91 research outputs found
Theoretical studies of interactions of transition metal anticancer complexes with DNA
No full textDensity functional theory (DFT) and combined quantum mechanics/molecular mechanics (QM/MM) calculations have been used to model inter- and intra-molecular non-covalent interactions of transition metal complexes and where applicable their interactions with DNA. Two DFT functionals, BHandH and B97-D, which have shown
to be efficient in modelling systems containing non-covalent interactions, have been tested against high level ab initio calculations on test transition metal complexes, designed to represent the intermolecular interactions present in the benzene dimer and
methane benzene systems. The DFT functionals above show good agreement with the benchmark calculations and have been used to study ruthenium arene 'piano stool' type
complexes, of the general form [6(arene)Ru(en)Cl]+, which have shown potential as anticancer agents. The intramolecular interactions of these ruthenium complexes
through coordination to guanine and adenine through the N7 nitrogen, has been explored using a selection of pure DFT, hybrid DFT, and post Hartree-Fock approaches
against benchmark correlated wavefunction methods, where the best methods were found to be BHandH, B97-D2, and MP2(0.25). The B97-D2 functional was used to
model these ruthenium complexes, with a selection of extended aromatic ligands with potential to act as intercalators, interacting with base pair steps. Calculated binding energies show a sensitivity to the nature of the arenes, where the more flexible ligands
form more non-covalent interactions with DNA, as demonstrated by QTAIM analysis.
Conformations and binding energies of a relatively new platinum anticancer drug, kiteplatin, with small single strand fragments of DNA, have been studied using B97-D
and semi-empirical methods and compared to established drugs cisplatin and oxaliplatin. Isotropic shielding values and J coupling constants have also been
calculated for these systems to relate these values to conformational data. Extended dual strand kiteplatin-DNA adducts have been studied using the QM/MM method ONIOM,
combining BHandH with AMBER, to calculate binding energies and optimised structures. These results show that as the DNA adduct increases in size the values of the
kiteplatin energies start to converge and comparison of base pair parameters show that around the site of coordination all fragments show comparable geometrical distortions
Modulation of stacking interactions by transition-metal coordination: ab initio benchmark studies
No full textA series of ab initio calculations are used to determine the CHπ and ππ-stacking interactions of aromatic rings coordinated to transition-metal centres. Two model complexes have been employed, namely, ferrocene and chromium benzene tricarbonyl. Benchmark data obtained from extrapolation of MP2 energies to the basis set limit, coupled with CCSD(T) correction, indicate that coordinated aromatic rings are slightly weaker hydrogen-bond acceptors but are significantly stronger hydrogen-bond donors than uncomplexed rings. It is found that ππ stacking to a second benzene is stronger than in the free benzene dimer, especially in the chromium case. This is assigned, by use of energy partitioning in the local correlation method, to dispersion interactions between metal d and benzene π orbitals. The benchmark data is also used to test the performance of more efficient theoretical methods, indicating that spin-component scaling of MP2 energies performs well in all cases, whereas various density functionals describe some complexes well, but others with errors of more than 1 kcal mol−1
Density functional theory studies of interactions of ruthenium arene complexes with base pair steps
No full textDensity functional theory (DFT) calculations have been performed to determine the strength and geometry of intermolecular interactions of “piano-stool” ruthenium arene complexes, which show potential as anticancer treatments. Model complexes with methane and benzene indicate that the coordinated arene has C–H···π acceptor ability similar to that of free benzene, whereas this arene acts as a much stronger C–H donor or partner in π-stacking than free benzene. The source of these enhanced interactions is identified as a combination of electrostatic and dispersion effects. Complexes of Ru-arene complexes with base-pair step fragments of DNA, in which the arene has the potential to act as an intercalator, have also been investigated. Binding energies are found to be sensitive to the size and nature of the arene, with larger and more flexible arenes having stronger binding. π-stacking and C–H···π interactions between arene and DNA bases and hydrogen bonds from coordinated N–H to DNA oxygen atoms, as well as covalent Ru–N bonding, contribute to the overall binding. The effect of complexation on DNA structure is also examined, with larger rise and more negative slide values than canonical B-DNA observed in all case
Molecular Dynamics Simulation on the Effect of Transition Metal Binding to the N-Terminal Fragment of Amyloid-β
