american chemical society 23rd annual northern california ... · chemistry, 1997-2002; journal of...

American Chemical Society 23rd Annual Northern California Undergraduate

Research Symposium

San José State University, San José Department of Chemistry

San José, CA May 14th 2011

Sponsors

SJSU Department of Chemistry

SJSU College of Science SJSU Student Affiliates of the American Chemical Society

SJSU Associated Students Santa Clara Valley Section of the American Chemical Society

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Thank you to our Sponsors

SJSU Department of Chemistry

SJSU College of Science

SJSU Student Affiliates of the

American Chemical Society

SJSU Associated Students

Santa Clara Valley Section of the

American Chemical Society

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American Chemical Society 23rd Annual Northern California Undergraduate Research

Symposium

San José State University, San José Department of Chemistry

San José, CA May 14th 2011

8:30am-9:00am Registration, Refreshments In front of Clark

Hall 8:45am-9:00am Student Oral Presentation Set-Up Clark Hall

9:00am-9:15am

Introductory Remarks Dr. Michael Parrish, COS Dean

Dr. Gerry Selter, Provost

Engineering Auditorium E189

9:20am-11:10am

Student Oral Presentations Session 1:

Biochemistry I Session 2:

Biochemistry II Session 3:

Physical and Computational Chemistry Session 4:

Organic Chemistry

Clark Hall

CL 202

CL 204

CL 216

CL 218

11:10am-11:15am Poster Set-Up Engineering

E285/287 11:15am- 12:10pm

Poster Session I (odd-numbered posters)

Engineering E285/287

12:10pm-1:10pm

Lunch provided to all registered attendees


1:10pm-1:55pm

Poster Session II (even-numbered posters)


2:00pm-3:00pm

Keynote Presentation Prof. Kenneth N. Raymond

UC Berkeley From Microbes to MRI: Some Roles of Metals in Medicine


3:00pm Concluding Remarks

Dr. Bradley Stone, Chair Department of Chemistry


Organizer: Dr. Lionel Cheruzel, San Jose State University

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KEYNOTE PRESENTATION

From Microbes to MRI: Some Roles of Metals in Medicine.

Prof. Kenneth N. Raymond

Department of Chemistry, University of California, Berkeley

The human serum iron transport protein, transferrin, maintains free serum ferric ion concentration at 10-24 M. Pathogenic bacteria must compete against this to obtain iron from their human host. It is difficult to overestimate the significance of iron as a limiting nutrient in microbial growth: enhancements of pathogenicity of over a million fold are seen when iron is supplemented. Small, but powerful and selective, iron chelators (siderophores) are produced by microbes as part of an arms race for iron between microbes and humans that will be generally described. These natural agents provide a biomimetic recipe for how to make selective complexing agents for other metal ion ions. For example, gadolinium(III) is an ideal magnetic resonance image (MRI) contrast agent due to its seven unpaired electrons combined with a suitable electronic relaxation rate. However, its high toxicity in vivo requires it to be complexed for bio-medical applications. Recent development of new classes of MRI agents, using the biomimetic approach, will be described. In another example, plutonium is feared as a human contaminant. Our approach to complexing Pu(IV) has been based on similarities in the chemical and biological properties of Fe(III) and Pu(IV). There is now a large scale program at LBNL to bring these agents into the clinic for emergency use. Finally, today’s technology and biotechnology use luminescent materials for high speed, and very sensitive, assays. Some lanthanide ions have unique electronic properties that enable time resolved detection; the difference between looking at a flashlight with the sun behind versus in a dark room. However these lanthanide ions must be complexed by an antenna ligand that can absorb light, efficiently transfer the energy to the lanthanide, and keep water away from the metal ion. There are now several commercial applications of the luminescence agents that have come out of our lab. Recent collaborations with Professor Muller and his group have used chiral derivatives of these agents to monitor circularly polarized luminescence.

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KENNETH N. RAYMOND

EDUCATION Institution Major Field Degree/Year Oregon public schools Matriculation/1959 Reed College Chemistry B.A./1964 Portland, Oregon Northwestern University Inorganic Ph.D/1968 Evanston, Illinois Advisors: Professors Fred Basolo and James A. Ibers

PROFESSIONAL CAREER Department of Chemistry, University of California, Berkeley: Assistant Professor, 1967-1974; Associate Professor, 1974-1978; Professor, 1978-; Vice Chair, 1982-1984, 1999-2000; Chair, 1993-1996, UC Berkeley Chancellor’s Professor, 2006- Chemical Sciences Division, Ernest Orlando Lawrence Berkeley National Laboratory: Faculty Scientist, 1976-1996; Faculty Senior Scientist, 1996-; Director, Seaborg Center, Chemical Sciences Division, 2002- HONORS Alfred P. Sloan Research Fellow, 1971–1973; Miller Research Professor, 1977–1978, 1996, 2004; Guggenheim Fellow, 1980-1981; Selected as one of the "Technology 100, 1981" by Technology Magazine; American Association for the Advancement of Science Fellow, 1984; DOE Ernest O. Lawrence Award, 1984; Lawrence Berkeley Laboratory Technology Transfer award, 1988, 1991; Humboldt Research Award for Senior U.S. Scientists, 1992; American Chemical Society Alfred Bader Award in Bioinorganic or Bioorganic Chemistry, 1994; Erskine Fellow, University of Canterbury, New Zealand, 1997; elected to National Academy of Sciences, 1997; Basolo Medal, Northwestern University, 1997; Max-Planck-Institut für Strahlenchemie “Frontiers in Biological Chemistry” Award, 1997; elected to the American Academy of Arts and Sciences, 2001; Reed College Howard Vollum Award, 2002; ACS Auburn Section G. M. Kosolapoff Award, 2004; Izatt-Christensen Award in Macrocyclic Chemistry, 2005; ACS Award in Inorganic Chemistry, 2008; Visiting Professor or Lecturer at many universities around the world. Recently: Joe L. Franklin Memorial Lectureship, 2006; Paulo Fasella Lectureship, 2006; 3M University Lecturer, University of Western Ontario, 2007; Frontiers in Chemistry Distinguished Lecturer, Case Western Reserve University, 2007; Watkins Lecturer, Wichita State University, 2007; Karcher Lecturer, University of Oklahoma, 2007; the Ramabrahman and

