High-accuracy extrapolated ab initio thermochemistry. III. Additional improvements and overview

Effects of increased basis-set size as well as a correlated treatment of the diagonal Born-Oppenheimer approximation are studied within the context of the high-accuracy extrapolated ab initio thermochemistry (HEAT) theoretical model chemistry. It is found that the addition of these ostensible improvements does little to increase the overall accuracy of HEAT for the determination of molecular atomization energies. Fortuitous cancellation of high-level effects is shown to give the overall HEAT strategy an accuracy that is, in fact, higher than most of its individual components. In addition, the issue of core-valence electron correlation separation is explored; it is found that approximate additive treatments of the two effects have limitations that are significant in the realm of <1 kJ mol(-1) theoretical thermochemistry.     

Metal-specific allosteric activation and deactivation of a diamine

The reaction of a potentially tetradentate bis(pyridyl-thiazole) ligand with acetone is allosterically activated upon complexation with Cd(II) but deactivated by reaction with Cu(I), demonstrating metal-specific allosteric controlled reactivity.     

Simulations of calcite crystallization on self-assembled monolayers

This paper presents simulations of calcium carbonate ordering in contact with self-assembled monolayers. The calculations use potential-based molecular dynamics to model the crystallization of calcium carbonate to calcite expressing both the (00.1) and (01.2) surfaces. The effect of monolayer properties: ionization; epitaxial matching; charge density; and headgroup orientation on the crystallization process are examined in detail. The results demonstrate that highly charged surfaces are vital to stimulate ordering and crystallization. Template directed crystallization requires charge epitaxy between both the crystal surface and the monolayer. The orientation of the headgroup appears to make no contribution to the selection of the crystal surface.     

The synthesis of azadirachtin: a potent insect antifeedant

We describe in full the first synthesis of the potent insect antifeedant azadirachtin through a highly convergent approach. An O-alkylation reaction is used to unite decalin ketone and propargylic mesylate fragments, after which a Claisen rearrangement constructs the central C8-C14 bond in a stereoselective fashion. The allene which results from this sequence then enables a second critical carbon-carbon bond forming event whereby the [3.2.1] bicyclic system, present in the natural product, is generated via a 5-exo-radical cyclisation process. Finally, using knowledge gained through our early studies into the reactivity of the natural product, a series of carefully designed steps completes the synthesis of this challenging molecule.     

Theoretical investigation of electronic excitation energy transfer in bichromophoric assemblies

Electronic excitation energy transfer (EET) rates in rylene diimide dyads are calculated using second-order approximate coupled-cluster theory and time-dependent density functional theory. We investigate the dependence of the EET rates on the interchromophoric distance and the relative orientation and show that Forster theory works quantitatively only for donor-acceptor separations larger than roughly 5 nm. For smaller distances the EET rates are over- or underestimated by Forster theory depending on the respective orientation of the transition dipole moments of the chromophores. In addition to the direct transfer rates we consider bridge-mediated transfer originating from oligophenylene units placed between the chromophores. We find that the polarizability of the bridge significantly enhances the effective interaction. We compare our calculations to single molecule experiments on two types of dyads and find reasonable agreement between theory and experiment.     

Design and synthesis of alpha-helical peptides and mimetics

The alpha-helix is the most abundant secondary structural element in proteins and is an important structural domain for mediating protein-protein and protein-nucleic acid interactions. Strategies for the rational design and synthesis of alpha-helix mimetics have not matured as well as other secondary structure mimetics such as strands and turns. This perspective will focus on developments in the design, synthesis and applications of alpha-helices and mimetics, particularly in the last 5 years. Examples where synthetic compounds have delivered promising biological results will be highlighted as well as opportunities for the design of mimetics of the type I alpha-helical antifreeze proteins.     

Polynuclear lanthanide complexes of a series of bridging ligands containing two tridentate N,N',O-donor units: structures and luminescence properties

A set of three potentially bridging ligands containing two tridentate chelating N,N',O-donor (pyrazole-pyridine-amide) donors separated by an o, m, or p-phenylene spacer has been prepared and their coordination chemistry with lanthanide(III) ions investigated. Ligand L(1) (p-phenylene spacer) forms complexes with a 2:3 M:L ratio according to the proportions used in the reaction mixture; the Ln(2)(L(1))(3) complexes contain two 9-coordinate Ln(III) centres with all three bridging ligands spanning both metal ions, and have a cylindrical (non-helical) 'mesocate' architecture. The 1:1 complexes display a range of structural types depending on the conditions used, including a cyclic Ln(4)(L(1))(4) tetranuclear helicate, a Ln(2)(L(1))(2) dinuclear mesocate, and an infinite one-dimensional coordination polymer in which metal ions and bridging ligands alternate along the sequence. ESMS studies indicate that the 1:1 complexes form a mixture of oligonuclear species {Ln(L(1))}(n) in solution (n up to 5) which are likely to be cyclic helicates. In contrast, ligands L(2) and L(3) (with o- and m-phenylene spacers, respectively) generally form dinuclear Ln(2)L(2) Ln(III) complexes in which the two ligands may be arranged in a helical or non-helical architecture about the two metal ions. These complexes also contain an additional exogenous bidentate bridging ligand, either acetate or formate, which has arisen from hydrolysis of solvent molecules promoted by the Lewis-acidity of the Ln(III) ions. Luminescence studies on some of the Nd(III) complexes showed that excitation into ligand-centred pi-pi* transitions result in the characteristic near-infrared luminescence from Nd(III) at 1060 nm.     

