Selectivity of bis(calix[4]diquinone) ionophores towards metal ions in solvent dimethylsulfoxide: a molecular mechanics and molecular dynamics study

Molecular modelling studies have been carried out on two bis(calix[4]diqu(inone) ionophores, each created from two (calix[4]diquinone)arenes bridged at their bottom rims via alkyl chains (CH2)(n), 1: n = 3, 2; n = 4, in order to understand the reported selectivity of these ligands towards different sized metal ions such as Na+, K+, Rb+, and Cs+ in dmso solution. Conformational. analyses have been carried out which show that in the lowest energy conformations of the two macrocycles, the individual calix[4]diquinones exhibit a combination of partial cone, 1,3-alternate and cone conformations. The interactions of these alkali metals with the macrocycles have been studied in the gas phase and in a periodic box of solvent dmso by molecular mechanics and molecular dynamics calculations. Molecular mechanics calculations have been carried out on the mode of entry of the ions into the macrocycles and suggest that this is likely to occur from the side of the central cavity, rather than through the main axis of the calix[4]diquinones. There are energy barriers of ca. 19 kcal mol(-1) for this entry path in the gas phase, but in solution no energy barrier is found. Molecular dynamics simulations show that in both 1 and 2, though particularly in the latter macrocycle, one or two solvent molecules are bonded to the metal throughout the course of the simulation, often to the exclusion, of one or more of the ether oxygen atoms. By contrast the carbonyl oxygen atoms remain bonded to the metal atoms throughout with bond lengths that remain significantly less than those to the ether oxygen atoms. Free energy perturbation studies have been carried out in dmso and indicate that for 1, the selectivity follows the order Rb+ approximate to K+ > Cs+ >> Na+, which is partially in agreement with the experimental results. The energy differences are small and indeed the ratio between stability constants found for Cs+ and K+ complexes is only 0.60, showing that 1 has only a slight preference for K+. For the larger receptor 2, which is better suited to metal complexation, the binding affinity follows the pattern Cs+ >> Rb+ >> K+ >> Na+, with energy differences of 5.75, 2.61, 2.78 kcal mol(-1) which is perfectly consistent with experimental results.

Design, synthesis and computational modelling of aromatic tweezer-molecules as models for chain-folding polymer blends

Novel 'tweezer-type' complexes that exploit the interactions between pi-electron-rich pyrenyl groups and pi-electron deficient diimide units have been designed and synthesised. The component molecules leading to complex formation were accessed readily from commercially available starting materials through short and efficient syntheses. Analysis of the resulting complexes, using the visible charge-transfer band, revealed association constants that increased sequentially from 130 to 11,000 M-1 as increasing numbers of pi-pi-stacking interactions were introduced into the systems. Computational modelling was used to analyse the structures of these complexes, revealing low-energy chain-folded conformations for both components, which readily allow close, multiple pi-pi-stacking and hydrogen bonding to be achieved. In this paper, we give details of our initial studies of these complexes and outline how their behaviour could provide a basis for designing self-healing polymer blends for use in adaptive coating systems. (C) 2008 Elsevier Ltd. All rights reserved.

Quantum mechanics studies of the tautomers of dlhydrodiacetylformoin, an important Maillard intermediate and the synthesis of furaneol

Conformational analyses have been carried out on the acyclic and cyclic forms of dihydrodiacetylformoin, an important Maillard intermediate and precursor for furaneol. For the acyclic forms, the 2,5-dicarbonyl isomers have the lowest energy, while for the cyclic forms, the 3-carbonyl are favoured over the 4-carbonyl isomers. The likely path for cyclisation is investigated and it is shown that the favoured path is dependent upon the relative chiralities of the carbon atoms and in particular that the reaction proceeds more readily if C2 and C3 have different chiralities. After cyclisation, the reaction path to produce furaneol proceeds via the loss of a water molecule. This reaction has been studied with a model including two water molecules and a hydroxide anion and shows relatively low-energy barriers. (C) 2008 Published by Elsevier B.V.

