Cation complexation by chemically modified calixarenes. 11. Complexation and extraction of alkali cations by calix[5]- and -[6]arene ketones. Crystal and molecular structures of calix[5]arene ketones and Na+ and Rb+ complexes

A series of four calix[5]arenes and three calix[6]arenes (R-calixarene-OCH2COR1) (R = H or Bu-t) with alkyl ketone residues (R-1 = Me or Bu-t) on the lower rim have been synthesized, and their affinity for complexation of alkali cations has been assessed through phase-transfer experiments and stability constant measurements. The conformations of these ketones have been probed by H-1 NMR and X-ray diffraction analysis, and by molecular mechanics calculations. Pentamer 3 (R R-1 = Bu-t) possesses a symmetrical cone conformation in solution and a very distorted cone conformation in the solid state. Pentamer 5 (R = H, R-1 = Bu-t) exists in a distorted 1,2-alternate conformation in the solid state, but in solution two slowly interconverting conformations, one a cone and the other presumed to be 1,2-alternate, can be detected. X-ray structure analysis of the sodium and rubidium perchlorate complexes of 3 reveal the cations deeply encapsulated by the ethereal and carbonyl oxygen atoms in distorted cone conformations which can be accurately reproduced by molecular mechanics calculations. The phase-transfer and stability constant data reveal that the extent of complexation depends on calixarene size and the nature of the alkyl residues adjacent to the ketonic carbonyls with tert-butyl much more efficacious than methyl.

Molecular modeling of calixarenes with group I metal ions

Molecular mechanics calculations have been used to model the geometries of the complexes of Group I metal ions with calix[n]arenes (n = 4,5). A simple procedure in which the calixarene atoms are assigned partial charges on the basis of AM1 calculations and the metal ions are allowed to bind electrostatically to the calixarenes produces surprising good results when the resulting structures are compared to known crystallographic data on the complexes. Encapsulated solvent molecules and/or counterions can be included in the calculations and, indeed, are necessary to reproduce the X-ray data.

Volumetric Properties, Viscosities, and Isobaric Heat Capacities of Imidazolium Octanoate Protic Ionic Liquid in Molecular Solvents

Densities (F), viscosities (?), and isobaric heat molar capacities (Cp) of binary mixtures containing imidazolium octanoate, [Im][C7CO2], a protic ionic liquid (PIL), with four molecular solvents, water, acetonitrile, ethanol, and 1-octanol, are determined as a function of temperature from (298.15 to 323.15) K and within the whole composition range at atmospheric pressure. Excess molar volumes, VE, excess molar heat capacities, Cp E, and the deviation from additivity rules of viscosities, ??, of imidazolium octanoate solutions were then deduced from the experimental results, as well as apparent molar volumes, Vfi, and partial molar volumes, V j m,i. Results are discussed according to the nature of the interaction between the PIL and the molecules and the effect of temperature. The excess Gibbs energies of activation of viscous flow (?G*E) for these systems were then calculated at 298.15 K. The excess isobaric heat capacities, Cp E, of binary ([Im][C7CO2] + solvent) systems, depend also of the nature of the molecular solvent in mixture. The excess properties were then correlated, at each temperature, as a function of composition by a Redlich-Kister-type equation. Finally results have been discussed in terms of molecular interactions and molecular structures in these binary mixtures, and thermodynamic properties of investigated binary mixtures were then compared to literature values together to investigate the impact of the nature of the solvent on these reported properties.

Molecular abundances in the magellanic clouds .1. A multiline study of five cloud cores

Nine H II regions of the LMC were mapped in (CO)-C-13(1-0) and three in (CO)-C-12(1-0) to study the physical properties of the interstellar medium in the Magellanic Clouds. For N113 the molecular core is found to have a peak position which differs from that of the associated H II region by 20 ''. Toward this molecular core the (CO)-C-12 and (CO)-C-13 peak T-MB line temperatures of 7.3 K and 1.2 K are the highest so far found in the Magellanic Clouds. The molecular concentrations associated with N113, N44BC, N159HW, and N214DE in the LMC and LIRS 36 in the SMC were investigated in a variety of molecular species to study the chemical properties of the interstellar medium. I(HCO+)/I(HCN) and I(HCN)/I(HNC) intensity ratios as well as lower limits to the I((CO)-C-13)/I((CO)-O-18) ratio were derived for the rotational 1-0 transitions. Generally, HCO+ is stronger than HCN, and HCN is stronger than HNC. The high relative HCO+ intensities are consistent with a high ionization flux from supernovae remnants and young stars, possibly coupled with a large extent of the HCO+ emission region. The bulk of the HCN arises from relatively compact dense cloud cores. Warm or shocked gas enhances HCN relative to HNC. From chemical model calculations it is predicted that I(HCN)/I(HNC) close to one should be obtained with higher angular resolution (less than or similar to 30 '') toward the cloud cores. Comparing virial masses with those obtained from the integrated CO intensity provides an H-2 mass-to-CO luminosity conversion factor of 1.8 x 10(20) mol cm(-2) (K km s(-1))(-1) for N113 and 2.4 x 10(20) mol cm(-2) (K km s(-1))(-1) for N44BC. This is consistent with values derived for the Galactic disk.

