Identifying optimal solvents for reactions using quantum mechanics and computer-aided molecular design

A new iterative hybrid methodology, incorporating quantum mechanics (QM) calculations and a computationally inexpensive computer-aided molecular design (CAMD) methodology, QM-CAMD, for identification of optimal solvents for reactions is presented. The methodology has been applied to a Menschutkin reaction, where pyridine and phenacyl bromide are the reactants. The QM calculations take on the form of density functional theory calculations with a given solvent treated using continuum solvation models. The accuracy of the solvent QM calculations is assessed by computing free energies of solvation for different solvation models; the IEF-PCM, SM8 and SMD models are studied and SMD is identified as the best model. Rate constants kQM, determined from QM calculations, are calculated based on conventional transition state theory (Eyring 1935, Evans & Polanyi 1935). By using the SMD solvation model and a statistical mechanics derivation of kQM, rate constant predictions within an order of magnitude are achieved. For a small set of solvents investigated by QM, selected solvent properties are predicted using group contribution (GC) methods. 38 structural groups are considered in this approach. The QM-computed rate constants and solvent properties determined by GC are used to obtain a computationally inexpensive reaction model, based on an empirical linear free energy relationship, which is used to predict reaction rate constants. This predictive reaction model is incorporated into an optimisation-based CAMD methodology. With an objective function of maximising the reaction rate constant subject to molecular and reaction condition constraints, optimal solvent candidates are identified. By considering a design space of over 1000 solvent molecules, solvent candidates containing nitro-groups are predicted to be optimal for the Menschutkin reaction. This outcome supports experimental results for a related reaction available in the literature (Lassau & Jungers 1968). For verification purposes, Ganase et al. (2011) have measured (based on 1H NMR data and kinetic analysis) the rate constant for the reaction of interest in a number of solvents and report a significant increase in the rate constant with nitromethane as the solvent

Senior Recital:Sharon Struebing, Pianist and Vocalist

Centennial Lecture Hall November 6, 1966 3:00p.m

Different Effect of Sox11 in Retinal Ganglion Cells Survival and Axon Regeneration

Purpose: The present study examines the role of Sox11 in the initial response of retinal ganglion cells (RGCs) to axon damage and in optic nerve regeneration in mouse.Methods: Markers of retinal injury were identified using the normal retina database and optic nerve crush (ONC) database on GeneNetwork2 (www.genenetwork.org). One gene, Sox11, was highly upregulated following ONC. We examined the role of this transcription factor, Sox11, following ONC and optic nerve regeneration in mice. In situ hybridization was performed using the Affymetrix 2-plex Quantigene View RNA In Situ Hybridization Tissue Assay System. Sox11 was partially knocked out by intravitreal injection of AAV2-CMV-Cre-GFP in Sox11f/f mice. Optic nerve regeneration model used Pten knockdown. Mice were perfused and the retinas and optic nerves were dissected and examined for RGC survival and axon growth.Results:Sox11 was dramatically upregulated in the retina following ONC injury. The level of Sox11 message increased by approximately eightfold 2 days after ONC. In situ hybridization demonstrated low-level Sox11 message in RGCs and cells in the inner nuclear layer in the normal retina as well as a profound increase in Sox11 message within the ganglion cells following ONC. In Sox11f/f retinas, partially knocking out Sox11 significantly increased RGC survival after ONC as compared to the AAV2-CMV-GFP control group; however, it had little effect on the ability of axon regeneration. Combinatorial downregulation of both Sox11 and Pten resulted in a significant increase in RGC survival as compared to Pten knockdown only. When Pten was knocked down there was a remarkable increase in the number and the length of regenerating axons. Partially knocking out Sox11 in combination with Pten deletion resulted in a fewer regenerating axons.Conclusion: Taken together, these data demonstrate that Sox11 is involved in the initial response of the retina to injury, playing a role in the early attempts of axon regeneration and neuronal survival. Downregulation of Sox11 aids in RGC survival following injury of optic nerve axons, while a partial knockout of Sox11 negates the axon regeneration stimulated by Pten knockdown

