Theoretical and experimental studies on the electronic, optical, and structural properties of poly-pyrrole-2-carboxylic acid films

A theoretical approach is used here to explain experimental results obtained from the electrosynthesis of polypyrrole-2-carboxylic acid (PPY-2-COOH) films in nonaqueous medium. An analysis of the Fukui function (reactivity index) indicates that the monomer (pyrrole-2-carboxylic acid, PY-2-COOH), and dimers and trimers are oxidized in the C4 or C5 positions of the heterocyclic ring of the PY-2-COOH structure. After calculating the heat of formation using semiempirical Austin Model 1 post-Hartree-Fock parameterization for dimer species, both C4 and C5 positions adjacent to the aromatic rings of PPY-2-COOH were considered the most susceptible ones to oxidative coupling reactions. The ZINDO-S/CI semiempirical method was used to simulate the electronic transitions typically seen in the UV-VIS-NIR range in monomer and oligomers with different conjugation lengths. The use of an electrochemical quartz crystal microbalance provides sufficient information to propose a polymerization mechanism of PY-2-COOH based on molecular modeling and experimental results.

Studio e sviluppo di un motore a 2 tempi diesel veloce di nuova concezione per applicazioni automobilistiche

The Department of Mechanical and Civil Engineering (DIMeC) of the University of Modena and Reggio Emilia is developing a new type of small capacity HSDI 2-Stroke Diesel engine (called HSD2), featuring a specifically designed combustion system, aimed to reduce weight, size and manufacturing costs, and improving pollutant emissions at partial load. The present work is focused on the analysis of the combustion and the scavenging process, investigated by means of a version of the KIVA-3V code customized by the University of Chalmers and modified by DIMeC. The customization of the KIVA-3V code includes a detailed combustion chemistry approach, coupled with a comprehensive oxidation mechanism for diesel oil surrogate and the modeling of turbulence/chemistry interaction through the PaSR (Partially Stirred Reactor) model. A four stroke automobile Diesel engine featuring a very close bore size is taken as a reference, for both the numerical models calibration and for a comparison with the 2-Stroke engine. Analysis is carried out trough a comparison between HSD2 and FIAT 1300 MultiJet in several operating conditions, at full and partial load. Such a comparison clearly demonstrates the effectiveness of the two stroke concept in terms of emissions reduction and high power density. However, HSD2 is still a virtual engine, and experimental results are needed to assume the reliability of numerical results.

Comparison between 2.5-D and 3-D realistic models for wind field adjustment

[EN]In previous works, many authors have widely used mass consistent models for wind field simulation by the finite element method. On one hand, we have developed a 3-D mass consistent model by using tetrahedral meshes which are simultaneously adapted to complex orography and to terrain roughness length. In addition, we have included a local refinement strategy around several measurement or control points, significant contours, as for example shorelines, or numerical solution singularities. On the other hand, we have developed a 2.5-D model for simulating the wind velocity in a 3-D domain in terms of the terrain elevation, the surface temperature and the meteorological wind, which is consider as an averaged wind on vertical boundaries...

Study of the thermal effects induced by magnetic resonance on endocardial leads: numerical models and experimental validation