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Balamani Guthikonda Award Lecturer, Columbia University, 2008; Graduate Program Distinguished Lecturer, Scripps Research Institute 2008; Douglas G. Hill Memorial Lecturer, Cornell University, 2009; University of Rochester Distinguished Lectureship, 2009; Bailar Lectureship, University of Illinois, Champaign-Urbana, 2009; The Jerry and Jean Mohrig Lecturer in Chemistry, Carleton College, Northfield, MN, 2010. PROFESSIONAL ACTIVITIES United States Editorial Advisor for Springer-Verlag in Chemistry, 1972-1991; Member, Editorial Boards: Journal of Inorganic and Nuclear Chemistry, 1974-1981; Inorganic Chemistry, 1979-1986, 2002-2004; Journal of Coordination Chemistry, 1981-; Topics in Current Chemistry, 1981-1996; Accounts of Chemical Research, 1982-1988, 2005-2007; Inorganica Chimica Acta f-Block Elements, 1984-1988; Advances in Inorganic Chemistry, 1985-2001; Journal of the American Chemical Society, 1988-1994; BioMetals, 1992-; Journal of Biological Inorganic Chemistry, 1996-2000, 2005-2007; Topics in Biological Inorganic Chemistry, 1997-2002; Journal of Supramolecular Chemistry, 1992-2001; Proceedings of the National Academy of Sciences, 2002-2003; Contrast Media and Molecular Imaging 2006-2009. Member, boards: "Metallobiochemistry" Study Section of the National Institutes of Health, 1983-1985; National Science Foundation Advisory Panel in Chemistry 1984-1987; Board on Chem. Sciences and Technology, Natl. Academy of Sciences, 1998-2003, Co-Chair, 2000-2003; Center for Green Materials Chemistry, University of Oregon, 2010-. Chair, Inorganic Division, American Chemical Society, 1996-1997; member; “Synthetic and Biological Chemistry A” Study Section of the National Institutes of Health, 2006-2010; member, Scientific Review Committee, NIH NIAID, 2010; Cofounder, Lumiphore, Inc., 2001. PUBLICATIONS—510 papers and edited books PATENTS GRANTED—18 US patents

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Student Oral Presentations

Session 1

Biochemistry I

Clark Hall CL 202

Session Chair: Dr. Jennifer Lillig, Sonoma State University

9:20 am

Danelle Reddy

Jennifer Lillig*

Sonoma State University

Killing Listeria: The Effectiveness of Two Antibacterial Peptides

9:40 am

Jeremy Beckford Sina Yadegarynia

Brandon White* Marc d'Alarcao*

San José State University

Flavonoids Can Be Cytotoxic to Breast Tumor

Cells Despite Inhibiting Caspase-3

10:00 am

Rebecca Spector Renee Kinkade

Jennifer Lillig* Jon Fukuto*


The Isolation and Purification of GAPDH from Different Tissues of Gallus

Gallus

10:20 am Coffee Break

10:30 am

Aileen Espinoza Mallory Kato

Amanda Rodriguez

Elaine Collins*


Expression and Purification of the Human Vitamin D

Receptor and Two Variants

10:50 am

Cinthya Cisneros Samantha J. Carrington

Kevin Harnden

Jon M. Fukuto*


The Chemical Biology of H2S: Persulfide Formation

and Reactivity

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Session 2

Biochemistry II

Clark Hall CL 204

Session Chair: Dr. Daryl Eggers, San José State University

9:20 am

Melanie Lomotan

Carmen Works*


Isolation and Purification of Chromate Reductase from Novel

Pseudomonas Veronii

9:40 am

Philip Calabretta Mitchell Chancellor

Daryl Eggers*


Retention of Protein Structure in Hydrophilic, Organically-modified

Silica Gels

10:00 am

Andrew Martinolich Rachel Gate

Korin Wheeler*

Santa Clara University

Biophysical Characterization of the Cu(II) Active site of

Pseudomonas aeuruginosa Azurin with Silver Nanoparticles


10:30 am

Ngoc Huynh Ngoc-Han Tran

Lionel Cheruzel*


A new approach to fatty acid hydroxylation using hybrid P450-

BM3 enzyme and light

10:50 am

Heather Wright Jonathan Grist

Elaine Collins*


Synthesis and Purification of Tat Peptides and TAR RNA from

Bovine Immunodeficiency Virus

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Session 3

Physical and Computational Chemistry

Clark Hall CL 216

Session Chair: Dr. Annalise Van Wyngarden, San José State University

9:20 am

Erin Lee Brian McNelis

Thorsteinn Adalsteinsson*


Evidence of solution aggregation of PCB-octyl and PCB-octadecyl

by diffusion resolved NMR spectroscopy

9:40 am

Anil Azad Sergio Yoc

Maria Matyska-Pesek*


Synthesis and Characterization of Alkyl Bonded Phases Based on Silica Hydride Via Hydrosilation with Nickel Complex Catalysts