Design, synthesis, characterization and application of rare-earth doped glass and glass ceramic scintillators

Single crystal scintillators have been the premier choice for gamma ray detecting applications due to their high luminescent efficiency and sharp energy resolutions. However, there remain downsides to the use of single crystal scintillators such as production expense, vulnerability to environmental factors, and rigid shaping. Industries have been searching for lower cost alternatives to single crystal scintillators in order to make more portable devices practical. Glass and glass-ceramic scintillators have gained attention for their lower production cost, scalability, and ease of shaping to fit complex geometries. By the nature of the glass matrix any crystalline phases within the material are self-encapsulated, which avoids the issue of hygroscopicity and reduces the impact of mechanical shock and high temperature exposure. The main issue holding back glass and glass-ceramic scintillators has been the low luminescent efficiency stemming from the inherent disorder in the non-crystalline glassy matrix. We believe this downside can be mitigated through increases to density, harnessing the innate energy transfer capabilities of constituent materials, and controlled nucleation of crystalline phases within the glass structure. Glass-ceramics combine the robust resilience of glass with the luminescent capabilities of crystalline nanoparticles by precipitating nano-sized crystals within the glass matrix. This study approaches the field of glass and glass-ceramic based scintillators with rare-earth rich, high density compositions modeled after known crystal systems in order to produce a glass ceramic scintillator that could compete with single crystals.Ph.D

A QM-CAMD approach to solvent design for optimal reaction rates

The choice of solvent in which to carry out liquid-phase organic reactions often has a large impact on reaction rates and selectivity and is thus a key decision in process design. A systematic methodology for solvent design that does not require any experimental data on the effect of solvents on reaction kinetics is presented. It combines quantum mechanical computations for the reaction rate constant in various solvents with a computer-aided molecular design (CAMD) formulation. A surrogate model is used to derive an integrated design formulation that combines kinetics and other considerations such as phase equilibria, as predicted by group contribution methods. The derivation of the mixed-integer nonlinear formulation is presented step-by-step. In the application of the methodology to a classic SN2 reaction, the Menschutkin reaction, the reaction rate is used as the key performance objective. The results highlight the tradeoffs between different chemical and physical properties such as reaction rate constant, solvent density and solid reactant solubility and lead to the identification of several promising solvents to enhance reaction performance

A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks

Aging is regarded as a major risk factor for neurodegenerative diseases. Thus, a better understanding of the similarities between the aging process and neurodegenerative diseases at the cellular and molecular level may reveal better understanding of this detrimental relationship. In the present study, we mined publicly available gene expression datasets from healthy individuals and patients affected by neurodegenerative diseases (Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease) across a broad age spectrum and compared those with mouse aging and mouse cell-type specific gene expression profiles. We performed weighted gene co-expression network analysis (WGCNA) and found a gene network strongly related with both aging and neurodegenerative diseases. This network was significantly enriched with a microglial signature as imputed from cell type-specific sequencing data. Since mouse models are extensively used for the study of human diseases, we further compared these human gene regulatory networks with age-specific mouse brain transcriptomes. We discovered significantly preserved networks with both human aging and human disease and identified 17 shared genes in the top-ranked immune/microglia module, among which we found five human hub genes TYROBP, FCER1G, ITGB2, MYO1F, PTPRC, and two mouse hub genes Trem2 and C1qa. Taken together, these results support the hypothesis that microglia are key players involved in human aging and neurodegenerative diseases, and suggest that mouse models should be appropriate for studying these microglial changes in human

