Table of Contents
- Chem 397, 497 or 498
- Faculty Research Interests
- Chemistry 397
- Chemistry 497
- Chemistry 498
This brochure describes the diverse research areas available in the Chemistry Department for undergraduate research. Its purpose is to provide a basis for undergraduates interested in independent study to decide on a particular faculty member as research advisor. Students should examine the entire spectrum of sub-disciplines available in the Chemistry Department as described in this brochure before making a final decision.
Undergraduate chemical education in the United States, and at SUNY Binghamton in particular, is designed to provide a sound theoretical understanding of the principles of chemistry through lecture courses and the application of these principles through laboratory courses. By its very nature, however, traditional chemistry courses cannot give an undergraduate the experience of working in a research group, in which current research areas are investigated using modern and sophisticated techniques. Furthermore, hands-on experience in a research group is essential for a student to gain the actual working knowledge required in an industrial, governmental, or academic research environment. For these reasons, the Chemistry Department offers Chem 397 (Independent Study) and Chem 497 (Advanced Independent Study) to provide undergraduates with this kind of research experience. Students considering a career in chemistry or related fields should seriously consider enrolling in these courses. For Chemistry majors, four credits of Chem 397 and twelve credits total of independent research can count toward satisfying the elective requirements for the BA and BS degree.
Chemistry 397 (Independent Study) provides an introduction to basic research. The actual format of the study will depend on the particular faculty research advisor, but typically will include a search of the relevant literature, an introduction to the pertinent experimental and/or computational methods, original research on a particular topic, and participation in research group meetings. Students who contribute significantly to a research project are included as co-authors in publications arising from the research.
Those students previously enrolled in Chem 397 may want to continue research on a more advanced level and enroll in Chem 497 (Advanced Independent Study). Chem 497 requires more extensive preparation than Chem 397, including a written summary of the proposed research. Students may wish to continue further with their research project and enroll in Chem 498 (Advanced Independent Study - Honors) during their last semester at Binghamton University. Chem 498 is the highest level of research an undergraduate can do. It is the baccalaureate equivalent of doctoral research, and requires a written thesis and defense of the thesis before a faculty committee.
To apply for Chem 397, 497 or 498, undergraduates should follow these steps:
- Please read the guidelines for Independent Study found at the back of this booklet.
- Peruse this brochure and identify several faculty members whose research interests you.
- Make an appointment and talk with the faculty members about their research and about the opportunities for undergraduate independent research in their research groups.
- Chose a faculty member willing to act as research supervisor.
- Fill out an application for independent study (available in the departmental office), have the faculty member sign the application, and submit the application to the departmental office (S2 236).
FACULTY RESEARCH INTERESTS
- Assistant Professor
- Organic Chemistry
Dr. An received his B.S. in Chemistry (Honors thesis) and Cellular Molecular Biology from the University of Michigan, Ann Arbor (1996). His Ph.D. in Chemistry focused on organic synthesis and mechanistic enzymology, received under the supervision of Prof. Paul A. Bartlett at the University of California, Berkeley (2003). He also did post¬doctoral research at the University of California, San Francisco, and he was Anna Fuller Fund Postdoctoral Fellow in Molecular Oncology with Prof. Donald M. Engelman at Yale University. He joine Binghamton University faculty in the fall of 2011.
My research interests are in the general areas of organic, bio-organic, biological, and pharmaceutical chemistry, as well as chemical biology. At present time, we are focused on the development of DMA and pHLIP prodrugs to improve cancer chemotherapy by targeting tumor acidosis.
DMA prodrugs. Many cancerous tumors have extracellular pH (pHe) in the range of 6.5-7.0, with average pHe of ~ 6.8, compared with that of 7.2-7.4 in healthy tissues. This small difference of about half pH unit presents an exciting novel opportunity, as well as a great challenge, for selective drug delivery to cancer cells. Tumor acidosis can reduce the effectiveness of chemotherapy by decreasing the membrane permeability of amine drugs such as doxorubicin (Dox), topotecan, and vinblastine. Current pH-sensitive cleavable linkers, such as ketal, acetal, cyclic orthoester, imine, acylhydrazone, boronate, and mono-substituted maleamic acid (i.e. cis-aconityl linker), can respond to endosomal acidity of pH 4.5-6.0, but they are not sensitive enough for triggering by tumor acidosis pHe. To address this need, we studied the super-sensitive, di-substituted maleamic acid (DMA) linker and found that it cleaves at pH 6.5 to release ~ 67% Dox (free drug) in 24 hr compared to ~18% Dox release at pH 7.4. The pH 6.5/7.4 release ratio is improved from the previous known best of 2:1 (in terms of drug released, using cyclic orthoester) to ~ 4:1 (using DMA). We also learned that the closed maleimide form (DMI) is a major side-product (15-60%) during drug release at all pH values, as well as a convenient synthetic precursor of DMA for ease of handling and storage. Finally, conjugating Dox to glutathione (used as a membrane-impermeable peptide) via DMA gave a prodrug of Dox that is more cytotoxic under acidic conditions than neutral pH, reversing the pH-profile of free drug cytotoxicity. Such DMA-linked prodrug of Dox may improve chemotherapy by reducing off target side-effects.
pHLIP prodrugs. Malignant tumors create acidic environments. The pH Low Insertion Peptide (pHLIP) can be used as a sensor for tumor acidic environments. In response to slight acidity, pHLIP forms a transmembrane helix in an unidirectional fashion with the C-terminus inserted through the lipid bilayer. Conjugating cargo molecules to the C-terminal region of pHLIP allows for cytoplasmic delivery of drugs. To evaluate pHLIP as a prodrug delivery system, Taxol or Doxorubicin (Dox) was conjugated to a C-terminal Cys via disulfide cleavable linkers for a number of pHLIP variants (WT, P20G, Asp14Gla/Asp25Aad, etc.). These pHLIP-drug conjugates were evaluated in anti-proliferation assays with various tumor cell lines (A549 lung cancer, PC-3 prostate cancer, MDA-MB-231 breast cancer, Skov3 ovarian cancer, and U87MG brain cancer) as well as noncancerous kidney cells (HK2). We learned that P20G and Asp14Gla/Asp25Aad pHLIP-Taxol exhibited greater anti-growth effects at pH 6.6 than 7.4. The effect of a hydrophobic cargo such as Taxol (MW 854, log P ~ 4) on pHLIP-membrane interactions was also studied using biophysical methods (CD, Trp fluorescence). For all pHLIP variants, pHLIP-Taxol demonstrated deeper imbedding in lipid bilayer in the membrane-adsorbed state at pH 7.4, as well as an increase in pH50 of insertion. Tumor acidosis can contribute to drug resistance as Dox is more membrane-impermeable, and thus more cytotoxic, at pH 7.4 than 6.6, exacerbating side-effects at healthy tissues. We showed that conjugation to pHLIP can reverse the pH-profile of Dox cytotoxicity. Two disulfide linkers were used either conjugating the linker to the amine group of Dox through a carbamate (self-immolative) or amide, both demonstrated pH dependents. Furthermore, various near IR dyes were conjugated to pHLIP-drug to study drug retention effects at the tumor in vivo, as well as nanoparticle formulation of pHLIP-drug for the purpose of bringing more pHLIP-drug to the tumor.
TYPES OF RESEARCH EXPERIENCE AVAILABLE
Organic synthesis, peptide synthesis and purification (HPLC), bio-conjugate and peptide chemistry, biophysical characterization (model membrane systems, liposomes, fluorescence, UV/vis, CD), and cell culture work.
Courses (none). The earlier you try out for research the better. Freshmen / sophomores preferred over juniors. Students should read the relevant publications before meeting with Professor. GPA 3.0 or above.
Interest leads to motivation, which in turn leads to commitment of time. Thus, genuine interest is of highest priority. Students should commit to at least two semesters (in the same lab), and are expected to do > 15 h per week of lab work (in > 4 h time blocks).
Real scientific research is frustrating most of the time (and the reward is often no more than the work itself). Therefore, self-motivation, patience (i.e. a balance between passion about the work at large and a cool detachment from negative results), attention to detail, and an ability to think about what you are doing (the experimental task at hand) are all very necessary to make this a safe and enjoyable experience.
Hanz, S. Z.; Shu, N. S.; Qian, J.; Christman, N.; Kranz, P.; An, M.; Grewer, C.; Qiang, W.; “Protonation-driven membrane insertion of the pH-low insertion peptide” Angew. Chem. Int. Ed. 2016, accepted. DOI: 10.1002/anie.201605203R1 and 10.1002/ange.201605203R1.
Shu, N. S.; Chung, M. S.; Yao, L.; An, M.; Qiang, W.; “Residue-specific Structures and Membrane Locations of the pH-Low Insertion Peptide by Solid-state NMR Spectroscopy” Nature Communications, 2015, 6, 7787. doi: 10.1038/ncomms8787.
Onyango, J. O.; Chung, M. S.; Eng, C.-H.; Klees, L. M.; Langenbacher, R.; Yao, L.; An, M.; “Noncanonical Amino Acids Improve the pH-response of pHLIP Insertion at Tumor Acidity” Angew. Chem. Int. Ed. 2015, 54, 3658-3663.
Karabadzhak, A. G.; An, M.; Yao, L.; Langenbacher, R.; Moshnikova, A.; Adochite, R.; Andreev, O. A.; Reshetnyak, Y. K.; and Engelman, D. M.; “pHLIP-FIRE, a Cell Insertion-Triggered Fluorescent Probe for Imaging Tumors Demonstrates Targeted Cargo Delivery In Vivo” ACS Chem. Biol. 2014, 9, 2545-2553.
An, M.; Wijesinghe, D.; Andreev, O.; Reshetnyak, Y.; and Engelman, D. M.; “pHLIP Translocation of Membrane Impermeable Phalloidin Toxin Inhibits Cancer Cell Proliferation” Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 20246-20250.
- Bioorganic and Biophysical Chemistry
Dr. Bane received her B.S. in Chemistry from Davidson College (1980) and Ph.D. in Biochemistry from Vanderbilt University (1983). She did postdoctoral research in Bioorganic Chemistry at the University of Virginia, joining the SUNY Binghamton faculty in 1985.
My research interests are in Chemical Biology. Chemical Biology is a relatively new term used to describe the study of the chemistry that underlies all biological structure and processes. We use the principles, theories and tools that have been traditionally applied to small molecules and apply them to investigate biologically important systems. Consequently, we draw from diverse areas of chemistry and biology - ranging from computational chemistry to cell biology - to solve a biological problem.
We have two general areas of current interest: (1) Microtubules. Microtubules occupy a central role in the life of a cell. Examine any cellular function that involves movement - division, directional migration, transport - and microtubules are likely to be found. These structures are a dynamic assemblage of several proteins. The central core of the microtubule is composed entirely of the protein tubulin, which is also the most abundant protein in the tubule. The exterior of the microtubule is decorated with proteins collectively termed microtubule-associated proteins, which are implicated in interactions between microtubules and other elements of the cell. Virtually nothing is known about the interior of the microtubules. We are using organic chemistry, photochemistry, cell biology and protein techniques to discover and identify proteins in the microtubule lumen. (2) Bioorthogonal Chemistry. Bioorthogonal chemistry involves chemical reactions that can take place under conditions compatible with living organisms. A critical aspect of this chemistry is that the reactive species are selective for one another and do not irreversibly react with the myriad of functional groups in the natural system. There are many applications of this type of chemistry, such as coupling drugs to carriers (such as antibodies) for chemotherapy and tagging individual biomolecules with fluorophores to monitor their behavior inside cells,
TYPES OF RESEARCH EXPERIENCE AVAILABLE
Our studies require the use of protein biochemistry, synthetic organic chemistry, and spectroscopic (NMR, fluorescence, UV/vis and CD) techniques. More advanced students may be engaged in cell culture. An individual student's project will generally emphasize one of these areas, depending on the student's interest and the current needs of the program
Courses: Introductory Chemistry (107 and 108 or 111), Chemistry 231, 332 and 335. For students with interest in the biological aspects of this work, a course in Biochemistry is recommended but not required.
Students interested in research in our lab should read the following reviews prior to meeting with Professor Bane:
- Sletten, E. M., and Bertozzi, C. R. (2009) Bioorthogonal chemistry: fishing for selectivity in a sea of functionality, Angewandte Chemie (International ed. in English) 48, 6974-6998.
- E. Nogales “Structural insights into microtubule function.” Annual Review of Biochemistry, 2000, 69, 277-302.
