Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections

For (H2O)n where n = 1–10, we used a scheme combining molecular dynamics sampling with high level ab initio calculations to locate the global and many low lying local minima for each cluster. For each isomer, we extrapolated the RI-MP2 energies to their complete basis set limit, included a CCSD(T) correction using a smaller basis set and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled and unscaled harmonic vibrational frequencies. The vibrational scaling factors were determined specifically for water clusters by comparing harmonic frequencies with VPT2 fundamental frequencies. We find the CCSD(T) correction to the RI-MP2 binding energy to be small (<1%) but still important in determining accurate conformational energies. Anharmonic corrections are found to be non-negligble; they do not alter the energetic ordering of isomers, but they do lower the free energies of formation of the water clusters by as much as 4 kcal/mol at 298.15 K.

Use of the Supermolecule Approach To Model the Syn and Anti Conformations of Solvated Cyclic 3‘,5‘-Adenosine Monophosphate

The supermolecule approach has been used to model the hydration of cyclic 3‘,5‘-adenosine monophosphate, cAMP. Model building combined with PM3 optimizations predict that the anti conformer of cAMP is capable of hydrogen bonding to an additional solvent water molecule compared to the syn conformer. The addition of one water to the syn superstructure with concurrent rotation of the base about the glycosyl bond to form the anti superstructure leads to an additional enthalpy of stabilization of approximately −6 kcal/mol at the PM3 level. This specific solute−solvent interaction is an example of a large solvent effect, as the method predicts that cAMP has a conformational preference for the anti isomer in solution. This conformational preference results from a change in the number of specific solute−solvent interactions in this system. This prediction could be tested by NMR techniques. The number of waters predicted to be in the first hydration sphere around cAMP is in agreement with the results of hydration studies of nucleotides in DNA. In addition, the detailed picture of solvation about this cyclic nucleotide is in agreement with infrared experimental results.

The Role of Anharmonicity in Hydrogen-Bonded Systems: The Case of Water Clusters

The nature of vibrational anharmonicity has been examined for the case of small water clusters using second-order vibrational perturbation theory (VPT2) applied on second-order Møller–Plesset perturbation theory (MP2) potential energy surfaces. Using a training set of 16 water clusters (H2O)n=2–6,8,9 with a total of 723 vibrational modes, we determined scaling factors that map the harmonic frequencies onto anharmonic ones. The intermolecular modes were found to be substantially more anharmonic than intramolecular bending and stretching modes. Due to the varying levels of anharmonicity of the intermolecular and intramolecular modes, different frequency scaling factors for each region were necessary to achieve the highest accuracy. Furthermore, new scaling factors for zero-point vibrational energies (ZPVE) and vibrational corrections to the enthalpy (ΔHvib) and the entropy (Svib) have been determined. All the scaling factors reported in this study are different from previous works in that they are intended for hydrogen-bonded systems, while others were built using experimental frequencies of covalently bonded systems. An application of our scaling factors to the vibrational frequencies of water dimer and thermodynamic functions of 11 larger water clusters highlights the importance of anharmonic effects in hydrogen-bonded systems.

Comparison of CBS-QB3, CBS-APNO, G2, and G3 thermochemical predictions with experiment for formation of ionic clusters of hydronium and hydroxide ions complexed with water

The GAUSSIAN 2, GAUSSIAN 3, complete basis set-QB3, and complete basis set-APNO methods have been used to calculate ΔH∘ and ΔG∘ values for ionic clusters of hydronium and hydroxide ions complexed with water. Results for the clusters H3O+(H2O)n andOH−(H2O)n, where n=1–4 are reported in this paper, and compared against experimental values contained in the National Institutes of Standards and Technology (NIST) database. Agreement with experiment is excellent for the three ab initio methods for formation of these clusters. The high accuracy of these methods makes them reliable for calculating energetics for the formation of ionic clusters containing water. In addition this allows them to serve as a valuable check on the accuracy of experimental data reported in the NIST database, and makes them useful tools for addressing unresolved issues in atmospheric chemistry.

Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes

A series of oligodeoxyribonucleotides and oligoribonucleotides containing single and multiple tricyclo(tc)-nucleosides in various arrangements were prepared and the thermal and thermodynamic transition profiles of duplexes with complementary DNA and RNA evaluated. Tc-residues aligned in a non-continuous fashion in an RNA strand significantly decrease affinity to complementary RNA and DNA, mostly as a consequence of a loss of pairing enthalpy DeltaH. Arranging the tc-residues in a continuous fashion rescues T(m) and leads to higher DNA and RNA affinity. Substitution of oligodeoxyribonucleotides in the same way causes much less differences in T(m) when paired to complementary DNA and leads to substantial increases in T(m) when paired to complementary RNA. CD-spectroscopic investigations in combination with molecular dynamics simulations of duplexes with single modifications show that tc-residues in the RNA backbone distinctly influence the conformation of the neighboring nucleotides forcing them into higher energy conformations, while tc-residues in the DNA backbone seem to have negligible influence on the nearest neighbor conformations. These results rationalize the observed affinity differences and are of relevance for the design of tc-DNA containing oligonucleotides for applications in antisense or RNAi therapy.

The Repairing of Misconceptions through the Use of Inquiry-Based Activities

Misconceptions exist in all fields of learning and develop through a person’s preconception of how the world works. Students with misconceptions in chemical engineering are not capable of correctly transferring knowledge to a new situation and will likely arrive at an incorrect solution. The purpose of this thesis was to repair misconceptions in thermodynamics by using inquiry-based activities. Inquiry-based learning is a method of teaching that involves hands-on learning and self-discovery. Previous work has shown inquiry-based methods result in better conceptual understanding by students relative to traditional lectures. The thermodynamics activities were designed to guide students towards the correct conceptual understanding through observing a preconception fail to hold up through an experiment or simulation. The developed activities focus on the following topics in thermodynamics: “internal energy versus enthalpy”, “equilibrium versus steady state”, and “entropy”. For each topic, two activities were designed to clarify the concept and assure it was properly grasped. Each activity was coupled with an instructions packet containing experimental procedure as well as pre- and post-analysis questions, which were used to analyze the effect of the activities on the students’ responses. Concept inventories were used to monitor students’ conceptual understanding at the beginning and end of the semester. The results did not show a statistically significant increase in the overall concept inventory scores for students who performed the activities compared to traditional learning. There was a statistically significant increase in concept area scores for “internal energy versus enthalpy” and “equilibrium versus steady state”. Although there was not a significant increase in concept inventory scores for “entropy”, written analyses showed most students’ misconceptions were repaired. Students transferred knowledge effectively and retained most of the information in the concept areas of “internal energy versus enthalpy” and “equilibrium versus steady state”.

LakeMIP Kivu: evaluating the representation of a large, deep tropical lake by a set of one-dimensional lake models

The African great lakes are of utmost importance for the local economy (fishing), as well as being essential to the survival of the local people. During the past decades, these lakes experienced fast changes in ecosystem structure and functioning, and their future evolution is a major concern. In this study, for the first time a set of one-dimensional lake models are evaluated for Lake Kivu (2.28°S; 28.98°E), East Africa. The unique limnology of this meromictic lake, with the importance of salinity and subsurface springs in a tropical high-altitude climate, presents a worthy challenge to the seven models involved in the Lake Model Intercomparison Project (LakeMIP). Meteorological observations from two automatic weather stations are used to drive the models, whereas a unique dataset, containing over 150 temperature profiles recorded since 2002, is used to assess the model’s performance. Simulations are performed over the freshwater layer only (60 m) and over the average lake depth (240 m), since salinity increases with depth below 60 m in Lake Kivu and some lake models do not account for the influence of salinity upon lake stratification. All models are able to reproduce the mixing seasonality in Lake Kivu, as well as the magnitude and seasonal cycle of the lake enthalpy change. Differences between the models can be ascribed to variations in the treatment of the radiative forcing and the computation of the turbulent heat fluxes. Fluctuations in wind velocity and solar radiation explain inter-annual variability of observed water column temperatures. The good agreement between the deep simulations and the observed meromictic stratification also shows that a subset of models is able to account for the salinity- and geothermal-induced effects upon deep-water stratification. Finally, based on the strengths and weaknesses discerned in this study, an informed choice of a one-dimensional lake model for a given research purpose becomes possible.