PROTONATED HCN IN MOLECULAR CLOUDS

Observations of protonated HCN (HCNH+) in a selection of galactic molecular clouds are reported. This species plays a key role in understanding the chemistry of the important high density tracer HCN. HCNH+ has been detected in the nearby cold dust cloud TMC-1 with an ratio relative to HCN of [HCNH+]/[HCN] between 0.015 and 0.26 (preferred value 0.03) and tentatively in DR21(OH) with a ratio of approximately 0.01. This is about 100 times higher than the ratio of protonated carbon monoxide to CO [HCO+]/[CO], but comparable to the [HCS+]/[CS] ratio. Possible explanations of these high abundance ratios are discussed in the light of model calculations.

Time delay between photoemission from the 2p and 2s subshells of neon

The R-matrix incorporating time (RMT) method is a method developed recently for solving the time-dependent Schrödinger equation for multielectron atomic systems exposed to intense short-pulse laser light. We have employed the RMT method to investigate the time delay in the photoemission of an electron liberated from a 2p orbital in a neon atom with respect to one released from a 2s orbital following absorption of an attosecond xuv pulse. Time delays due to xuv pulses in the range 76-105 eV are presented. For an xuv pulse at the experimentally relevant energy of 105.2 eV, we calculate the time delay to be 10.2±1.3 attoseconds (as), somewhat larger than estimated by other theoretical calculations, but still a factor of 2 smaller than experiment. We repeated the calculation for a photon energy of 89.8 eV with a larger basis set capable of modeling correlated-electron dynamics within the neon atom and the residual Ne ion. A time delay of 14.5±1.5 as was observed, compared to a 16.7±1.5 as result using a single-configuration representation of the residual Ne⁺ ion. 

Strong-field photodetachment of H- by few-cycle laser pulses

The recent adiabatic saddle-point method of Shearer et al. [ Phys. Rev. A 84 033409 (2011)] is applied to study strong-field photodetachment of H- by few-cycle linearly polarized laser pulses of frequencies near the two-photon detachment threshold. The behavior of the saddle points in the complex-time plane for a range of laser parameters is explored. A detailed analysis of the influence of laser intensities [(2×1011)–(6.5 × 1011) W/cm2], midinfrared laser wavelengths (1800–2700 nm), and various values of the carrier envelope phase (CEP) on (i) three-dimensional probability detachment distributions, (ii) photoangular distributions (PADs), (iii) energy spectra, and (iv) momentum distributions are presented. Examination of the probability distributions and PADs reveal main lobes and jetlike structures. Bifurcation phenomena in the probability distributions and PADs are also observed as the wavelength and intensity increase. Our simulations show that the (i) probability distributions, (ii) PADs, and (iii) energy spectra are extremely sensitive to the CEP and thus measuring such distributions provides a useful tool for determining this phase. The symmetrical properties of the electron momentum distributions are also found to be strongly correlated with the CEP and this provides an additional robust method for measuring the CEP of a laser pulse. Our calculations further show that for a three-cycle pulse inclusion of all eight saddle points is required in the evaluation of the transition amplitude to yield an accurate description of the photodetachment process. This is in contrast to recent results for a five-cycle pulse.

Selective Hydrogenation of alpha,beta-Unsaturated Aldehydes and Ketones using Novel Manganese Oxide and Platinum Supported on Manganese Oxide Octahedral Molecular Sieves as Catalysts

The selective hydrogenation of ,-unsaturated aldehydes and ketones has been studied using ketoisophorone and cinnamaldehyde as model substrates using manganese oxide octahedral molecular sieve (OMS-2) based catalysts. For the first time, OMS-2 has been shown to be an efficient and selective hydrogenation catalyst. High selectivities for either the CC or CO double bond at approximate to 100% conversion were achieved by using OMS-2 and platinum supported on OMS-2 catalysts. Density functional theory (DFT) calculations showed that the dissociation of H2 on OMS-2 was water assisted and occurred on the surface Mn of OMS-2(001) that had been modified by an adsorbed H2O molecule. The theoretically calculated activation barrier was in good agreement with the experimentally determined value for the hydrogenation reactions, indicating that H2 dissociation on OMS-2 is likely to be the rate-determining step. A significant increase in the rate of reaction was observed in the presence of Pt as a result of the enhancement of H2 dissociative adsorption and subsequent reaction on the Pt or spillover of the hydrogen to the OMS-2 support. The relative adsorption strengths of ketoisophorone and cinnamaldehyde on the OMS-2 support compared with the Pt were found to determine the product selectivity.