Geometrical isomers of [TEAH][Co(L-Se)(2)]center dot xH(2)O: synthesis, structural, spectroscopic and computational studies

Trans-1, [HNEt3][Co-III(L-Se)(2)]center dot H2O and cis-1, [HNEt3][Co-III(L-Se)(2)]center dot 3H(2)O have been synthesized and characterized by single-crystal X-ray studies. The counter ion Et3NH+ plays a crucial role in the crystal packing leading to the formation of two distinctly different supramolecular assemblies in the two complexes. In trans-1, Co-bisphenolate units and triethylamine molecules are arranged in a linear fashion leading to a supramolecular columnar assembly along the crystallographic a-axis. In this assembly, triethylammonium ions are sandwiched between successive Co-bisphenolate units and act as gluing agents joining Co-bisphenolate units on either side through C-H center dot center dot center dot pi interactions. In sharp contrast to trans-1, Co-bisphenolate units and triethylammonium ions in cis-1 are arranged in a helical supramolecular assembly through similar C-H center dot center dot center dot pi interactions along the crystallographic b-axis. The Se center dot center dot center dot Se van der Waals interactions may be responsible for the predominant occurrence of the cis-isomer. The cyclic voltammetric studies showed quasi-reversible waves for the cobalt(III) -> cobalt(II) reductions with E-1/2 = 0.635 and 0.628 V vs. Ag/AgCl for cis-1 (at similar to 5 degrees C) and trans-1 (at similar to 25 degrees C), respectively. DFT calculations show that the trans-form is the thermodynamic product with higher stability than the cis-one, which is consistent with the variable temperature H-1 NMR studies

Discovery of three polymorphs of 7-fluoroisatin reveals challenges in using computational crystal structure prediction as a complement to experimental screening

A combined computational and experimental polymorph search was undertaken to establish the crystal forms of 7-fluoroisatin, a simple molecule with no reported crystal structures, to evaluate the value of crystal structure prediction studies as an aid to solid form discovery. Three polymorphs were found in a manual crystallisation screen, as well as two solvates. Form I ( P2(1)/c, Z0 1), found from the majority of solvent evaporation experiments, corresponded to the most stable form in the computational search of Z0 1 structures. Form III ( P21/ a, Z0 2) is probably a metastable form, which was only found concomitantly with form I, and has the same dimeric R2 2( 8) hydrogen bonding motif as form I and the majority of the computed low energy structures. However, the most thermodynamically stable polymorph, form II ( P1 , Z0 2), has an expanded four molecule R 4 4( 18) hydrogen bonding motif, which could not have been found within the routine computational study. The computed relative energies of the three forms are not in accord with experimental results. Thus, the experimental finding of three crystalline polymorphs of 7- fluoroisatin illustrates the many challenges for computational screening to be a tool for the experimental crystal engineer, in contrast to the results for an analogous investigation of 5- fluoroisatin.

C-H...O hydrogen bonding in 4-phenyl-benzaldehyde: a comprehensive crystallographic, spectroscopic and computational study

The crystal structure of 4-phenyl-benzaldehyde reveals the presence of a dimer linked by the C=O and C( 9)-H groups of adjacent molecules. In the liquid phase, the presence of C-(HO)-O-... bonded forms is revealed by both vibrational and NMR spectroscopy. A Delta H value of - 8.2 +/- 0.5 kJ mol(-1) for the dimerisation equilibrium is established from the temperature-dependent intensities of the bands assigned to the carbonyl-stretching modes. The NMR data suggest the preferential engagement of the C(2,6)-H and C(10/12)/C(11)-H groups as hydrogen bond donors, instead of the C(9)-H group. While ab initio calculations for the isolated dimers are unable to corroborate these NMR results, the radial distribution functions obtained from molecular dynamics simulations show a preference for C(2,6)-H and C(10/12)/C(11)-(HO)-O-... contacts relative to the C(9)-(HO)-O-... ones.

