Density functional energy decomposition into one- and two-atom contributions

The present work provides a generalization of Mayer's energy decomposition for the density-functional theory (DFT) case. It is shown that one- and two-atom Hartree-Fock energy components in Mayer's approach can be represented as an action of a one-atom potential VA on a one-atom density ρ A or ρ B. To treat the exchange-correlation term in the DFT energy expression in a similar way, the exchange-correlation energy density per electron is expanded into a linear combination of basis functions. Calculations carried out for a number of density functionals demonstrate that the DFT and Hartree-Fock two-atom energies agree to a reasonable extent with each other. The two-atom energies for strong covalent bonds are within the range of typical bond dissociation energies and are therefore a convenient computational tool for assessment of individual bond strength in polyatomic molecules. For nonspecific nonbonding interactions, the two-atom energies are low. They can be either repulsive or slightly attractive, but the DFT results more frequently yield small attractive values compared to the Hartree-Fock case. The hydrogen bond in the water dimer is calculated to be between the strong covalent and nonbonding interactions on the energy scale

A tale of two elements: P1ncP1 and RTO

The and RT0 finite element schemes are among the most promising low order elements for use in unstructured mesh marine and lake models. They are both free of spurious elevation modes, have good dispersive properties and have a relatively low computational cost. In this paper, we derive both finite element schemes in the same unified framework and discuss their respective qualities in terms of conservation, consistency, propagation factor and convergence rate. We also highlight the impact that the local variables placement can have on the model solution. The main conclusion that we can draw is that the choice between elements is highly application dependent. We suggest that the element is better suited to purely hydrodynamical applications while the RT0 element might perform better for hydrological applications that require scalar transport calculations.

Sampling uncertainties in surface radiation budget calculations in RADAGAST

In the Radiative Atmospheric Divergence Using ARM Mobile Facility GERB and AMMA Stations (RADAGAST) project we calculate the divergence of radiative flux across the atmosphere by comparing fluxes measured at each end of an atmospheric column above Niamey, in the African Sahel region. The combination of broadband flux measurements from geostationary orbit and the deployment for over 12 months of a comprehensive suite of active and passive instrumentation at the surface eliminates a number of sampling issues that could otherwise affect divergence calculations of this sort. However, one sampling issue that challenges the project is the fact that the surface flux data are essentially measurements made at a point, while the top-of-atmosphere values are taken over a solid angle that corresponds to an area at the surface of some 2500 km2. Variability of cloud cover and aerosol loading in the atmosphere mean that the downwelling fluxes, even when averaged over a day, will not be an exact match to the area-averaged value over that larger area, although we might expect that it is an unbiased estimate thereof. The heterogeneity of the surface, for example, fixed variations in albedo, further means that there is a likely systematic difference in the corresponding upwelling fluxes. In this paper we characterize and quantify this spatial sampling problem. We bound the root-mean-square error in the downwelling fluxes by exploiting a second set of surface flux measurements from a site that was run in parallel with the main deployment. The differences in the two sets of fluxes lead us to an upper bound to the sampling uncertainty, and their correlation leads to another which is probably optimistic as it requires certain other conditions to be met. For the upwelling fluxes we use data products from a number of satellite instruments to characterize the relevant heterogeneities and so estimate the systematic effects that arise from the flux measurements having to be taken at a single point. The sampling uncertainties vary with the season, being higher during the monsoon period. We find that the sampling errors for the daily average flux are small for the shortwave irradiance, generally less than 5 W m−2, under relatively clear skies, but these increase to about 10 W m−2 during the monsoon. For the upwelling fluxes, again taking daily averages, systematic errors are of order 10 W m−2 as a result of albedo variability. The uncertainty on the longwave component of the surface radiation budget is smaller than that on the shortwave component, in all conditions, but a bias of 4 W m−2 is calculated to exist in the surface leaving longwave flux.