No full textMolecular dynamics trajectories in PDB format for 3x Cu-Aβ, 3x Zn-Aβ and 9x Fe-Aβ simulations.</p
Interpretations of Data in Ethical vs. Unethical Data Visualizations
No full textabstract: This paper presents the results of an empirical analysis of deceptive data visualizations paired with explanatory text. Data visualizations are used to communicate information about important social issues to large audiences and are found in the news, social media, and the Internet (Kirk, 2012). Modern technology and software allow people and organizations to easily produce and publish data visualizations, contributing to data visualizations becoming more prevalent as a means of communicating important information (Sue & Griffin, 2016). Ethical transgressions in data visualizations are the intentional or unintentional use of deceptive techniques with the potential of altering the audience’s understanding of the information being presented (Pandey et al., 2015). While many have discussed the importance of ethics in data visualization, scientists have only recently started to look at how deceptive data visualizations affect the reader. This study was administered as an on-line user survey and was designed to test the deceptive potential of data visualizations when they are accompanied by a paragraph of text. The study consisted of a demographic questionnaire, chart familiarity assessment, and data visualization survey. A total of 256 participants completed the survey and were evenly distributed between a control (non-deceptive) survey or a test (deceptive) survey in which participant were asked to observe a paragraph of text and data visualization paired together. Participants then answered a question relevant to the observed information to measure how they perceived the information to be. The individual differences between demographic groups and their responses were analyzed to understand how these groups reacted to deceptive data visualizations compared to the control group. The results of the study confirmed that deceptive techniques in data visualizations caused participants to misinterpret the information in the deceptive data visualizations even when they were accompanied by a paragraph of explanatory text. Furthermore, certain demographics and comfort levels with chart types were more susceptible to certain types of deceptive techniques. These results highlight the importance of education and practice in the area of data visualizations to ensure deceptive practices are not utilized and to avoid potential misinformation, especially when information can be called into question.Dissertation/ThesisMasters Thesis Technical Communication 201
Civic Community, Population Change, and Violent Crime in Rural Communities
No full textThis analysis investigates the relationships between measures of civic community, population change, and violent crime rates in rural communities. Rural communities that are civically robust are hypothesized to have lower violent crime rates and to experience less change in violent crime over time. Alternatively, sustained population change is hypothesized to elevate violent crime rates and to moderate the protective effect that civic robustness provides against violent crime over time. Results from both lagged panel and cross-sectional negative binomial regression models of county-level data support these expectations. In substantive terms, these findings suggest that civically robust communities are much better positioned to weather population change than civically weak communities, but continuous change over time compromises the protective effect that civic robustness provides against serious crime. © The Author(s) 2010
Histories, Horizons, and the Theatre Arts: A Hermeneutic Study of the Theatre Texts An Actor Prepares and Theatre of the Oppressed
No full textabstract: The purpose of this study is to explore the question: what are the ways in which the texts An Actor Prepares (1936) by Constantin Stanislavski and Theatre of the Oppressed (1985) by Augusto Boal intersect with each other and diverge from each other such that in their intersection/divergence a new horizons of understanding may emerge? This question is important in the context of rethinking theatre education. The principle methodology of analysis used is what Shaun Gallagher (1992) terms a "moderate hermeneutics" in which the aim is a "dialogical conversation" leading to a "creative communication between the reader and the text" (p.10). The reason for undertaking a hermeneutical analysis of the two texts is that hermeneutics offers an approach in which the researcher may deeply analyze texts and therefore create new understandings and meanings from those texts. Through the use of hermeneutical analysis, the relationship between the writer and text, and a reader and text becomes a dialectical relationship. A "dialectical relationship" is a conversation between writer, reader and the text. This conversation leads to new interpretations.Dissertation/ThesisPh.D. Curriculum and Instruction 201
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