10:00 am

Hyunsuk Yoo Anthony De Crisci

Robert M. Waymouth*

Stanford University

An Investigation on the Thermodynamic Characteristics of

Ring Opening Polymerization of δ-Valerolactone


10:30 am

Kyle Tubbs Vincent T. Nguyen

Paul J. Henry

Thorsteinn Adalsteinsson*


The thermodynamic properties of encapsulated binary n-

Hexadecane/1-Octanol solutions within poly(t-butyl methacrylate)

nanocapsules

10:50 am

Gal Marcan

Jennifer Lillig*


Determining binding constant for pentagastrin with phospholipid

vesicles

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Session 4

Organic Chemistry

Clark Hall CL 218

Session Chair: Dr. Roy Okuda, San José State University

9:20 am

Angel Resendez Jaime Saavedra

Bakthan Singaram*

UC Santa Cruz

Reduction of Nitriles to Primary Amines Using InCl3-NaBH4 in

Tetrahydrofuran

9:40 am

Amanda Wong

Michael Carrasco*


The practical synthesis of aminooxy and N-methylaminooxy amines for

used in peptoid chemistry and bioconjugation

10:00 am

Alexander Rovira Jaime Saavedra

Bakthan Singaram*

UC Santa Cruz

Borohydride reactions with metal salts and the deoxygenation of

benzophenone derivatives using NaBH4/InCl3


10:30 am

Hoang Ly Oliver Oliverio

David J. R. Brook*


Metal Complexes of pyridine-2-carboxaldehyde-2’-pyridyl-

hydrazone, papyH, and its formation of Mixed Metal MOFs

10:50 am

Joseph B. Yu Darshan Manix

Ketwee Saksrithai Nguyen N. Nguyen

Hosea D. Matel

Krishnan P. Nambiar*

UC Davis

The conversion of α-Ionone to 4-Hydroxy-β-Ionone

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List of Presentation Abstracts

1. Killing Listeria: The Effectiveness of Two Antibacterial Peptides....p.14 Danelle Reddy and Jennifer Lillig* Department of Chemistry, Sonoma State University

2. Flavonoids Can Be Cytotoxic to Breast Tumor Cells Despite Inhibiting Caspase-3………………………………………………………………..…p.14 Jeremy Beckford; Sina Yadegarynia; Brandon White* and Marc d'Alarcao* Department of Chemistry, San José State University

3. The Isolation and Purification of GAPDH from Different Tissues of Gallus Gallus……………………………………………………………….p.15 Rebecca Spector; Renee Kinkade; Jennifer Lillig* and Jon Fukuto* Department of Chemistry, Sonoma State University

4. Expression and Purification of the Human Vitamin D Receptor and Two Variants………………………………………………………………..p.15 Aileen Espinoza; Mallory Kato; Amanda Rodriguez and Elaine Collins* Department of Chemistry, San José State University

5. The Chemical Biology of H2S: Persulfide Formation and Reactivity……………………………………………………………………p.16 Cinthya Cisneros; Samantha J. Carrington; Kevin Harnden and Jon M. Fukuto* Department of Chemistry, Sonoma State University

6. Isolation and Purification of Chromate Reductase from Novel Pseudomonas veronii……………………………………………………...p.17 Melanie Lomotan and Carmen Works* Department of Chemistry, Sonoma State University

7. Retention of Protein Structure in Hydrophilic, Organically-modified Silica Gels………………………………………………………………..…p.17 Philip Calabretta; Mitchell Chancellor and Daryl Eggers* Department of Chemistry, San José State University

8. Biophysical Characterization of the Cu(II) Active site of Pseudomonas aeuruginosa Azurin with Silver Nanoparticles…………………………..p.18 Andrew Martinolich; Rachel Gate and Korin Wheeler* Department of Chemistry, Santa Clara University

9. A new approach to fatty acid hydroxylation using hybrid P450-BM3 enzyme and light…..…………………………………………………….…p.19 Ngoc Huynh; Ngoc-Han Tran and Lionel Cheruzel* Department of Chemistry, San José State University

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10. Synthesis and Purification of Tat Peptides and TAR RNA from Bovine Immunodeficiency Virus……………………………………….…p.19 Heather Wright; Jonathan Grist and Elaine Collins* Department of Chemistry, San José State University

11. Evidence of solution aggregation of PCB-octyl and PCB-octadecyl by diffusion resolved NMR spectroscopy…………………………………...p.20 Erin Lee; Brian McNelis and Thorsteinn Adalsteinsson* Department of Chemistry & Biochemistry, Santa Clara University

12. Synthesis and Characterization of Alkyl Bonded Phases Based on Silica Hydride Via Hydrosilation with Nickel Complex Catalysts……...p.20 Anil Azad; Sergio Yoc and Maria Matyska-Pesek* Department of Chemistry, San José State University

13. An Investigation on the Thermodynamic Characteristics of Ring Opening Polymerization of δ-Valerolactone………………………….…p.21 Hyunsuk Yoo; Anthony De Crisci and Robert M. Waymouth* Department of Chemistry, Stanford University

14. The thermodynamic properties of encapsulated binary n-Hexadecane/1-Octanol solutions within poly(t-butyl methacrylate) nanocapsules……………………………………………………………….p.22 Kyle Tubbs; Vincent T. Nguyen; Paul J. Henry and Thorsteinn Adalsteinsson* Department of Chemistry & Biochemistry, Santa Clara University

15. Determining binding constant for pentagastrin with phospholipid vesicles…………………………………………………………………...…p.22 Gal Marcan and Jennifer Lillig* Department of Chemistry, Sonoma State University

16. Reduction of Nitriles to Primary Amines Using InCl3-NaBH4 in Tetrahydrofuran…………………………………………………………….p.23 Angel Resendez; Jaime Saavedra and Bakthan Singaram* Department of Chemistry and Biochemistry, University of California Santa Cruz

17. The practical synthesis of aminooxy and N-methylaminooxy amines for used in peptoid chemistry and bioconjugation……………………...p.23 Amanda Wong and Michael Carrasco* Department of Chemistry & Biochemistry, Santa Clara University