Theory of enhanced magnetic anisotropy induced by Pt adatoms on two-dimensional Co clusters supported on a Pt(111) substrate

Calculations are reported of the magnetic anisotropy energy of two-dimensional (2D) Co nanostructures on a Pt(111) substrate. The perpendicular magnetic anisotropy (PMA) of the 2D Co clusters strongly depends on their size and shape, and rapidly decreases with increasing cluster size. The PMA calculated is in reasonable agreement with experimental results. The sensitivity of the results to the Co-Pt spacing at the interface is also investigated and, in particular, for a complete Co monolayer we note that the value of the spacing at the interface determines whether PMA or in-plane anisotropy occurs. We find that the PMA can be greatly enhanced by the addition of Pt adatoms to the top surface of the 2D Co clusters. A single Pt atom can induce in excess of 5 meV to the anisotropy energy of a cluster. In the absence of the Pt adatoms the PMA of the Co clusters falls below 1 meV/Co atom for clusters of about 10 atoms whereas, with Pt atoms added to the surface of the clusters, a PMA of 1 meV/Co atom can be maintained for clusters as large as about 40 atoms. The effect of placing Os atoms on the top of the Co clusters is also considered. The addition of 5d atoms and clusters on the top of ferromagnetic nanoparticles may provide an approach to tune the magnetic anisotropy and moment separately.

The impact of a closed-loop electronic prescribing and automated dispensing system on the ward pharmacist’s time and activities

Objective To assess the impact of a closed-loop electronic prescribing and automated dispensing system on the time spent providing a ward pharmacy service and the activities carried out. Setting Surgical ward, London teaching hospital. Method All data were collected two months pre- and one year post-intervention. First, the ward pharmacist recorded the time taken each day for four weeks. Second, an observational study was conducted over 10 weekdays, using two-dimensional work sampling, to identify the ward pharmacist's activities. Finally, medication orders were examined to identify pharmacists' endorsements that should have been, and were actually, made. Key findings Mean time to provide a weekday ward pharmacy service increased from 1 h 8 min to 1 h 38 min per day (P = 0.001; unpaired t-test). There were significant increases in time spent prescription monitoring, recommending changes in therapy/monitoring, giving advice or information, and non-productive time. There were decreases for supply, looking for charts and checking patients' own drugs. There was an increase in the amount of time spent with medical and pharmacy staff, and with 'self'. Seventy-eight per cent of patients' medication records could be assessed for endorsements pre- and 100% post-intervention. Endorsements were required for 390 (50%) of 787 medication orders pre-intervention and 190 (21%) of 897 afterwards (P < 0.0001; chi-square test). Endorsements were made for 214 (55%) of endorsement opportunities pre-intervention and 57 (30%) afterwards (P < 0.0001; chi-square test). Conclusion The intervention increased the overall time required to provide a ward pharmacy service and changed the types of activity undertaken. Contact time with medical and pharmacy staff increased. There was no significant change in time spent with patients. Fewer pharmacy endorsements were required post-intervention, but a lower percentage were actually made. The findings have important implications for the design, introduction and use of similar systems.

Analytical potentials for triatomic molecules VIII. A two valued surface for the lowest 1A¢ surfaces of H2O

Ab initio calculations of the energy have been made at approximately 150 points on the two lowest singlet A' potential energy surfaces of the water molecule, 1A' and 1A', covering structures having D∞h, C∞v, C2v and Cs symmetries. The object was to obtain an ab initio surface of uniform accuracy over the whole three-dimensional coordinate space. Molecular orbitals were constructed from a double zeta plus Rydberg basis, and correlation was introduced by single and double excitations from multiconfiguration states which gave the correct dissociation behaviour. A two-valued analytical potential function has been constructed to fit these ab initio energy calculations. The adiabatic energies are given in our analytical function as the eigenvalues of a 2 2 matrix, whose diagonal elements define two diabatic surfaces. The off-diagonal element goes to zero for those configurations corresponding to surface intersections, so that our adiabatic surface exhibits the correct Σ/II conical intersections for linear configurations, and singlet/triplet intersections of the O + H2 dissociation fragments. The agreement between our analytical surface and experiment has been improved by using empirical diatomic potential curves in place of those derived from ab initio calculations.

