iDEA Collection: Faculty Research and Publications (Chemistry)

Reaction Attempts Edition 1: the UsefulChem Project

Wed, 28 Apr 2010 23:39:47 GMT

Title: Reaction Attempts Edition 1: the UsefulChem Project

Authors: Bradley, Jean-Claude; Mirza, Khalid; Lang, Andrew; Bohinski, Tim; Bulger, David; Merchant, Alicia; Messner, Emily; Moritz, Marshall; Oseback, Shannon; Parikh, Rikesh; Shah, Mitesh

Abstract: This book is a compilation of Ugi reactions attempted for the UsefulChem Project mainly in the Bradley laboratory at Drexel University. The entries are sorted alphabetically based on reactants. Links are provided to the relevant lab notebook pages.

Description: For more information: http://onsbooks.wikispaces.com/Reaction+Attempts Licensed under a Creative Commons Attribution 2.5 License

ONS Solubility Challenge Notebook Archive 2010-02-11

Fri, 12 Feb 2010 21:06:42 GMT

Title: ONS Solubility Challenge Notebook Archive 2010-02-11

Authors: Lang, Andrew; Neylon, Cameron; Guha, Rajarshi; Williams, Antony; Hooker, Bill; Friesen, Brent; Bohinski, Tim; Bulger, David; Federici, Matthew; Hale, Jenny; Mancinelli, Jenna; Mirza, Khalid; Moritz, Marshall; Rein, Daniel; Tchakounte, Cedric; Truong, Hai

Abstract: This is the first edition to include a full archive of the ONS Challenge notebook. A space export from Wikispaces provides an initial version of all the HTML pages in the notebook with local hyperlinks to copies of all images and files uploaded onto the wiki. All of the Google Spreadsheets are automatically downloaded as Excel spreadsheets and placed in the same "files" folder as the images. NMR spectra, stored as JCAMP-DX files, are placed in the "spectra" folder. All of the HTML pages are reformatted to provide local references to both Excel spreadsheets and the JCAMP-DX files. The notebook archive is meant to represent a snapshot of the state of all source documents at the time of the publication of an edition of this book. When used from a server with web services running, clicking on links to the spectra will allow interaction via a browser interface, including zooming in or out and integration of the NMR spectrum. When accessed in stand-alone mode after downloading or directly from a CD, everything will work the same, except that JCAMP-DX files must be open from JSpecView running on the desktop. Excel files will retain any calculations in the cells of the original Google Spreadsheets but dynamic values generated from calling web services - such the script that automatically integrates NMR spectra - will be frozen as simple values. However the link to the web service used will be stored in the cell as a comment. Links to external websites are not crawled and embedded Google Spreadsheets or videos are not copied. These will work but will reflect live data on the web.

Description: This archive contains the source files for the book "Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents" (3RD) available from http://www.lulu.com/content/paperback-book/open-notebook-science-challenge-solubilities-of-organic-compounds-in-organic-solvents-%283rd%29/8337972 Begin with the file entitled List of Experiments.html

Identification of a novel lysophospholipid acyltransferase in Saccharomyces cerevisiae

Sun, 29 Oct 2006 22:58:59 GMT

Title: Identification of a novel lysophospholipid acyltransferase in Saccharomyces cerevisiae

Authors: Shilpa, Jain; Stanford, NaTaza; Bhagwat, Neha; Seiler, Brian; Costanzo, Michael; Boone, Charles; Oelkers, Peter

