Highly accurate quantum chemistry : spin-orbit splittings via multireference coupled-cluster methods and applications in heavy-atom main-group chemistry

Diese Dissertation demonstriert und verbessert die Vorhersagekraft der Coupled-Cluster-Theorie im Hinblick auf die hochgenaue Berechnung von Moleküleigenschaften. Die Demonstration erfolgt mittels Extrapolations- und Additivitätstechniken in der Single-Referenz-Coupled-Cluster-Theorie, mit deren Hilfe die Existenz und Struktur von bisher unbekannten Molekülen mit schweren Hauptgruppenelementen vorhergesagt wird. Vor allem am Beispiel von cyclischem SiS_2, einem dreiatomigen Molekül mit 16 Valenzelektronen, wird deutlich, dass die Vorhersagekraft der Theorie sich heutzutage auf Augenhöhe mit dem Experiment befindet: Theoretische Überlegungen initiierten eine experimentelle Suche nach diesem Molekül, was schließlich zu dessen Detektion und Charakterisierung mittels Rotationsspektroskopie führte. Die Vorhersagekraft der Coupled-Cluster-Theorie wird verbessert, indem eine Multireferenz-Coupled-Cluster-Methode für die Berechnung von Spin-Bahn-Aufspaltungen erster Ordnung in 2^Pi-Zuständen entwickelt wird. Der Fokus hierbei liegt auf Mukherjee's Variante der Multireferenz-Coupled-Cluster-Theorie, aber prinzipiell ist das vorgeschlagene Berechnungsschema auf alle Varianten anwendbar. Die erwünschte Genauigkeit beträgt 10 cm^-1. Sie wird mit der neuen Methode erreicht, wenn Ein- und Zweielektroneneffekte und bei schweren Elementen auch skalarrelativistische Effekte berücksichtigt werden. Die Methode eignet sich daher in Kombination mit Coupled-Cluster-basierten Extrapolations-und Additivitätsschemata dafür, hochgenaue thermochemische Daten zu berechnen.

Aerosol-cloud interactions studied with a chemistry-climate model

This study aims at a comprehensive understanding of the effects of aerosol-cloud interactions and their effects on cloud properties and climate using the chemistry-climate model EMAC. In this study, CCN activation is regarded as the dominant driver in aerosol-cloud feedback loops in warm clouds. The CCN activation is calculated prognostically using two different cloud droplet nucleation parameterizations, the STN and HYB CDN schemes. Both CDN schemes account for size and chemistry effects on the droplet formation based on the same aerosol properties. The calculation of the solute effect (hygroscopicity) is the main difference between the CDN schemes. The kappa-method is for the first time incorporated into Abdul-Razzak and Ghan activation scheme (ARG) to calculate hygroscopicity and critical supersaturation of aerosols (HYB), and the performance of the modied scheme is compared with the osmotic coefficient model (STN), which is the standard in the ARG scheme. Reference simulations (REF) with the prescribed cloud droplet number concentration have also been carried out in order to understand the effects of aerosol-cloud feedbacks. In addition, since the calculated cloud coverage is an important determinant of cloud radiative effects and is influencing the nucleation process two cloud cover parameterizations (i.e., a relative humidity threshold; RH-CLC and a statistical cloud cover scheme; ST-CLC) have been examined together with the CDN schemes, and their effects on the simulated cloud properties and relevant climate parameters have been investigated. The distinct cloud droplet spectra show strong sensitivity to aerosol composition effects on cloud droplet formation in all particle sizes, especially for the Aitken mode. As Aitken particles are the major component of the total aerosol number concentration and CCN, and are most sensitive to aerosol chemical composition effect (solute effect) on droplet formation, the activation of Aitken particles strongly contribute to total cloud droplet formation and thereby providing different cloud droplet spectra. These different spectra influence cloud structure, cloud properties, and climate, and show regionally varying sensitivity to meteorological and geographical condition as well as the spatiotemporal aerosol properties (i.e., particle size, number, and composition). The changes responding to different CDN schemes are more pronounced at lower altitudes than higher altitudes. Among regions, the subarctic regions show the strongest changes, as the lower surface temperature amplifies the effects of the activated aerosols; in contrast, the Sahara desert, where is an extremely dry area, is less influenced by changes in CCN number concentration. The aerosol-cloud coupling effects have been examined by comparing the prognostic CDN simulations (STN, HYB) with the reference simulation (REF). Most pronounced effects are found in the cloud droplet number concentration, cloud water distribution, and cloud radiative effect. The aerosol-cloud coupling generally increases cloud droplet number concentration; this decreases the efficiency of the formation of weak stratiform precipitation, and increases the cloud water loading. These large-scale changes lead to larger cloud cover and longer cloud lifetime, and contribute to high optical thickness and strong cloud cooling effects. This cools the Earth's surface, increases atmospheric stability, and reduces convective activity. These changes corresponding to aerosol-cloud feedbacks are also differently simulated depending on the cloud cover scheme. The ST-CLC scheme is more sensitive to aerosol-cloud coupling, since this scheme uses a tighter linkage of local dynamics and cloud water distributions in cloud formation process than the RH-CLC scheme. For the calculated total cloud cover, the RH-CLC scheme simulates relatively similar pattern to observations than the ST-CLC scheme does, but the overall properties (e.g., total cloud cover, cloud water content) in the RH simulations are overestimated, particularly over ocean. This is mainly originated from the difference in simulated skewness in each scheme: the RH simulations calculate negatively skewed distributions of cloud cover and relevant cloud water, which is similar to that of the observations, while the ST simulations yield positively skewed distributions resulting in lower mean values than the RH-CLC scheme does. The underestimation of total cloud cover over ocean, particularly over the intertropical convergence zone (ITCZ) relates to systematic defficiency of the prognostic calculation of skewness in the current set-ups of the ST-CLC scheme.rnOverall, the current EMAC model set-ups perform better over continents for all combinations of the cloud droplet nucleation and cloud cover schemes. To consider aerosol-cloud feedbacks, the HYB scheme is a better method for predicting cloud and climate parameters for both cloud cover schemes than the STN scheme. The RH-CLC scheme offers a better simulation of total cloud cover and the relevant parameters with the HYB scheme and single-moment microphysics (REF) than the ST-CLC does, but is not very sensitive to aerosol-cloud interactions.