Magnetic resonance imaging (MRI) is today precluded to patients bearing active implantable medical devices AIMDs). The great advantages related to this diagnostic modality, together with the increasing number of people benefiting from implantable devices, in particular pacemakers(PM)and carioverter/defibrillators (ICD), is prompting the scientific community the study the possibility to extend MRI also to implanted patients. The MRI induced specific absorption rate (SAR) and the consequent heating of biological tissues is one of the major concerns that makes patients bearing metallic structures contraindicated for MRI scans. To date, both in-vivo and in-vitro studies have demonstrated the potentially dangerous temperature increase caused by the radiofrequency (RF) field generated during MRI procedures in the tissues surrounding thin metallic implants. On the other side, the technical evolution of MRI scanners and of AIMDs together with published data on the lack of adverse events have reopened the interest in this field and suggest that, under given conditions, MRI can be safely performed also in implanted patients. With a better understanding of the hazards of performing MRI scans on implanted patients as well as the development of MRI safe devices, we may soon enter an era where the ability of this imaging modality may be more widely used to assist in the appropriate diagnosis of patients with devices. In this study both experimental measures and numerical analysis were performed. Aim of the study is to systematically investigate the effects of the MRI RF filed on implantable devices and to identify the elements that play a major role in the induced heating. Furthermore, we aimed at developing a realistic numerical model able to simulate the interactions between an RF coil for MRI and biological tissues implanted with a PM, and to predict the induced SAR as a function of the particular path of the PM lead. The methods developed and validated during the PhD program led to the design of an experimental framework for the accurate measure of PM lead heating induced by MRI systems. In addition, numerical models based on Finite-Differences Time-Domain (FDTD) simulations were validated to obtain a general tool for investigating the large number of parameters and factors involved in this complex phenomenon. The results obtained demonstrated that the MRI induced heating on metallic implants is a real risk that represents a contraindication in extending MRI scans also to patient bearing a PM, an ICD, or other thin metallic objects. On the other side, both experimental data and numerical results show that, under particular conditions, MRI procedures might be consider reasonably safe also for an implanted patient. The complexity and the large number of variables involved, make difficult to define a unique set of such conditions: when the benefits of a MRI investigation cannot be obtained using other imaging techniques, the possibility to perform the scan should not be immediately excluded, but some considerations are always needed.

Substructuring approache in state space models for dynamic system parameters identification

In the recent decade, the request for structural health monitoring expertise increased exponentially in the United States. The aging issues that most of the transportation structures are experiencing can put in serious jeopardy the economic system of a region as well as of a country. At the same time, the monitoring of structures is a central topic of discussion in Europe, where the preservation of historical buildings has been addressed over the last four centuries. More recently, various concerns arose about security performance of civil structures after tragic events such the 9/11 or the 2011 Japan earthquake: engineers looks for a design able to resist exceptional loadings due to earthquakes, hurricanes and terrorist attacks. After events of such a kind, the assessment of the remaining life of the structure is at least as important as the initial performance design. Consequently, it appears very clear that the introduction of reliable and accessible damage assessment techniques is crucial for the localization of issues and for a correct and immediate rehabilitation. The System Identification is a branch of the more general Control Theory. In Civil Engineering, this field addresses the techniques needed to find mechanical characteristics as the stiffness or the mass starting from the signals captured by sensors. The objective of the Dynamic Structural Identification (DSI) is to define, starting from experimental measurements, the modal fundamental parameters of a generic structure in order to characterize, via a mathematical model, the dynamic behavior. The knowledge of these parameters is helpful in the Model Updating procedure, that permits to define corrected theoretical models through experimental validation. The main aim of this technique is to minimize the differences between the theoretical model results and in situ measurements of dynamic data. Therefore, the new model becomes a very effective control practice when it comes to rehabilitation of structures or damage assessment. The instrumentation of a whole structure is an unfeasible procedure sometimes because of the high cost involved or, sometimes, because it’s not possible to physically reach each point of the structure. Therefore, numerous scholars have been trying to address this problem. In general two are the main involved methods. Since the limited number of sensors, in a first case, it’s possible to gather time histories only for some locations, then to move the instruments to another location and replay the procedure. Otherwise, if the number of sensors is enough and the structure does not present a complicate geometry, it’s usually sufficient to detect only the principal first modes. This two problems are well presented in the works of Balsamo [1] for the application to a simple system and Jun [2] for the analysis of system with a limited number of sensors. Once the system identification has been carried, it is possible to access the actual system characteristics. A frequent practice is to create an updated FEM model and assess whether the structure fulfills or not the requested functions. Once again the objective of this work is to present a general methodology to analyze big structure using a limited number of instrumentation and at the same time, obtaining the most information about an identified structure without recalling methodologies of difficult interpretation. A general framework of the state space identification procedure via OKID/ERA algorithm is developed and implemented in Matlab. Then, some simple examples are proposed to highlight the principal characteristics and advantage of this methodology. A new algebraic manipulation for a prolific use of substructuring results is developed and implemented.