Exchange potential from the common energy denominator approximation for the Kohn-Sham Green's function: Application to (hyper)polarizabilities of molecular chains

An approximate Kohn-Sham (KS) exchange potential v(xsigma)(CEDA) is developed, based on the common energy denominator approximation (CEDA) for the static orbital Green's function, which preserves the essential structure of the density response function. v(xsigma)(CEDA) is an explicit functional of the occupied KS orbitals, which has the Slater v(Ssigma) and response v(respsigma)(CEDA) potentials as its components. The latter exhibits the characteristic step structure with "diagonal" contributions from the orbital densities \psi(isigma)\(2), as well as "off-diagonal" ones from the occupied-occupied orbital products psi(isigma)psi(j(not equal1)sigma). Comparison of the results of atomic and molecular ground-state CEDA calculations with those of the Krieger-Li-Iafrate (KLI), exact exchange (EXX), and Hartree-Fock (HF) methods show, that both KLI and CEDA potentials can be considered as very good analytical "closure approximations" to the exact KS exchange potential. The total CEDA and KLI energies nearly coincide with the EXX ones and the corresponding orbital energies epsilon(isigma) are rather close to each other for the light atoms and small molecules considered. The CEDA, KLI, EXX-epsilon(isigma) values provide the qualitatively correct order of ionizations and they give an estimate of VIPs comparable to that of the HF Koopmans' theorem. However, the additional off-diagonal orbital structure of v(xsigma)(CEDA) appears to be essential for the calculated response properties of molecular chains. KLI already considerably improves the calculated (hyper)polarizabilities of the prototype hydrogen chains H-n over local density approximation (LDA) and standard generalized gradient approximations (GGAs), while the CEDA results are definitely an improvement over the KLI ones. The reasons of this success are the specific orbital structures of the CEDA and KLI response potentials, which produce in an external field an ultranonlocal field-counteracting exchange potential. (C) 2002 American Institute of Physics.

Mechanistic Study of 1,3-Butadiene Formation in Acetylene Hydrogenation over the Pd-Based Catalysts Using Density Functional Calculations

Green oil, which leads to the deactivation of the catalysts used for the selective hydrogenation of acetylene, has long been observed but its formation mechanism is not fully understood. In this work, the formation of 1,3-butadiene, known to be the precursor of green oil, on both Pd(111) and Pd(211) surfaces is examined using density functional theory calculations. The pathways containing C-2 + C-2 coupling reactions as well as the corresponding hydrogenation reactions are studied in detail. Three pathways for 1,3-butadiene production, namely coupling plus hydrogenation and further hydrogenation, hydrogenation plus coupling plus hydrogenation, and a two step hydrogenation followed by coupling, are determined. By comparing the effective barriers, we identify the favored pathway on both surfaces. A general understanding toward the deactivation process of the industrial catalysts is also provided. In addition, the effects of the formation of subsurface carbon atoms as well as the Ag alloying on the 1,3-butadiene formation on Pd-based catalysts are also investigated and compared with experimental results.

Robust nonadiabatic molecular dynamics for metals and insulators

We present a new formulation of the correlated electron-ion dynamics (CEID) scheme, which systematically improves Ehrenfest dynamics by including quantum fluctuations around the mean-field atomic trajectories. We show that the method can simulate models of nonadiabatic electronic transitions and test it against exact integration of the time-dependent Schrodinger equation. Unlike previous formulations of CEID, the accuracy of this scheme depends on a single tunable parameter which sets the level of atomic fluctuations included. The convergence to the exact dynamics by increasing the tunable parameter is demonstrated for a model two level system. This algorithm provides a smooth description of the nonadiabatic electronic transitions which satisfies the kinematic constraints (energy and momentum conservation) and preserves quantum coherence. The applicability of this algorithm to more complex atomic systems is discussed.