Appropriate interests, motivation and responsible commitment of time are essential. Students interested in independent study should plan on spending at least two semesters in the research lab and expect to devote a minimum of 15 hours/week to research. In my lab, it is essential that a student have large blocks of time available between 9 am and 5 pm, as most experiments require at least 4 hours to perform.
A research lab is very different from a laboratory class. It is rare for an experiment to work the first time (or the second time or even the third time). The research student must be prepared and willing to engage in a great deal of troubleshooting!
"Dissecting paclitaxel-microtubule association: Quantitative assessment of the 2 '-OH group." Sharma S, Lagisetti C, Poliks B, Coates RM, Kingston DGI, Bane S. 2013. Biochemistry 52, 2328-2336.
"Site-specific fluorescent labeling of tubulin." Mukherjee K, Bane SL. 2013. Methods in Cell Biology (Microtubules, In Vitro) 115, 1-12
“Aromatic Hydrazine-Based Fluorophores: Synthesis, Spectroscopy and Bioapplications.” Dilek O, Bane S. 2013. In Fluorophores: Characterization, Synthesis and Applications, ed. S Watanabe, pp. 53-76: Nova Science Publishers
"Aurones: Small Molecule Visible Range Fluorescent Probes Suitable for Biomacromolecules." Shanker N, Dilek O, Mukherjee K, McGee DW, Bane SL. 2011. Journal of Fluorescence 21, 2173-2184.
"4-Aminophenylalanine as a biocompatible nucleophilic catalyst for hydrazone ligations at low temperature and neutral pH." Blanden AR, Mukherjee K, Dilek O, Loew M, Bane SL. 2011. Bioconjugate Chemistry 22, 1954-1961.
"Site-specific orthogonal labeling of the carboxy terminus of alpha-tubulin." Banerjee A, Panosian TD, Mukherjee K, Ravindra R, Gal S, Sackett DL, Bane S. 2010. ACS Chemical Biology 5, 777-785.
"Characterization of the Colchicine Binding Site on Avian Tubulin Isotype beta VI." Sharma S, Poliks B, Chiauzzi C, Ravindra R, Blanden AR, Bane S. 2010. Biochemistry 49, 2932-2942.
"Synthesis, biological activity and tubulin binding poses of 1-deoxy-9-(R)-dihydrotaxane analogs." Yuan TH, Jiang Y, Wang XH, Wang DL, Bannerjee A, Bane S, Snyder JP, Lin HX. 2009. Bioorganic & Medicinal Chemistry Letters 19, 1148-1151.
"Synthesis of boron dipyrromethene fluorescent probes for bioorthogonal labeling." Dilek Ö, Bane SL. 2008. Tetrahedron Letters 49, 1413-1416.
"Rotational-echo double-resonance NMR distance measurements for the tubulin-bound paclitaxel conformation." Paik Y, Yang C, Metaferia B, Tang SB, Bane S, Ravindra R, Shanker N, Alcaraz AA, Johnson SA, Schaefer J, O'Connor RD, Cegelski L, Snyder JP, Kingston DGI. 2007. Journal of the American Chemical Society 129, 361-370.
"Molecular Features of the Interaction of Colchicine and Related Structures with Tubulin." Bane S. 2008. In The Role of Microtubules in Cell Biology, Neurobiology, and Oncology, ed. T Fojo, pp. 259-279: Humana Press
"Design, synthesis, and bioactivity of simplified paclitaxel analogs based on the T-Taxol bioactive conformation." Thota Ganesh, A. Norris, Susan Bane, A. A. Alcaraz, James P. Snyder, and David G. I. Kingston 2006. Bioorganic & Medicinal Chemistry, 14, 3447-3454.
- Assistant Professor of Chemistry and Biochemistry
- Interests in Chemical Biology
Dr. Callahan received his B.S. magna cum laude from SUNY Cortland (1996) and his PhD in Biochemistry and Biophysics from the University of North Carolina, Chapel Hill (2005). His postdoctoral research (2006-2012) was carried out at the Wadsworth Center and at the University at Albany, funded in part by an NIH fellowship in Biodefense and Emerging Infectious Disease. He joined the Chemistry Department at Binghamton University in the Fall of 2012.
Synopsis: We investigate the chemical biology of protein biogenesis and protein degradation, two essential events in the expression of genetic information.
Protein Biogenesis: A number of disease-related genes encode precursor polypeptides that require specific chemical processing to yield biologically active proteins. We investigate the chemical biology of this event, called protein biogenesis. Of particular interest is the autocatalytic biogenesis of proteins by HINT domains. These ~25 kDa sequences activate hedgehog and intein-containing precursors through an intricate self-splicing reaction. HINT domains are conserved in evolution and have been implicated in a wide-range of important human diseases, including tuberculosis, birth defects, and cancer. The absence of solution assays to monitor HINT activity together with a paucity of high-resolution structural data on eukaryotic HINT domains have presented major roadblocks to detailed studies in this area. We aim to address these gaps and thereby pursue our research objectives, which include:
- To exploit HINT domains as therapeutic targets for birth defects and for sporadic tumors.
- To engineer HINT domains for the biosynthesis of chemically modified proteins for imaging and medicine.
- To identify and characterize the structure of reactive intermediates formed during HINT self-splicing.
Protein Degradation: An additional area of research centers on the design of genetically encoded biosensors. We are particularly interested in designing biosensors to detect the action of proteolytic enzymes, or proteases. Recently we engineered green fluorescent protein (GFP) to function as the first fluorogenic biosensor of protease activity. We are now developing a variegated family of protease biosensors from spectrally distinct fluorescent proteins to facilitate assay multiplexing. A related project seeks to exploit our GFP biosensor to define the substrate specificity of novel proteases as well as to "breed" proteases that cleave at user-defined sequences. Future studies in this area will involve adapting the technology for use in cultured mammalian cells and in animals, with the goal of visualizing protease-initiated cell signaling pathways, such as apoptosis.
Student-driven research projects in these areas may involve enzyme kinetics, site-directed mutagenesis, small-molecule chemistry, bioseperations, and multiple types of spectroscopy. Highly motivated students willing to dedicate 12-15 hrs per week of laboratory time are encouraged to apply.
Required course work: Students will have completed Organic chemistry I and Organic lab. Courses in Biochemistry and Bioorganic Chemistry are also recommended
Callahan B.P.; Topilina, N., Stanger M.; Van Roey; P., Belfort M. Structure of a catalytically competent intein caught in a redox trap with functional and biological implications. Nat. Struct. Mol. Biol. (2011b) 18, 630-3.
Zhang L, Zheng, Y, Callahan B., Belfort M., Liu, Y. Cisplatin as a protein splicing inhibitor suggesting inteins as therapeutic targets in mycobacteria J. Biol. Chem. (2011a) 286, 1277-82 (Highlighted in Nature Chemical Biology)
Callahan B.P., Stanger M., Belfort M. Protease activation of split green fluorescent protein ChemBioChem (2010b) 11, 2259-63.
Callahan B., Nguyen K., Gormley A., Valdes K., Caplow M., Crossman D.K., Steyn A.J.C., Eisele L., Derbyshire K. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriology. (2010a) 192, 326-35.
Amitai G., Callahan B.P., Stanger M., Belfort G., Belfort M. Modulation of intein activity by its neighboring extein substrates.. Proc. Natl. Acad. Sci. USA (2009) 106, 11005-10.
Callahan B.P., Miller B.G. OMP decarboxylase—An enigma persists. Bioorg. Chem. (2007) 35, 465-9.
Callahan B.P., Lomino, J.V., Wolfenden R. Nanomolar inhibition of the enterobactin biosynthesis enzyme, EntE: Synthesis, substituent effects, and additivity. Bioorg. Med. Chem. Lett. (2006) 16, 3802-05.
Callahan B.P., Yaun, Y., Wolfenden, R. The Burden Borne by Urease J. Am. Chem. Soc. (2005) 127, 10828-9. (Highlighted in Science)
Callahan B.P., Wolfenden, R. OMP Decarboxylase: an Experimental Test of Ground State Destabilization of the Enzyme-Substrate Complex J. Am. Chem. Soc (2004) 126, 14698-9. (Highlighted in Faculty of 1000)
- Professor of Chemistry and Materials Science
- Interests in Analytical Chemistry, Electrochemistry, Materials Science
Dr. Nikolay Dimitrov received his PhD degree in chemistry from Bulgarian Academy of Sciences, Sofia, BULGARIA in 1993. He did his postdoctoral research in electrochemistry and corrosion of materials at Arizona State University (1996-1999). Next he was appointed as a research assistant professor at Arizona State University for the period 2000-2003. He joined the chemistry faculty at SUNY Binghamton in the fall of 2003.
RESEARCH INTERESTSKinetic and Thermodynamic Aspects of Thin Film Growth - NSF-DMR, CAREER Award
Surface defects corresponding to adatoms, vacancies, and steps together with misfit dislocations are known to interact with one another affecting and often dominating kinetic processes. This research examines various issues related to the role of defect interactions in determining thin-film growth modes. Most recently, a long-term research activity was established aimed at realizing multistep galvanic displacement processes for the growth of epitaxial metal films and successive layered assemblies of different metals and/or alloys. A proof-of-concept study, marked the beginning of the development of a new thin film growth method realizing as an elementary step monolayer limited, galvanic displacement. While displacement reactions have been used recently for sub-monolayer to a monolayer surface modification, the new outcome that warrants the innovative aspect of our study is associated with the application of this strategy for metal thin film deposition. This method, called Surface Limited Redox Replacement (SLRR) is now applied for growth of thin metal films of Ag, Cu and Pt by at least four research groups nationwide.All Electrochemical Processing of Nanoscale Materialsand Catalysts - funded by NSF-Chemistry
Motivated by the ever-increasing demand for development of cost-effective, highly active and durable catalysts a research founded on my expertise with nanoporous metals, introduces all-electrochemical synthetic approach for catalysts that could be an alternative to the most established nanoparticle based ones. The new synthetic route enables production of ultra thin and continuous nanoporous catalysts with tunable thickness and length scale of interconnected porosity along with reliable composition control and high processing efficiency. The protocols under development include electrodeposition of ultra thin and continuous film of single-phase alloy followed by a selective electrochemical dissolution (de-alloying) intended for the less-noble component removal that generates a nanoporous metal (NPM) with thickness of less than 20 nm. Depending upon its nature, the NPM could then be either used as catalyst or electrochemically functionalized with a catalytically active layer with a variety of practical applications.Development of Glass Interposers – industrial funding (IEEC Binghamton, NY STAR)
Glass interposers have been developed as alternative to Si ones. Key steps in the development effort are be aimed at (i) identifying the most appropriate electroless protocol for deposition of ultrathin and continuous metal seed layer with satisfactory adhesion on glass and (ii) optimizing the solution chemistry and electroplating regimes for superconformal (SC) through-via Cu plating on patterned and metal/Cu seeded glass substrates. Main achievements associated with our development of glass interposers to date have been the establishment of feasible glass-metallization protocol, the implementation of working plating routines for conformal metallization of through glass vias (TGV), and the proof of concept level demonstration of a viable circuitization approach. Another remarkable success in our resent work has been the development of electrodeposition approach for SC plating in TGV drilled in samples with ever finer via holes with aspect ratio of 6 and its ongoing extension to 10:1 and higher AR holes. A primary goal of future work is to develop a complete and accurate model of processing parameters and shorten the time required to SC fill holes. The ultimate goal is to reduce process costs while providing void-free filling and low surface Cu thickness to minimize the time needed for surface planarization.
Interested students must be highly motivated and able to devote at least 12-15 hours/week to the research. An experiment in our Lab would require at least four hours of uninterrupted time. Also, prospective students should have very good to excellent performance in the laboratory activities associated with the core chemistry courses. Participation in all group meeting is mandatory as well.
MOST RECENT PUBLICATIONS / REPRESENTATIVE PUBLICATIONS
S. Ambrozik, B. Rawlings, N. Vasiljevic, and N. Dimitrov, Metal Deposition via Electroless Surface Limited Redox Replacement, Electrochemistry Communications, 2014, 44, 19-22.
L. Bromberg, J. Xia, M. Fayette, and N. Dimitrov, Synthesis of Ultrathin and Continuous Layers of Nanoporous Au on Glassy Carbon Substrates, Journal of the Electrochemical Society, 2014, 161 (7), D3001-D3010.