Parametric Sensitivity Analysis of the Most Recent Computational Models of Rabbit Cardiac Pacemaking

The cellular basis of cardiac pacemaking activity, and specifically the quantitative contributions of particular mechanisms, is still debated. Reliable computational models of sinoatrial nodal (SAN) cells may provide mechanistic insights, but competing models are built from different data sets and with different underlying assumptions. To understand quantitative differences between alternative models, we performed thorough parameter sensitivity analyses of the SAN models of Maltsev & Lakatta (2009) and Severi et al (2012). Model parameters were randomized to generate a population of cell models with different properties, simulations performed with each set of random parameters generated 14 quantitative outputs that characterized cellular activity, and regression methods were used to analyze the population behavior. Clear differences between the two models were observed at every step of the analysis. Specifically: (1) SR Ca2+ pump activity had a greater effect on SAN cell cycle length (CL) in the Maltsev model; (2) conversely, parameters describing the funny current (If) had a greater effect on CL in the Severi model; (3) changes in rapid delayed rectifier conductance (GKr) had opposite effects on action potential amplitude in the two models; (4) within the population, a greater percentage of model cells failed to exhibit action potentials in the Maltsev model (27%) compared with the Severi model (7%), implying greater robustness in the latter; (5) confirming this initial impression, bifurcation analyses indicated that smaller relative changes in GKr or Na+-K+ pump activity led to failed action potentials in the Maltsev model. Overall, the results suggest experimental tests that can distinguish between models and alternative hypotheses, and the analysis offers strategies for developing anti-arrhythmic pharmaceuticals by predicting their effect on the pacemaking activity.

Micro-FEM models based on micro-CT reconstructions for the in vitro characterization of the elastic properties of trabecular bone tissue.

This master’s thesis describes the research done at the Medical Technology Laboratory (LTM) of the Rizzoli Orthopedic Institute (IOR, Bologna, Italy), which focused on the characterization of the elastic properties of the trabecular bone tissue, starting from october 2012 to present. The approach uses computed microtomography to characterize the architecture of trabecular bone specimens. With the information obtained from the scanner, specimen-specific models of trabecular bone are generated for the solution with the Finite Element Method (FEM). Along with the FEM modelling, mechanical tests are performed over the same reconstructed bone portions. From the linear-elastic stage of mechanical tests presented by experimental results, it is possible to estimate the mechanical properties of the trabecular bone tissue. After a brief introduction on the biomechanics of the trabecular bone (chapter 1) and on the characterization of the mechanics of its tissue using FEM models (chapter 2), the reliability analysis of an experimental procedure is explained (chapter 3), based on the high-scalable numerical solver ParFE. In chapter 4, the sensitivity analyses on two different parameters for micro-FEM model’s reconstruction are presented. Once the reliability of the modeling strategy has been shown, a recent layout for experimental test, developed in LTM, is presented (chapter 5). Moreover, the results of the application of the new layout are discussed, with a stress on the difficulties connected to it and observed during the tests. Finally, a prototype experimental layout for the measure of deformations in trabecular bone specimens is presented (chapter 6). This procedure is based on the Digital Image Correlation method and is currently under development in LTM.

Biomolecular studies in Alzheimer’s Disease models: investigations in vitro and in vivo

The Alzheimer’s disease (AD), the most prevalent form of age-related dementia, is a multifactorial and heterogeneous neurodegenerative disease. The molecular mechanisms underlying the pathogenesis of AD are yet largely unknown. However, the etiopathogenesis of AD likely resides in the interaction between genetic and environmental risk factors. Among the different factors that contribute to the pathogenesis of AD, amyloid-beta peptides and the genetic risk factor apoE4 are prominent on the basis of genetic evidence and experimental data. ApoE4 transgenic mice have deficits in spatial learning and memory associated with inflammation and brain atrophy. Evidences suggest that apoE4 is implicated in amyloid-beta accumulation, imbalance of cellular antioxidant system and in apoptotic phenomena. The mechanisms by which apoE4 interacts with other AD risk factors leading to an increased susceptibility to the dementia are still unknown. The aim of this research was to provide new insights into molecular mechanisms of AD neurodegeneration, investigating the effect of amyloid-beta peptides and apoE4 genotype on the modulation of genes and proteins differently involved in cellular processes related to aging and oxidative balance such as PIN1, SIRT1, PSEN1, BDNF, TRX1 and GRX1. In particular, we used human neuroblastoma cells exposed to amyloid-beta or apoE3 and apoE4 proteins at different time-points, and selected brain regions of human apoE3 and apoE4 targeted replacement mice, as in vitro and in vivo models, respectively. All genes and proteins studied in the present investigation are modulated by amyloid-beta and apoE4 in different ways, suggesting their involvement in the neurodegenerative mechanisms underlying the AD. Finally, these proteins might represent novel potential diagnostic and therapeutic targets in AD.