Effects of phosphorus intake on phosphorus flow in growing pigs: Application and comparison of two models

A comparison of the models of Vitti et al. (2000, J. Anim. Sci. 78, 2706-2712) and Fernandez (1995c, Livest. Prod. Sci. 41, 255-261) was carried out using two data sets on growing pigs as input. The two models compared were based on similar basic principles, although their aims and calculations differed. The Vitti model employs the rate:state formalism and describes phosphorus (P) flow between four pools representing P content in gut, blood, bone and soft tissue in growing goats. The Fernandez model describes flow and fractional recirculation between P pools in gut, blood and bone in growing pigs. The results from both models showed similar trends for P absorption from gut to blood and net retention in bone with increasing P intake, with the exception of the 65 kg results from Date Set 2 calculated using the FernAndez model. Endogenous loss from blood back to gut increased faster with increasing P intake in the FernAndez than in the Vitti model for Data Set 1. However, for Data Set 2, endogenous loss increased with increasing P intake using the Vitti model, but decreased when calculated using the FernAndez model. Incorporation of P into bone was not influenced by intake in the FernAndez model, while in the Vitti model there was an increasing trend. The FernAndez model produced a pattern of decreasing resorption in bone with increasing P intake, with one of the data sets, which was not observed when using the Vitti model. The pigs maintained their P homeostasis in blood by regulation of P excretion in urine. (c) 2005 Elsevier Ltd. All rights reserved.

A conserved basic loop in hepatitis C virus p7 protein is required for amantadine-sensitive ion channel activity in mammalian cells but is dispensable for localization to mitochondria

We previously identified the function of the hepatitis C virus (HCV) p7 protein as an ion channel in artificial lipid bilayers and demonstrated that this in vitro activity is inhibited by amantadine. Here we show that the ion channel activity of HCV p7 expressed in mammalian cells can substitute for that of influenza virus M2 in a cell-based assay. This was also the case for the p7 from the related virus, bovine viral diarrhoea virus (BVDV). Moreover, amantadine was shown to abrogate HCV p7 function in this assay at a concentration that specifically inhibits M2. Mutation of a conserved basic loop located between the two predicted trans-membrane alpha helices rendered HCV p7 non-functional as an ion channel. The intracellular localization of p7 was unaffected by this mutation and was found to overlap significantly with membranes associated with mitochondria. Demonstration of p7 ion channel activity in cellular membranes and its inhibition by amantadine affirm the protein as a target for future anti-viral chemotherapy.

Molecular structures of benzoic acid and 2-hydroxybenzoic acid, obtained by gas-phase electron diffraction and theoretical calculations

The structures of benzoic acid (C6H5COOH) and 2-hydroxybenzoic acid (C6H4OHCOOH) have been determined in the gas phase by electron diffraction using results from quantum chemical calculations to inform restraints used on the structural parameters. Theoretical methods (HF and MP2/6-311+G(d, p)) predict two conformers for benzoic acid, one which is 25.0 kJ mol(-1) (MP2) lower in energy than the other. In the low-energy form, the carboxyl group is coplanar with the phenyl ring and the O-H group eclipses the C=O bond. Theoretical calculations (HF and MP2/6-311+ G(d, p)) carried out for 2-hydroxybenzoic acid gave evidence for seven stable conformers but one low-energy form (11.7 kJ mol-1 lower in energy (MP2)) which again has the carboxyl group coplanar with the phenyl ring, the O-H of the carboxyl group eclipsing the C=O bond and the C=O of the carboxyl group oriented toward the O-H group of the phenyl ring. The effects of internal hydrogen bonding in 2-hydroxybenzoic acid can be clearly observed by comparison of pertinent structural parameters between the two compounds. These differences for 2-hydroxybenzoic acid include a shorter exocyclic C-C bond, a lengthening of the ring C-C bond between the substituents, and a shortening of the carboxylic single C-O bond.