The d4/d3 redox pairs [MX(CO)(eta-RC[triple bond, length as m-dash]CR)Tp']z (z=0 and 1): structural consequences of electron transfer and implications for the inverse halide order

The d4 halide complexes [MX(CO)(eta-RC[triple bond, length as m-dash]CR)Tp'] {X=F, Cl, Br or I; R=Me or Ph; M=Mo or W; Tp'=hydrotris(3,5-dimethylpyrazolyl)borate} undergo one-electron oxidation to the d3 monocations [MX(CO)(eta-RC[triple bond, length as m-dash]CR)Tp']+, isolable for M=W, R=Me. X-Ray structural studies on the redox pairs [WX(CO)(eta-MeC[triple bond, length as m-dash]CMe)Tp']z (X=Cl and Br, z=0 and 1), the ESR spectra of the cations [WX(CO)(eta-RC[triple bond, length as m-dash]CR)Tp']+ (X=F, Cl, Br or I; R=Me or Ph), and DFT calculations on [WX(CO)(eta-MeC[triple bond, length as m-dash]CMe)Tp']z (X=F, Cl, Br and I; z=0 and 1) are consistent with electron removal from a HOMO (of the d4 complexes) which is pi-antibonding with respect to the W-X bond, pi-bonding with respect to the W-C(O) bond, and delta-bonding with respect to the W-Calkyne bonds. The dependence of both oxidation potential and nu(CO) for [MX(CO)(eta-RC[triple bond, length as m-dash]CR)Tp'] shows an inverse halide order which is consistent with an ionic component to the M-X bond; the small size of fluorine and its closeness to the metal centre leads to the highest energy HOMO and the lowest oxidation potential. In the cations [MX(CO)(eta-RC[triple bond, length as m-dash]CR)Tp']+ electronegativity effects become more important, leading to a conventional order for Cl, Br and I. However, high M-F pi-donation is still facilitated by the short M-F distance.     

Kinetics of the reaction of methyl radical with hydroxyl radical and methanol decomposition

The CH3 + OH bimolecular reaction and the dissociation of methanol are studied theoretically at conditions relevant to combustion chemistry. Kinetics for the CH3 + OH barrierless association reaction and for the H + CH2OH and H + CH3O product channels are determined in the high-pressure limit using variable reaction coordinate transition state theory and multireference electronic structure calculations to evaluate the fragment interaction energies. The CH3 + OH --> 3CH2 + H2O abstraction reaction and the H2 + HCOH and H2 + H2CO product channels feature localized dynamical bottlenecks and are treated using variational transition state theory and QCISD(T) energies extrapolated to the complete basis set limit. The 1CH2 + H2O product channel has two dynamical regimes, featuring both an inner saddle point and an outer barrierless region, and it is shown that a microcanonical two-state model is necessary to properly describe the association rate for this reaction over a broad temperature range. Experimental channel energies for the methanol system are reevaluated using the Active Thermochemical Tables (ATcT) approach. Pressure dependent, phenomenological rate coefficients for the CH3 + OH bimolecular reaction and for methanol decomposition are determined via master equation simulations. The predicted results agree well with experimental results, including those from a companion high-temperature shock tube determination for the decomposition of methanol.     

Catalytic cracking of alkylcyclohexanes: Modeling the reaction pathways and mechanisms

The cracking reaction pathways and mechanisms of ethylcyclohexane and 1-cyclohexyloctane with a rare earth Y (REY) catalyst were studied. Experiments at 500°C indicated that the dominant reactions were ring opening with subsequent secondary cracking, cracking in the alkyl side chain, isomerization, and hydrogen transfer. A kinetic model of the catalytic cracking of 1-cyclohexyloctane was developed using a novel mechanism-based lumping scheme that exploits the chemical similarities within reaction families. The formal application of 17 reaction family matrices, which correspond to 13 reaction family classes, to the matrix representations of the reactants and derived products generated the model. The reaction family concept was further exploited to constrain the kinetics within each reaction family to follow a quantitative structure/reactivity Polanyi relationship. Ultimately, nine Polanyi relationship parameters and three coking/deactivation parameters were determined by optimizing the model fit to the experimental data. The resulting model correlations were excellent, as the overall parity between experimental and model values was y_Model=−0.000470+0.986y_Exp with a correlation coefficient of 0.971. © 1997 John Wiley & Sons, Inc. Int J Chem Kinet 29: 545–560, 1997.