Measurement of the elastic electron-proton cross section and separation of the electric and magnetic form factor in the Q 2 range from 0.004 to 1 (GeV/c) 2

The electromagnetic form factors of the proton are fundamental quantities sensitive to the distribution of charge and magnetization inside the proton. Precise knowledge of the form factors, in particular of the charge and magnetization radii provide strong tests for theory in the non-perturbative regime of QCD. However, the existing data at Q^2 below 1 (GeV/c)^2 are not precise enough for a hard test of theoretical predictions.rnrnFor a more precise determination of the form factors, within this work more than 1400 cross sections of the reaction H(e,e′)p were measured at the Mainz Microtron MAMI using the 3-spectrometer-facility of the A1-collaboration. The data were taken in three periods in the years 2006 and 2007 using beam energies of 180, 315, 450, 585, 720 and 855 MeV. They cover the Q^2 region from 0.004 to 1 (GeV/c)^2 with counting rate uncertainties below 0.2% for most of the data points. The relative luminosity of the measurements was determined using one of the spectrometers as a luminosity monitor. The overlapping acceptances of the measurements maximize the internal redundancy of the data and allow, together with several additions to the standard experimental setup, for tight control of systematic uncertainties.rnTo account for the radiative processes, an event generator was developed and implemented in the simulation package of the analysis software which works without peaking approximation by explicitly calculating the Bethe-Heitler and Born Feynman diagrams for each event.rnTo separate the form factors and to determine the radii, the data were analyzed by fitting a wide selection of form factor models directly to the measured cross sections. These fits also determined the absolute normalization of the different data subsets. The validity of this method was tested with extensive simulations. The results were compared to an extraction via the standard Rosenbluth technique.rnrnThe dip structure in G_E that was seen in the analysis of the previous world data shows up in a modified form. When compared to the standard-dipole form factor as a smooth curve, the extracted G_E exhibits a strong change of the slope around 0.1 (GeV/c)^2, and in the magnetic form factor a dip around 0.2 (GeV/c)^2 is found. This may be taken as indications for a pion cloud. For higher Q^2, the fits yield larger values for G_M than previous measurements, in agreement with form factor ratios from recent precise polarized measurements in the Q2 region up to 0.6 (GeV/c)^2.rnrnThe charge and magnetic rms radii are determined as rn⟨r_e⟩=0.879 ± 0.005(stat.) ± 0.004(syst.) ± 0.002(model) ± 0.004(group) fm,rn⟨r_m⟩=0.777 ± 0.013(stat.) ± 0.009(syst.) ± 0.005(model) ± 0.002(group) fm.rnThis charge radius is significantly larger than theoretical predictions and than the radius of the standard dipole. However, it is in agreement with earlier results measured at the Mainz linear accelerator and with determinations from Hydrogen Lamb shift measurements. The extracted magnetic radius is smaller than previous determinations and than the standard-dipole value.

Evolution of the structural and fracture design of the ISS payloads due to the new launchers, specifically applied to Biolab IEC-2 projects

