Metal complexes of a tetraazacyclophane: solution and molecular modelling studies

An alternative synthetic approach to yield the compound 2,3,5,6,8,9,11,14-octahydrobenzo[1][ 1,4,7,10]tetraazacyclotetradecine (bz[14]N-4) is presented. The protonation constants of bz[14]N-4 and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+, Pb2+ were determined in H2O at 25degreesC with ionic strength 0.10 mol dm(-3) in KNO3 and they were compared with structurally related macrocycles cyclam (1,4,8,11-tetraazacyclotetradecane) and cyclen (1,4,7,10-tetraazacyclododecane). These studies indicate that only 1 : 1 ( M : L) species are formed in solution, and the ligand exhibits a high affinity for larger ions such as Cd2+ and Pb2+. The X-ray study of [bz[14]N4H3](3+) shows that an inclusion compound with a chloride counter-anion is formed through NH...Cl hydrogen bonds. Spectroscopic data in solution ( electronic and NMR spectra) showed that the macrocycle adopts a planar arrangement upon metal complexation. Molecular mechanics calculations reveal that in spite of the presence of the benzene ring in the macrocyclic framework this ligand can encapsulate metal ions with different stereo-electronic sizes in square planar arrangements. Our results indicate that the presence of the benzene ring in the backbone of the bz[14]N-4 confers a coordination behaviour intermediate between that of cyclam and cyclen.

Metal complexes of a dipyridine octaazamacrocycle: stability constants, structural and modelling studies

Two 28-membered octaazamacrocycles, [28]py(2)N(6) and Me-2[28]py(2)N(6), have been synthesized. The protonation constants of the N-methyl. derivative and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+, and Pb2+ were determined at 25degreesC in 0.10 mol dm(-3) KNO3. The high overall basicity of Me-2[28]py(2)N(6) is ascribed to the weaker repulsion between protonated contiguous charged ammonium sites separated by propyl chains. These studies together with NMR, UV-vis and EPR spectroscopies indicated the presence of mono- and di-nuclear species, The single crystal structure of the complex [Ni-2([28]py(2)N(6))(H2O)(4)]Cl-4.3H(2)O was determined, and showed each nickel centre in a distorted octahedral co-ordination environment. The nickel centres are held within the macrocycle at a large distance of 6.991(g) Angstrom from each other. The formation of mononuclear complexes was evaluated theoretically via molecular mechanics (MM) and molecular dynamics (MD) calculations and showed that these large macrocycles have sufficient flexibility to encapsulate metal ions with different stereo-electronic sizes. Structures for small and large metal ions are proposed.

Crumpet structures: experimental and modelling studies

Crumpets are made by heating fermented batter on a hot plate at around 230°C. The characteristic structure dominated by vertical pores develops rapidly: structure has developed throughout around 75% of the product height within 30s, which is far faster than might be expected from transient heat conduction through the batter. Cooking is complete within around 3 min. Image analysis based on results from X-ray tomography shows that the voidage fraction is approximately constant and that there is continual coalescence between the larger pores throughout the product although there is also a steady level of small bubbles trapped within the solidified batter. We report here experimental studies which shed light on some of the mechanisms responsible for this structure, together with some models of key phenomena.Three aspects are discussed here: the role of gas (carbon dioxide and nitrogen) nuclei in initiating structure development; convective heat transfer inside the developing pores; and the kinetics of setting the batter into an elastic solid structure. It is shown conclusively that the small bubbles of carbon dioxide resulting from the fermentation stage play a crucial role as nuclei for pore development: without these nuclei, the result is not a porous structure, but rather a solid, elastic, inedible, gelatinized product. These nuclei are also responsible for the tiny bubbles which are set in the final product. The nuclei form the source of the dominant pore structure which is largely driven by the, initially explosive, release of water vapour from the batter together with the desorption of dissolved carbon dioxide. It is argued that the rapid evaporation, transport and condensation of steam within the growing pores provides an important mechanism, as in a heat pipe, for rapid heat transfer, and models for this process are developed and tested. The setting of the continuous batter phase is essential for final product quality: studies using differential scanning calorimetry and on the kinetics of change in the visco-elastic properties of the batter suggest that this process is driven by the kinetics of gelatinization. Unlike many thermally driven food processes the rates of heating are such that gelatinization kinetics cannot be neglected. The implications of these results for modelling and for the development of novel structures are discussed.

Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Model studies of the interannual variability of the northern-hemisphere stratospheric winter circulation: the role of the quasi-biennial oscillation

A series of experiments are described that examine the sensitivity of the northern-hemisphere winter evolution to the equatorial quasi-biennial oscillation (QBO). The prime tool for the experiments is a stratosphere-mesosphere model. The model is integrated over many years with the modelled equatorial winds relaxed towards observed values in order to simulate a realistic QBO. In experiment A the equatorial winds are relaxed towards Singapore radiosonde observations in the height region 16-32 km. In contrast to previous modelling studies, the Holton-Tan relationship (warm/cold winters associated with easterly/westerly QBO winds in the lower stratosphere) is absent. However, in a second experiment (run B) in which the equatorial winds are relaxed towards rocketsonde data over the extended height range 16-58 km, a realistic Holton-Tan relationship is reproduced. A series of further studies are described that explore in more detail the sensitivity to various equatorial height regions and to the bottom-boundary forcing. The experiments suggest that the evolution of the northern-hemisphere winter circulation is sensitive to equatorial winds throughout the whole depth of the stratosphere and not just to the lower-stratospheric wind direction as previously assumed.

Numerical modelling of the energy and water cycle of the Baltic Sea

This paper will introduce the Baltex research programme and summarize associated numerical modelling work which has been undertaken during the last five years. The research has broadly managed to clarify the main mechanisms determining the water and energy cycle in the Baltic region, such as the strong dependence upon the large scale atmospheric circulation. It has further been shown that the Baltic Sea has a positive water balance, albeit with large interannual variations. The focus on the modelling studies has been the use of limited area models at ultra-high resolution driven by boundary conditions from global models or from reanalysis data sets. The programme has further initiated a comprehensive integration of atmospheric, land surface and hydrological modelling incorporating snow, sea ice and special lake models. Other aspects of the programme include process studies such as the role of deep convection, air sea interaction and the handling of land surface moisture. Studies have also been undertaken to investigate synoptic and sub-synoptic events over the Baltic region, thus exploring the role of transient weather systems for the hydrological cycle. A special aspect has been the strong interests and commitments of the meteorological and hydrological services because of the potentially large societal interests of operational applications of the research. As a result of this interests special attention has been put on data-assimilation aspects and the use of new types of data such as SSM/I, GPS-measurements and digital radar. A series of high resolution data sets are being produced. One of those, a 1/6 degree daily precipitation climatology for the years 1996–1999, is such a unique contribution. The specific research achievements to be presented in this volume of Meteorology and Atmospheric Physics is the result of a cooperative venture between 11 European research groups supported under the EU-Framework programmes.

Effects of plant pathogens on population dynamics and community composition in grassland ecosystems: two case studies

Grassland ecosystems comprise a major portion of the earth’s terrestrial surface, ranging from high-input cultivated monocultures or simple species mixtures to relatively unmanaged but dynamic systems. Plant pathogens are a component of these systems with their impact dependent on many interacting factors, including grassland species population dynamics and community composition, the topics covered in this paper. Plant pathogens are affected by these interactions and also act reciprocally by modifying their nature. We review these features of disease in grasslands and then introduce the 150-year long-term Park Grass Experiment (PGE) at Rothamsted Research in the UK. We then consider in detail two plant-pathogen systems present in the PGE, Tragopogon pratensis-Puccinia hysterium and Holcus lanata-Puccinia coronata. These two systems have very different life history characteristics: the first, a biennial member of the Asteraceae infected by its host-specific, systemic rust; the second, a perennial grass infected by a host-non-specific rust. We illustrate how observational, experimental and modelling studies can contribute to a better understanding of population dynamics, competitive interactions and evolutionary outcomes. With Tragopogon pratensis-Puccinia hysterium, characterised as an “outbreak” species in the PGE, we show that pathogen-induced mortality is unlikely to be involved in host population regulation; and that the presence of even a short-lived seed-bank can affect the qualitative outcomes of the host-pathogen dynamics. With Holcus lanata-Puccinia coronata, we show how nutrient conditions can affect adaptation in terms of host defence mechanisms, and that co-existence of competing species affected by a common generalist pathogen is unlikely.