P. Ogutu, E. Fey, P. Borgesen, and N. Dimitrov, Hybryd Method for Metallization of Glass Interposers, Journal of the Electrochemical Society , 2013, 160(12),D3228-D3236.
J. Nutariya, M. Fayette, N. Dimitrov, and N. Vasiljevic, Growth of Platinum by Surface Limited Redox Replacement of Underpotentially Deposited Hydrogen, Electrochimica Acta, 2013, 112, 813-823.
M. Fayette, J. Nutariya, N. Vasiljevic, and N. Dimitrov, A Study of Pt Dissolution during Formic Acid Oxidation, ACS Catalysis, 2013, 3, 1709-1718.
L. Yin, F. Wafula, N. Dimitrov, and P. Borgesen, Toward a Better Understanding of the Effect of Cu Electroplating Process Parameters on Cu3Sn Voiding, Journal of Electronic Materials, 2012, 41, 1898
D. A. McCurry, M.Kamundi, M. Fayette, F. Wafula, N. Dimitrov, All Electrochemical Fabrication of a Platinized Nanoporous Au Thin-Film Catalyst, ACS Applied Materials and Interfaces, 2011, 3, 4459.
M. Fayette, Y. Liu, D. Bertrand, J. Nutariya, N. Vasiljevic, N. Dimitrov, From Au to Pt via Surface Limited Redox Replacement of Pb UPD in One-Cell Configuration, Langmuir, 2011, 27(9), 5650.
F. Wafula, Y. Liu, L. Yin, P. Borgesen, E.J. Cotts, and N. Dimitrov, Effect of the deposition parameters on the voiding propensity of solder joints with Cu electroplated in a Hull cell, Journal of Applied Electrochemistry, 2011, 41, 469.
Y. Liu, S. Bliznakov and N. Dimitrov, Factors Controlling the Less Noble Metal Retention in Nanoporous Structures Processed by Electrochemical Dealloying, Journal of the Electrochemical Society, 2010, 157 (8), K168.
F. Wafula, Y. Liu, L. Yin, S. Bliznakov, P. Borgesen, E.J. Cotts, and N. Dimitrov, Impact of Key Deposition Parameters on the Voiding, Sporadically Occurring in Solder Joints with Electroplated Copper, Journal of the Electrochemical Society, 2010, 157(2), 111.
Y. Liu, L. Yin, S. Bliznakov, P. Kondos, P. Borgesen, D.W. Henderson, C. Parks, J. Wang, E.J. Cotts, and N. Dimitrov, Improving Copper Electrodeposition in the Microelectronics Industry, IEEE Transactions on Components and Packaging Technologies , 2010, 33(1) 127.
Dan Xu, S. Bliznakov, Zhaoping Liu, Jiye Fang, and N. Dimitrov, Composition-Dependent Electrocatalytic Activity of Pt-Cu Nanocube Catalysts towards Formic Acid Oxidation, Angewandte Chemie, 2010, 49, 1.
Y. Liu, S. Bliznakov and N. Dimitrov, Comprehensive Study of the Application of a Pb Underpotential Deposition-Assisted Method for Surface Area Measurement of Metallic Nanoporous Materials, Journal of Physical Chemistry C, 2009, 113 (28), 12362.
L.T. Viyannalage, S. Bliznakov, and N. Dimitrov, Electrochemical Method for Quantitative Determination of Trace Amounts of Lead, Analytical Chemistry A, 2008, 80, 2042.
N. Vasiljevic, L.T. Viyannalage, N. Dimitrov, and K. Sieradzki High resolution electrochemical STM: New structural results for underpotentially deposited Cu on Au(111) in acid sulfate solution, Journal of Electroanalytical Chemistry, 2008, 613, 118.
N. Dimitrov, R. Vasilic, N. Vasiljevic, A kinetic model for redox replacement of UPD layers, Electrochemical and Solid State Letters, 2007, 10(7), D79.
L.T. Viyannalage, R.Vasilic, and N. Dimitrov, Epitaxial Growth of Cu on Ag(111) and Au(111) by Surface Limited Redox Replacement - An Electrochemical and STM Study, Journal of Physical Chemistry, 2007, 111, 4036.
R.Vasilic, L.T. Viyannalage, and N. Dimitrov, Epitaxial Growth of Ag on Au(111) by Galvanic Displacement of Pb and Tl Monolayers, Journal of the Electrochemical Society, 2006, 153(9), C648.
- Associate Professor
- Materials Chemistry, Inorganic Chemistry, Nanotechnology
After he graduated from Lanzhou University, Dr. Fang received his M.Sc. (Chemistry) and Ph.D. (Materials Science) degrees from the National University of Singapore in 1994 and 1998, respectively. Following a postdoctoral/research specialist training in Advanced Materials Research Institute, he joined University of New Orleans as an Assistant Professor of Chemistry in 2002. He was a National Science Foundation Career award winner in 2005. He serves as a director of Materials Science Program/track at BU fro 2009 to 2015.
Dr. Fang’s interdisciplinary research is focused on shape-controlled synthesis of functional low-dimensional inorganic materials and manipulation of nanocrystals via a wet-chemical pathway, as well as on the understanding of their relevant physical and chemical phenomena. The emphases are (1) to produce high-quality nanocrystals (size- and shape-control) and to develop advanced processing technology; (2) to study superstructure of self-assembled nanopolyhedral systems; (3) to explore novel physical properties of functional materials (such as perovskite photovoltaic materials) under pressure; (4) to support energy-related applications of nanocrystals and functional materials in emerging fields such as energy storage and sustainability. Present projects include fuel cell catalysts, perovskite solar cell materials, high-pressure phase transition, high-capacity cathode materials for Li-ion batteries and supercapacitors, self-assembly and supercrystals.
His synthetic strategy is based on a high-temperature organic solution approach, in which various chemical reactions are designed using organometallic precursors and carried out in an organic solvent at high reaction temperature in the presence of appropriate capping ligand and stabilizing agent. In other words, developed techniques that used to use in organic synthesis (e.g. air-/moisture-sensitive operation) are adopted in the inorganic nanocrystals synthesis with well-defined high-quality (size-, shape-, phase- and composition-control). Knowledge from Coordination Chemistry, Organometallic Chemistry, Crystallography and Colloidal Processing may add an advantage to this study. Characterization performance may include phase/nanostructural (e.g. XRD, TEM, SEM, AFM), optical (e.g. UV-Vis, FTIR, NIR, PL), compositional (e.g. ICP, EDS), magnetic (e.g. SQUID, VSM, EPR), thermal (e.g. TGA, DTA), electrochemical, synchrotron and high-pressure investigations.
“Pressure Dependent Polymorphism and Bandgap Tuning of Methylammonium Lead Iodide Perovskite”, Shaojie Jiang, Yanan Fang, Ruipeng Li, Hai Xiao, Jason Crowley, Chenyu Wang, Timothy J. White, William A. Goddard III*, Zhongwu Wang, Tom Baikie* and Jiye Fang*, Angew. Chem. Int. Ed. 55 (22) 6540-6544, (2016).
"Pressure Processing of Naocube Assembly towards Harvesting of Metastable PbS Phase", Tie Wange,Ruipeng Li, Zewei Quan, Welley Siu Loc, William A. Basset, Y. Charles Cao, Jiye Fand and Zhongwu Wang, Link
“Understanding the forces acting in self-assembly and the implications for constructing three-dimensional (3D) supercrystals”, Chenyu Wang, Carrie Siu, Jun Zhang and Jiye Fang*, Nano Res., 8 (8), 2445-2466, (2015).
“Solvent-Mediated Self-Assembly of Nanocube Superlattices”, Zewei Quan, Hongwu Xu, Chenyu Wang, Xiaodong Wen, Yuxuan Wang, Jinlong Zhu, Ruipeng Li, Chris Sheehan, Zhongwu Wang, Detlef-M. Smilgies, Zhiping Luo* and Jiye Fang*, J. Am. Chem. Soc. 136 (4) 1352-1359, (2014).
“Solution-Based Synthesis of III-V Quantum Dots and Their Applications in Gas Sensing and Bio-Iamging”, Guangyin Fan, Chenyu Wang and Jiye Fang*, NanoToday, 9 (1) 69-84, (2014).
“Pressure-Induced Switching between Amorphization and Crystallization in PbTe Nanoparticles”, Zewei Quan, Zhiping Luo, Yuxuan Wang, Hongwu Xu, Chenyu Wang, Zhongwu Wang and Jiye Fang*, Nano. Lett. 13 (8) 3729-3735, (2013).
“Shape-Controlled and Electrocatalytic Activity-Enhancement of Pt-Based Bimetallic Nanocrystals” (invited review), Nathan S. Porter, Hong Wu, Zewei Quan* and Jiye Fang*, Acc. Chem. Res. 46 (8) 1867-1877, (2013).
“High-Indexed Noble Metal Nanocrystals”, Zewei Quan, Yuxuan Wang, and Jiye Fang*, Acc. Chem. Res, 46(2) 191-202, (2013).
“Tilted Face-Centered-Cubic Superscrystals of PbS Nanocubes”, Zewei Quan, Welley Siu Loc, Cuikun Lin, Zhiping Luo, Kaikun Yang, Yuxuan Wang, Howard Wang, Zhongwu Wang* and Jiye Fang*, Nano Lett. 12 (8) 4409-4413, (2012).
“Reversible Kirkwood-Alder Transition Observed in Pt3Cu2 Nanoctahedron Assemblies under Controlled Solvent Annealing/Drying Conditions”, Jun Zhang, Zhiping Luo, Benjamin Martens, Zewei Quan, Amar Kumbhar, Nathan Porter, Yuxuan Wang, Detlef-M. Smilgies* and Jiye Fang*, J. Am. Chem. Soc., 134 (34) 14043-14049, (2012).
“Selective Epitaxial Growth of Silver Nanoplates”, Yuxuan Wang and Jiye Fang*, Angew. Chem. Int. Ed. 50 (5) 992-993, (2011).
“Composition-Dependent Electrocatalytic Activity of Pt-Cu Nanocube Catalysts towards Formic Acid Oxidation”, Dan Xu, Stoyan Bliznakov, Zhaoping Liu, Jiye Fang* and Nikolay Dimitrov*, Angew. Chem. Int. Ed. 49 (7) 1282-1285, (2010).
“Synthesis and Oxygen Reduction Activity of Shape-Controlled Pt3Ni Nanopolyhedra”, Jun Zhang, Hongzhou Yang, Jiye Fang* and Shouzhong Zou*, Nano Lett. 10 (2) 638-644, (2010).
“Assembling Non-Spherical 2D Binary Nanoparticle Superlattices by Opposite Electrical Charges: The Role of Coulomb Forces”, Zhaoyong Sun, Zhiping Luo* and Jiye Fang*, ACS NANO 4(4) 1821-1828, (2010).
“Enhancing by Weakening: Electrooxidation of Methanol on Pt3Co and Pt Nanocubes”, Hongzhou Yang, Jun Zhang, Kai Sun, Shouzhong Zou* and Jiye Fang*, Angew. Chem. Int. Ed. 49 (38) 6848-6851, (2010).
“Solution-Based Evolution and Enhanced Methanol Oxidation Activity of Monodisperse Pt-Cu Nanocubes”, Dan Xu, Zhaoping Liu, Hongzhou Yang, Qingsheng Liu, Jun Zhang, Jiye Fang*, Shouzhong Zou* and Kai Sun, Angew. Chem. Int. Ed. 48 (23) 4217-4221, (2009).
“A General Strategy for Preparation of Pt-3d-transition Metal (Co, Fe, Ni) Nanocubes”, Jun Zhang and Jiye Fang*, J. Am. Chem. Soc., 131 (51) 18543-18547, (2009).
“Co-reduction Colloidal Synthesis of III-V Nanocrystals: The Case of InP”, Zhaoping Liu, Amar Kumbhar, Dan Xu, Jun Zhang, Zhaoyong Sun and Jiye Fang*, Angew. Chem. Int. Ed. 47 (19) 3540-3542 (2008).
“p-Type Field-Effect Transistors of Single-Crystal ZnTe Nanobelts”, Jun Zhang, Po-Chiang Chen, Guozhen Shen, Jibao He, Amar Kumbhar, Chongwu Zhou and Jiye Fang*, Angew. Chem. Int. Ed. 47(49) 9469-9471, (2008).