18. Borohydride reactions with metal salts and the deoxygenation of benzophenone derivatives using NaBH4/InCl3…………………….……p.24 Alexander Rovira; Jaime Saavedra and Bakthan Singaram* Department of Chemistry and Biochemistry, University of California Santa Cruz

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19. Metal Complexes of pyridine-2-carboxaldehyde-2’-pyridyl-hydrazone, papyH, and its formation of Mixed Metal MOFs…………………..……p.24 Hoang Ly; Oliver Oliverio and David J. R. Brook* Department of Chemistry, San José State University

20. The conversion of α-Ionone to 4-Hydroxy-β-Ionone……………….p.25 Joseph B. Yu; Darshan Manix; Ketwee Saksrithai; Nguyen N. Nguyen; Hosea D. Matel and Krishnan P. Nambiar* Department of Chemistry, University of California, Davis, CA

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Student Oral Presentation Abstracts

1. Killing Listeria: The Effectiveness of Two Antibacterial Peptides

Danelle Reddy and Jennifer Lillig*

Department of Chemistry, Sonoma State University Class IIa bacteriocins are peptides known to kill various Listeria species, especially the foodborne pathogen L. monocytogenes. The lactic acid bacteria Carnobacterium piscicola V1 (C. piscicola) produces two of these: Piscicocins V1a and V1b. To determine how well these peptides kill Listeria I performed a liquid killing assay in which I mixed L. ivanovii with either piscicocin V1a, piscicocin V1b, V1a’s C-terminus, V1b’s C-terminus, or pipes buffer (as a control); incubated; plated serial dilutions of the mixtures; and counted the resulting bacterial colonies. The exact numerical results are yet to be determined via statistical analysis, but it appears as though V1a and V1b were both effective killers, with V1a being the most effective, and that the C-terminal domains alone were not effective killers. Using the knowledge gained from this and other experiments, these antilisterial peptides may one day be used as food preservatives and antibiotics to prevent and treat Listeria infections.

2. Flavonoids Can Be Cytotoxic to Breast Tumor Cells Despite Inhibiting Caspase-3

Jeremy Beckford; Sina Yadegarynia; Brandon White* and Marc d'Alarcao*

Department of Chemistry, San José State University Flavonoids are polyphenolic plant natural products found extensively in the human diet. This class of compounds has been of considerable medicinal interest because of numerous reports of anti-inflammatory and anti-cancer activities. However, a detailed understanding of the biochemical mechanism of these activities is lacking. We have undertaken a study to determine which of the various cellular activites are necessary to induce cell death in a variety of breast cancer cell lines. As part of this study, we have evaluated the ability of various flavonoids to induce apoptosis by evaluating their effect on various markers, including caspase 3/7. Caspases are cysteine proteases responsible for mediating cellular apoptosis and several flavonoids have been reported to induce apoptosis in cancer cells. We hypothesized that the addition of flavonoids would result in increased caspase activity. To test the effect of flavonoids on caspase activity, we utilized Promega’s Caspase-Glo 3/7 assay system based on the fluorogenic substrate Ac-DEVD-AMC

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that generates fluorescent AMC upon caspase-induced cleavage. MDA-MB-231 cells were treated with staurosporine alone, flavonoid alone, flavonoid/staurosporine together for 24 h, or staurosporine first with flavonoid added immediately before the assay was conducted. From these data, it was evident that not only did some flavonoids fail to activate caspases, but some showed significant, dose-dependent inhibition of caspase 3 activity. The results showed that some flavonoids are cytotoxic to cells despite inhibiting caspase 3. The differential inhibition of the caspases by some flavonoids suggests the possibility of designing highly selective caspase inhibitors for possible medicinal use.

3. The Isolation and Purification of GAPDH from Different Tissues of Gallus Gallus

Rebecca Spector; Renee Kinkade; Jennifer Lillig* and Jon Fukuto*

Department of Chemistry, Sonoma State University Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays diverse and vital roles in the cell. Along with being a glycolitic enzyme it also know as a “housekeeping” gene due to its diversity and high concentration. It is extremely diverse due to many post-translational modifications involving oxidation. Since liver is the site of gluconeogenesis and it has been reported that bovine liver and rabbit skeletal muscle GAPDH have different Km values. We suggest that the liver GAPDH will have a higher Km than the muscle GAPDH from the same species. We are purifying GAPDH from liver tissue and skeletal muscle of Gallus Gallus (chicken) and a comparison will be made between the enzyme kinetics of the different sources. Purification began by the homogenization of the enzyme followed by an addition of ammonium sulfate. We will continue purification by subjecting the protein to DEAE anion exchange column.

4. Expression and Purification of the Human Vitamin D Receptor and Two Variants

Aileen Espinoza; Mallory Kato; Amanda Rodriguez and Elaine Collins*

Department of Chemistry, San José State University The hormonally active form of vitamin D, 1-25 dihyroxyvitamin D (1, 25(OH)2D3, regulates cell proliferation and differentiation, maintains phosphorous levels and stimulates intestinal absorption of calcium essential for bone growth and preservation. The nuclear vitamin D receptor (VDR) is a ligand-dependent transcription factor that acts with other coactivators to regulate gene expression. After vitamin D3 binds the VDR, biological effects are mediated via a vitamin D-responsive

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element (VDRE). Thermodynamic characterization of the vitamin D receptor (VDR) and variants would aid in the development of analogs useful for pharmaceuticals specific for vitamin D-related disease. In order to investigate the thermodynamic parameters for the binding of the VDR to 1,25(OH)2D3 and other analogs, we have cloned the cDNA for the full-length wild-type receptor (1-427), the C-terminal ligand binding domain of the receptor (118-427), and the fokI (F) polymorphism VDR (4-427) using polymerase chain reaction (PCR) and inserted the cDNAs into the pE-SUMOstar vector(Lifesensors). Resulting plasmids were then transformed into Rosetta cells (Novagen) to enhance eukaryotic proteins expression. Isolated proteins were confirmed using SDS-PAGE and SimpleBlue staining (Invitrogen) and will be purified by nickel affinity chromatography. Characterization of purified VDR proteins will be accomplished through binding assays and isothermal microcalorimetry.