The Madden-Julian Oscillation and the diurnal cycle over the Maritime Continent: scale interactions and modelling

The Maritime Continent archipelago, situated on the equator at 95-165E, has the strongest land-based precipitation on Earth. The latent heat release associated with the rainfall affects the atmospheric circulation throughout the tropics and into the extra-tropics. The greatest source of variability in precipitation is the diurnal cycle. The archipelago is within the convective region of the Madden-Julian Oscillation (MJO), which provides the greatest variability on intra-seasonal time scales: large-scale (∼10^7 km^2) active and suppressed convective envelopes propagate slowly (∼5 m s^-1) eastwards between the Indian and Pacific Oceans. High-resolution satellite data show that a strong diurnal cycle is triggered to the east of the advancing MJO envelope, leading the active MJO by one-eighth of an MJO cycle (∼6 days). Where the diurnal cycle is strong its modulation accounts for 81% of the variability in MJO precipitation. Over land this determines the structure of the diagnosed MJO. This is consistent with the equatorial wave dynamics in existing theories of MJO propagation. The MJO also affects the speed of gravity waves propagating offshore from the Maritime Continent islands. This is largely consistent with changes in static stability during the MJO cycle. The MJO and its interaction with the diurnal cycle are investigated in HiGEM, a high-resolution coupled model. Unlike many models, HiGEM represents the MJO well with eastward-propagating variability on intra-seasonal time scales at the correct zonal wavenumber, although the inter-tropical convergence zone's precipitation peaks strongly at the wrong time, interrupting the MJO's spatial structure. However, the modelled diurnal cycle is too weak and its phase is too early over land. The modulation of the diurnal amplitude by the MJO is also too weak and accounts for only 51% of the variability in MJO precipitation. Implications for forecasting and possible causes of the model errors are discussed, and further modelling studies are proposed.

Improving the TanDEM-X Digital Elevation Model for flood modelling using flood extents from Synthetic Aperture Radar images

The topography of many floodplains in the developed world has now been surveyed with high resolution sensors such as airborne LiDAR (Light Detection and Ranging), giving accurate Digital Elevation Models (DEMs) that facilitate accurate flood inundation modelling. This is not always the case for remote rivers in developing countries. However, the accuracy of DEMs produced for modelling studies on such rivers should be enhanced in the near future by the high resolution TanDEM-X WorldDEM. In a parallel development, increasing use is now being made of flood extents derived from high resolution Synthetic Aperture Radar (SAR) images for calibrating, validating and assimilating observations into flood inundation models in order to improve these. This paper discusses an additional use of SAR flood extents, namely to improve the accuracy of the TanDEM-X DEM in the floodplain covered by the flood extents, thereby permanently improving this DEM for future flood modelling and other studies. The method is based on the fact that for larger rivers the water elevation generally changes only slowly along a reach, so that the boundary of the flood extent (the waterline) can be regarded locally as a quasi-contour. As a result, heights of adjacent pixels along a small section of waterline can be regarded as samples with a common population mean. The height of the central pixel in the section can be replaced with the average of these heights, leading to a more accurate estimate. While this will result in a reduction in the height errors along a waterline, the waterline is a linear feature in a two-dimensional space. However, improvements to the DEM heights between adjacent pairs of waterlines can also be made, because DEM heights enclosed by the higher waterline of a pair must be at least no higher than the corrected heights along the higher waterline, whereas DEM heights not enclosed by the lower waterline must in general be no lower than the corrected heights along the lower waterline. In addition, DEM heights between the higher and lower waterlines can also be assigned smaller errors because of the reduced errors on the corrected waterline heights. The method was tested on a section of the TanDEM-X Intermediate DEM (IDEM) covering an 11km reach of the Warwickshire Avon, England. Flood extents from four COSMO-SKyMed images were available at various stages of a flood in November 2012, and a LiDAR DEM was available for validation. In the area covered by the flood extents, the original IDEM heights had a mean difference from the corresponding LiDAR heights of 0.5 m with a standard deviation of 2.0 m, while the corrected heights had a mean difference of 0.3 m with standard deviation 1.2 m. These figures show that significant reductions in IDEM height bias and error can be made using the method, with the corrected error being only 60% of the original. Even if only a single SAR image obtained near the peak of the flood was used, the corrected error was only 66% of the original. The method should also be capable of improving the final TanDEM-X DEM and other DEMs, and may also be of use with data from the SWOT (Surface Water and Ocean Topography) satellite.