The adsorption of biomolecules to multi-walled carbon nanotubes is influenced by both pulmonary surfactant lipids and surface chemistry

Background During production and processing of multi-walled carbon nanotubes (MWCNTs), they may be inhaled and may enter the pulmonary circulation. It is essential that interactions with involved body fluids like the pulmonary surfactant, the blood and others are investigated, particularly as these interactions could lead to coating of the tubes and may affect their chemical and physical characteristics. The aim of this study was to characterize the possible coatings of different functionalized MWCNTs in a cell free environment. Results To simulate the first contact in the lung, the tubes were coated with pulmonary surfactant and subsequently bound lipids were characterized. The further coating in the blood circulation was simulated by incubating the tubes in blood plasma. MWCNTs were amino (NH2)- and carboxyl (-COOH)-modified, in order to investigate the influence on the bound lipid and protein patterns. It was shown that surfactant lipids bind unspecifically to different functionalized MWCNTs, in contrast to the blood plasma proteins which showed characteristic binding patterns. Patterns of bound surfactant lipids were altered after a subsequent incubation in blood plasma. In addition, it was found that bound plasma protein patterns were altered when MWCNTs were previously coated with pulmonary surfactant. Conclusions A pulmonary surfactant coating and the functionalization of MWCNTs have both the potential to alter the MWCNTs blood plasma protein coating and to determine their properties and behaviour in biological systems.

Channels and transporters. Mini-symposium of the Division of Medicinal Chemistry (DMC) of the Swiss Chemical Society (SCS) at the Department of Chemistry, University of Basel, May 27, 2010

During a half-day symposium, the topic 'Channels and Transporters' was covered with five lectures, including a presentation on 'Introduction and Basics of Channels and Transporters' by Beat Ernst, lectures on structure, function and physiology of channels and transporters ('The Structural Basis for Ion Conduction and Gating in Pentameric Ligand-Gated Ion Channels' by Raimund Dutzler and 'Uptake and Efflux Transporters for Endogenous Substances and for Drugs' by Dietrich Keppler), and a case study lecture on 'Avosentan' by Werner Neidhart. The program was completed by Matthias Hediger who introduced to the audience the National Center of Competence in Research (NCCR)-TransCure in his lecture entitled 'From Transport Physiology to Identification of Therapeutic Targets'.

Thermodynamics of Forming Water Clusters at Various Temperatures and Pressures by Gaussian-2, Gaussian-3, Complete Basis Set-QB3, and Complete Basis Set-APNO Model Chemistries; Implications for Atmospheric Chemistry

The Gaussian-2, Gaussian-3, complete basis set- (CBS-) QB3, and CBS-APNO methods have been used to calculate ΔH° and ΔG° values for neutral clusters of water, (H2O)n, where n = 2−6. The structures are similar to those determined from experiment and from previous high-level calculations. The thermodynamic calculations by the G2, G3, and CBS-APNO methods compare well against the estimated MP2(CBS) limit. The cyclic pentamer and hexamer structures release the most heat per hydrogen bond formed of any of the clusters. While the cage and prism forms of the hexamer are the lowest energy structures at very low temperatures, as temperature is increased the cyclic structure is favored. The free energies of cluster formation at different temperatures reveal interesting insights, the most striking being that the cyclic trimer, cyclic tetramer, and cyclic pentamer, like the dimer, should be detectable in the lower troposphere. We predict water dimer concentrations of 9 × 1014 molecules/cm3, water trimer concentrations of 2.6 × 1012 molecules/cm3, tetramer concentrations of approximately 5.8 × 1011 molecules/cm3, and pentamer concentrations of approximately 3.5 × 1010 molecules/cm3 in saturated air at 298 K. These results have important implications for understanding the gas-phase chemistry of the lower troposphere.