Adsorption interaction of carrier-free thallium species with gold and quartz surfaces

The adsorption interactions of thallium and its compounds with gold and quartz surfaces were investigated. Carrier-free amounts of thallium were produced in nuclear fusion reactions of alpha particles with thick gold targets. The method chosen for the studies was gas thermochromatography and varying the redox potential of the carrier gases. It was observed that thallium is extremely sensitive to trace amounts of oxygen and water, and can even be oxidized by the hydroxyl groups located on the quartz surface. The experiments on a quartz surface with O2, He, H2 gas in addition with water revealed the formation and deposition of only one thallium species – TlOH. The adsorption enthalpy was determined to be Δ HSiO2ads(TlOH) = −134 ± 5 kJ mol−1. A series of experiments using gold as stationary surface and different carrier gases resulted in the detection of two thallium species – metallic Tl (H2 as carrier gas) and TlOH (O2, O2+H2O and H2+H2O as pure carrier gas or carrier gas mixture) with Δ HAuads(Tl) = −270 ± 10 kJ mol− and Δ HAuads(TlOH) = −146 ± 3 kJ mol−1. These data demonstrate a weak interaction of TlOH with both quartz and gold surfaces. The data represent important information for the design of future experiments with the heavier homologue of Tl in group 13 of the periodic table – element 113 (E113).

Mass spectrometric study of molecular and ionic sublimation of lanthanum triiodide

The molecular and ionic composition of saturated vapor over lanthanum triiodide was studied by Knudsen effusion mass spectrometry. The (LaI3)n molecules (n = 1–3) and the [I(LaI3)n]− ions (n = 0–4) were observed. The partial pressures of the molecules were determined and the enthalpies of sublimation, ΔsH° (298.15 K) in kJ mol−1, in the form of monomers (304 ± 7), dimers (428 ± 25), and trimers (455 ± 50) were obtained by the second and third laws of thermodynamics. The enthalpy of formation, ΔfH° (298.15 K) in kJ mol−1, of the LaI3 (−376 ± 10), La2I6 (−932 ± 25), La3I9 (−1585 ± 50) molecules and the LaI4− (−841 ± 24), La2I7− (−1486 ± 32) ions were determined. The electron work function, φe = 3.5 ± 0.3 eV, for the LaI3 crystal was calculated from the thermochemical cycle.

Energía geotérmica de baja entalpía

El actual aumento de concentraciones de gases de efecto invernadero, el agotamiento y encarecimiento de combustibles fósiles, y el cuidado del ambiente, son los motivos principales por los cuales el uso de las energías a partir de fuentes renovables está incrementando. La energía geotérmica es un tipo de energía potencialmente renovable. La misma presenta varias tipologías, siendo la de baja entalpía la que posee mayor disponibilidad en todo el mundo. Este tipo de energía se puede utilizar para climatizar ambientes, durante todo el año, debido a la estabilidad térmica que la misma brinda. Se ha realizado un análisis del recurso presente en los primeros metros de profundidad de suelo, bajo determinadas condiciones externas y de extracción, y dentro de estas circunstancias se obtuvieron datos de temperatura de suelo, y de aire (tanto arriba como debajo de la tierra), los cuales, luego de ser estudiados, fueron comprobados matemáticamente y pudieron brindar un ábaco que sirve como herramienta para ser utilizado en distintos aprovechamientos utilizando el prototipo elaborado, pudiendo reflejar en la realidad práctica las investigaciones realizadas.

The CMCC Eddy-permitting Global Ocean Physical Reanalysis (C-GLORS v5, 1980-2014), links to NetCDF files

The CMCC Global Ocean Physical Reanalysis System (C-GLORS) is used to simulate the state of the ocean in the last decades. It consists of a variational data assimilation system (OceanVar), capable of assimilating all in-situ observations along with altimetry data, and a forecast step performed by the ocean model NEMO coupled with the LIM2 sea-ice model. KEY STRENGTHS: - Data are available for a large number of ocean parameters - An extensive validation has been conducted and is freely available - The reanalysis is performed at high resolution (1/4 degree) and spans the last 30 years KEY LIMITATIONS: - Quality may be discontinuos and depend on observation coverage - Uncertainty estimates are simply derived through verification skill scores

Late Miocene palaeoflora and palaeoclimate of Lincang (China)