“Simple Cubic Super Crystals Containing PbTe Nanocubes and Their Core-Shell Building Blocks”, Jun Zhang, Amar Kumbhar, Jibao He, Narayan Chandra Das, Kaikun Yang, Jian-Qing Wang, Howard Wang, Kevin L. Stokes and Jiye Fang*, J. Am. Chem. Soc., 130 (45) 15203-15209, (2008).
“Super-Crystal Structures of Octahedral c-In2O3 Nanocrystals”, Weigang Lu, Qingsheng Liu, Zhaoyong Sun, Jibao He, Chidi Ezeolu and Jiye Fang*, J. Am. Chem. Soc., 130 (22) 6983-6991, (2008).
“Single Crystalline Magnetite Nanotubes”, Zuqin Liu, Daihua Zhang, Song Han, Chao Li, Bo Lei, Weigang Lu, Jiye Fang and Chongwu Zhou*, J. Am. Chem. Soc., 127, 6-7 (2005).
“Study of Quasi-Monodisperse In2O3 Nanocrystals: Synthesis and Optical Determination”, Qingsheng Liu, Weigang Lu, Aihui Ma, Jingke Tang, Jin Lin and Jiye Fang*, J. Am. Chem. Soc., 127(15), 5276-5277 (2005).
“Bismuth Telluride Hexagonal Nanoplatelets and Their Two-Step Epitaxial Growth”, Weigang Lu, Yong Ding, Yuxi Chen, Zhong Lin Wang and Jiye Fang, J. Am. Chem. Soc., 127(28), 10112 - 10116 (2005).
- Biophysical Chemistry
Dr. Grewer received his Ph.D. in Physical Chemistry from the University of Frankfurt, Germany, in 1993. He subsequently was a Postdoctoral Fellow at Cornell University and a Senior Research Associate at the Max-Planck-Institute for Biophysics in Frankfurt, Germany. He is joining the BU faculty in 2008 after a 4-year appointment as Assistant Professor in the Department of Physiology and Biophysics at the University of Miami School of Medicine.
My laboratory focuses on research in the field of Biophysical Chemistry, at the interface between the chemical, biological, and physical sciences. We are interested in elucidating the physical principles underlying the movement of ions and small, organic molecules across biological membranes. In living cells, specific membrane proteins, such as ion channels and transport proteins, catalyze transmembrane movement of ions and organic molecules. We are specifically interested in transporters that “pump” substrates uphill against a transmembrane concentration and/or electrical gradient, by coupling this movement to an energy source. Proteins performing such tasks are called active transporters.
Transporters studied in the lab: Our current research focuses mainly on secondary-active Na+-coupled transporters, which are energized by coupling of substrate transport to the cotransport of Na+ ions down their electrochemical potential gradient across the membrane. Neurotransmitter transporters and amino acid transporters belong to this class of transport proteins. The systems investigated are: Glutamate transporters, - aminobutyric acid transporters, dopamine transporters, and neutral amino acid transporters (system ASC, system A, system N). Most of these transport systems are highly relevant for physiological processes, including chemical signal transmission in the brain, and they may be targets for future drug development.
Techniques: In many cases, transmembrane transport is associated with stationary or transient transport of charge. We measure this charge transport with electrophysiological techniques, such as current recording from transporter-expressing, voltage-clamped cells or patches excised from the cell membrane. In order to investigate transient charge transport, we perturb a pre-existing transporter steady state by applying voltage or rapid substrate concentration jumps and subsequently measuring the kinetics of the relaxation to a new steady state with a sub-millisecond time resolution. In addition to investigating the transport mechanism of wild-type transporters, rapid kinetic studies are extended to transporters that are fused to fluorescent proteins or site-specifically mutated. The combination of these techniques allows us to understand the relationship between the structure and the function of the transport proteins. The experimental techniques are supplemented with kinetic modeling to simulate transporter function and predict transporter behavior in their physiological environment.
In an additional project, we are interested in developing methods to investigate transmembrane flux of transported molecules, by using fluorescent microscopy, with the aim of performing flux measurements in single cells. To this extent, we are synthesizing fluorescent markers to be used for bio-orthogonal labeling of the transported molecules.
We are also using computational methods to study the biophysics of transport processes. This includes lower level approaches based on solving the Poisson-Boltzmann equation to all atom models using molecular dynamics (MD). MD simulations are performed in unbiased mode, as well as using steered MD to explore conformation changes and binding/unbinding events. To this extent, the laboratory hosts a small cluster for high-performance computations.
Development of pharmacological tools: One of our projects aims at discovering new pharmacological tools for the investigation of neutral amino acid transporters in vitro and in vivo. We are using computational approaches, such as in-silico ligand docking and Molecular Dynamics simulations to identify modes and mechanisms of ligand interaction with their transporter binding site(s). Promising ligands generated through the computational methods are then synthesized by using the methods of classical synthetic organic chemistry, and functionally tested with respect to their action on the transport proteins. We also perform structure-activity relationship studies to predict ligand behavior without knowledge of the transporter binding site.
Grewer C, Gameiro A. How do glutamate transporters function as transporters and ion channels? Biophys J. (2014) (3):546-7.
2. Grewer C, Gameiro A, Rauen T. SLC1 glutamate transporters. Pflugers Arch. (2014) 466:3-24
Zander, C. B., Albers, T., Grewer, C. Voltage-dependent processes in the electroneutral amino acid exchanger ASCT2. J. Gen. Physiol. (2013) 14; 659-672.
Grewer C, Zhang Z, Mwaura J, Albers T, Schwartz A, Gameiro A. Charge Compensation Mechanism of a Na+-coupled, Secondary Active Glutamate Transporter. J Biol Chem. (2012) 287; 26921-31.
Albers T, Marsiglia W, Thomas T, Gameiro A, Grewer C. Defining substrate and blocker activity of alanine-serine-cysteine transporter 2 (ASCT2) Ligands with Novel Serine Analogs. Mol Pharmacol. (2012) 81; 356-65.
Gameiro, A., Braams, S., Rauen, T., and Grewer, C. The Discovery of Slowness1 : Low capacity transport and slow anion channel gating by the glutamate transporter EAAT5, Biophys. J. (2011) in press.Zhang, Z., Zander, C. B. and Grewer, C. The C-terminal domain of the neutral amino acid transporter SNAT2 regulates transport activity through voltage-dependent processes, Biochem. J. (2011) 434; 287-296.
Tao, Z., Rosental, N., Kanner, B. I., Gameiro, A., Mwaura, J., Grewer, C. Mechanism of cation binding to the glutamate transporter EAAC1 probed with mutation of the conserved amino acid residue T101. J. Biol. Chem. (2010) 285; 17725-17733.
Zhang Z, Albers T, Fiumer H, Gameiro A, Grewer C. A conserved Na+ binding site of the sodium-coupled neutral amino acid transporter 2 (SNAT2). J. Biol. Chem., (2009) in press.
Tao Z, Gameiro A, Grewer C. Thallium ions can replace both sodium and potassium ions in the glutamate transporter excitatory amino acid carrier 1. Biochemistry. (2008) 47, 12923- 30.
Grewer C, Gameiro A, Zhang Z, Tao Z, Braams S, Rauen T. Glutamate forward and reverse transport: from molecular mechanism to transporter-mediated release after ischemia. IUBMB Life. (2008) 60, 609-19.
Zhang Z, Gameiro A, Grewer C. Highly conserved asparagine 82 controls the interaction of Na+ with the sodium-coupled neutral amino acid transporter SNAT2. J Biol Chem. (2008) 283,12284-92.
Erreger K, Grewer C, Javitch JA, Galli A. Currents in response to rapid concentration jumps of amphetamine uncover novel aspects of human dopamine transporter function. J Neurosci. (2008) 28, 976-89.
Zhang, Z., Tao, Z., Gameiro, A., Barcelona, S., Braams, S., Rauen, T., and Grewer, C., The transport direction determines the kinetics of substrate transport by the glutamate transporter EAAC1. Proc. Natl. Acad. Sci. USA (2007) 104, 18025-30.
1Title adapted from: Nadolny, S., The Discovery of Slowness, 1997, Penguin
- Inorganic Chemistry
Dr. Lees received his B.Sc. (Honors) and Ph.D. degrees from the University of Newcastle-upon-Tyne. He did postdoctoral research with Professor Arthur Adamson at the University of Southern California, and joined the faculty at SUNY-Binghamton in 1981. He was Visiting Professor at the University of Cambridge with Professor Lord Jack Lewis in 1989 and was Professor and Dean of Science at the University of Central Lancashire in 1992 -94 and Visiting Professor at the University of York with Professor Robin Perutz in 1997 and 2004-05.
Our research interests are in organometallic photochemistry with a current emphasis on transition-metal photophysics, photochemical mechanisms, photoinitiation and photocatalytic processes. Recent work (funded by the Department of Energy) has included measuring quantitative photochemical data for a number of important intermolecular Si-H and C-H bond activation processes, determining the photochemistry of metal cluster complexes that present new avenues for activation and catalysis, a photochemical investigation of the distinct singlet and triplet excited-state reactivities of W(CO)4(en) (en = ethylenediamine), characterization of the luminescent complex, W(CO)4(4-Me-phen) (phen = 1,10-phenantholine), in room-temperature and low-temperature glassy solutions and in acrylate thin films and demonstrating its usefulness as a spectroscopic probe, exploring the long-wavelength photochemistry of CpFe(CO)2I and facilitating an improved synthetic pathways to azaferrocene, and an investigation of the wavelength-dependence photochemistry of [CpFe(arene)]X (arene = benzene, toluene, napthalene, pyrene; X= PF6, BF4, SbF6, AsF6, CF3SO3), a well-recognized photocatalyst/photoinitiator in thin films. Also, we have recently begun to investigate a number of molecular squares and other configurations involving organometallic species as potential sensors. Our most current research is investigating both inorganic and organic molecules as possible anions sensors. This involves first preparing the compounds and then studying their spectroscopic responses to added anions, including fluoride and cyanide. Detecting such anions is of importance with respect to their environmental issues.
TYPES OF RESEARCH EXPERIENCE AVAILABLE
Synthesis and/or physical study (spectroscopy/ photochemistry) of organometallic complexes. Students will have an opportunity to learn FT-IR, UV-vis, fluorescence and photochemical techniques in the research laboratory.
Courses: Introductory Chemistry (107 and 108 or 111) and Analytical Chemistry (221) are recommended.
Students must be highly motivated and willing to devote at least 12-15 hours/week to the research.
"Quantitative Wavelength Dependent Photochemistry of the [CpFe(6-ipb)]PF6 (ipb = isopropylbenzene) Photoinitiator," Vladimír Jakúbek and Alistair J. Lees, Inorg. Chem. 2000, 39, 5779-5786.
"One-Step Self-Assembly Organometallic Molecular Cages from 11 Components," Shih-Sheng Sun and Alistair J. Lees, Chem. Commun., 2001, 103-104.
"Luminescent Metal Complexes as Spectroscopic Probes of Monomer/Polymer Environments," Alistair J. Lees, in Sensors and Optical Switching Phenomena, V. Ramamurthy and Kirk S. Schanze, Eds.
"Molecular and Supramolecular Photochemistry Series, Vol. 7, Marcel Dekker, New York, 2001, Chapter 5, 209-255.
"Self-Assembly Organometallic Squares with Terpyridyl Metal Complexes as Bridging Ligands," Shih-Sheng Sun and Alistair J. Lees, Inorg. Chem., 2001, 40, 3154-3160.
"Synthesis and Photophysical Properties of Dinuclear Organometallic Rhenium(I) Diimine Complexes Linked by Pyridine-Containing Macrocyclic Phenylacetylene Ligands," Shih-Sheng Sun and Alistair J. Lees, Organometallics, 2001, 20, 2353-2358.
"Synthesis, Photophysical Properties and Photoinduced Luminescence Switching of Trinuclear Diimine Rhenium(I) Tricarbonyl Complexes Linked by an Isomerizable Stilbene-Like Ligand," Shih-Sheng Sun and Alistair J. Lees, Organometallics, 2002, 21, 39-49.
"Synthesis and Electrochemical, Photophysical and Anion Binding Properties of Self- Assembly Heterometallic Cyclophanes," Shih-Sheng Sun, Jason A. Anspach, Alistair J. Lees, and Peter Y. Zavalij, Organometallics, 2002, 21, 685-693. 109.
"Transition Metal Based Supramolecular Systems: Synthesis, Photophysics, Photochemistry and their Potential Applications as Luminescent Anion Chemosensors," Shih-Sheng Sun and Alistair J. Lees, Coord. Chem. Revs., 2002, 230, 162-183.