Abstract: The incorporation of unsaturated acyl chains into phospholipids during de novo synthesis is primarily mediated by the 1-acylsn- glycerol-3-phosphate acyltransferase reaction. In S. cerevisiae, Slc1 has been shown to mediate this reaction but distinct activity remains after its removal from the genome. To identify the enzyme that mediates the remaining activity, we performed synthetic genetic array analysis using a slc1Δ strain. One of the genes identified by the screen, LPT1, was found to encode for an acyltransferase that uses a variety of lysophospholipid species, including 1-acyl-sn-glycerol-3-phosphate. Deletion of LPT1 had a minimal effect on 1-acyl-snglycerol- 3-phosphate acyltransferase activity but over-expression increased activity 7-fold. Deletion of LPT1 abrogated the esterification of other lysophospholipids and over-expression increased lysophosphatidylcholine acyltransferase activity 7-fold. The majority of this activity co-purified with microsomes. To test the putative role for this enzyme in selectively incorporating unsaturated acyl chains into phospholipids, in vitro, substrate concentration series experiments were performed with the four acyl-CoA species commonly found in yeast. While the saturated palmitoyl-CoA and stearoyl-CoA showed a lower apparent Km, the monounsaturated palmitoleoyl-CoA and oleoyl-CoA showed a higher apparent Vmax. Arachidonyl-CoA, although not abundant in yeast, also had a high apparent Vmax. Pulse-labeling of lpt1Δ strains showed a 30% reduction in [3H]oleate incorporation into phosphatidylcholine only. Therefore, Lpt1p, a member of the membrane bound o-acyltransferase gene family, seems to work in conjunction with Slc1 to mediate the incorporation of unsaturated acyl-chains into the sn-2 position of phospholipids.

Asymmetric band profile of the Soret band of deoxymyoglobin is caused by electronic and vibronic perturbations of the heme group rather than by a doming deformation

Wed, 03 Oct 2007 22:58:59 GMT

Title: Asymmetric band profile of the Soret band of deoxymyoglobin is caused by electronic and vibronic perturbations of the heme group rather than by a doming deformation

Authors: Schweitzer-Stenner, Reinhard; Gorden, John Paul; Hagarman, Andrew

Abstract: We measured the Soret band of deoxymyoglobin deoxyMb , myoglobin cyanide MbCN , and aquo-metmyoglobin all from horse heart with absorption and circular dichroism CD spectroscopies. A clear non-coincidence was observed between the absorption and CD profiles of deoxyMb and MbCN, with the CD profiles red- and blueshifted with respect to the absorption band position, respectively. On the contrary, the CD and absorption profiles of aquametMb were nearly identical. The observed noncoincidence indicates a splitting of the excited B state due to heme-protein interactions. CD and absorption profiles of deoxyMb and MbCN were self-consistently analyzed by employing a perturbation approach for weak vibronic coupling as well as the relative intensities and depolarization ratios of seven bands in the respective resonance Raman spectra measured with B-band excitation. The respective By component was found to dominate the observed Cotton effect of both myoglobin derivatives. The different signs of the noncoincidences between CD and absorption bands observed for deoxyMb and MbCN are due to different signs of the respective matrix elements of A1g electronic interstate coupling, which reflects an imbalance of Gouterman’s 50:50 states. The splitting of the B band reflects contributions from electronic and vibronic perturbations of B1g symmetry. The results of our analysis suggest that the broad and asymmetric absorption band of deoxyMb results from this band splitting rather than from its dependence on heme doming. Thus, we are able to explain recent findings that the temperature dependences of CO rebinding to myoglobin and the Soret band profile are uncorrelated Ormos et al., Proc. Natl. Acad. Sci U.S.A. 95, 6762 1998 .

Interactions of methane, ethane and pentane with the (110C) surface of γ−alumina

Sun, 08 Apr 2007 22:58:59 GMT

Title: Interactions of methane, ethane and pentane with the (110C) surface of γ−alumina

Authors: Cai, Shu-Hui; Chihaia, Viorel; Sohlberg, Karl

Abstract: Adsorptions of methane, ethane and pentane on the γ-alumina (110C) surface are investigated with semi-empirical (PM3) cluster calculations. It is found that the abstraction of an H atom accompanied by the formation of a C-O bond is the most favorable reaction for methane on the alumina surface. For ethane- and pentane-alumina interactions, the abstraction of two H atoms accompanied by the formation of an alkene is the most favorable reaction. The surface Al atoms help to promote the reactions, but are not directly involved in the bond formation.

