Physical Sciences and Mathematics Commons^™

Open Data, Open Source, And Open Standards In Chemistry: The Blue Obelisk Five Years On, Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, Peter Murray-Rust

College of Science and Engineering Faculty Research and Scholarship

Background: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions: We show that the Blue …

The Regulation Of Skeletal Muscle Protein Turnover During The Progression Of Cancer Cachexia In The ApcMin/+ Mouse, James P. White, John W. Baynes, Stephen L. Welle, Matthew C. Kostek, Lydia E. Matesic, Shuichi Sato, James A. Carson

Faculty Publications

Muscle wasting that occurs with cancer cachexia is caused by an imbalance in the rates of muscle protein synthesis and degradation. The Apc(Min/+) mouse is a model of colorectal cancer that develops cachexia that is dependent on circulating IL-6. However, the IL-6 regulation of muscle protein turnover during the initiation and progression of cachexia in the Apc(Min/+) mouse is not known. Cachexia progression was studied in Apc(Min/+) mice that were either weight stable (WS) or had initial (≤5%), intermediate (6-19%), or extreme (≥20%) body weight loss. The initiation of cachexia reduced %MPS 19% and a further ∼50% with additional weight …

Cucurbit[8]Uril Rotaxanes, Vijayakumar Ramalingam, Adam R. Urbach

Chemistry Faculty Research

The synthesis of [2]rotaxanes, each comprising a viologen core threaded through a cucurbit[8]uril (Q8, Figure 1) macrocycle and stoppered by tetraphenylmethane groups, and their binding to second guests as inclusion complexes in organic and aqueous media are described. Stoppering was observed to have little effect on binding. Chemical modification of the threaded guest was used to control solubility and binding characteristics, thus demonstrating a novel approach to making artificial receptors with readily modifiable properties.

Efficient Quantum Trajectory Representation Of Wavefunctions Evolving In Imaginary Time, Sophya V. Garashchuk, James Mazzuca, Tijo Vazhappilly

Faculty Publications

The Boltzmann evolution of a wavefunction can be recast as imaginary-time dynamics of the quantum trajectory ensemble. The quantum effects arise from the momentum-dependent quantum potential – computed approximately to be practical in high-dimensional systems – influencing the trajectories in addition to the external classical potential [S. Garashchuk, J. Chem. Phys.132, 014112 (2010)]. For a nodelesswavefunction represented as ψ(x, t) = exp ( − S(x, t)/ℏ) with the trajectory momenta defined by ∇S(x, t), analysis of the Lagrangian and Eulerian evolution shows that for bound potentials the former …

Green Decarbonylation Of Aldehydes Using Palladium (Ii) Acetate, Jessica Konopka

Pell Scholars and Senior Theses

Decarbonylation reactions are important reactions in the chemical industry with typical methods being costly and wasteful. It is important to determine an effective catalyst and to see how general the reaction is with varying aldehydes, as well as to reduce the waste and make the reaction more cost effective. Several different aldehydes were studied using palladium (II) acetate as a catalyst. The samples were analyzed using Gas Chromatography Mass Spectroscopy (GC-MS) to determine if a product was formed based on the percent report obtained. Palladium (II) acetate was found to be an effective catalyst, yielding 100% product for several aldehydes …

Utilizing Service-Learning In The Analytical Chemistry Laboratory: Soil And Water Analysis In Rochester, New York, Kimberly D. Chichester, Irene Kimaru, Lynn Donahue, Maryann Herman

Chemistry Faculty/Staff Publications

For an analytical chemistry course at St. John Fisher College, instructors designed a servicelearning project on soil and water analysis to achieve the following two goals: 1) to introduce analytical chemistry students to soil- and water-testing methods by working in collaboration with surrounding neighborhoods residents and government agencies and 2) to prepare written reports of the results for the designated community partners. Service-learning students conducted soil testing for lead on homes and perspective community garden sites around Rochester, NY with plans to establish planting methods to revitalize polluted soil. Four different communities contributed soil samples. The entire project was performed …

Chemistry In Second Life. Part 2. A World Of Education And Networking, Andrew Lang, Jean-Claude Bradley

College of Science and Engineering Faculty Research and Scholarship

Second Life visualisations can be scripted for immersive educational activities and real-life collaborative research. Social networking through Second Life is another spin-off for both chemists and chemistry students.

Cacao Use And The San Lorenzo Olmec, Terry G. Powis, Ann Cyphers, Nilesh W. Gaikwad, Louis Grivetti, Kong Cheong

Faculty and Research Publications

Mesoamerican peoples had a long history of cacao use—spanning more than 34 centuries—as confirmed by previous identification of cacao residues on archaeological pottery from Paso de la Amada on the Pacific Coast and the Olmec site of El Manatí on the Gulf Coast. Until now, comparable evidence from San Lorenzo, the premier Olmec capital, was lacking. The present study of theobromine residues confirms the continuous presence and use of cacao products at San Lorenzo between 1800 and 1000 BCE, and documents assorted vessels forms used in its preparation and consumption. One elite context reveals cacao use as part of a …

Chemistry In Second Life. Part 1. A World Of Visualisation, Andrew Lang, Jean-Claude Bradley

College of Science and Engineering Faculty Research and Scholarship

The multi-user virtual environment of Second Life is not limited tothe realms of role-play or romance. It can be a platform for the interactive and collaborative visualisation of molecules, spectraand experimental data.