"Self-Assembly Transition Metal Based Macrocycles Linked by Photoisomerizable Ligands: Examples of Photoinduced Conversion of Tetranuclear-Dinuclear Squares," Shih-Sheng Sun, Jason Anspach, and Alistair J. Lees, Inorg. Chem., 2002, 41, 1862-1869.
"Highly Sensitive Luminescent Metal-Complex Receptors for Anions through Charge-Assisted Amide ydrogen Bonding," Shih-Sheng Sun, Alistair J. Lees and Peter Y. Zavalij, Inorg. Chem., 2003, 42, 3445-3453.
“Directed Assembly Metallocyclic Supramolecular Systems for Molecular Recognition and Chemical Sensing,” Arvind Kumar, Shih-Sheng Sun and Alistair J. Lees, Coord. Chem. Revs., 2008, 252, 922-939.
“A Simple Thiourea Based Colorimetric Sensor for Cyanide Ion,” Maurice O. Odago, Diane M. Colabello and Alistair J. Lees, Tetrahedron Letts., 2010, 66, 7565-7461.
"Photoswitching Tetranuclear Rhenium (I) Tricarbonyl Diimine Complexes with a Stilbene-Like Bridging Ligand", Ju-Ling Lin, Chih-Wei Chen, Shih-Sheng Sun and Alistair J. Lees, Chem. Commun., 2011, 47, 6030-6032.
"Thioamide, Urea and Thiourea Bridged Rhenium(I) Complexes as Luminescent Anion Receptors", Maurice O. Odago, Amanda E. Hoffman, Russell L. Carpenter, Douglas Chi Tak Tse, Shih-Sheng Sun and Alistair J. Lees, Inorg. Chim. Acta, 2011, 374, 558-565.
"Anion Sensing by Rhenium(I) Carbonyls with Polarized N-H Recognition Motifs", Kai-Chi Chang, Shih-Sheng Sun and Alistair J. Lees, Inorg. Chim. Acta, 2012, 389, 16-28.
- Assistant Professor
- Physical Chemistry
- Interests in Computational Chemistry, Artifical PHotosynthesis, Electro- and Photocatalysis
Dr. Panetier received his BSc in Physical Chemistry (2005) at the Université de Reims Champagne-Ardenne, France. He obtained both his MChem (2008) and PhD (2012) from Heriot-Watt University, UK, working under the supervision of Prof. Stuart Macgregor on computational studies of C–X bond activation at transition-metal centers. In recent years, Dr. Panetier has been working as a postdoctoral scholar at the University of California, Berkeley, and at the Joint Center for Artificial Photosynthesis (JCAP) at Lawrence Berkeley National Laboratory under the advisement of Prof. Martin Head-Gordon. His research focused on the design of electrocatalysts for H+ and CO2 reduction, using electronic structure calculations. He joined SUNY Binghamton as Assistant Professor in Physical Chemistry in the Fall 2015.
The primary research goal is to use computational methods to design novel catalysts with optimized activity and high selectivity for (i) the conversion of solar energy to fuels, and (ii) the activation of small molecules. Electronic structure calculations provide both kinetic and thermodynamic information. Most of the work is performed in close collaboration with experimentalists.
Design of Electro- and Photocatalysts for Artificial Photosynthesis using Computational Modeling: The growing interest in renewable energy, coupled with the continuing rise of CO2 emissions from the burning of fossil fuels have focused considerable attention on artificial photosynthesis for the conversion of solar energy to fuels and commodity chemicals. The objective of this endeavor is to focus on the development of new electro- and photocatalysts for H+ and CO2 reduction, by using electronic structure calculations. Computational modeling includes the ability to identify rate-determining steps and critical intermediates, such as which factors control the bond breaking and bond making processes that occur at the active site(s).
Computational Modeling of Transition-Metal Complexes for the Activation of Small Molecules: The purpose of this project is to perform electronic structure calculations to guide the efforts in designing catalysts for the activation of small molecule such as the conversion of N2 into NH3. N2 is abundant in the earth’s atmosphere, however, in order to be integrated into biological systems, the conversion into NH3 is required. Fixation of the strong N N triple bond is a challenging task due to both thermodynamic (bond dissociation enthalpy = 225 kcal/mol, negative electron affinity and high ionization energy), and kinetic factors (absence of dipole moment, poor nucleophilicity and electrophilicity). Electronic structure calculations can (i) provide vital insight in determining which supporting ligands and transition metals will allow the activation of N2, (ii) reveal essential mechanistic insight for N2 reduction, and (iii) potentially uncover new reaction pathways.
Appropriate interests, motivation and responsible commitment of time are essential. Highly motivated students willing to devote a minimum of 15 hours/week to research are encouraged to apply. Courses in Computational Chemistry and/or Inorganic Chemistry are also recommended.
J.W. Jurss, R.S. Khnayzer, J.A. Panetier, K.A. El Roz, M. Head-Gordon, J.R. Long, F.N. Castellano and C.J. Chang "Bioinspired design of redox-active ligands for multielectron catalysis: effects of positioning pyrazine reservoirs on cobalt for electro- and photocatalytic generation of hydrogen from water" Chem. Sci. 2015, 6, 4954
C.S. Letko, J.A. Panetier, M. Head-Gordon and T.D. Tilley "Mechanism of the electrocatalytic reduction of protons with diaryldithiolene cobalt complexes" J. Am. Chem. Soc. 2014, 136, 9364
A.W. Hauser, N. Mardirossian, J.A. Panetier, M. Head-Gordon, A.T. Bell, and P. Schwerdtfeger "Functionalized graphene as a gatekeeper for chiral molecules: an alternative concept for chiral separation" Angew. Chem. Int. Ed. 2014, 53, 9957
M. Nippe, R.S. Khnayzer, J.A. Panetier, D.Z. Zee, B.S. Olaiya, M. Head-Gordon, C.J. Chang, F.N. Castellano and J.R. Long "Catalytic proton reduction with transition metal complexes of the redox-active ligand bpy2PYMe" Chem. Sci. 2013, 4, 3934
J.A. Panetier, S.A. Macgregor and M.K. Whittlesey "Catalytic hydrodefluorination of pentafluorobenzene by [Ru(NHC)(PPh3)2(CO)H2]: a nucleophilic attack by a metal-bound hydride ligand explains an unusual ortho-regioselectivity" Angew. Chem. Int. Ed. 2011, 50, 2783
- Assistant Professor
- Biophysical Chemistry
Dr. Qiang received his B.S. in Chemistry from Tsinghua University (Beijing, China) in 2004. He obtained his Ph.D. in physical chemistry in 2009 from Michigan State University (East Lansing, MI). His graduate research, which was focused on the application of solid state nuclear magnetic resonance (NMR) spectroscopy in HIV membrane fusion, was conducted under the supervision of Professor David Weliky. He continued as a postdoctoral fellow at the National Institutes of Health after graduation, under the supervision of Dr. Robert Tycko. One of his postdoctoral research was about the spectroscopic studies of fibrillation process in Alzheimer's diseases. Dr. Qiang joined Binghamton University faculty in the spring of 2014.
In general, my research interests focus on the biological and medicinal applications of solid state nuclear magnetic resonance (NMR) spectroscopy and other biophysical techniques including fluorescence spectroscopy, electron microscopy and atomic force microscopy. There are three distinct projects:
Structural basis of the amyloidosis-induced membrane disruption. We are interested in understanding the fundamental question of how the membrane bilayer get disrupted during the aggregation process of amyloid peptides. Current efforts focus on the AΒamyloidosis process. Using a combination of solid-state NMR spectroscopy and other techniques, we investigate all possible pathways that lead to membrane disruption as well as the crucial factors that modulate the AΒ elution process. The long-term goal is to fill in the knowledge gap between the producing of Aβ and the severe consequences of its aggregation such as cell membrane disruption.
Molecular mechanisms of the pH-low Insertion Peptides (pHLIPs) as biomarker and drug deliver for cancer treatment. The structures and membrane interactions of pHLIPs are sensitive to the local pH variation, and therefore they are considered as potential universal biomarkers for identifying cancer cells as well as useful anti-cancer drug delivers. Our goal is to understand the key structural factors that modulate the pH-dependent function of pHLIP, and to design bioactive pHLIP sequences that are suitable for the local environment of cancer cells.
Structural-specific inhibitor design for β amyloid (Aβ) fibrils. Formation of Aβ fibrils is an important clinic hallmark of Alzheimer's disease (AD). The fibrils are neurotoxic, and the levels of neurotoxicity are related to their atomic-level structures. In this project, we are hoping to utilize computational and experimental approaches to design small molecules (peptides, small organic compounds, etc.) which will selectively bind to distinct fibrillar species. These molecules are potential inhibitors which may regulate the toxicity of fibrils.
TYPES OF RESEARCH EXPERIENCE AVAILABLE
The projects will utilize:
- Peptide chemistry including solid phase peptide synthesis, purification, and more advanced peptide preparation with non-native amino acids.
- Spectroscopic technique including solid state NMR spectroscopy, transmission electron microscopy, atomic force microscopy fluorescence spectroscopy, and circular dichroism spectroscopy.
- Computational simulation using packages such as Rosetta and Xplor-NIH.
An individual student will pick one of the above projects, and the necessary research training (including background knowledge and experimental techniques) will be given for the student in order to make progress in the project.
S.Z. Hanz, N.S. Shu, J. Qian, N. Christman, P. Kranz, M. An, C. Grewer, and W. Qiang, "Protonation-driven membrane insertion of the pH-low insertion peptide", Angew. Chem. Int. Ed., 2016, in press.
D.A. Delgado, K.E. Doherty, Q. Cheng, H. Kim, D. Xu, H. Dong, C. Grewer, and W. Qiang, "Distinct membrane disruption pathways induced by the 40-residue beta-amyloid peptides", J. Biol. Chem., 2016, 291(23), 12233-44.
N.S. Shu, M. S. Chung, L. Yao, M. An, and W. Qiang, "Residue-specific structures and membrane locations of pH-low insertion peptide by solid-state nuclear magnetic resonance", Nat. Commun., 2015, 6, 7787.
R.D. Akinlolu, M. Nam, and W. Qiang, "Competition between fibrillation and induction of vesicle fusion for the membrane-associated 40-residue beta-amyloid peptide", Biochemistry, 2015, 54, 3416-19. - Highlighted on Biochemistry Webpage.
N. Sgourakis, W.M. Yau, and W. Qiang, "Modeling an in-register, parallel "Iowa" Abeta fibril structure using solid-state NMR data from sparsely labeled samples with Rosetta", Structure, 2015, 23, 216-27.
W. Qiang, W.M. Yau, and J. Schulte, "Fibrillation of Β amyloid peptides in the presence of phospholipid bilayers and the consequent membrane disruption", BBA-Biomembranes, 2015, 1848, 266-76.
W. Qiang, R.D. Akinlolu, M. Nam, “Solid-state NMR studies of the membrane disruption induced by the Β amyloid peptides: perspective and difficulties”, eMagRes (invited review), 2015, 4, 2.W. Qiang, R.D. Akinlolu, M. Nam, and N.S. Shu, "Structural evolution and membrane interaction of the 40-residue Β-amyloid peptide: differences in the initial proximity between peptides and the membrane bilayer studied by solid-state nuclear magnetic resonance spectroscopy", Biochemistry, 2014, 53, 7503-14.
J.X. Lu, W. Qiang, W.M. Yau, C.D. Schwieters, S.C. Meredith, and R. Tycko, “Molecular structure of Β-amyloid fibrils in Alzheimer’s disease brain tissue”, Cell, 2013, 154, 1257-68.
W. Qiang, K. Kelley, and R. Tycko, “Polymorph-specific kinetics and thermodynamics of Β-amyloid fibril growth”, J. Am. Chem. Soc., 2013, 135, 6860-71.
- Associate Professor
- Organic and Bioorganic Chemistry
Dr. Rozners received his B.S. and Ph.D. degrees from Riga Technical University (Latvia) in 1990 and 1993, respectively. He was a Postdoctoral Fellow with Prof. Roger Stromberg at Stockholm University and Karolinska Institute (Sweden) from 1994 to 1997 and with Prof. Edwin Vedejs at University of Wisconsin Madison and University of Michigan from 1997 to 2000. Before joining Binghamton University in 2008, Dr. Rozners was Assistant Professor at Northeastern University in Boston.