5. The Chemical Biology of H2S: Persulfide Formation and Reactivity

Cinthya Cisneros; Samantha J. Carrington; Kevin Harnden and Jon M. Fukuto*

Department of Chemistry, Sonoma State University Numerous reports indicate an important biological signaling function associated with hydrogen sulfide (H2S). For example, endogenously produced H2S has been demonstrated to be a regulator of vascular tone and cardiac inotropy (possibly via interactions with potassium and/or calcium channels) among other important functions. In spite of the physiological importance of H2S very little is known about the chemistry responsible for its actions. As the simplest of all biological thiols, it is hypothesized that H2S can participate in thiol redox processes, some of which may be responsible for some of its activity. The reaction of H2S with an oxidized thiol (e.g. RSSR) results in the formation of a persulfide (RSSH). Thus, the formation of persulfides in biological systems appears likely and the unique chemistry of persulfides may be important to the biology of H2S. However, as a metastable species, knowledge of persulfide chemistry and biology is scant. Thus, the biological chemistry and prevalence of persulfides are being investigated.

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6. Isolation and Purification of Chromate Reductase from Novel Pseudomonas veronii

Melanie Lomotan and Carmen Works*

Department of Chemistry, Sonoma State University Hexavalent chromium (Cr(VI)) is a toxic metal that is not naturally present in the environment; it is a byproduct of many industrial processes and is a source of contamination for soils and water supplies. Chromium(VI) is extremely water soluble and readily passes through cell membranes. Remediation of contaminated areas has proven to be difficult, but studies have shown that certain bacteria can enzymatically reduce Cr(VI) to the less soluble, less toxic, trivalent chromium. The purpose of this study is to isolate, purify and characterize a chromate reductase from a novel strain of Pseudomonas veronii. Results indicate that the molecule is a homodimer with a molecular weight of approximately 50 kDa, and is an anion at pH 7.00. Purification techniques used size selective filtration and anion exchange chromatography; enzyme activity was monitored by DPC method and purity was checked by SDS-PAGE.

7. Retention of Protein Structure in Hydrophilic, Organically-modified Silica Gels

Philip Calabretta; Mitchell Chancellor and Daryl Eggers*

Department of Chemistry, San José State University Considering that the reactions of life do not occur at infinite dilution, it is important to take into account how surface interactions affect the structure and reactivity of biomolecules. In an attempt to better understand surface phenomena and crowding effects, apomyoglobin was immobilized in the pores of amorphous silica prepared by polycondensation of tetramethylorthosilicate (TMOS). Initially, it was found by circular dichroism spectroscopy that encapsulation leads to denaturation of this model protein. In an attempt to alter this result and to study the effects of surface chemistry on protein structure in general, various functionalized trimethoxysilanes were incorporated into gels at different mole ratios (2.5-10%). In this particular study, hydrophilic functional groups were targeted for testing (both charged and polar uncharged). Such substitutions were found to have a range of effects on protein structure compared to a control gel of 100% TM! OS. Most notably, three of the silica modifying reagents caused the encapsulated protein to adopt a structure similar to that observed in dilute solution. However, a possible issue was realized for one of these reagents, (3-glycidoxypropyl) trimethoxysilane, since this modifier can

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react with nucleophiles and, therefore, can potentially crosslink the protein to the silica matrix. To explore this issue further, a series of mass spectrometry experiments were designed to test the reactivity of the silica modifying reagent in water. Results show that crosslinking is possible at high concentrations of a model nucleophile (isoelectric glycine) relative to the concentration of (3-glycidoxypropyl) trimethoxysilane. 8. Biophysical Characterization of the Cu(II) Active site of Pseudomonas

aeuruginosa Azurin with Silver Nanoparticles

Andrew Martinolich; Rachel Gate and Korin Wheeler*

Department of Chemistry, Santa Clara University Silver nanoparticles (AgNPs) are being utilized commercially for their antibacterial properties, with applications ranging from apparel to plastic food storage containers. Although effective as an antimicrobial additive, little is known about their human health and environmental impacts. Cellular studies of AgNPs demonstrate toxicity resulting from surface oxidation. Ag(I) binds strongly to biological thiols, such as Cys and Met. As a result, essential pathways such as the respiratory chain are disrupted, including the function of many metalloproteins. Our investigations focus upon characterization of AgNP interactions with a model Cu(II) electron transport protein, Pseudomonas aeuruginosa azurin. Displacement of Cu(II) active site of azurin was monitored by UV-Vis spectroscopy. Preliminary results demonstrate a concentration dependent decrease in the Cu(II)-Cys LMCT band upon exposure to AgNPs. Studies across a range of AgNP sizes show increasing e! ffects upon the LMCT band as AgNP size was decreased. A maximum 68% decrease in the LMCT band was observed as a result of exposure to 10 nm AgNPs. The addition of AgNPs of various sizes resulted in minimal secondary structural changes in azurin, as monitored by circular dichroism. Preliminary mechanistic studies suggest direct AgNP interaction is necessary for Cu-displacement, rather than a mechanism that is dependent upon AgNP dissolution. These direct and indirect mechanisms of interaction will be discussed.