The relatively young discipline of astronautics represents one of the scientifically most fascinating and technologically advanced achievements of our time. The human exploration in space does not offer only extraordinary research possibilities but also demands high requirements from man and technology. The space environment provides a lot of attractive experimental tools towards the understanding of fundamental mechanism in natural sciences. It has been shown that especially reduced gravity and elevated radiation, two distinctive factors in space, influence the behavior of biological systems significantly. For this reason one of the key objectives on board of an earth orbiting laboratory is the research in the field of life sciences, covering the broad range from botany, human physiology and crew health up to biotechnology. The Columbus Module is the only European low gravity platform that allows researchers to perform ambitious experiments in a continuous time frame up to several months. Biolab is part of the initial outfitting of the Columbus Laboratory; it is a multi-user facility supporting research in the field of biology, e.g. effect of microgravity and space radiation on cell cultures, micro-organisms, small plants and small invertebrates. The Biolab IEC are projects designed to work in the automatic part of Biolab. In this moment in the TO-53 department of Airbus Defence & Space (formerly Astrium) there are two experiments that are in phase C/D of the development and they are the subject of this thesis: CELLRAD and CYTOSKELETON. They will be launched in soft configuration, that means packed inside a block of foam that has the task to reduce the launch loads on the payload. Until 10 years ago the payloads which were launched in soft configuration were supposed to be structural safe by themselves and a specific structural analysis could be waived on them; with the opening of the launchers market to private companies (that are not under the direct control of the international space agencies), the requirements on the verifications of payloads are changed and they have become much more conservative. In 2012 a new random environment has been introduced due to the new Space-X launch specification that results to be particularly challenging for the soft launched payloads. The last ESA specification requires to perform structural analysis on the payload for combined loads (random vibration, quasi-steady acceleration and pressure). The aim of this thesis is to create FEM models able to reproduce the launch configuration and to verify that all the margins of safety are positive and to show how they change because of the new Space-X random environment. In case the results are negative, improved design solution are implemented. Based on the FEM result a study of the joins has been carried out and, when needed, a crack growth analysis has been performed.

Gespeicherte Ionen in der Paulfalle: Voruntersuchungen zur Lebensdauermessung des metastabilen 6D-3/2-Zustands des 226 Ra +, Speichereigenschaften von 138 Ba + und 28 N 2 + bei Variation des Puffergasdrucks

Auf Paulfallen basierende Experimente spielen eine wichtige Rolle in verschiedenen Bereichen der Physik, z.B. der Atomphysik zum Test theoretischer Modelle und der Massenspektroskopie. Die vorliegende Arbeit widmet sich beiden Themengebieten und gliedert sich entsprechend in zwei Teilbereiche: 1) Erdalkali-Ionen sind aufgrund ihrer Energieniveaus optimale Kandidaten für Laserspektroskopie-Experimente mit Ionenfallen und bestens geeignet, um mittels der spektroskopischen Daten die theoretischen Modelle zu testen. Lediglich für Ra+ fehlen bislang als einzigem Erdalkali-Ion diese Daten wie z.B. die Lebensdauern der metastabilen Niveaus. Diese wären auch von Interesse für bereits geplante Radium-Experimente zur Paritätsverletzung. Im ersten Teil dieser Arbeit wird der Aufbau eines Laser-Paulfallenexperiments zur Messung der Lebensdauer des 6D3/2 Zustands von 226Ra+ dokumentiert und es werden Testmessungen mit 138Ba+ vorgestellt. 2) Für die Verwendung der Paulfalle in der Massenspektroskopie und zur Analyse von Reaktionsprodukten ist die Kenntnis der Lage der im Speicherbereich auftretenden nichtlinearen Resonanzen wesentlich, ebenso wie deren Veränderung durch Dämpfung und Raumladung. Im zweiten Teil dieser Arbeit werden detaillierte Untersuchungen der Speicherung großer puffergasgekühlter Ionenwolken an zwei unterschiedlichen Paulfallen-Experimenten vorgestellt. Am ersten wurden 138Ba+-Ionenwolken kontinuierlich durch Laserspektroskopie bzw. über einen elektronischen Nachweis beobachtet, während das zweite N2+-Molekülionen automatisiert destruktiv nachwies. Am N2+-Experiment wurden zwei hochaufgelöste Messungen des ersten Speicherbereichs durchgeführt, die erstmals eine direkte Überprüfung der theoretisch berechneten Verläufe der Resonanzen mit experimentellen Daten erlauben. Die Nachweiseichung ermöglichte dabei zum ersten Mal die Angabe absoluter Ionenzahlen. Im Gegensatz zu vergleichbaren früheren Messungen wurden hierbei die sich überlagernden Speicherbereiche von 4 simultan gespeicherten Ionensorten beobachtet und zur Analyse der Resonanzen herangezogen. Die nichtlinearen Resonanzen wurden untersucht bei Variation von Puffergasdruck und Ionenzahl, wobei kollektive Resonanzen ohne zusätzliche externe Anregung beobachtet wurden. Die gemessenen Raumladungsverschiebungen wurden mit theoretischen Modellen verglichen. Bei Variation des Puffergasdrucks wurde mit Bariumionen die räumliche Ausdehnung der Ionenwolke gemessen und mit Stickstoffionen die Verschiebung des Punktes optimaler Speicherung bestimmt. Dabei wurde festgestellt, daß der zum Ioneneinfang optimale Puffergasdruck kleiner ist als der, bei dem die längsten Speicherdauern erzielt werden. Mit gespeicherten N2+-Ionen wurde die Position extern angeregter kollektiver und individueller Resonanzen im Frequenzspektrum bei Änderung der Parameter Ionenzahl, Puffergasdruck und Dauer der Anregung untersucht, ebenso wie die Resonanzform, die mit theoretischen Linienformen verglichen wurde. Bei Änderung der Fallenparameter wurden verstärkende Effekte zwischen nahen kollektiven Resonanzen festgestellt. Die Beobachtung, welche der im Frequenzspektrum vorher identifizierten Bewegungs-Resonanzen sich bei Variation der Fallenparameter a bzw. q überlagern, ermöglicht eine bislang nicht beschriebene einfache Methode der Bestimmung von nichtlinearen Resonanzen im Stabilitätsdiagramm.