Solid state annular tautomerism in a molecule containing two imidazole moieties

The X-ray crystal structure of the 1:2 condensate (1) of hydrazine hydrate and 4-methyl-imidazole-5-carboxaldehyde has been determined. The molecule is centrosymmetric crystallising in the space group Fddd with cell dimensions: a = 10.557(14), b = 17.062(22), c = 24.759(27) angstrom. Fourier map shows that the NH hydrogen atom of each imidazole moiety has equal possibility of occupying any of its two ring N atoms. This poses the possibility of finding three tautomers in 1 in the solid state. Consideration of the H-bonding pattern observed in 1 and related B3LYP/6-311+G(2d, p) calculations show that only two tautomers are present in the solid state. The situation is compared with that in the structure of 4(5)-nitro-5(4)-methoxy-imidazole reported previously by Kubicki.

Solvent extraction and lanthanide complexation studies with new terdentate ligands containing two 1,3,5-triazine moieties

The extracting agent 2,6-bis(4,6-di-pivaloylamino-1,3,5-triazin-2-yl)-pyridine (L-5) in n-octanol was found, in synergy with 2-bromodecanoic acid, to give D-Am/D-Eu separation factors (SFs) between 2.4 and 3.7 when used to extract the metal ions from 0.02-0.12 M HNO3. Slightly higher SFs (4-6) were obtained in the absence of the synergist when the ligand was used to extract Am(III) and Eu(III) from 0.98 M HNO3. In order to investigate the possible nature of the extracted species crystal structures of L-5 and the complex formed between Yb(III) with 2,6-bis(4,6-di-amino-1,3,5-triazin-2-yl)-pyridine (L-4) were also determined. The structure of L-5 shows 3 methanol solvent molecules all of which form 2 or 3 hydrogen bonds with triazine nitrogen atoms, amide nitrogen or oxygen atoms, or pyridine nitrogen atoms. However, L-5 is relatively unstable in metal complexation reactions and loses amide groups to form the parent tetramine L-4. The crystal structure of Yb(L-4)(NO3)(3) shows ytterbium in a 9-coordinate environment being bonded to three donor atoms of the ligand and three bidentate nitrate ions. The solvent extraction properties of L-4 and L-5 are far inferior to those found for the 2,6-bis-(1,2,4-triazin-3-yl)-pyridines (L-1) which have SF values of ca. 140 and theoretical calculations have been made to compare the electronic properties of the ligands. The electronic charge distribution in L-4 and L-5 is similar to that found in other terdentate ligands such as terpyridine which have equally poor extraction properties and suggests that the unique properties of L-1 evolve from the presence of two adjacent nitrogen atoms in the triazine rings.

Antimalarial drugs based on artemisinin: DFT calculations on the principal reactions

Theoretical calculations have been carried out on the interactions of several endoperoxides which are potential antimalarials, including the clinically useful artemisinin, with two possible sources of iron in the parasite, namely the hexa-aquo ferrous ion [Fe(H2O)(6)](2+) and haeme. DFT calculations show that the reactions of all endoperoxides considered, with both sources of iron, initially generate a Fe-O bond followed by cleavage of the O-O bond to oxygen radical species. Subsequently, they can be transformed into carbon-centred radicals of greater stability. However, with [Fe(H2O)(6)](2+) as the iron source, the oxygen-centred radical species are more likely to react further akin to Fenton's reagent, whereby iron salts encourage hydrogen peroxide to act as an oxidizing agent, and that solvent plays a major role. In contrast, when reacting with haeme, the oxygen-centred radicals interconvert to more stable carbon-centred radicals, which can then alkylate haeme. Subsequent cleavage of the Fe-O bond leads to stable and inactive antimalarial products. These results indicate that the reactivity of the endoperoxides as antimalarials is greater with iron hexahydrates for radical-mediated damage as opposed to haeme, which leads to unreactive species. Since only nanomolar quantities of hydrated metal ions could catalyse the reactions leading to damage to the parasites, this could be an alternative or competitive reaction responsible for the antimalarial activity. (c) 2005 Elsevier B.V. All rights reserved.

