Summer Science Research at Bryn Mawr

'2008' Archive

Exploration of the Conjugate Addition Reactions of Carbon Nucleophiles

Posted May 14, 2010

Generally, I will be experimenting with different carbon nucleophiles of Birch Cope sequence products for multiple conjugate addition reactions. Below [Scheme 1] includes the outline of the starting materials that I have been synthesizing in order to do this. The last three steps of this scheme illustrate the Birch Cope sequence that will produce the starting material necessary for the aforementioned reactions.

Modeling the Molybdenum Cofactor

Posted May 14, 2010

The second row transition metal molybdenum, atomic number 42, is a naturally occurring element in a countless number of biological reactions. Assuming the role as a biological catalytic center, molybdenum occupies the catalytic site in more than forty essential enzymes, which control the oxidation-reduction reactions for a broad range of inorganic and organic substrates. Considering the ubiquitous nature of molybdenum enzymes, with its presence in everything from simple bacteria to human beings, it is no wonder that the element has a profound evolutionary history, contributing significantly to the biological function of virtually every living organism. From the human perspective alone, three molybdoenzymes—sulfite oxidase, xanthine oxidase and aldehyde oxidase—are essential for proper health.

A Thermal Denaturation method for distinguishing between K-turn and non-K-turn RNA

Posted May 14, 2010

Protein-RNA interactions are important for cellular growth and regulation. Proper interactions between protein and RNA require both of their interfacial sites to be conserved for specific recognition and binding. Organisms, like Saccharomyces cerevisiae (yeast), have evolved in ways that condense multi-component and multi-step pathways into more self-contained processes. This allows the cell machinery to maintain, if not improve, its specificity and regulation, while increasing the efficiency of these vital mechanisms. Knowledge of protein and RNA interactions continues to aid in the development of therapeutic approaches for the treatment of various diseases.

Functionalization of a Variety of Carbon Surfaces with Transition Metal Complexes: Glassy Carbon, HOPG and SWNT

Posted May 14, 2010

The behavior of several carbon surface types functionalized with the compound below (1) will be explored.

A sample of complex 1 was synthesized and re-crystallized to obtain a workable powder. Polished glassy carbon, highly oriented pyrolytic graphite, and single-walled carbon nanotubes (SWNT), were functionalized using 1 by dissolving the complex in acetonitrile and exposing the carbon surface to a dilute solution of 1. The HOPG and glassy carbon functionalized surfaces were characterized by the observed redox behavior on an electrode surface using cyclic voltammetry. Experiments used a range of concentrations from 0.1μM to 2.0μM, and were conducted over the period of 1.5 hours. For each data point the reduction peak height was recorded. The equation was used to obtain the electrode coverage for each data point. The kinetics and thermodynamics of the adsorption process can be determined by an analysis of coverage (Γ) versus time and coverage versus concentration. In order to study the adsorption behavior of 1 on SWNT, an additional step was required to disperse and separate the SWNT material. Suspensions of SWNT were created using several solvents, including Milli-Q water, chloroform, ethanol, and isopropanol. A range of surfactants, SDS, PVP, PVA, and Triton X-100, were also used and compared as to their relative utilities for suspension formation. Suspensions that appeared to be well-distributed were diluted and filtered. Atomic force microscopy was used to characterize the appearance of the SWNT suspensions. The dispersions will also be cast onto metal electrodes to study their adsorption behavior.

Functionalizing Surfaces with Transition Metal Complexes

Posted May 13, 2010

The nanotechnology field is growing rapidly thus novel methods in modulating behavior on the nanoscale is necessary for the development of nanoelectronics. In order to control the behavior of this technology, one must appeal to redox chemistry. Adding functionality to surfaces is possible through the synthesis of metal complexes with the appropriate substituents, allowing adsorption to various surfaces.

The focus of this research is to achieve the synthesis of a transition metal complex capable of the aforementioned functionalization. First, a bromoalkyl chain of varying lengths is to be added to a 4,4’-dimethyl-2,2’-bipyridine molecule giving 4-bromobutyl-4-methyl-2,2’-bipyridine or 4-bromononyl-4-methyl-2,2’-bipyridine. The added bromine will then be replaced with a thiol, an SH group, which has the capability of adsorbing to gold surfaces. The bipyridine portion of the molecule also enables the formation of a stable metal complex. In this case the transition metal is ruthenium as shown in Figure 1.