Modelling metal cutting using modern ductile fracture mechanics: Quantitative explanations for some longstanding problems

The assumption that negligible work is involved in the formation of new surfaces in the machining of ductile metals, is re-examined in the light of both current Finite Element Method (FEM) simulations of cutting and modern ductile fracture mechanics. The work associated with separation criteria in FEM models is shown to be in the kJ/m2 range rather than the few J/m2 of the surface energy (surface tension) employed by Shaw in his pioneering study of 1954 following which consideration of surface work has been omitted from analyses of metal cutting. The much greater values of surface specific work are not surprising in terms of ductile fracture mechanics where kJ/m2 values of fracture toughness are typical of the ductile metals involved in machining studies. This paper shows that when even the simple Ernst–Merchant analysis is generalised to include significant surface work, many of the experimental observations for which traditional ‘plasticity and friction only’ analyses seem to have no quantitative explanation, are now given meaning. In particular, the primary shear plane angle φ becomes material-dependent. The experimental increase of φ up to a saturated level, as the uncut chip thickness is increased, is predicted. The positive intercepts found in plots of cutting force vs. depth of cut, and in plots of force resolved along the primary shear plane vs. area of shear plane, are shown to be measures of the specific surface work. It is demonstrated that neglect of these intercepts in cutting analyses is the reason why anomalously high values of shear yield stress are derived at those very small uncut chip thicknesses at which the so-called size effect becomes evident. The material toughness/strength ratio, combined with the depth of cut to form a non-dimensional parameter, is shown to control ductile cutting mechanics. The toughness/strength ratio of a given material will change with rate, temperature, and thermomechanical treatment and the influence of such changes, together with changes in depth of cut, on the character of machining is discussed. Strength or hardness alone is insufficient to describe machining. The failure of the Ernst–Merchant theory seems less to do with problems of uniqueness and the validity of minimum work, and more to do with the problem not being properly posed. The new analysis compares favourably and consistently with the wide body of experimental results available in the literature. Why considerable progress in the understanding of metal cutting has been achieved without reference to significant surface work is also discussed.

An investigation into the mechanics of cutting using data from orthogonally cutting Nylon 66

Cutting force data for Nylon 66 has been examined in terms of various different models of cutting. Theory that includes significant work of separation at the tool tip was found to give the best correlation with experimental data over a wide range of rake angles for derived primary shear plane angle. A fracture toughness parameter was used as the measure of the specific work of separation. Variation in toughness with rake angle determined from cutting is postulated to be caused by mixed mode separation at the tool tip. A rule of mixtures using independently determined values of toughness in tension (mode 1) and shear (mode 11) is found to describe well the variation with rake angle. The ratio of modes varies with rake angle and, in turn, with the primary shear plane angle. Previous suggestions that cutting is a means of experimentally determining fracture toughness are now seen to be extended to identify the mode of fracture toughness as well.

Quantum mechanics studies of the tautomers of diacetylformoin, an important maillard product and odorant

Diacetylformoin (3,4-dihydroxy-3-hexene-2,5-dione) has 16 tautomers, many with several possible conformations and all have been geometry optimised using quantum mechanics at the HF/6-31+G* level. Eleven structures have been identified with energies within 10 kcal mol(-1) of the minimum energy structure. Of these eight are acyclic and three cyclic. Calculations of NMR spectra have clarified the identity of the acyclic and cyclic structures found experimentally. The mechanism for cyclisation has been investigated and transition states obtained. The lowest energy reaction path requires the loss and gain of a proton during cyclisation. (c) 2006 Elsevier B.V. All rights reserved.

Swarms of computational resources and swarms of tasks for building reliable systems

Space applications demand the need for building reliable systems. Autonomic computing defines such reliable systems as self-managing systems. The work reported in this paper combines agent based and swarm robotic approaches leading to swarm-array computing, a novel technique to achieve autonomy for distributed parallel computing systems. Two swarm-array computing approaches based on swarms of computational resources and swarms of tasks are explored. FPGA is considered as the computing system. The feasibility of the two proposed approaches that binds the computing system and the task together is simulated on the SeSAm multi-agent simulator.