A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks

Aging is regarded as a major risk factor for neurodegenerative diseases. Thus, a better understanding of the similarities between the aging process and neurodegenerative diseases at the cellular and molecular level may reveal better understanding of this detrimental relationship. In the present study, we mined publicly available gene expression datasets from healthy individuals and patients affected by neurodegenerative diseases (Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease) across a broad age spectrum and compared those with mouse aging and mouse cell-type specific gene expression profiles. We performed weighted gene co-expression network analysis (WGCNA) and found a gene network strongly related with both aging and neurodegenerative diseases. This network was significantly enriched with a microglial signature as imputed from cell type-specific sequencing data. Since mouse models are extensively used for the study of human diseases, we further compared these human gene regulatory networks with age-specific mouse brain transcriptomes. We discovered significantly preserved networks with both human aging and human disease and identified 17 shared genes in the top-ranked immune/microglia module, among which we found five human hub genes TYROBP, FCER1G, ITGB2, MYO1F, PTPRC, and two mouse hub genes Trem2 and C1qa. Taken together, these results support the hypothesis that microglia are key players involved in human aging and neurodegenerative diseases, and suggest that mouse models should be appropriate for studying these microglial changes in human

Neuropathology of incidental Lewy body & prodromal Parkinson's disease

Background Background Parkinson's disease (PD) is a progressive neurodegenerative disorder associated with a loss of dopaminergic (DA) neurons. Despite symptomatic therapies, there is currently no disease-modifying treatment to halt neuronal loss in PD. A major hurdle for developing and testing such curative therapies results from the fact that most DA neurons are already lost at the time of the clinical diagnosis, rendering them inaccessible to therapy. Understanding the early pathological changes that precede Lewy body pathology (LBP) and cell loss in PD will likely support the identification of novel diagnostic and therapeutic strategies and help to differentiate LBP-dependent and -independent alterations. Several previous studies identified such specific molecular and cellular changes that occur prior to the appearance of Lewy bodies (LBs) in DA neurons, but a concise map of such early disease events is currently missing. Methods Here, we conducted a literature review to identify and discuss the results of previous studies that investigated cases with incidental Lewy body disease (iLBD), a presumed pathological precursor of PD. Results Collectively, our review demonstrates numerous cellular and molecular neuropathological changes occurring prior to the appearance of LBs in DA neurons. Conclusions Our review provides the reader with a summary of early pathological events in PD that may support the identification of novel therapeutic and diagnostic targets and aid to the development of disease-modifying strategies in PD

A participatory action research approach to strengthening health managers’ capacity at district level in Eastern Uganda

BACKGROUND: Many approaches to improving health managers’ capacity in poor countries, particularly those pursued by external agencies, employ non-participatory approaches and often seek to circumvent (rather than strengthen) weak public management structures. This limits opportunities for strengthening local health managers’ capacity, improving resource utilisation and enhancing service delivery. This study explored the contribution of a participatory action research approach to strengthening health managers’ capacity in Eastern Uganda. METHODS: This was a qualitative study that used open-ended key informant interviews, combined with review of meeting minutes and observations to collect data. Both inductive and deductive thematic analysis was undertaken. The Competing Values Framework of organisational management functions guided the deductive process of analysis and the interpretation of the findings. The framework builds on four earlier models of management and regards them as complementary rather than conflicting, and identifies four managers’ capacities (collaborate, create, compete and control) by categorising them along two axes, one contrasting flexibility versus control and the other internal versus external organisational focus. RESULTS: The findings indicate that the participatory action research approach enhanced health managers’ capacity to collaborate with others, be creative, attain goals and review progress. The enablers included expanded interaction spaces, encouragement of flexibility, empowerment of local managers, and the promotion of reflection and accountability. Tension and conflict across different management functions was apparent; for example, while there was a need to collaborate, maintaining control over processes was also needed. These tensions meant that managers needed to learn to simultaneously draw upon and use different capacities as reflected by the Competing Values Framework in order to maximise their effectiveness. CONCLUSIONS: Improved health manager capacity is essential if sustained improvements in health outcomes in lowincome countries are to be attained. The expansion of interaction spaces, encouragement of flexibility, empowerment of local managers, and the promotion of reflection and accountability were the key means by which participatory action research strengthened health managers’ capacity. The participatory approach to implementation therefore created opportunities to strengthen health managers’ capacity