The Miocene Lincang leaf assemblage is used in this paper as proxy data to reconstruct the palaeoclimate of southwestern Yunnan (SW China) and the evolution of monsoon intensity. Three quantitative methods were chosen for this reconstruction, i.e. Leaf Margin Analysis (LMA), Climate Leaf Analysis Multivariate Program (CLAMP), and the Coexistence Approach (CA). These methods, however, yield inconsistent results, particularly for the precipitation, as also shown in European and other East Asian Cenozoic floras. The wide range of the reconstructed climatic parameters includes the Mean Annual Temperature (MAT) of 18.5-24.7 °C and the Mean Annual Precipitation (MAP) of 1213-3711 mm. Compared with the modern Lincang climate (MAT, 17.3 °C; MAP, 1178.7 mm), the Miocene climate is slightly warmer, wetter and has a higher temperature seasonality. A detailed comparison on the palaeoclimatic variables with the coeval Late Miocene Xiaolongtan flora from the eastern part of Yunnan allows us to investigate the development and interactions of both South Asian and East Asian monsoons during the Late Miocene in southwest China, now under strong influence of these monsoon systems. Our results suggest that the monsoon climate has already been established in southwest Yunnan during the Late Miocene. Furthermore, our results support that both Southeast Asian and East Asian monsoons co-occurred in Yunnan during the Late Miocene.

Laser ablation modelling of aluminium, silver and crystalline silicon for applications in photovoltaic technologies

Laser material processing is being extensively used in photovoltaic applications for both the fabrication of thin film modules and the enhancement of the crystalline silicon solar cells. The two temperature model for thermal diffusion was numerically solved in this paper. Laser pulses of 1064, 532 or 248 nm with duration of 35, 26 or 10 ns were considered as the thermal source leading to the material ablation. Considering high irradiance levels (108–109 W cm−2), a total absorption of the energy during the ablation process was assumed in the model. The materials analysed in the simulation were aluminium (Al) and silver (Ag), which are commonly used as metallic electrodes in photovoltaic devices. Moreover, thermal diffusion was also simulated for crystalline silicon (c-Si). A similar trend of temperature as a function of depth and time was found for both metals and c-Si regardless of the employed wavelength. For each material, the ablation depth dependence on laser pulse parameters was determined by means of an ablation criterion. Thus, after the laser pulse, the maximum depth for which the total energy stored in the material is equal to the vaporisation enthalpy was considered as the ablation depth. For all cases, the ablation depth increased with the laser pulse fluence and did not exhibit a clear correlation with the radiation wavelength. Finally, the experimental validation of the simulation results was carried out and the ability of the model with the initial hypothesis of total energy absorption to closely fit experimental results was confirmed.

Effects of high hydrostatic pressure on rheological and termal properties of chickpea Cicer arietinum L. flour slurry and heat-induced paste.

Thermorheological changes in high hydrostatic pressure (HHP)-treated chickpea flour (CF) slurries were studied as a function of pressure level (0.1, 150, 300, 400, and 600 MPa) and slurry concentration (1:5, 1:4, 1:3, and 1:2 flour-to-water ratios). HHP-treated slurries were subsequently analyzed for changes in properties produced by heating, under both isothermal and non-isothermal processes. Elasticity (G′) of pressurized slurry increased with pressure applied and concentration. Conversely, heat-induced CF paste gradually transformed from solid-like behavior to liquid-like behavior as a function of moisture content and pressure level. The G′ and enthalpy of the CF paste decreased with increasing pressure level in proportion with the extent of HHP-induced starch gelatinization. At 25 °C and 15 min, HHP treatment at 450 and 600 MPa was sufficient to complete gelatinization of CF slurry at the lowest concentration (1:5), while more concentrated slurries would require higher pressures and temperature during treatment or longer holding times. Industrial relevance Demand for chickpea gel has increased considerably in the health and food industries because of its many beneficial effects. However, its use is affected by its very difficult handling. Judicious application of high hydrostatic pressure (HHP) at appropriate levels, adopted as a pre-processing instrument in combination with heating processes, is presented as an innovative technology to produce a remarkable decrease in thermo-hardening of heat-induced chickpea flour paste, permitting the development of new chickpea-based products with desirable handling properties and sensory attributes.