GAIA: An easy-to-use web-based application for interaction analysis of case-control data

BACKGROUND: The advent of cheap, large scale genotyping has led to widespread adoption of genetic association mapping as the tool of choice in the search for loci underlying susceptibility to common complex disease. Whilst simple single locus analysis is relatively trivial to conduct, this is not true of more complex analysis such as those involving interactions between loci. The importance of testing for interactions between loci in association analysis has been highlighted in a number of recent high profile publications. RESULTS: Genetic Association Interaction Analysis (GAIA) is a web-based application for testing for statistical interactions between loci. It is based upon the widely used case-control study design for genetic association analysis and is designed so that non-specialists may routinely apply tests for interaction. GAIA allows simple testing of both additive and additive plus dominance interaction models and includes permutation testing to appropriately correct for multiple testing. The application will find use both in candidate gene based studies and in genome-wide association studies. For large scale studies GAIA includes a screening approach which prioritizes loci (based on the significance of main effects at one or both loci) for further interaction analysis. CONCLUSION: GAIA is available a

Computational study of the hydrodefluorination of fluoroarenes at [Ru(NHC)(PR₃)<sub style="vertical-align: sub;">2</sub>(CO)(H)<sub style="vertical-align: sub;">2</sub>]: predicted scope and regioselectivities

Density functional theory calculations have been employed to investigate the scope and selectivity of the hydrodefluorination (HDF) of fluoroarenes, C6F6-nHn (n = 0-5), at catalysts of the type [Ru(NHC)(PR3)(2)(CO)(H)(2)]. Based on our previous study (Angew. Chem., Int. Ed., 2011, 50, 2783) two mechanisms featuring the nucleophilic attack of a hydride ligand at a fluoroarene substrate were considered: (i) a concerted process with Ru-H/C-F exchange occurring in one step; and (ii) a stepwise pathway in which the rate-determining transition state involves formation of HF and a Ru-sigma-fluoroaryl complex. The nature of the metal coordination environment and, in particular, the NHC ligand was found to play an important role in both promoting the HDF reaction and determining the regioselectivity of this process. Thus for the reaction of C6F5H, the full experimental system (NHC = IMes, R = Ph) promotes HDF through (i) more facile initial PR3/fluoroarene substitution and (ii) the ability of the NHC N-aryl substituents to stabilise the key C-F bond breaking transition state through F center dot center dot center dot HC interactions. This latter effect is maximised along the lower energy stepwise pathway when an ortho-H substituent is present and this accounts for the ortho-selectivity seen in the reaction of C6F5H to give 1,2,3,4-C6F4H2. Computed C-F bond dissociation energies (BDEs) for C6F6-nHn substrates show a general increase with larger n and are most sensitive to the number of ortho-F substituents present. However, HDF is always computed to remain significantly exothermic when a silane such as Me3SiH is included as terminal reductant. Computed barriers to HDF also generally increase with greater n, and for the concerted pathway a good correlation between C-F BDE and barrier height is seen. The two mechanisms were found to have complementary regioselectivities. For the concerted pathway the reaction is directed to sites with two ortho-F substituents, as these have the weakest C-F bonds. In contrast, reaction along the stepwise pathway is directed to sites with only one ortho-F substituent, due to difficulties in accommodating ortho-F substituents in the C-F bond cleavage transition state. Calculations predict that 1,2,3,5-C6F4H2 and 1,2,3,4-C6F4H2 are viable candidates for HDF at [Ru(IMes)(PPh3)(2)(CO)(H)(2)] and that this would proceed selectively to give 1,2,4-C6F3H3 and 1,2,3-C6F3H3, respectively.</p

Redox-mediated reactions of vinylferrocene: Toward redox auxiliaries

Chemical redox reactions have been exploited to transform unreactive vinylferrocene into a powerful dienophile for the Diels–Alder reaction and reactive substrate for thiol addition reactions upon conversion to its ferrocenium state. We have further investigated the ability of these reactions to facilitate redox-auxiliary-like reactivity by further hydrogenolyisis of the Diels–Alder adduct to the corresponding cyclopentane derivative

Isomerisation of nido-[C₂B₁₀H₁₂]²⁻ dianions::Unprecedented rearrangements and new structural motifs in carborane cluster chemistry

We thank the EPSRC for support (DMcK funded by project EP/E02971X/1).Dianionic nido-[C2B10]2- species are key intermediates in the polyhedral expansion from 12- to 13-vertex carboranes and metallacarboranes, and the isomer adopted by these nido intermediates dictates the isomeric form of the 13-vertex product. Upon reduction and metallation of para-carborane up to five MC2B10 metallacarboranes can be produced (Angew. Chem., Int. Ed., 2007, 46, 6706), the structures of which imply the intermediacy of 1,7-, 3,7-, 4,7-, 7,9- and 7,10-isomers of the nido-[C2B10]2- species. In this paper we use density functional theory (DFT) calculations to characterise the reduction of closo-C2B10H12 carboranes and the subsequent isomerisations of the nido-[C2B10H12]2- dianions. Upon reduction para-carborane initially opens to [1,7-nido-C2B10H12]2- (abbreviated to 1,7) and [4,7-nido-C2B10H12]2- (4,7) and isomerisation pathways connecting 1,7 to 7,9, 4,7 to 7,10 and 1,7 to 3,7 have been characterised. For ortho- and meta-carborane the experimental reduction produces 7,9 in both cases and computed pathways for both processes are also defined; with ortho-carborane rearrangement occurs via 7,8, whereas with meta-carborane 7,9 is formed directly. The 7,9 isomer is the global minimum nido-structure. The characterisation of these isomerisation processes uncovers intermediates that adopt new structural motifs that we term basket and inverted nido. Basket intermediates feature a two-vertex basket handle bridging the remaining 10 vertices; inverted nido intermediates are related to known nido species, in that they have 5- and 6-membered belts, but where the latter, rather than the former, is capped, leaving a 5-membered open face. These new intermediates exhibit similar stability to the nido species, which is attributed to their relation to the 13-vertex docosahedron through the removal of 5-connected vertices. Isomerisation pathways starting from nido geometries are most often initiated by destabilisation of the cluster through a DSD process causing the 3-connected C7 vertex to move into a 4-connected site and a neighbouring B vertex to become 3-connected. The ensuing rearrangement of the cluster involves processes such as the pivoting of a 4-vertex diamond about its long diagonal, the pivoting of two 3-vertex triangles about a shared vertex and DSD processes. These processes are all ultimately driven by the preference for carbon to occupy low-connected vertices on the open 6-membered face of the resulting nido species.Publisher PDFPeer reviewe