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9. A new approach to fatty acid hydroxylation using hybrid P450-BM3 enzyme and light

Ngoc Huynh; Ngoc-Han Tran and Lionel Cheruzel*

Department of Chemistry, San José State University Cytochromes P450 are a superfamily of heme-thiolate monooxygenases, found in almost all living organisms that play an important role in the biosynthesis and biodegradation of endogenous compounds. The P450 reaction is the introduction of an oxygen atom, derived from molecular oxygen, into a substrate unactivated carbon center. The mechanism involves the reductive scission of the O-O bond at the iron center, leading to the formation of a highly oxidative heme radical ferryl species, namely Compound I. Our long-term goal is to develop hybrid P450 heme domain enzymes that selectively hydroxylate C-H bonds in various substrates upon light activation with enhanced activity and stability compared to the current available systems. Our first generation of hybrid enzymes are constituted of a Ru(II)-diimine photosensitizer covalently attached to the heme domain of P450-BM3 mutants. Our preliminary results indicate that the novel hybrid enzymes can oxidize long chain fatty acids under constant visible light irradiation with enhanced activity (20 times better than the peroxide shunt). Optimization of the photocatalytic reactions will also be presented.

10. Synthesis and Purification of Tat Peptides and TAR RNA from Bovine Immunodeficiency Virus

Heather Wright; Jonathan Grist and Elaine Collins*

Department of Chemistry, San José State University Bovine immunodeficiency virus (BIV) is an advantageous model system for studying human immunodeficiency virus (HIV) due to their similar structure and mechanism. The key to pathogenicity is the interaction between the trans-activating (Tat) peptide and the transactivator response element (TAR) RNA. The interaction of the viral Tat protein and TAR RNA cause viral RNA to be transcribed more efficiently and accumulate in the nucleus of its host. We have used PCR-assisted gene assembly to clone cDNA for the wild-type (WT), R78G, K75G and double mutant BIV Tat peptide cDNA as well as BIV TAR RNA. The Tat peptides were cloned into the expression vector pTwin-1 (NEB) at the Pst1 and Sap1 restriction sites. The TAR DNA construct included the hepatitis delta virus (HDV) ribozyme sequence 3’ to the Tar sequence. The construct was cloned in pUC18 at the BamHI and HindIII restriction sites. The HDV ribozyme is self-cleaved from the TAR RNA as the RNA

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is transcribed. This ensures that the TAR RNA is homogeneous. RNA transcribed by T7 polymerase is otherwise heterogeneous since the T7 polymerase can up to 3 template-independent nucleotides at the 3’ end of the sequence. The tat peptides were expressed in BL21(DE3)pLsyS cells. Peptides were purified by affinity chromatography with chitin resin. TAR RNA was transcribed by T7 RNA polymerase. RNA was purified using SDS-PAGE. The mass of the each Tat peptide and TAR RNA was confirmed by mass spectrometry. The binding interactions between TAR RNA and the Tat peptides will be determined by isothermal titration calorimetry (ITC). The goal is to develop therapeutic agents that interfere with the interaction between TAR RNA and Tat peptides. 11. Evidence of solution aggregation of PCB-octyl and PCB-octadecyl by

diffusion resolved NMR spectroscopy

Erin Lee; Brian McNelis and Thorsteinn Adalsteinsson*

Department of Chemistry & Biochemistry, Santa Clara University In recent years, a growing demand for renewable energy sources has increased the need for solar cells and photovoltaic systems. The applicability of organic molecules, such as C60 analogs, to these systems is currently limited by a tendency towards low durability as well as low efficiency. By determining and correcting for the cause of the short shelf-life, we will be able to drastically improve the durability and efficiency of these organic systems. We believe that aggregation of the C60 molecules leads to this decrease in performance. In order to investigate this theory, we used diffusion NMR to follow the aggregation behavior of several C60 analogs in varying compositions of deuterobenzene and deutero methanol. We found that multiple factors, including solvent composition, impacted the aggregation of the molecules, suggesting that if conditions for the organic molecules are optimized, these molecules can be much more durable and efficient energy producers in photovoltaic systems.

12. Synthesis and Characterization of Alkyl Bonded Phases Based on Silica Hydride Via Hydrosilation with Nickel Complex Catalysts.

Anil Azad; Sergio Yoc and Maria Matyska-Pesek*

Department of Chemistry, San José State University Hydrosilation of silica hydride using two novel catalysts was evaluated. The hydrophilic and hydrophobic behavior of this material was determined by studying the retention characteristics of three amino analytes and four polyaromatic hydrocarbons analytes, respectively. Retention maps of the tested solutes revealed good selectivity and

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retention in the ANP (Aqueous Normal Phase) and RP-HPLC (Reversed Phase –High Performance Liquid Chromatography) mode.

13. An Investigation on the Thermodynamic Characteristics of Ring Opening Polymerization of δ-Valerolactone

Hyunsuk Yoo; Anthony De Crisci and Robert M. Waymouth*

Department of Chemistry, Stanford University Computational methods were used to calculate the thermodynamic parameters of ring opening polymerization (ROP) reaction of lactones and cyclic carbonates. Calculations were performed with Gaussian 09, Density Functional Theory (DFT) using B3LYP functional and CC-PVTZ basis set. For a simple reaction in which methanol reacted with δ-valerolactone to form a ring opened monomer in the gas phase, it was shown that the enthalpy of ring-opening was ΔH = -7.20 kcal/mol. Calculations for the same reaction were done in different solvents (benzene, acetonitrile, chloroform, and dichloromethane) that had different dielectric constants. The enthalpy of ROP was calculated to be smaller in solvents with higher dielectric constants (see Fig. 1). The trend predicted by the DFT calculations was tested by running ROP experiments of δ-valerolactone at different temperatures and determining the equilibrium monomer concentration ([M]eq) by NMR spectroscopy. Experimental results showed that ΔH of ROP decreased as the dielectric constant of the solvent increased, as was initially predicted by the DFT calculations. This study demonstrates that DFT calculations can provide qualitative predictions on the role of solvation on the thermodynamics of ring opening polymerization reactions.