Prof. Rozners's research interests are in the chemistry and biochemistry of nucleic acids with a focus on elucidation of RNA?s structure and function. The research philosophy is to use organic chemistry as the enabling discipline to create unique model systems and tools for fundamental studies and practical applications in nucleic acid biochemistry, biophysics and biomedicine. The current projects include design, synthesis, and biophysical exploration of RNA analogs having non-phosphorous internucleoside linkages and development of novel RNA binders for biomedical applications. Amide-linked RNA has the structural features of both nucleic acids and proteins and is of particular interest as an intriguing model system to study biopolymer recognition and for design of artificial enzymes and therapeutic agents. Other interesting modifications are RNA analogues having formacetal internucleoside linkages. Modified RNAs have therapeutic potential in antisense, antigene and RNA interference applications. More efficient routes to make highly modified nucleic acid analogs are being sought to make them more readily available for further evaluation.
Prof. Rozners's research is interdisciplinary in nature, involving exploratory studies on synthetic organic methodology including combinatorial chemistry, catalytic enantioselective Nozaki-Hiyama-Kishi reaction, total synthesis of natural products and their analogues (e.g., modified RNA and peptides), and the study of biochemical and biophysical properties of the synthesized analogues. Methods such as UV thermal denaturation, fluorescence spectroscopy and osmotic stress are used to characterize modified oligonucleotides.
Zengeya, T.; Gupta, P.; Rozners, E. Triple Helical Recognition of RNA Using 2-Aminopyridine-Modified PNA at Physiologically Relevant Conditions. Angew. Chem., Int. Ed. 2012, 51, 12593-12596
Selvam, C.; Thomas, S.; Abbott, J.; Kennedy, S. D.; Rozners, E. Amides Are Excellent Mimics of Phosphate Linkages in RNA Angew. Chem. Int. Ed. 2011, 50, 2068-2070.
Li, M.; Zengeya, T.; Rozners, E., Short Peptide Nucleic Acids Bind Strongly to Homopurine Tract of Double Helical RNA at pH 5.5. J. Am. Chem. Soc. 2010, 132, 8676- 8681.
Tanui, P.; Kullberg, M.; Song, N.; Chivate, Y.; Rozners, E., Monomers for preparation of amide linked RNA: synthesis of C3'-homologated nucleoside amino acids from D-xylose. Tetrahedron 2010, 66, 4961-4964.
Kolarovic, A.; Schweizer, E.; Greene, E.; Gironda, M.; Pallan, P. S.; Egli, M.; Rozners, E. Interplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Nonionic Modifications Better than DNA. J. Am. Chem. Soc. 2009, 131, 14932-14937.
- Bioanalytical, Environmental and Materials Chemistry
Dr. Sadik received her Ph.D. in Chemistry from the University of Wollongong in Australia and did her postdoctoral research at the US Environmental Protection Agency (US-EPA) in Las Vegas, Nevada. Dr. Sadik has held appointments at Harvard University, Cornell University and Naval Research Laboratories in Washington, DC. Sadik's research currently centers on the design and development of chemical and biological sensors that are inspired by the recognition processes found in nature. She holds five U.S. patents for her work on biosensors, which are being licensed for commercial products. Sadik is recognized for her research innovation (https://en.wikipedia.org/wiki/Omowunmi_Sadik) and sustainable nanotechnology. Other career recognitions include the recipient of Harvard University's Distinguished Radcliffe Fellowship, National Science Foundation's Discovery Corps Senior Fellowship, SUNY Chancellor Award for Research, Australian Merit Scholar Award, Chancellor Award for Outstanding Inventor, and the National Research Council COBASE fellowship. In addition, I am a Fellow of the Royal Society of Chemistry and a Fellow of the American Institute for Medical and Biological Engineering (AIMBE) and a 2015-2017 Sigma Xi Distinguished Lecturer
She chaired the inaugural "Gordon Conference on Environmental Nanotechnology in 2011 and has served as the nanotechnology editor for the RSC Journal of Environmental Science Processes and Impact. As the President and co-founder of the Sustainable Nanotechnology Organization-SNO (www.susnano.org), Sadik is promoting the responsible growth of nanotechnology around the world through research, education and outreach. Sadik is the co-author of over 160 publications and has given over 350 invited lectures and conference contributions world-wide.
RESEARCH INTERESTS (For additional information please visit our group website: http://www.chem.binghamton.edu/S ADIK/sadik.htm
We are interested in the design and development of chemical and biological sensors that are inspired by the recognition processes found in nature. Perhaps the best and most sophisticated recognition process is found in the human body. For example, our senses of smell, tastes and ability to respond to temperature variation all occur via living polymer interfaces. Even cellular processes are regulated by cell walls, comprising dynamic macromolecules that are capable of sensing and responding to specific chemical stimuli. Hence, by learning from nature, we are developing smart sensors that can be used for applications in environmental monitoring, homeland security, process control and biomedical testing. Selected projects are discussed below.
CHEMICAL BIOSENSORS. The design of biosensors requires the successful immobilization of biological reagents such as antigen, antibody, enzymes, DNA or cells. A number of approaches for immobilizing antibody and dsDNA layers on electrodes have been reported, yet the quest for a molecularly organized, but reproducible immobilization continues to pose a challenge. A major research question is how to design the interface between the transducer and the biospecific layer for efficient molecular recognition. Basic questions include the exact nature of the intermolecular forces at the sensor/biospecific layer and sensor/analyte interfaces, and also whether these forces are responsible for the partial discrimination between different chemical and biochemical compounds. Understanding, engineering and predicting the interactions between molecules require the knowledge of the available types of interactions and a rational design of the sensor chemistries. Our current focus is on the design of smartphone-based biosensors, low-cost, low power biosensors, microbial biosensors, pain biosensors and UPAC instrument.
SUSTAINABLE NANOSYNTHESIS. The concept of sustainable nanotechnology involves the nanoscale control of synthesis and processing of matter without footprints that give rise to environmental degradation. Hence there is a search for synthetic methods that utilize fewer amounts of materials, water, and energy; while reducing or replacing the need for organic solvents. In this area, we are preparing, characterizing and conducting the antimicrobial/cytotoxicity studies of nanoparticles of different shapes and sizes using water soluble, phosphorylated and sulfonated Quercetin derivatives. These flavonoids served as the reducing and capping agent thereby forming stable spherical, triangular, and hexagonal, cubicle and rectangular nanoparticles. In this case the flavonoid derivatives are also being used as a stabilizer thereby avoiding use of organic chemicals.
MEMBRANES WITH EXPERIMENTALLY-CONTROLLED TRANSPORT & DISINFECTION PROPERTIES. Polymer materials are attractive hosts that can control the morphology of nanoparticles (NPs), and generate ordered and hierarchical structures. Moreover, polymers do not simply template the ordering of nanoparticles. Rather, the final morphology is determined by a complex interplay between the entropy and enthalpy within the system. The optical, electrical, mechanical, and rheological properties of NP–polymer–composite materials can change dramatically, which is largely due to the spatial distribution of NPs in the polymer matrix. We are designing, and creating novel polymers with unique control properties and testing these as packaging and sensing materials. We have developed new materials for selective removal of certain metals and organics and tested these materials for catalytic conversion of high-valent heavy metals into their low oxidation state equivalents. Research opportunities exist to explore the use nanostructured materials for the rapid conversion of Cr (VI) to Cr(III), design/testing of nanoreactors for environmental monitoring including the understanding of the fate, transport, and transformation of emerging contaminants with cells and complex matrices.
RECENT PUBLICATIONS (* denotes undergraduate co-authors)
Victor Murithi Kariuki, Julien Panetier, Jurgen Schulte, and Omowunmi A. Sadik, Directional Templating Mechanisms of Anisotropic Nanoparticles Using Poly (Pyromellitic Dianhydride-p-Phenylene Diamine), J. Phys. Chem. C, Just Accepted Manuscript,. DOI: 10.1021/acs.jpcc.6b03369.
Francis J. Osonga, Idris Yazgan, Victor Kariuki, *David Luther, *Apryl Jimenez, *Phuong Le & Omowunmi A. Sadik, Greener Synthesis and Characterization, Antimicrobial and Cytotoxicity Studies of Gold Nanoparticles of Novel Shapes and Sizes, RSC Advances, 2016, 6, 2302 – 2313.
Kun Xiang, Yinglei Li, William Ford, Walker Land, David Schaffer, Robert Congdon, Omowunmi Sadik Automated Analysis of Food-borne Pathogens using a Novel Microbial Cell Culture, Sensing and Classification System, Analyst, 2016, 141, 1472 – 1482.
Victor M. Kariuki , *Sohaib A Fasih-Ahmad, Francis J Osonga and Omowunmi A. Sadik, Electrochemical Sensor for Nitrobenzene using π-conjugated Polymer-embedded Nanosilver, Analyst 2016, 14, 2259-2269, DOI: 10.1039/C6an00029k.
Veronica Okello, Francis Osonga, *Michael Knipfing, *Victor Bushlyar & Omowunmi Sadik, Total Removal of Lead in Water and Sediments using Quercetin and Other Flavonoids, . Environmental Science: Processes & Impacts, 2016, 18, 306 – 313, DOI: 10.1039/C5EM00580A.
Cinelli M, Coles SR, Sadik O, Karn B, Kirwan K, A Framework of Criteria for the Sustainability Assessment of Nanoproducts, Journal of Cleaner Production (2016), 126, 277-287, doi: 10.1016/j.jclepro.2016.02.118.
Francis J. Osonga, Idris Yazgan, Victor Kariuki, *David Luther, *Apryl Jimenez, *Phuong Le & Omowunmi A. Sadik, Greener Synthesis and Characterization, Antimicrobial and Cytotoxicity Studies of Gold Nanoparticles of Different Shapes and Sizes, Journal of Total Environment, 563-564, 977-986, 2016, doi:10.1016/j.scitotenv.2015.12.064.
Vicki H. Grassian, Amanda J. Haes, Imali A. Mudunkotuwa, Philip Demokritou, Agnes B. Kane, Catherine J. Murphy, James E. Hutchison, Jacqueline A. Isaacs, Young-Shin Jun, Barbara Karn, Saiful I. Khondaker, Sarah C. Larsen, Boris L. T. Lau, John M. Pettibone, Omowunmi A. Sadik, Navid B. Saleh and Clayton Teague, Environmental Science: Nano 3 (1), 15-27, 2016.
Kariuki V., Yazgan I., Akgul A., Kowal A., Parlinska M., Sadik O. Synthesis, Catalytic and Biological Evaluation of Gold and Silver Nanoparticles using Poly(amic) Acid, Environmental Science: Nano, Environmental Science: Nano, 2015, 2, 518 – 527.
Magdalena Parlinska-Wojtan, Małgorzata Kus-Liskiewicz, Joanna Depciuch, Omowunmi Sadik, Green synthesis and antibacterial effects of aqueous colloidal solutions of silver nanoparticles using camomile terpenoids as a combined reducing and capping agent, Bioprocess & Biosystems Engineering, 2016, DOI: 10.1007/s00449-016-1599-4
Victor M. Kariuki · Jing Zhang , Andrzej Kowal , Magdalena Parlinska, Sadik O. A., 3D π-Conjugated Poly (amic) Acid Polymer as Support Matrices for Ethanol Electro-oxidation on Palladium and Platinum Catalysts, Electrocatalysis, July 2016, Volume 7, Issue 4, pp 317-325, 2016, DOI 10. 1007/s12678-016-0307-0.back to top
- Assistant Professor
- Chemistry and Biochemistry
Dr. Solmaz received her M.S. degree in Biochemistry from the Leibniz University of Hannover, Germany in 2001, and performed her M.S. thesis work with Nobel laureate Robert Huber, Ph.D., at the Max Planck Institute of Biochemistry in Martinsried, Germany. She received her Ph.D. degree in 2006 from the Max Planck Institute of Biophysics and the Goethe University in Frankfurt, Germany, where she was a Ph.D. student with Nobel laureate Hartmut Michel, Ph.D., supervised by Carola Hunte, Ph.D. As a Postdoctoral Researcher with Nobel laureate Gunter Blobel, Ph.D., at Howard Hughes Medical Institute at the Rockefeller University in New York, she developed an interest for the nuclear pore complex. She joined the Chemistry Department at Binghamton University in the Fall of 2014.