The second goal is to synthesize a molecule with the capability of adsorbing to varying carbon surfaces. The first step is the same as the formation of the previous molecule. Once the molecule has a bromoalkyl substituent, the bromine will be converted to an amine. This NH2 group will allow the coupling of polyaromatic groups resulting in a ligand with an extended pi system. The ligands will then form a complex with a transition metal giving a product as seen in Figure 2 where the polyaromatic group shown is pyrene. The manner of how these molecules adsorb to gold, platinum surfaces, or carbon surfaces will then be observed by using electrochemistry.

Synthesis and Characterization of DNA-Intercalating and Potential Photocleaving Ru(II)-bis(bipyridine)-Pteridinyl Complexes and Similar Co(III) Complexes

Posted May 13, 2010

Small transition metal molecules have been the object of many studies due to their interactions with DNA and the resulting effects on the regulation of DNA transcription and replication, as well as their potential as pharmaceuticals. Ru(II) compounds are especially useful as probes due to their stability and photophysical properties. Bis(bipyridyl) Ru(II) complexes of pteridinyl-phenanthroline ligands have been of particular interest because pteridinyl ligands possess H-bonding patterns complementary to the purine and pyrimidine bases of DNA and RNA. The pteridinyl ligand of these Ru-pteridine complexes is capable of inserting itself between the base pairs of DNA, thus binding to DNA via intercalation. Other metal complexes, including certain Co(III) complexes, have been known to cleave DNA in the presence of light (photoactivated cleavage of DNA). Such metallointercalators are practical for their high affinity for double-stranded DNA and because they include a range of redox-active metal centers and ligands.

Syntheses of [n]Phenacenes

Posted May 13, 2010

[n]Phenacenes are compounds that contain n benzene rings fused together in a zigzag pattern. An example of a [7]phenacene derivative is shown below.

R=alkyl group

The synthesis of [n]phenacenes is of particular importance for the investigation of whether pseudo one-dimensional versions of the pseudo two-dimensional graphite sheets possess similar patterns of conductivity to the graphite sheets. Previously, an [n]phenacene having 11 fused rings has been synthesized by the Mallory group. [n]Phenacenes with n > 6 are extremely insoluble, so to produce larger [n]phenacenes by chemical synthesis, solubilizing groups (R) must be attached. [n]Phenacenes with n > 11 have been attempted, but have proved unsuccessful due to issues of solubility based on the various R-groups used.

Synthesis and Electrochemical Analysis of Transition Metal Complexes with Various Functionalities for Surface Modification

Posted May 13, 2010

It is possible to functionalize various surfaces by attaching various different types of organic ligands to them. The organic ligands are able to form complexes with transition metals, and an electrode composed of the surface material in question is placed into a solution containing a low concentration of the aforementioned metal complex. The interactions of various ligands with metal and carbon surfaces can be analyzed electrochemically, and in this manner the rate at which these ligands adhere to the surface, based on varying concentration, can be examined.

Ecological compensation mechanisms within pollinator communities in the face of species loss

Posted May 13, 2010

Ecosystem services are processes and contributions from the natural world that are essential to human well-being. Among the most important of these services is pollination, which is provided primarily by bees and is required for the successful production of half of the world’s crops. Recent declines in managed honeybees and concerns about food security in an increasingly populous world make it imperative that we understand the role of other wild bee species and the factors that influence pollination to ensure stable pollination. A series of recent articles suggest that pollination, like other ecosystem services, is dependent upon diversity and abundance of species within a system, thus loss of biodiversity may severely impact crop pollination and production. This may occur because the total level of pollination service provided depends on the number of individual bees visiting a crop and on the amount of pollination each individual provides.

The Effect of Instruction on Children’s Symbolic Understanding

Posted May 12, 2010

Symbols are everywhere in our world; we use them when we read and write, we see them in our homes and every time we step outside, and we need them to communicate to others. In the most general sense, a symbol is anything used to represent anything else. Because we use symbols in communicative contexts, a deeper understanding of symbolic thought tells us more about how children’s minds develop. Previous researchers have discussed pictorial representation as a complex interplay between several factors: the creator, the user, the picture, and the represented object. What remains to be shown is whether children flexibly adapt their symbols to the following conditions: (1) when they receive insight into the mind of the person who will be using their drawing, and (2) when they are made aware that a drawing is insufficient to communicate in a particular context. For instance, an inexperienced symbol-user may misunderstand a perfectly good drawing, and the failure should be attributed to the person, not the drawing. Similarly, if the drawing resembles both the intended object and another available object equally as well, failure could be attributed to the drawing (not the symbol-user). This study will investigate whether children are sensitive to the ways in which these factors influence effective drawing and communication.

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