Migration of aluminum atoms in the transformation of γ− to θ−alumina

Mon, 29 Oct 2001 22:58:59 GMT

Title: Migration of aluminum atoms in the transformation of γ− to θ−alumina

Authors: Cai, Shu-Hui; Sohlberg, Karl

Abstract: γ− and θ−alumina are two metastable phases of aluminum oxide observed along the thermal dehydration sequence of boehmite before conversion to the final product α−alumina. The transformation from γ− to θ−alumina was studied by using Al16O24 cells. Motion of some Al atoms from their γ−alumina positions to new positions and no O motions result in an approximate structure that, upon relaxation by first-principles calculations, becomes the known θ−alumina structure. Total-energy calculations along the paths of the atomic motions have been used to map out transformation pathways. The model accurately predicts experimentally observed domain boundaries in θ−alumina and the γ− to θ−alumina conversion rate.

Correlation of substituent parameter values to electronic properties of molecules

Tue, 29 Oct 2002 22:58:59 GMT

Title: Correlation of substituent parameter values to electronic properties of molecules

Authors: Carroll, Natalie R.; Matsunaga, Nikita; Sohlberg, Karl

Abstract: There are a vast number of organic compounds that could be considered for use in molecular electronics. Because of this, the need for efficient and economical screening tools has emerged. We have demonstrated that the substituent parameter values (σ), commonly found in advanced organic chemistry textbooks, correlate very strongly with features of the charge migration process. This result supports the use of the σ values as a low cost time saving tool in the selection of compounds for use in molecular electronic devices.

The thermodynamic stability of three near-degenerate phases of platinum dioxide

Fri, 29 Oct 2004 22:58:59 GMT

Title: The thermodynamic stability of three near-degenerate phases of platinum dioxide

Authors: Zhuo, Shuping; Sohlberg, Karl

Abstract: The thermodynamic stability of the three nearly energy degenerate crystal structures of PtO2 is studied here with first-principles-based calculations of their free energies. For P = 0 the α-(CdI2) structure is the thermodynamically stable phase at low temperature, while the β-(CaCl2) structure is stable at high pressure. The β'- (rutile) structure represents an unstable fixed point on the potential energy surface, or is possibly just barely bound. These results reconcile seemingly contradictory findings and answer longstanding questions about PtO2.

Gao et al. Reply

Fri, 28 Sep 2001 22:58:59 GMT

Title: Gao et al. Reply

Authors: Gao, H. J.; Sohlberg, Karl; Xue, Z. Q.; Chen, H.Y.; Hou, S. M.; Ma, L. P.; Fang, X.W.; Pennycook, Stephen J.

The Influence of Surface Reconstruction and C-impurities on Photocatalytic Water Dissociation by TiO2

Wed, 29 Oct 2003 22:58:59 GMT

Title: The Influence of Surface Reconstruction and C-impurities on Photocatalytic Water Dissociation by TiO2

Authors: Nie, Xiliang; Sohlberg, Karl

Abstract: TiO2 is well known as a prototype photocatalyst for water dissociation. To understand the mechanism of its photocatalytic water dissociation we performed first-principles calculations. We find that the surface of the catalytically favorable (TiO) termination is very different from the physically favorable (oxygen) termination. The calculated surface energy of the catalytically favorable (TiO) termination is about 10 times larger than that of the physically favorable (oxygen) termination. Analysis of the surface band structure suggests that while O-vacancies are intrinsic active sites for water dissociation into H2 and O2 gas, they are not essential for photocatalytic water dissociation. We also find that carbon impurities decrease the band-gap of TiO2, in agreement with previously reported experimental results. Moreover, we identify the origin of the arcane “double band gap” in carbon doped TiO2. The two onsets seen in the photoabsorption spectrum result from excitations from two of three C p-states within the band gap, not from domains of different composition.