Fig 1. DFT calculation result showing how solvation affects ΔH of ROP of

δ-valerolactone

-8

-6

-4

-2

0

2.3 4.8 8.9 37.5

ΔH

Dielectric Constant

ΔH of ROP vs Dielectric Constant

Enthalpy Change

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14. The thermodynamic properties of encapsulated binary n-

Hexadecane/1-Octanol solutions within poly(t-butyl methacrylate) nanocapsules.

Kyle Tubbs; Vincent T. Nguyen; Paul J. Henry and Thorsteinn Adalsteinsson*

Department of Chemistry & Biochemistry, Santa Clara University We study the phase transition behavior of binary solutions of n-Hexadecane and 1-Octanol that are encapsulated with sub-micron sized poly(t-butyl methacrylate) polymer capsules. Systematic variation of the diameter of the encapsulated oil droplet from 75 nm to 150 nm allows us to observe how the increase in the particle surface to volume ratio affects the phase transition behavior of the oil. The synthetic handle of the polymer capsules also allows us to vary the thickness of the encapsulating polymer film, and the chemical composition of the film. This allows us to change the flexibility of the film, and the surface tension between the polymer and the oil. The phase transition of the encapsulated oil is investigated through differential scanning calorimetry and variable temperature NMR spectroscopy. This gives us a broad experimental basis in observing the actual transition temperature, the enthalpy of the phase transition, how much of the oil remains in liquid form (perceivably the surface-phase in the system) and how the composition of remaining encapsulated liquid changes during the freezing of the oil. The experiments show a dramatic change in the phase behavior and surface-liquid composition as a function of the size of the confinement. The onset of the phase transition is shifted toward lower temperatures as the confinement gets smaller, while simultaneously more liquid remains unfrozen after the main transition. The composition of the unfrozen liquid appears to be enriched in n-hexadecane, rather than 1-octanol.

15. Determining binding constant for pentagastrin with phospholipid vesicles

Gal Marcan and Jennifer Lillig*

Department of Chemistry, Sonoma State University The binding of pentagastrin to phospholipid vesicles has been studied by fluorescence spectroscopy. Fluorescence changes are seen due to the tryptophan residue of this peptide upon binding to phospholipids vesicles. This is accompanied by a blue shift of the maximum emission indicative of the incorporation of the tryptophan residue into a more hydrophobic environment. The hydrophobic nature and the electrostatic

23

charge have significant influence on the nature of the binding. Zwitterionic DMPC and acidic phospholipid DMPG phospholipids have been tested for binding affinity to pentagastrin. Fluorecence titration curves have been used to determine the binding constant. A more conclusive binding curve has been shown for acidic DMPG compared to zwitterionic DMPC.

16. Reduction of Nitriles to Primary Amines Using InCl3-NaBH4 in Tetrahydrofuran

Angel Resendez; Jaime Saavedra and Bakthan Singaram*

Department of Chemistry and Biochemistry, University of California Santa Cruz

Current methods for the reduction of nitriles consists of working with pyrophoric compounds or toxic heavy metals, currently in the lab a new method for reducing nitriles to primary amines has been developed using InCl3-NaBH4 in Tetrahydrofuran, which is relatively low toxic in comparison to the usage of Lewis acid reductions and transition metal salt hydrides. A variety of aromatic, aliphatic, and hetero-aromatic nitriles were successfully reduced to their corresponding primary amines obtaining yields of up to 99% under ambient conditions. Products were isolated by acid-base extraction. 17. The practical synthesis of aminooxy and N-methylaminooxy amines

for used in peptoid chemistry and bioconjugation

Amanda Wong and Michael Carrasco*

Department of Chemistry & Biochemistry, Santa Clara University Aminooxy and N-alkylaminooxy groups incorporated into peptides have proven extremely useful for bioconjugation. The aminooxy groups react chemoselectively with aldehydes and ketones to form oximes, and N-alkylaminooxy groups react with unprotected reducing sugars to effect peptide glycosylation. In order to extend this bioconjugation chemistry to peptoids, we have developed a practical synthesis for five aminooxy and N-alkylaminooxy amines. These amines can be incorporated into peptoids via the submonomer synthesis method. The resulting peptoids can then be chemoselectively modified to provide lipidated and glycosylated analogs. Here we present the details of the optimized synthetic procedures for the amines and our current progress in incorporating the amines into peptoids.

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18. Borohydride reactions with metal salts and the deoxygenation of benzophenone derivatives using NaBH4/InCl3

Alexander Rovira; Jaime Saavedra and Bakthan Singaram*

Department of Chemistry and Biochemistry, University of California Santa Cruz

Various metal salts were reacted with borohydrides, such as lithium aminoborohydride (LAB) and sodium borohydride (NaBH4), to compare their effectiveness for converting metal salts into metals or metal hydrides. LAB reagents are effective in converting several metal salts into the corresponding metals through the intermediate formation of metal hydrides. However, NaBH4 converted most of the metal salts to the corresponding metal borides with one exception. Sodium borohydride reacted with indium trichloride (InCl3) and generated diborane. A systematic study revealed that InCl3/NaBH4 mixture is effective in deoxygenating benzophenone derivatives to the corresponding benzhydryl compound with isolated yields of up to 95%. The reaction could be carried out in one pot using one equivalent of InCl3 and three equivalents of NaBH4 in refluxing methylene chloride.