An Assessment Of Stable Hydrogen-Isotope Analysis Methods To Assign Geographic Origin To Migratory Red-Tailed Hawks (Buteo Jamaicensis), Carla Marie Ahlschwede

Department of Environmental Studies: Undergraduate Student Theses

Stable-hydrogen isotopes are becoming an increasingly popular method of studying migratory birds, though sample preparation methods may affect results. In this study I examined feathers from red-tailed hawks (Buteo jamaicensis) to determine the relationship between measure of δD due to inter-feather variation or drying methods, assessed the accuracy of results by using two birds of known-origin and estimated possible natal origins of migratory red-tailed hawks. Two feathers per individual were taken from 81 wild hawks caught at Hitchcock Nature Center near Crescent IA and from 2 rescued red-tailed hawks, Raptor Recovery Nebraska near Eagle, NE. 119 of the …

Slow Magnetic Relaxation And Electron Delocalization In An S = 9/2 Iron(Ii/Iii) Complex With Two Crystallographically Inequivalent Iron Sites, Susanta Hazra, Sujit Sasmal, Michel Fleck, Fernande Grandjean, Moulay T. Sougrati, Meenakshi Ghosh, T. David Harris, Pierre Bonville, Gary J. Long, Sasankasekhar Mohanta

Chemistry Faculty Research & Creative Works

The magnetic, electronic, and Mössbauer spectral properties of Fe ₂L(µ-OAc)₂ClO₄, 1, where L is the dianion of the tetraimino-diphenolate macrocyclic ligand, H₂L, indicate that 1 is a class III mixed valence iron(II/III) complex with an electron that is fully delocalized between two crystallographically inequivalent iron sites to yield a [Fe₂]^V cationic configuration with a S_t 9/2 ground state. Fits of the dc magnetic susceptibility between 2 and 300K and of the isofield variable-temperature magnetization of 1 yield an isotropic magnetic exchange parameter, J, of -32(2) cm^-1 for an …

A Bis-Urea Naphthalene Macrocycle Displaying Two Crystal Structures With Parallel Ureas, Michael F. Geer, Mark D. Smith, Linda S. Shimizu

Faculty Publications

Herein we synthesized a bis-urea macrocycle from 2,7-dimethylnaphthalene that displays an unusual parallel urea conformation. The naphthalenes also adopt a bowl shape over the anticipated parallel planar orientation. Crystallization of the macrocycle from different solvent systems affords two solvated forms. 1·DMSO·(H₂O)₂ has an extended columnar structure where parallel macrocycles are linked by intervening hydrogen bonded water molecules. In 1·(MeOH)₂direct hydrogen-bonds link the macrocycles into chains, which hydrogen-bond with methanolmolecules to form a layered structure.

Her2 Targeted Molecular Mr Imaging Using A De Novo Designed Protein Contrast Agent, Jingjuan Qiao, Shunyi Li, Lixia Wei, Jie Jiang, Robert Long, Hui Mao, Ling Wei, Liya Wang, Hua Yang, Hans E. Grossniklaus, Zhi-Ren Liu, Jenny J. Yang

Chemistry Faculty Publications

The application of magnetic resonance imaging (MRI) to non-invasively assess disease biomarkers has been hampered by the lack of desired contrast agents with high relaxivity, targeting capability, and optimized pharmacokinetics. We have developed a novel MR imaging probe targeting to HER2, a biomarker for various cancer types and a drug target for anti-cancer therapies. This multimodal HER20targeted MR imaging probe integrates a de novo designed protein contrast agent with a high affinity HER2 affibody and a near IR fluorescent dye. Our probe can differentially monitor tumors with different expression levels of HER2 in both human cell lines and xenograft mice …

Joule, John A. Heterocyclic Chemistry (Book Review), Jeffrey H. Glans

Chemistry & Physics Faculty Publications

Book review by Jeffrey H. Glans.

Joule, John A. and Keith Mills. "A Heterocyclic Chemistry. 5th ed. Wiley-Blackwell, 2010.

ISBN 9781405193658 (hardcover); 9781405133005 (pbk.)

Study Of The Interactions Between Elodea Canadensis And Cuo Nanoparticles, M. E. Johnson, S. A. Ostroumov, Julian Tyson, B. Xing

Chemistry Department Faculty Publication Series

No abstract provided.

The Complexity Of Reform Efforts In Science Curriculum And Instruction: A Case Study Of The Illinois Mathematics And Science Academy Chemistry Teacher, Tang Wee Teo

IMSA History

This study explores how teacher-initiated site-based reform in a specialized STEM school is conceptualized and enacted, how and why curriculum reform ideas change in the process of enactment, what qualities of teacher agency are entailed, how these qualities are acquired, interplayed, become generative, and/or are influenced to effect different curriculum reform outcomes, and how different conditions support and further teacher agency to make a more defensible curriculum.

In a critical case study of a highly experienced and qualified science teacher, I follow a teacher who initiated efforts to reform the advanced chemistry curriculum. This teacher wanted to make the curriculum …