Full-dimensional vibrational calculations for H5O2+ using an ab initio potential energy surface

We report quantum diffusion Monte Carlo (DMC) and variational calculations in full dimensionality for selected vibrational states of H5O2+ using a new ab initio potential energy surface [X. Huang, B. Braams, and J. M. Bowman, J. Chem. Phys. 122, 044308 (2005)]. The energy and properties of the zero-point state are focused on in the rigorous DMC calculations. OH-stretch fundamentals are also calculated using "fixed-node" DMC calculations and variationally using two versions of the code MULTIMODE. These results are compared with infrared multiphoton dissociation measurements of Yeh [L. I. Yeh, M. Okumura, J. D. Myers, J. M. Price, and Y. T. Lee, J. Chem. Phys. 91, 7319 (1989)]. Some preliminary results for the energies of several modes of the shared hydrogen are also reported.

Tuning of redox potential and visible absorption band of ruthenium(II) complexes of (benzimidazolyl) derivatives: synthesis, characterization, spectroscopic and redox properties, X-ray structures and DFT calculations

Six ruthenium(II) complexes have been prepared using the tridentate ligands 2,6-bis(benzimidazolyl) pyridine and bis(2-benzimidazolyl methyl) amine and having 2,2'-bipyridine, 2,2':6',2 ''-terpyridine, PPh3, MeCN and chloride as coligands. The crystal structures of three of the complexes trans-[Ru(bbpH(2))(PPh3)(2)(CH3CN)I(ClO4)(2) center dot 2H(2)O (2), [Ru(bbpH(2))(bpy)Cl]ClO4 (3) and [Ru(bbpH(2))(terpy)](ClO4)(2) (4) are also reported. The complexes show visible region absorption at 402-517 nm, indicating that it is possible to tune the visible region absorption by varying the ancillary ligand. Luminescence behavior of the complexes has been studied both at RT and at liquid nitrogen temperature (LNT). Luminescence of the complexes is found to be insensitive to the presence of dioxygen. Two of the complexes [Ru(bbpH(2))(bpy)Cl]ClO4 (3) and [Ru(bbpH(2))(terpy]ClO4)(2) (4) show RT emission in the NIR region, having lifetime, quantum yield and radiative constant values suitable for their application as NIR emitter in the solid state devices. The DFT calculations on these two complexes indicate that the metal t(2g) electrons are appreciably delocalized over the ligand backbone. (C) 2006 Elsevier B.V. All rights reserved.

Synthesis and structural characterization of two nostoclide analogues

The vinylogous aldol reaction between appropriate aldehydes and furan-based silyloxy diene synthon generated from 3-benzyl-5H-furan-2-one (3) afforded two truncated lactone analogues [compounds (4) and (5)] of nostoclides (2). The compounds were fully characterized by IR, NMR (H-1 and C-13), 2D NMR spectroscopy experiments (HMBC, HSQC and NOESY), MS spectrometry and X-ray crystallography. Compounds (4) and (5) crystallized in the space group P2(1)2(1)2(1) and P2(1)/c, respectively. Although expected correlations between hydrogen atoms in spatial close proximity were not observed for compound (5) using NMR, the stereochemistry of the exocyclic double bond of both (4) and (5) was unambiguously determined to be Z and E, respectively, using X-ray crystallography. The packing of both compounds within the crystal are stabilized by non-classical inter-molecular hydrogen bonds. DFT calculations (B3LYP/6-31+G* level) confirmed that the crystal structures possessed the lowest energies in the gas phase when compared to their geometric isomers. (c) 2006 Elsevier B.V. All rights reserved.