upon ring substituents, which is in stark contrast with the hydrolysis rates of substituted benzyl halides in water, which vary 10(7) fold. The rate of substitution of benzyl chloride by substituted phenoxide ions is first order in the concentration of the nucleophile indicative of a S(N)2 process, and the dependence of the rate constants on the pK(a) of the phenol in liquid ammonia generates a Br?nsted β(nuc) = 0.40. Contrary to the solvolysis reaction, the reaction of phenoxide ion with 4-substituted benzyl chlorides gives a Hammett ρ = 1.1, excluding the 4-methoxy derivative, which shows the normal positive deviation. The second order rate constants for the substitution of benzyl chlorides by neutral and anionic amines show a single Br?nsted β(nuc) = 0.21 (based on the aqueous pK(a) of amine), but their dependence on the substituent in substituted benzyl chlorides varies with a Hammett ρ of 0 for neutral amines, similar to that seen for solvolysis, whereas that for amine anions is 0.93, similar to that seen for phenoxide ion.     

Anti-inflammatory and antimalarial meroterpenoids from the New Zealand ascidian Aplidium scabellum

Bioassay-directed fractionation of an extract of the New Zealand ascidian Aplidium scabellum has afforded the anti-inflammatory secondary metabolite 2-geranyl-6-methoxy-1,4-hydroquinone-4-sulfate (1) and a family of pseudodimeric meroterpenoids scabellones A (2)-D (5). The benzo[c]chromene-7,10-dione scaffold contained within scabellones A-D is particularly rare among natural products. The structures were elucidated by interpretation of NMR data. Scabellone B was also identified as a moderately potent, nontoxic inhibitor of Plasmodium falciparum.     

Bead diffusion assay for discovering antimicrobial cyclic peptides

A combinatorial library of 15,536 cyclic decapeptide analogues of tyrocidine A and gramicidin S was prepared on photocleavable TentaGel beads. The beads were photolyzed without solvent, and spread onto an agar plate inoculated with bacterial lawn. Clear zones were formed around beads carrying antimicrobially active peptides such as E18 c(kVOrnLfThiYOrnLq), which inhibited growth of B. subtilis and selected MRSA strains.     

Copper(I)-catalyzed amination of aryl halides in liquid ammonia

The amination of aryl halides in liquid ammonia (LNH(3)) is catalyzed by a copper(I) salt/ascorbate system to yield primary aromatic amines in good to excellent yields. The low concentrations of catalyst required and the ease of product isolation suggest that this process has potential industrial applications. Commonly used ligands for analogous metal-catalyzed reactions are not effective. The rate of amination of iodobenzene in liquid ammonia is first order in copper(I) catalyst concentration. The small Hammett ρ = 0.49 for the amination of 4-substituted iodobenzenes in liquid ammonia at 25 °C indicates that the C-I bond is not significantly broken in the transition state structure and that there is a small generation of negative charge in the aryl ring, which is compatible with the oxidative addition of the copper ion being rate limiting.     

Sub-surface nucleation of graphene precursors near a Ni(111) step-edge

Graphene nucleation on Ni(111) has been modeled using QM/MD simulations. We demonstrate that graphene precursor nucleation can occur underneath the catalyst surface. In addition, a Ni(111) step-edge is not a static structure, as is often assumed; it is instead highly malleable, being deformed and subsequently healed during graphene nucleation.     

Reassignment of fundamental vibrational modes of cyclic S4N3 cation

MP2/6 31G* calculations were carried out to investigate the vibrational spectrum of cyclic S4N3+. The results indicate that previous assignments of several fundamental vibrational modes are in error. On the basis of the calculated results, reassignments of these modes are proposed.     

The correlation of molecular orientation in liquid water by neutron and X-ray scattering

The neutron diffraction structure factor for heavy water at 22°c has been measured for momentum transfers, ?Q, up to a Q of 13 å ^-1. The results have been interpreted by abstracting the molecular structure effects as far as possible and using models for the correlation of orientation of pairs of molecules ranging from completely uncorrelated orientation to that for adjacent molecules in ice I. Neither these nor any of the popular models for the structure of water, nor a non-hydrogen bonded model, fit the neutron diffraction data over the whole range of Q. Nevertheless, information about the molecular-centres structure factor is obtained, especially for Q up to about 3 å ^-1.

The method of analysis is generalized and applied to x-ray diffraction data and in particular to x-ray data for liquid water. It is shown that this method of analysis has some advantages over the conventional one. The effect of correlation of molecular orientation is less than that of molecular structure on x-ray scattering by water and rather more extensive information is obtained for the molecular-centres structure factor than from neutron data—if the conventional assumption of atomic electron clouds is accepted.

A comparison of the x-ray and neutron scattering data for liquid heavy water shows that the two sets of data are reasonably consistent for any of the usual models for water, except for the region of Q between 3 and 5 å ^-1. The molecular-centres structure factor of water has a weak double humped first maximum with peaks at 2·0 å ^-1 and 2·9å ^-1, probably followed by a damped oscillation. This contrasts with atomic liquids but is similar to that found in liquid carbon tetrachloride. The structure of liquid water is not, therefore, necessarily unique or unusual.     

Dynamics of local chirality during SWCNT growth: armchair versus zigzag nanotubes

We present an analysis of the dynamics of single-walled carbon nanotube (SWCNT) chirality during growth, using the recently developed local chirality index (LOCI) method [ Kim et al. Phys. Rev. Lett. 2011 , 107 , 175505 ] in conjunction with quantum chemical molecular dynamics (QM/MD) simulations. Using (5,5) and (8,0) SWCNT fragments attached to an Fe(38) catalyst nanoparticle, growth was induced by periodically placing carbon atoms at the edge of the SWCNT. For both armchair and zigzag SWCNTs, QM/MD simulations indicate that defect healing-the process of defect removal during growth-is a necessary, but not sufficient, condition for chirality-controlled SWCNT growth. Time-evolution LOCI analysis shows that healing, while restoring the pristine hexagon structure of the growing SWCNT, also leads to changes in the local chirality of the SWCNT edge region and thus of the entire SWCNT itself. In this respect, we show that zigzag SWCNTs are significantly inferior in maintaining their chirality during growth compared to armchair SWCNTs.     

Heterogeneous nucleation in and out of pores

We study the nucleation of a new thermodynamic phase in pores and find that the nucleation often proceeds via two steps: nucleation of pore filling, and nucleation out of the pore. These two rates have opposing dependencies on pore size, resulting in a pore size at which the nucleation rate of the new phase is maximal. This finding is relevant to attempts to design and use porous media to crystallize proteins.