The effect of doubled CO2 and model basic state biases on the monsoon-ENSO system. II: Changing ENSO regimes

Integrations of a fully-coupled climate model with and without flux adjustments in the equatorial oceans are performed under 2×CO2 conditions to explore in more detail the impact of increased greenhouse gas forcing on the monsoon-ENSO system. When flux adjustments are used to correct some systematic model biases, ENSO behaviour in the modelled future climate features distinct irregular and periodic (biennial) regimes. Comparison with the observed record yields some consistency with ENSO modes primarily based on air-sea interaction and those dependent on basinwide ocean wave dynamics. Simple theory is also used to draw analogies between the regimes and irregular (stochastically forced) and self-excited oscillations respectively. Periodic behaviour is also found in the Asian-Australian monsoon system, part of an overall biennial tendency of the model under these conditions related to strong monsoon forcing and increased coupling between the Indian and Pacific Oceans. The tropospheric biennial oscillation (TBO) thus serves as a useful descriptor for the coupled monsoon-ENSO system in this case. The presence of obvious regime changes in the monsoon-ENSO system on interdecadal timescales, when using flux adjustments, suggests there may be greater uncertainty in projections of future climate, although further modelling studies are required to confirm the realism and cause of such changes.

Crop yield reduction in the tropics under climate change: Processes and uncertainties

Many modelling studies examine the impacts of climate change on crop yield, but few explore either the underlying bio-physical processes, or the uncertainty inherent in the parameterisation of crop growth and development. We used a perturbed-parameter crop modelling method together with a regional climate model (PRECIS) driven by the 2071-2100 SRES A2 emissions scenario in order to examine processes and uncertainties in yield simulation. Crop simulations used the groundnut (i.e. peanut; Arachis hypogaea L.) version of the General Large-Area Model for annual crops (GLAM). Two sets of GLAM simulations were carried out: control simulations and fixed-duration simulations, where the impact of mean temperature on crop development rate was removed. Model results were compared to sensitivity tests using two other crop models of differing levels of complexity: CROPGRO, and the groundnut model of Hammer et al. [Hammer, G.L., Sinclair, T.R., Boote, K.J., Wright, G.C., Meinke, H., and Bell, M.J., 1995, A peanut simulation model: I. Model development and testing. Agron. J. 87, 1085-1093]. GLAM simulations were particularly sensitive to two processes. First, elevated vapour pressure deficit (VPD) consistently reduced yield. The same result was seen in some simulations using both other crop models. Second, GLAM crop duration was longer, and yield greater, when the optimal temperature for the rate of development was exceeded. Yield increases were also seen in one other crop model. Overall, the models differed in their response to super-optimal temperatures, and that difference increased with mean temperature; percentage changes in yield between current and future climates were as diverse as -50% and over +30% for the same input data. The first process has been observed in many crop experiments, whilst the second has not. Thus, we conclude that there is a need for: (i) more process-based modelling studies of the impact of VPD on assimilation, and (ii) more experimental studies at super-optimal temperatures. Using the GLAM results, central values and uncertainty ranges were projected for mean 2071-2100 crop yields in India. In the fixed-duration simulations, ensemble mean yields mostly rose by 10-30%. The full ensemble range was greater than this mean change (20-60% over most of India). In the control simulations, yield stimulation by elevated CO2 was more than offset by other processes-principally accelerated crop development rates at elevated, but sub-optimal, mean temperatures. Hence, the quantification of uncertainty can facilitate relatively robust indications of the likely sign of crop yield changes in future climates. (C) 2007 Elsevier B.V. All rights reserved.

Sensitivity of tropospheric forecasts to stratospheric initial conditions

A number of recent papers in the atmospheric science literature have suggested that a dynamical link exists between the stratosphere and troposphere. Numerical modelling studies have shown that the troposphere has a time-mean response to changes to the stratospheric climatological state. In this study the response of the troposphere to an imposed transient stratospheric change is examined. The study uses a high horizontal and vertical resolution numerical weather-prediction model. Experiments compare the tropospheric forecasts of two medium-range forecast ensembles which have identical tropospheric initial conditions and different stratospheric initial conditions. In three case studies described here, stratospheric initial conditions have a statistically significant impact on the tropospheric flow. The mechanism for this change involves, in its most basic step, a change to tropospheric synoptic-scale systems. A consistent change to the tropospheric synoptic-scale systems occurs in response to the stratospheric initial conditions. The aggregated impact of changes to individual synoptic systems maps strongly onto the structure of the Arctic Oscillation, particularly over the North Atlantic storm track. The relationship between the stratosphere and troposphere, while apparent in Arctic Oscillation diagnostics, does not occur on coherent, hemispheric scales.