Semi-synthetic bile acids as novel drug candidate in liver diseases: physico-chemical characterization and HPLC-ES-MS/MS methods for their quali-quantitative analysis in different experimental animal models

The physico-chemical characterization, structure-pharmacokinetic and metabolism studies of new semi synthetic analogues of natural bile acids (BAs) drug candidates have been performed. Recent studies discovered a role of BAs as agonists of FXR and TGR5 receptor, thus opening new therapeutic target for the treatment of liver diseases or metabolic disorders. Up to twenty new semisynthetic analogues have been synthesized and studied in order to find promising novel drugs candidates. In order to define the BAs structure-activity relationship, their main physico-chemical properties (solubility, detergency, lipophilicity and affinity with serum albumin) have been measured with validated analytical methodologies. Their metabolism and biodistribution has been studied in “bile fistula rat”, model where each BA is acutely administered through duodenal and femoral infusion and bile collected at different time interval allowing to define the relationship between structure and intestinal absorption and hepatic uptake ,metabolism and systemic spill-over. One of the studied analogues, 6α-ethyl-3α7α-dihydroxy-5β-cholanic acid, analogue of CDCA (INT 747, Obeticholic Acid (OCA)), recently under approval for the treatment of cholestatic liver diseases, requires additional studies to ensure its safety and lack of toxicity when administered to patients with a strong liver impairment. For this purpose, CCl4 inhalation to rat causing hepatic decompensation (cirrhosis) animal model has been developed and used to define the difference of OCA biodistribution in respect to control animals trying to define whether peripheral tissues might be also exposed as a result of toxic plasma levels of OCA, evaluating also the endogenous BAs biodistribution. An accurate and sensitive HPLC-ES-MS/MS method is developed to identify and quantify all BAs in biological matrices (bile, plasma, urine, liver, kidney, intestinal content and tissue) for which a sample pretreatment have been optimized.

Kinetische Studien zur OH-Bildung über die Reaktionen von HO 2 mit organischen Peroxyradikalen