Automated tumour annotation and analysis for molecular pathology using TissueMark (R)

Objective: Molecular pathology relies on identifying anomalies using PCR or analysis of DNA/RNA. This is important in solid tumours where molecular stratification of patients define targeted treatment. These molecular biomarkers rely on examination of tumour, annotation for possible macro dissection/tumour cell enrichment and the estimation of % tumour. Manually marking up tumour is error prone. Method: We have developed a method for automated tumour mark-up and % cell calculations using image analysis called TissueMark® based on texture analysis for lung, colorectal and breast (cases=245, 100, 100 respectively). Pathologists marked slides for tumour and reviewed the automated analysis. A subset of slides was manually counted for tumour cells to provide a benchmark for automated image analysis. Results: There was a strong concordance between pathological and automated mark-up (100 % acceptance rate for macro-dissection). We also showed a strong concordance between manually/automatic drawn boundaries (median exclusion/inclusion error of 91.70 %/89 %). EGFR mutation analysis was precisely the same for manual and automated annotation-based macrodissection. The annotation accuracy rates in breast and colorectal cancer were 83 and 80 % respectively. Finally, region-based estimations of tumour percentage using image analysis showed significant correlation with actual cell counts. Conclusion: Image analysis can be used for macro-dissection to (i) annotate tissue for tumour and (ii) estimate the % tumour cells and represents an approach to standardising/improving molecular diagnostics.

Density functional theory study on the activation of molecular oxygen on a stepped gold surface in an aqueous environment: a new approach for simulating reactions in solution

The activation of oxygen molecules is an important issue in the gold-catalyzed partial oxidation of alcohols in aqueous solution. The complexity of the solution arising from a large number of solvent molecules makes it difficult to study the reaction in the system. In this work, O-2 activation on an Au catalyst is investigated using an effective approach to estimate the reaction barriers in the presence of solvent. Our calculations show that O-2 can be activated, undergoing OOH* in the presence of water molecules. The OOH* can readily be formed on Au(211) via four possible pathways with almost equivalent free energy barriers at the aqueous-solid interface: the direct or indirect activation of O-2 by surface hydrogen or the hydrolysis of O-2 following a Langmuir-Hinshelwood mechanism or an Eley-Rideal mechanism. Among them, the Eley-Rideal mechanism may be slightly more favorable due to the restriction of the low coverage of surface H on Au(211) in the other mechanisms. The results shed light on the importance of water molecules on the activation of oxygen in gold-catalyzed systems. Solvent is found to facilitate the oxygen activation process mainly by offering extra electrons and stabilizing the transition states. A correlation between the energy barrier and the negative charge of the reaction center is found. The activation barrier is substantially reduced by the aqueous environment, in which the first solvation shell plays the most important role in the barrier reduction. Our approach may be useful for estimating the reaction barriers in aqueous systems.

GRADIENT CORRECTIONS IN DENSITY-FUNCTIONAL THEORY CALCULATIONS FOR SURFACES - CO ON PD(110)

Ab initio total energy calculations have been performed for CO chemisorption on Pd(110). Local density approximation (LDA) calculations yield chemisorption energies which are significantly higher than experimental values but inclusion of the generalised gradient approximation (GGA) gives better agreement. In general, sites with higher coordination of the adsorbate to surface atoms lead to a larger degree of overbinding with LDA, and give larger corrections with GGA. The reason is discussed using a first-order perturbation approximation. It is concluded that this may be a general failure of LDA for chemisorption energy calculations. This conclusion may be extended to many surface calculations, such as potential energy surfaces for diffusion.

Molecular subtyping of primary prostate cancer reveals specific and shared target genes of different ETS rearrangements

This work aimed to evaluate whether ETS transcription factors frequently involved in rearrangements in prostate carcinomas (PCa), namely ERG and ETV1, regulate specific or shared target genes. We performed differential expression analysis on nine normal prostate tissues and 50 PCa enriched for different ETS rearrangements using exon-level expression microarrays, followed by in vitro validation using cell line models. We found specific deregulation of 57 genes in ERG-positive PCa and 15 genes in ETV1-positive PCa, whereas deregulation of 27 genes was shared in both tumor subtypes. We further showed that the expression of seven tumor-associated ERG target genes (PLA1A, CACNA1D, ATP8A2, HLA-DMB, PDE3B, TDRD1, and TMBIM1) and two tumor-associated ETV1 target genes (FKBP10 and GLYATL2) was significantly affected by specific ETS silencing in VCaP and LNCaP cell line models, respectively, whereas the expression of three candidate ERG and ETV1 shared targets (GRPR, KCNH8, and TMEM45B) was significantly affected by silencing of either ETS. Interestingly, we demonstrate that the expression of TDRD1, the topmost overexpressed gene of our list of ERG-specific candidate targets, is inversely correlated with the methylation levels of a CpG island found at -66 bp of the transcription start site in PCa and that TDRD1 expression is regulated by direct binding of ERG to the CpG island in VCaP cells. We conclude that ETS transcription factors regulate specific and shared target genes and that TDRD1, FKBP10, and GRPR are promising therapeutic targets and can serve as diagnostic markers for molecular subtypes of PCa harboring specific fusion gene rearrangements.