Pople's Gaussian-3 model chemistry applied to an investigation of (H2O)8 water clusters

The Gaussian-3 method developed by Pople and coworkers has been used to calculate the free energy of neutral octamer clusters of water, (H2O)8. The most energetically stable structures are in excellent agreement with those determined from experiment and those predicted from previous high-level calculations. Cubic structures are favored over noncubic structures over all temperature ranges studied. The D2d cubic structure is the lowest free energy structure and dominates the potential energy and free energy hypersurfaces from 0 K to 298 K.

CCSD(T), W1, and other model chemistry predictions for gas-phase deprotonation reactions

A series of CCSD(T) single-point calculations on MP4(SDQ) geometries and the W1 model chemistry method have been used to calculate ΔH° and ΔG° values for the deprotonation of 17 gas-phase reactions where the experimental values have reported accuracies within 1 kcal/mol. These values have been compared with previous calculations using the G3 and CBS model chemistries and two DFT methods. The most accurate CCSD(T) method uses the aug-cc-pVQZ basis set. Extrapolation of the aug-cc-pVTZ and aug-cc-pVQZ results yields the most accurate agreement with experiment, with a standard deviation of 0.58 kcal/mol for ΔG° and 0.70 kcal/mol for ΔH°. Standard deviations from experiment for ΔG° and ΔH° for the W1 method are 0.95 and 0.83 kcal/mol, respectively. The G3 and CBS-APNO results are competitive with W1 and are much less expensive. Any of the model chemistry methods or the CCSD(T)/aug-cc-pVQZ method can serve as a valuable check on the accuracy of experimental data reported in the National Institutes of Standards and Technology (NIST) database.

Experimental and Theoretical Study of the OH Vibrational Spectra and Overtone Chemistry of Gas-Phase Vinylacetic Acid

In this study we present the gas-phase vibrational spectrum of vinylacetic acid with a focus on the ν = 1−5 vibrational states of the OH stretching transitions. Cross sections for ν = 1, 2, 4 and 5 of the OH stretching vibrational transitions are derived on the basis of the vapor pressure data obtained for vinylacetic acid. Ab initio calculations are used to assist in the band assignments of the experimental spectra, and to determine the threshold for the decarboxylation of vinylacetic acid. When compared to the theoretical energy barrier to decarboxylation, it is found that the νOH = 4 transition with thermal excitation of low frequency modes or rotational motion and νOH = 5 transitions have sufficient energy for the reaction to proceed following overtone excitation.

Comparison of Model Chemistry and Density Functional Theory Thermochemical Predictions with Experiment for Formation of Ionic Clusters of the Ammonium Cation Complexed with Water and Ammonia; Atmospheric Implications

The G2, G3, CBS-QB3, and CBS-APNO model chemistry methods and the B3LYP, B3P86, mPW1PW, and PBE1PBE density functional theory (DFT) methods have been used to calculate ΔH° and ΔG° values for ionic clusters of the ammonium ion complexed with water and ammonia. Results for the clusters NH4+(NH3)n and NH4+(H2O)n, where n = 1−4, are reported in this paper and compared against experimental values. Agreement with the experimental values for ΔH° and ΔG° for formation of NH4+(NH3)n clusters is excellent. Comparison between experiment and theory for formation of the NH4+(H2O)n clusters is quite good considering the uncertainty in the experimental values. The four DFT methods yield excellent agreement with experiment and the model chemistry methods when the aug-cc-pVTZ basis set is used for energetic calculations and the 6-31G* basis set is used for geometries and frequencies. On the basis of these results, we predict that all ions in the lower troposphere will be saturated with at least one complete first hydration shell of water molecules.

Fine-tuning of substrate architecture and surface chemistry promotes muscle tissue development

Tissue engineering has been increasingly brought to the scientific spotlight in response to the tremendous demand for regeneration, restoration or substitution of skeletal or cardiac muscle after traumatic injury, tumour ablation or myocardial infarction. In vitro generation of a highly organized and contractile muscle tissue, however, crucially depends on an appropriate design of the cell culture substrate. The present work evaluated the impact of substrate properties, in particular morphology, chemical surface composition and mechanical properties, on muscle cell fate. To this end, aligned and randomly oriented micron (3.3±0.8 μm) or nano (237±98 nm) scaled fibrous poly(ε-caprolactone) non-wovens were processed by electrospinning. A nanometer-thick oxygen functional hydrocarbon coating was deposited by a radio frequency plasma process. C2C12 muscle cells were grown on pure and as-functionalized substrates and analysed for viability, proliferation, spatial orientation, differentiation and contractility. Cell orientation has been shown to depend strongly on substrate architecture, being most pronounced on micron-scaled parallel-oriented fibres. Oxygen functional hydrocarbons, representing stable, non-immunogenic surface groups, were identified as strong triggers for myotube differentiation. Accordingly, the highest myotube density (28±15% of total substrate area), sarcomeric striation and contractility were found on plasma-coated substrates. The current study highlights the manifold material characteristics to be addressed during the substrate design process and provides insight into processes to improve bio-interfaces.