Simulating SOC changes in 11 land use change chronosequences from the Brazilian Amazon with RothC and Century models

Land use and land cover changes in the Brazilian Amazon have major implications for regional and global carbon (C) cycling. Cattle pasture represents the largest single use (about 70%) of this once-forested land in most of the region. The main objective of this study was to evaluate the accuracy of the RothC and Century models at estimating soil organic C (SOC) changes under forest-to-pasture conditions in the Brazilian Amazon. We used data from 11 site-specific 'forest to pasture' chronosequences with the Century Ecosystem Model (Century 4.0) and the Rothamsted C Model (RothC 26.3). The models predicted that forest clearance and conversion to well managed pasture would cause an initial decline in soil C stocks (0-20 cm depth), followed in the majority of cases by a slow rise to levels exceeding those under native forest. One exception to this pattern was a chronosequence in Suia-Missu, which is under degraded pasture. In three other chronosequences the recovery of soil C under pasture appeared to be only to about the same level as under the previous forest. Statistical tests were applied to determine levels of agreement between simulated SOC stocks and observed stocks for all the sites within the 11 chronosequences. The models also provided reasonable estimates (coefficient of correlation = 0.8) of the microbial biomass C in the 0-10 cm soil layer for three chronosequences, when compared with available measured data. The Century model adequately predicted the magnitude and the overall trend in delta C-13 for the six chronosequences where measured 813 C data were available. This study gave independent tests of model performance, as no adjustments were made to the models to generate outputs. Our results suggest that modelling techniques can be successfully used for monitoring soil C stocks and changes, allowing both the identification of current patterns in the soil and the projection of future conditions. Results were used and discussed not only to evaluate soil C dynamics but also to indicate soil C sequestration opportunities for the Brazilian Amazon region. Moreover, modelling studies in these 'forest to pasture' systems have important applications, for example, the calculation of CO, emissions from land use change in national greenhouse gas inventories. (0 2007 Elsevier B.V. All rights reserved.

Use of a crop model ensemble to quantify CO2 stimulation of water-stressed and well-watered crops

Increased atmospheric concentrations of carbon dioxide (CO2) will benefit the yield of most crops. Two free air CO2 enrichment (FACE) meta-analyses have shown increases in yield of between 0 and 73% for C3 crops. Despite this large range, few crop modelling studies quantify the uncertainty inherent in the parameterisation of crop growth and development. We present a novel perturbed-parameter method of crop model simulation, which uses some constraints from observations, that does this. The model used is the groundnut (i.e. peanut; Arachis hypogaea L.) version of the general large-area model for annual crops (GLAM). The conclusions are of relevance to C3 crops in general. The increases in yield simulated by GLAM for doubled CO2 were between 16 and 62%. The difference in mean percentage increase between well-watered and water-stressed simulations was 6.8. These results were compared to FACE and controlled environment studies, and to sensitivity tests on two other crop models of differing levels of complexity: CROPGRO, and the groundnut model of Hammer et al. [Hammer, G.L., Sinclair, T.R., Boote, K.J., Wright, G.C., Meinke, H., Bell, M.J., 1995. A peanut simulation model. I. Model development and testing. Agron. J. 87, 1085-1093]. The relationship between CO2 and water stress in the experiments and in the models was examined. From a physiological perspective, water-stressed crops are expected to show greater CO2 stimulation than well-watered crops. This expectation has been cited in literature. However, this result is not seen consistently in either the FACE studies or in the crop models. In contrast, leaf-level models of assimilation do consistently show this result. An analysis of the evidence from these models and from the data suggests that scale (canopy versus leaf), model calibration, and model complexity are factors in determining the sign and magnitude of the interaction between CO2 and water stress. We conclude from our study that the statement that 'water-stressed crops show greater CO2 stimulation than well-watered crops' cannot be held to be universally true. We also conclude, preliminarily, that the relationship between water stress and assimilation varies with scale. Accordingly, we provide some suggestions on how studies of a similar nature, using crop models of a range of complexity, could contribute further to understanding the roles of model calibration, model complexity and scale. (C) 2008 Elsevier B.V. All rights reserved.