Es wurde untersucht, wie sich das Substitutionsmuster organischer Peroxyradikale (RO2) auf die Ratenkonstante k1 und die Verzweigungsverhältnisse α, β und γ der Reaktionen von RO2 mit HO2 auswirkt. Die Effekte der Deuterierung von HO2 wurden ebenfalls studiert. Für zwei RO2 wurde zusätzlich das UV-Absorptionsspektrum bestimmt.rnrn αrnRO2 + HO2 → RO + OH + O2 R1arnrn βrn → RO2H + O2 R1brnrn γrn → ROH + O3 R1crnrnIn dieser Arbeit wurde ein neues Experiment aufgebaut. Für die direkte und zeitaufgelöste Messung der OH-Konzentration wurde das Verfahren der Laser-induzierten Fluoreszenz angewendet. Die Radikalerzeugung erfolgte mittels gepulster Laserphotolyse, wodurch unerwünschte Nebenreaktionen weitgehend unterdrückt werden konnten. Mittels transienter Absorptionsspektroskopie konnten die Menge der photolytisch erzeugten Radikale bestimmt und die Ozonbildung über R1c quantifiziert werden. Für die Auswertung wurden kinetische Modelle numerisch an die Messdaten angepasst. Um die experimentellen Unsicherheiten abzuschätzen, wurde ein Monte-Carlo-Ansatz gewählt.rnrnk1 und α reagieren sehr empfindlich auf Veränderungen des RO2-Substitutionsmusters. Während sich eine OH-Bildung für das unsubstituierte C2H5O2 (EtP) mit α EtP ≤ 5 % nicht nachweisen lässt, stellt R1a bei den α-Oxo-substituierten H3CC(O)O2 (AcP) und HOCH2C(O)O2 (HAP) mit α AcP = (63 ± 11) % bzw. α HAP = (69 ± 12) % den Hauptkanal dar. Wie die mit α HEP = (10 ± 4) % geringfügige OH-Bildung bei HOC2H4O2 (HEP) zeigt, nimmt die OH-Gruppe in β-Stellung weniger Einfluss auf den Wert von α als die Oxogruppe in α-Stellung. Bei der Erzeugung α-Oxo-substituierter RO2 kann ebenfalls OH entstehen (R+O2→RO2/OH). Die Druckabhängigkeit dieser OH-Quelle wurde mit einem innovativen Ansatz bestimmt. Mit γ AcP = (15+5-6) % bzw. γ HAP = (10+2-3) % lässt sich für die Reaktionen der α-Oxo-substituierten RO2 eine erhebliche Ozonbildung nachweisen. Durch die Einführung der α-Oxogruppe steigt k1 jeweils um 1,3 • 10-11 cm3s-1 an, der Effekt der β-Hydroxygruppe ist halb so groß (k1 AcP = (2,0 ± 0,4) • 10-11 cm3s-1, k1 HAP = (2,6 ± 0,4) • 10-11 cm3s-1). Das Verzweigungsverhältnis α steigt weiter, wenn das HO2 deuteriert wird (α AcP,iso = (80 ± 14) %, k1 AcP,iso = (2,1 ± 0,4) • 10-11 cm3s-1). Vergleiche mit älteren Studien zeigen, dass die OH-Bildung über R1a bislang deutlich unterschätzt worden ist. Die möglichen Ursachen für die Unterschiede zwischen den Studien werden ebenso diskutiert wie die Hintergründe der beobachteten Substituenteneffekte.

Visualization and validation of (Q)SAR models

Analyzing and modeling relationships between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects in chemical datasets is a challenging task for scientific researchers in the field of cheminformatics. Therefore, (Q)SAR model validation is essential to ensure future model predictivity on unseen compounds. Proper validation is also one of the requirements of regulatory authorities in order to approve its use in real-world scenarios as an alternative testing method. However, at the same time, the question of how to validate a (Q)SAR model is still under discussion. In this work, we empirically compare a k-fold cross-validation with external test set validation. The introduced workflow allows to apply the built and validated models to large amounts of unseen data, and to compare the performance of the different validation approaches. Our experimental results indicate that cross-validation produces (Q)SAR models with higher predictivity than external test set validation and reduces the variance of the results. Statistical validation is important to evaluate the performance of (Q)SAR models, but does not support the user in better understanding the properties of the model or the underlying correlations. We present the 3D molecular viewer CheS-Mapper (Chemical Space Mapper) that arranges compounds in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kinds of features, like structural fragments as well as quantitative chemical descriptors. Comprehensive functionalities including clustering, alignment of compounds according to their 3D structure, and feature highlighting aid the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. Even though visualization tools for analyzing (Q)SAR information in small molecule datasets exist, integrated visualization methods that allows for the investigation of model validation results are still lacking. We propose visual validation, as an approach for the graphical inspection of (Q)SAR model validation results. New functionalities in CheS-Mapper 2.0 facilitate the analysis of (Q)SAR information and allow the visual validation of (Q)SAR models. The tool enables the comparison of model predictions to the actual activity in feature space. Our approach reveals if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs. The CheS-Mapper software is freely available at http://ches-mapper.org.