Nuclear transport: Nuclear pore complexes consist of 30 proteins, the nups. Their transport channel is arguably the largest and most complex transport conduit in the eukaryotic kingdom, and it is likely composed of the three channel nups. One of the most central questions of nuclear transport is: how can the huge protein scaffold of the nuclear pore complex adjust the diameter of its transport channel from 10 to 50 nm to accommodate cargoes of different sizes? To address this question, we have determined the protein structures of portions of the channel nups. Based on these structures, we have proposed a 'ring cycle hypothesis' for dilating and constricting the transport channel of the nuclear pore complex from 10-50 nm. Our goal is to obtain more structural data of the channel nups, in order to elucidate the molecular design of the transport channel, which will help us understand how large cargo and viruses, such as HIV, cross the nuclear pore complex. This research can inform therapies that block viral entry to the nucleus or promote it to improve gene therapy in non-dividing cells, where the nuclear pore complex is a major barrier for gene delivery to the nucleus.
Roles of nups in mitosis: Nups are multi-functional proteins that regulate many processes in the cell. During the 'mitosis' period of the cell cycle, chromosomes are segregated into two daughter cells. During mitosis in multi-cellular organisms, nuclear pore complexes are disassembled, and many of its 30 proteins, the nups, become part of a different kind of macromolecular machinery, the mitotic spindle apparatus. The mitotic spindle apparatus ensures faithful segregation of chromosomes to daughter cells. As part of this machinery, the nups interact with other proteins and participate in this process. It is unknown, how the structure of the nups sustains such multi-functionality. Thus, we plan to identify and characterize interactions of nups with components of the mitotic spindle apparatus and we will determine their crystal structures. Several of these nups were linked to cancers and especially leukemia. Investigating the mitotic functions of nups will reveal how they contribute to cancer generation and help devise therapies for cancer. Ultimately, the interplay between the roles of nups in nuclear transport, mitosis and gene regulation will be crucial for many aspects of the fate of the cell.
TYPES OF RESEARCH EXPERIENCES AVAILABLE
We use an interdisciplinary approach that combines x-ray crystallography to determine protein structures, biophysical methods to characterize protein-protein interactions, and cell biology for functional studies. A typical undergraduate project would involve expressing and purifying a protein of interest, and characterizing the protein by biophysical methods, such as light scattering or isothermal calorimetry. Students will also crystallize their protein of interest. The ultimate goal is to determine a protein structure, which involves collection of x-ray diffraction data at a synchrotron source
Highly motivated students are welcome in our lab and should expect to devote at least 2 semesters and a minimum of 15 hours a week to research. Most experiments take more than 4 hours to perform, but individual schedules can be accommodated.
Sharma, A1, Solmaz, SR1, Blobel, G and Melcak, I (2015). Ordered Regions of Channel Nucleoporins Nup62, Nup54 and Nup58 Form Dynamic Complexes in Solution. J Biol Chem 2015, 290, 18370. 1First authors, equally contributed. Selected as Journal cover.
Solmaz, SR*, Blobel, G* and Melcak, I*. Ring cycle for dilating and constricting the nuclear pore. Proc Natl Acad Sci U S A 2013 110: 5858-5863**.
Solmaz, SR, Chauhan, R, Blobel, G, and Melcak, I. Molecular architecture of the transport channel of the nuclear pore complex. Cell 2011 147: 590-602.
Solmaz, SR, and Hunte, C. Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. J Biol Chem 2008 283: 17542-17549.
Hunte, C, Solmaz, S, Palsdottir, H, and Wenz, T. A structural perspective on mechanism and function of the cytochrome bc1 complex. Results Probl Cell Differ 2008 45: 253-278.
Hunte, C, Solmaz, S, and Lange, C. Electron transfer between yeast cytochrome bc1 complex and cytochrome c: a structural analysis. Biochim Biophys Acta 2002 1555: 21-28.
- Assistant Professor
- Organic Chemistry
Dr. Vetticatt received his Ph.D. in physical organic chemistry with Prof. Daniel A. Singleton at Texas A&M University (2005-2009). His doctoral work was focused on the determination of organic reaction mechanisms using a combination of experimental and theoretical approaches. He applied these techniques to enzymatic reactions during his postdoctoral research in mechanistic enzymology and drug design with Prof. Vern L. Schramm at the Albert Einstein College of Medicine (2009-2011). Following this, he did postdoctoral research in organic synthesis and asymmetric catalysis with Prof. William D. Wulff at Michigan State University (2011-2013). He joined Binghamton as Assistant Professor of Organic Chemistry in the Fall of 2013.
Organocatalysis – catalysis by small organic molecules – is one of the fastest growing research areas in enantioselective synthesis, with over 2000 manuscripts published just within the last decade. Mechanistic understanding of these reaction has followed at a significantly diminished pace. Our research group utilizes a mechanism-based approach to the rational design of enantioselective reactions – with a specific focus on organocatalysis. Experimental and theoretical kinetic isotope effects (KIEs) and transition state analysis are used as design tools towards this end. This conceptually novel approach to methodology development is at the cutting-edge of this fast-expanding research area in enantioselective catalysis.
Another aspect of my research program involves an aggressive approach to develop a collaborative research effort focusing on mechanistic studies of contemporary organic reactions. This program gives my students an opportunity to interact with the top synthetic methodology groups around the world. Our collaborators, in turn, benefit from our mechanistic expertise, namely experimental determination of 13C KIEs, interpretation of KIEs using calculations and transition state modeling to understand mechanisms and selectivity in organic reactions. This concerted effort minimizes the time lag between discovery and mechanistic description of new organic reactions.
A third area of research focus involves the ‘transition state analogue’ approach to drug design. We develop transition state models, based on experimental KIEs, for a specific enzyme target. A density functional theory (DFT) based computational approach is utilized to generate libraries of small molecules that could potentially inhibit the activity of the enzyme by mimicking the electrostatics of the relevant transition state. The most promising inhibitor candidates are then synthesized and their efficacy evaluated.
In my lab, students will be trained in experimental and theoretical organic chemistry. Collaborations are an integral part of research in my group. In addition to furthering our research projects, students will be encouraged to identify problems of broad interest and establish independent collaborative efforts to successfully solve these problems. This will give the student an opportunity to showcase his/her expertise while gaining valuable inter-disciplinary research experience.
Sauer, G. S., Bandar, J. S., Wulff, W. D., Lambert, T. H., Vetticatt, M. J.*; Transition State Analysis of Enantioselective Brønsted Base Catalysis by Chiral Cycloprenimines. Submitted to J. Am. Chem. Soc. on 05/10/2014 (Collaborative project with Prof. Tristan Lambert at Columbia University, NY)
Vetticatt, M. J.; Itin, B.; Evans, G. B.; Schramm, V. L. Distortional Binding of Transition State Analogues to Human PNP probed by MAS Solid State NMR. Proc. Natl. Acad. Sci. USA. 2013, Accepted
Vetticatt, M. J.; Desai A. A.; Wulff, W. D. Isotope Effects and Mechanism of the Asymmetric BOROX Brønsted Acid Catalyzed Aziridination Reaction. in J. Org. Chem. 2013, 78, 5142–5152.
Burgos, E. S.; Vetticatt, M. J.; Schramm, V. L. Recycling Nicotinamide. The Transition-State Structure of Human Nicotinamide Phosphoribosyltransferase. J. Am. Chem. Soc. 2013, 135, 3485–3493.
Vetticatt, M. J.; Singleton, D. A. Isotope Effects and Heavy-Atom Tunneling in the Roush Allylboration of Aldehydes. Org. Lett. 2012, 14, 2370–2373.
Silva, R. G.; Vetticatt, M. J.; Merino, E. F.; Cassera, M. B.; Schramm, V. L. Transition-State Analysis of Trypanosoma cruzi Uridine Phosphorylase-Catalyzed Arsenolysis of Uridine. J. Am. Chem. Soc. 2011, 133, 9923–9931.
Schwartz, P. A.; Vetticatt, M. J.; Schramm, V. L. Transition State Analysis of the Arsenolytic Depyrimidination of Thymidine by Human Thymidine Phosphorylase. Biochemistry 2011, 50, 1412-1420.
Schwartz, P. A.; Vetticatt, M. J.; Schramm, V. L. Transition State Analysis of Thymidine Hydrolysis by Human Thymidine Phosphorylase. J. Am. Chem. Soc. 2010, 132, 13425-13433.
Vetticatt, M. J.; Desai A. A.; Wulff, W. D. How the Binding of Substrates to a Chiral Polyborate Counterion Governs Diastereoselection in an Aziridination Reaction: H-Bonds in Equipoise. J. Am. Chem. Soc. 2010, 132, 13104-13107. (Highlighted in C&EN)
- Distinguished Professor
- Inorganic and Materials Chemistry, and Materials Science & Engineering
Dr. Whittingham received his B.A., M.A. and D.Phil. degrees in chemistry from Oxford University in England. He did postdoctoral research in materials at Stanford University in California, then worked at Exxon and Schlumberger in basic energy related research before joining the chemistry faculty at SUNY Binghamton in 1988. He is also the Director of the Institute for Materials Research here, and of the Northeastern Center for Chemical Energy Storage at Binghamton.
The research interests of the Materials Chemistry group are in the preparation and chemical and physical properties of novel inorganic materials and all aspects of nanomaterials. Our long term goals are to solve the energy issues facing the United States.
The Nanochemistry of Materials is one of the two areas of chemistry experiencing the greatest growth at the present time both in academic institutions and industry. This popularity can be associated with the pervasiveness of solids throughout our lives from semiconductors through energy storage to geological/ biological systems, and to a number of recent breakthroughs, including high temperature inorganic superconductors.
One aspect of our work is in finding new synthetic routes to prepare metastable compounds that cannot be prepared by traditional techniques. Primary emphasis is on reacting ions in solution often using large organic species as templates around which he inorganic solid forms. In some cases it is possible to form previously unknown open structures by diffusing ions out of existing structures creating vacant tunnels or layers in which chemistry may be performed or separations/catalysis carried out. These reactions can be followed using electrochemical, x-ray, gravimetric and standard chemical methods, among others.
A second aspect is the study of ionic motion in solids and its use in batteries and fuel cells. Here much emphasis is on the intercalation compounds of the transition metal oxides, and the research involves both high and low temperature chemistry. Of particular interest are the vanadium and manganese oxides, which can be prepared with a variety of layer structures and with tunnels. Different ions and molecules can be intercalated into these structures allowing the controlled modification of chemical and physical properties. In addition these intercalation reactions can be the basis for high energy density storage devices and have the potential for revolutionizing the field of nanoscience.
An interest in chemistry and solids and a desire to go to graduate school in chemistry or materials. The expectation is that you will have taken or are planning to take Chem 341 and 444.
M. Stanley Whittingham, “The Ultimate Limits to Intercalation Reactions for Lithium Batteries”, Chem. Rev., 2014, 114: 11414-11443. DOI: 10.1021/cr5003003
M. Stanley Whittingham, “History, Evolution, and Future Status of Energy Storage”, IEEE Proceedings, 2012, 100: 1518-1534.
Frederik Omenya, Joel K. Miller, Jin Fang, Bohua Wen, Ruibo Zhang, Qi Wang, Natasha A. Chernova, and M. Stanley Whittingham, “Single-Phase Lithiation and Delithiation of Simferite Compounds Li(Mg,Mn,Fe)PO4”, Chemistry of Materials, 2014, 26: 626-6212. DOI: 10.1021/cm502832bNathalie Pereira, Glenn G. Amatucci, M. Stanley Whittingham, and Robert Hamlen, "Lithium titanium disulfide rechargeable cell performance after 35 years of storage", J. Power Sources, 2015, 280: 18-22. DOI: 10.1016/j.jpowsour.2015.01.056
Bohua Wen, Qi Wang, Yuhchieh Lin, Natasha A. Chernova, Khim Karki, Youngmin Chung, Fredrick Omenya, Shawn Sallis, Louis F. J. Piper, Shyue Ping Ong, and M. S. Whittingham, "Molybdenum Substituted Vanadyl Phosphate ε‑VOPO4 with Enhanced Two-Electron Transfer Reversibility and Kinetics for Lithium-Ion Batteries", Chem. Mater., 2016, 28: 3159-3170. DOI: 10.1021/acs.chemmater.6b00891
Zhixin Dong, Ruibo Zhang, Dongsheng Ji , Natasha A. Chernova , Khim Karki, Shawn Sallis , Louis Piper , and M. Stanley Whittingham, "The Anode Challenge for Lithium-Ion Batteries: A Mechanochemically Synthesized Sn–Fe–C Composite Anode Surpasses Graphitic Carbon", Advanced Science, 2016, 3: 1500229. DOI: 10.1002/advs.201500229.