Combined experimental and computational investigations of rhodium-catalysed C-H functionalisation of pyrazoles with alkenes

Detailed experimental and computational studies have been carried out on the oxidative coupling of the alkenes C(2)H(3)Y (Y=CO(2)Me (a), Ph (b), C(O)Me (c)) with 3-aryl-5-R-pyrazoles (R=Me (1 a), Ph (1 b), CF(3) (1 c)) using a [Rh(MeCN)(3)Cp*][PF(6)](2)/Cu(OAc)(2)⋅H(2)O catalyst system. In the reaction of methyl acrylate with 1 a, up to five products (2 aa–6 aa) were formed, including the trans monovinyl product, either complexed within a novel Cu(I) dimer (2 aa) or as the free species (3 aa), and a divinyl species (6 aa); both 3 aa and 6 aa underwent cyclisation by an aza-Michael reaction to give fused heterocycles 4 aa and 5 aa, respectively. With styrene, only trans mono- and divinylation products were observed, whereas with methyl vinyl ketone, a stronger Michael acceptor, only cyclised oxidative coupling products were formed. Density functional theory calculations were performed to characterise the different migratory insertion and β-H transfer steps implicated in the reactions of 1 a with methyl acrylate and styrene. The calculations showed a clear kinetic preference for 2,1-insertion and the formation of trans vinyl products, consistent with the experimental results

Gold(I)-Catalysed Direct Thioetherifications Using Allylic Alcohols: an Experimental and Computational Study

A gold(I)-catalysed direct thioetherification reaction between allylic alcohols and thiols is presented. The reaction is generally highly regioselective (S(N)2′). This dehydrative allylation procedure is very mild and atom economical, producing only water as the by-product and avoiding any unnecessary waste/steps associated with installing a leaving or activating group on the substrate. Computational studies are presented to gain insight into the mechanism of the reaction. Calculations indicate that the regioselectivity is under equilibrium control and is ultimately dictated by the thermodynamic stability of the products

The simplest amino‐borane H2B=NH2 trapped on a rhodium dimer : pre‐catalysts for amine–borane dehydropolymerization

Funding: The EPSRC (A.S.W. and S.A.M., EP/M024210/1; N.A.B., DTP Studentship), the Rhodes Trust (A.K.), G. M. Adams (G. P. C. analysis).The μ‐amino–borane complexes [Rh2(LR)2(μ‐H)(μ‐H2B=NHR′)][BArF4] (LR=R2P(CH2)3PR2; R=Ph, iPr; R′=H, Me) form by addition of H3B⋅NMeR′H2 to [Rh(LR)(η6‐C6H5F)][BArF4]. DFT calculations demonstrate that the amino–borane interacts with the Rh centers through strong Rh‐H and Rh‐B interactions. Mechanistic investigations show that these dimers can form by a boronium‐mediated route, and are pre‐catalysts for amine‐borane dehydropolymerization, suggesting a possible role for bimetallic motifs in catalysisPublisher PDFPeer reviewe

Understanding electronic effects on carboxylate-assisted C-H activation at ruthenium:the importance of kinetic and thermodynamic control

Meta-and para-substituted 1-phenylpyrazoles (R-phpyz-H) react with [RuCl2(p-cymene)]2 in the presence of NaOAc to form cyclometallated complexes [M(R-phpyz)Cl(p-cymene)] (where R = NMe2, OMe, Me, H, F, CF3 and NO2). Experimental and DFT studies indicate that product formation can be reversible or irreversible depending on the substituents and the reaction conditions. Competition experiments show that the kinetic selectivity favours electron-donating substituents and correlate well with the Hammett parameter, giving a negative slope (ρ =-2.4) that is consistent with a cationic transition state. However, surprisingly, the thermodynamic selectivity is completely opposite, with substrates featuring electron-withdrawing groups being favoured. These trends are reproduced with DFT calculations that locate a rate-limiting transition state dominated by Ru-O bond dissociation and minimal C-H bond elongation. Detailed computational analysis of these transition states shows that C-H activation proceeds by an AMLA/CMD mechanism through a synergic combination of a C-H→Ru agostic interaction and C-H⋯O H-bonding. NBO calculations also highlight a syndetic bonding term, and the relative weights of these three components vary in a complementary fashion depending on the nature of the substituent. With meta-substituted ligands H/D exchange experiments signal kinetically accessible ortho-C-H activation when R = NMe2, OMe and Me. This is also modelled computationally and the calculations highlight the kinetic relevance of the HOAc/Cl exchange that occurs post C-H bond cleavage, in particular with the bulkier NMe2 and Me substituents. Our study highlights that the experimental substituent effects are dependent on the reaction conditions and so using such studies to assign the mechanism of C-H activation in either stoichiometric or catalytic reactions may be misleading.</p