Yiqing Huang, Yuh-Chieh Lin, David M. Jenkins, Natasha A. Chernova, Youngmin Chung, Balachandran Radhakrishnan, Iek-Heng Chu, Jin Fang, Qi Wang, Fredrick Omenya, Shyue Ping Ong, and M. Stanley Whittingham "Thermal Stability and Reactivity of Cathode Materials for Li-Ion Batteries", Appl. Mater. Interfaces, 2016, 8: 7013-7021. DOI: 10.1021/acsami.5b12081.
Lin, Yuh-Chieh; Wen, Bohua; Wiaderek, Kamila; Sallis, Shawn; Liu, Hao; Lapidus, Saul; Borkiewicz, Olaf; Quackenbush, Nicholas; Chernova, Natasha; Karki, Khim; Omenya, Fredrick; Chupas, Peter; Piper, Louis; Whittingham, M.; Chapman, Karena; Ong, Shyue Ping, "Thermodynamics, Kinetics and Structural Evolution of LiVOPO4 over Multiple Lithium Intercalation", Chem. Mater., 2016, 28: 1794-1805. DOI: 10.1021/acs.chemmater.5b04880.
Fredrick Omenya, Natasha A. Chernova, Shailesh Upreti, Peter Y. Zavalij, Kyung-Wan Nam, Xiao-Qing Yang, and M. Stanley Whittingham, "Can Vanadium Be Substituted into LiFePO4?", Chem. Mater., 2011, 23: 4733-4740.
Heng Yang, Qi Wang, Ruibo Zhang, Bryan Trimm and M Stanley Whittingham, "The Electrochemical Behaviour of TTF in Li-O2 Batteries using TEGDME-based Electrolyte", ChemComm., 2016, 52: 7580-7583. DOI: 10.1039/C6CC01120A
Yiqing Huang, Yuh-Chieh Lin, David M. Jenkins, Natasha A. Chernova, Youngmin Chung, Balachandran Radhakrishnan, Iek-Heng Chu, Jin Fang, Qi Wang, Fredrick Omenya, Shyue Ping Ong, and M. Stanley Whittingham "Thermal Stability and Reactivity of Cathode Materials for Li-Ion Batteries", Appl. Mater. Interfaces, 2016, 8: 7013-7021. DOI: 10.1021/acsami.5b12081.
Ruibo Zhang, Tefaya Abtew, Nicholas Quackenbush, Linda Wangoh, Matthew Huie, Alexander Brady, David Bock, Harry Efstathiadis, M. Stanley Whittingham, Amy Marschilok, Kenneth Takeuchi, Esther Takeuchi, Peihong Zhang, Louis Piper, "Electrode Reaction Mechanism of Ag2VO2PO4 Cathode", Chem. Mater., 2016, 28: 3428-3434.
Sung-Wook Kim, Nathalie Pereira, Natasha A. Chernova, Fredrick Omenya, Peng Gao, M. Stanley Whittingham, Glenn G. Amatucci, Dong Su, Feng Wang, "Structure Stabilization by Mixed Anions in Oxyfluoride Cathodes for High-Energy Lithium Batteries", ACS Nano 2015, 9: 10076–10084. 10.1021/acsnano.5b03643.
Anna M. Wise, Chunmei Ban, Johanna Nelson Weker, Sumohan Misra, Andrew S. Cavanagh, Zhuangchun Wu, Zheng Li, M. Stanley Whittingham, Kang Xu, Steven George, Michael Toney, "Effect of Al2O3 Coating on Stabilizing LiNi0.4Mn0.4Co0.2O2 Cathodes", Chem. Mater., 2015, 27: 6146-6154. 10.1021/acs.chemmater.5b02952
F. Omenya, B. Wen, J. Fang, R. Zhang, Q. Wang, N. A. Chernova, J. Schneider-Haefner, F. Cosandey, M. S. Whittingham, "Mg Substitution Clarifies the Reaction Mechanism of Olivine LiFePO4", Advanced Energy Materials, 2015, 5: 1401204. DOI: 10.1002/aenm.201401204.
Zheng Li, Chunmei Ban, Natasha A. Chernova, Zhuangchun Wu, Shailesh Upreti, Anne Dillon, M. Stanley Whittingham, "Towards understanding the rate capability of layered transition metal oxides LiNiyMnyCo1-2yO2", J. Power Sources, 2014, 268: 106-112.
- Materials and Analytical Chemistry, Catalysis, and Nanotechnology
Interdisciplinary areas of materials and analytical chemistry, focusing on nanomaterials, chemical and biological sensors, electrochemical energy conversion and storage, and advanced catalysts. Examples of recent research include nanoalloy catalysts for fuel cells, lithium-air batteries and thermoelectrics, nanostructured sensor arrays for detecting volatile organic compounds and biomarkers of human breaths, functional nanoprobes for detecting, delivering or targeting amino acids, proteins, DNAs, miRNAs and bacteria, and flexible devices for energy, sensing and medical applications.
S. Shan, V. Petkov, L. Yang, J. Luo, P. Joseph , D. Mayzel, B. Prasai, L. Wang, M. Engelhard, C.J. Zhong, “Atomic-Structural Synergy for Catalytic CO Oxidation over Palladium-Nickel Nanoalloys”, J. Am. Chem. Soc., 2014, 136, 7140-7151.
L.Q. Lin, E. Crew, H. Yan, S. Shan, Z. Skeete, D. Mott, T. Krentsel, J. Yin, N.A. Chernova, J.Luo, M.H. Engelhard, C. Wang, Q.B. Li, C.J. Zhong, “Bifunctional Nanoparticles for SERS Monitoring and Magnetic Intervention of Assembly and Enzyme Cutting of DNAs”, J. Mater. Chem. B, 2013, 1, 4320 - 4330.
L. Yang, S. Shan, R. Loukrakpam, V. Petkov, Y. Ren, B. Wanjala, M. Engelhard, J. Luo, J. Yin, Y. Chen, C.J. Zhong, "Role of support-nanoalloy interactions in the atomic-scale structural and chemical ordering for tuning catalytic sites", J. Am. Chem. Soc., 2012, 134, 15048−15060.
J. Yin, S. Shan, L. Yang, D. Mott, O. Malis, V. Petkov, F. Cai, M. S. Ng, J. Luo, B. H. Chen, M. Engelhard, C. J. Zhong, "Gold-Copper Nanoparticles: Nanostructural Evolution and Bifunctional Catalytic Sites", Chem. Mater., 2012, 24, 4662−4674.
E. Crew, S. Rahman, A. Razzak-Jaffar, D. Mott, M. Kamundi, G. Yu, N. Tchah, J. Lee, M. Bellavia, and C. J. Zhong, "MicroRNA Conjugated Gold Nanoparticles and Cell Transfection", Anal. Chem., 2012, 34, 26-29.
J. Yin, P. Hu, J. Luo, L. Wang, M. F. Cohen, C. J. Zhong, “Thin Film Assembly of Nanoparticles on Flexible Devices: Electrical Conductivity vs. Device Strains in Different Gas/Vapor Environment”, ACS Nano, 2011, 5, 6516 - 6526.
B. Wanjala, B. Fang, J. Luo, Y. Chen, J. Yin, M. Engelhard, R. Loukrakpam, C.J. Zhong, "Correlation between Atomic Coordination Structure and Enhanced Electrocatalytic Activity for Trimetallic Alloy Catalysts", J. Am. Chem. Soc., 2011, 133, 12714–12727.
L. Wang, X. Wang, J. Luo, B.N. Wanjala, C. Wang, N. Chernova, M. H. Engelhard, Y. Liu, I.-T. Bae, C. J. Zhong. “Core-Shell Structured Ternary Magnetic Nanocubes ", J. Am. Chem. Soc., 2010, 132, 17686–17689.
S. Lim, C.J. Zhong, “Molecularly-Mediated Processing and Assembly of Nanoparticles: Exploring the Interparticle Interactions and Structures”, Acc. Chem. Res., 2009, 42, 798-808.
Revised Summer 2014
CHEMISTRY 397, INDEPENDENT WORK - Variable Credit
Individual research under supervision of faculty member. Not limited to chemistry majors. Students must make formal application and receive approval of instructor and Department before the end of the drop/add period.
May be repeated for credit. No more than four credits of CHEM 397 may be used to satisfy major requirements for chemistry. Written report of work required.
NOTE: Chem 397 cannot be used to satisfy the organic, physical or analytical chemistry laboratory requirements for a chemistry major. Four credits of Chem 397 can be used to satisfy the Math-Science elective requirement for the BS degree and the chemistry elective for the BA degree.
- Consent of instructor.
- See restrictions in the catalog description above.
- Enrollment in CHEM 397 for a maximum of 2 credits in the second half of any semester is permitted upon approval of an application submitted and approved prior to the established deadline for registration for "second-half" courses.
- Credit for research not performed in the Chemistry Department requires written application and justification for study and sponsorship of a Chemistry faculty member who will assign the grade.
- Stipend and credit for the same work will normally not be allowed.
CHEMISTRY 497, ADVANCED INDEPENDENT WORK - Variable Credit
Individual research under direct supervision of faculty member. Requires more extensive preparation than CHEM 397, including prerequisites CHEM 221, 332, 341, and 351/351 (one can be taken as a co-requisite). Required for Honors Program in Chemistry.
*If you are considering Honors Program in Chemistry, you should examine the Guidelines early in your Junior year.
Before advanced registration, student must make formal application and receive approval of instructor and department. May be repeated for credit. No more than twelve credits total of CHEM 397 and 497 may be used to satisfy major requirements for chemistry. Written report of work required.
- Consent of instructor and approval of the UPC Chair.
- Demonstrated potential for independent study.
- See restrictions in the catalog description above.
- Credit for research not performed in the Chemistry Department requires written application and justification from study and sponsorship of a Chemistry faculty member who will assign the grade.
- Stipend and credit for the same work will normally not be allowed.
- Average of "B" or better in the last twelve courses.
- Junior standing.
- Application must be made to the Independent Work and Honors Advisor of the Chemistry Department no later than the end of the drop/add period.
- Application forms are available for the Chemistry Department Office (S2-236), and
- list all chemistry and science division courses taken to date;
- list the last twelve courses attempted and the grades received;
- present a one to two page prospectus of the proposed project which includes background information, experimental methods, and appropriate literature references; and
- include approval by the faculty member proposed to be the supervisor of the project.
CHEMISTRY 498, ADVANCED INDEPENDENT WORK (HONORS)
Application and registration procedures are the same as for CHEM 397 and/or 497. In addition, the following guidelines have been established.
- For admission, a student must meet the following criteria:
- shall be entering his/her last semester and be an undergraduate major in chemistry.
- shall have completed at least two credits of CHEM 497.
- shall have been approved and registered for 4 credits of CHEM 498 during the last semester.
- shall be recommended for the Honors Program by the faculty member who is supervising the research project.
- Application must be made to the Undergraduate Program Committee Chair no later than the first day of classes of the student's last semester.
- The application must include a prospectus of about five pages, complete with references, which will summarize work completed to date and will describe plans for completion of the project.
- To receive Honors, the candidate must successfully write and defend a thesis based on his or her research. Successful defense is indicated by signatures of the defense committee on the signature page of your thesis.
- The thesis shall conform to the editorial standards for theses established by the Graduate School.
- Copies of the thesis must be submitted to the thesis advisor and members of the oral examination committee at least one week prior to the oral examination.
- The defense of the thesis shall be by an oral examination by a committee of no less than three faculty members approved by the Undergraduate Program Committee Chair and chaired by the faculty supervisor.
- Candidates whose theses are accepted and defended successfully will be awarded the honor "Distinguished Independent Work in Chemistry."
- A successful defense of your thesis is indicated by signatures of members of your defense committee on the signature page of your thesis. You must show the signature page, signed by your committee, to either the secretary in the Department Office (Science 2, Room 226) or the Undergraduate Program Director.
- You need to submit the original and one copy of your thesis, in final form, to the Glenn G. Bartle Library, Acquisitions, for binding. One bound copy will be placed in the Library, and the other will be returned to the Chemistry Department. In addition please provide copies for any personal copies you wish to have bound. Personal copies will be bound for $10.00 per copy.