19. Metal Complexes of pyridine-2-carboxaldehyde-2’-pyridyl-hydrazone, papyH, and its formation of Mixed Metal MOFs

Hoang Ly; Oliver Oliverio and David J. R. Brook*

Department of Chemistry, San José State University Pyridine-2-carboxaldehyde-2’-pyridyl-hydrazone, papyH, was first reported over 40 years ago largely in the context of analytical chemistry. More recently, because of their simple synthesis and ability to undergo self-assembly to form polymetallic grids, interest in hydrazones and related ligands has re-emerged but their metal complexes are still poorly characterized. We are working to rectify this situation with studies involving spectroscopy, electrochemistry, and nucleophilicity of nickel, cobalt, and iron complexes of papy. We report full characterization of these complexes using magnetic susceptibility, 1H NMR, UV-vis, cyclic voltammetry, MS, and kinetic analyses with CH3I. Furthermore, we will report on the potential for Metal Organic Frameworks, MOFs, based on hydrazones; in particular the possibility of a mixed metal system.

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20. The conversion of α-Ionone to 4-Hydroxy-β-Ionone

Joseph B. Yu; Darshan Manix; Ketwee Saksrithai; Nguyen N. Nguyen; Hosea D. Matel and Krishnan P. Nambiar*

Department of Chemistry, University of California, Davis, CA In our attempts to synthesize Lutein, we investigated using selenium dioxide in the allylic hydroxylation of α-ionone. Direct hydroxylation of α-ionone yielded 4-hydroxy-β-ionone and a small number of side products. This reaction is proposed to proceed through isomerization of the ε-ring of α-ionone to form the β-ring of β-ionone followed by hydroxylation at the Carbon-4 (C4) position. In all conditions tested, formation of 3-hydroxy-α-ionone or 3-hydroxy-β-ionone was not detected. These observations demonstrate that the doubly allylic hydrogen at the C6 position is more reactive than the hydrogen at the C3 and the methyl hydrogens at C5. In modifying the reaction parameters, we found that carrying out the reaction at -40 °C did not yield any product. Yields typically increased with larger amounts of selenium dioxide. Addition of hydrogen peroxide and tert-butyl hydrogen peroxide decreased yields of 4-hydroxy-β-ionone. The produced 4-hydroxy-β-ionone can be used as a precursor for the facile synthesis of isozeaxanthin, canthaxanthin and asthaxanthin -carotenoids found in avian plumage.

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List of Poster Abstracts

1. Synthesis and characterization of polymer nanocapsules by surface initiated polymerization from a nano-drop template…………………....p.30 Emily Tran; Paul J. Henry; Lauren E. Tracy and Thorsteinn Adalsteinsson* Department of Chemistry & Biochemistry, Santa Clara University

2. Synthesis and Characterization of Microspherical Imprinted Polymers as P450 Enzyme Mimic………………………………………………..….p.30 Austin Roberts; Alvin Thai and Lionel Cheruzel* Department of Chemistry, San José State University

3. Thermodynamic properties of encapsulated binary n-Hexadecane/1-Octanol solutions within poly(t-butyl methacrylate) nanocapsules…...p.31 Vincent Nguyen; Kyle W. Tubbs; Paul J. Henry and Thorsteinn Adalsteinsson* Department of Chemistry & Biochemistry, Santa Clara University

4. The Fabrication of Single Walled Carbon Nanotubes (SWCNT) in an Electrolyte Gate Field Effect Transistor (EGFET)………………………p.32 Khanh-Van Tu; Hsiao-Chu Lin; Cattien Nguyen; Roger H. Terrill* and Daniel Straus* Department of Chemistry, San José State University

5. Synthesis of polymer nanocapsules via surface initiation from mini-emulsions…………………………………………………………………...p.32 Paul Henry; Emily M. Tran; Lauren E. Tracy and Thorsteinn Adalsteinsson* Department of Chemistry & Biochemistry, Santa Clara University

6. Formation of Colored Solutes, Precipitates and Films by Reactions of Organics in Sulfuric Acid Particles in the Upper Troposphere/Lower Stratosphere………………………………………………………………..p.33 Kieu Ha; Nathan Feick; Jeffrey Berry; Saul Perez Montano; Linda Leong; Hoang Le; Khaled Khaled; Riyanto Dwisaksono; Laura T. Iraci* and Annalise Van Wyngarden* Department of Chemistry, San José State University

7. Characterization of Metal-Binding Sites of Calmodulin Utilizing Europium (III)……………………………………………………………….p.33 Truman Jefferson; Farah Memom and Gilles Muller* Department of Chemistry, San José State University

8. Photochemical Studies of Iron-Only Hydrogenase……………….…p.34 Melinda Pope and Carmen Works* Department of Chemistry, Sonoma State University

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9. Photophysical and Chiroptical Properties of Chiral Lanthanide(III) Complexes…………………………………………………………...……..p.34 Bao Le and Gilles Muller* Department of Chemistry, San José State University

10. Using Solvatochromic Fluorophores to Study Peptoid Structure...p.35 Stanley Hiew; Frederick J. Seidl; Marisa A. Plescia and Amelia Fuller* Department of Chemistry & Biochemistry, Santa Clara University

11. Investigation of fluorescent molecules from Naematoloma Fasciculare………………………………………………….………………p.35 Jeffery Verde; Rosie Geranio and Steve Farmer* Department of Chemistry, Sonoma State University

12. Factors Effecting the Chiral Recognition of Amino Acids…....……p.36 Jamie Lunkley; Brian T. Nguyen and Gilles Muller* Department of Chemistry, San José State University

13. Detailed Characterization of a Tridentate Ligand for Circularly Polarized Luminescent Ln(III)-Containing Probes………………….…..p.36 Andrew Ingram; Alexander Dunlap and Gilles Muller* Department of Chemistry, San José State University

14. Determination of Stability Constants of Lanthanide(III)-Based Systems for Circularly Polarized Luminescence…………....……….…p.37 Eliseo Quiroz; Andrew J. Ingram; Angela Tisch and Gilles Muller* Department of Chemistry, San José State University

15. Computational Study of the Thermal Rearrangement of Allylic Sulfinates to Sulfones…………………………………………………..…p.37 Christina McCulley; Randy M. Miller and David B. Ball* Department of Chemistry and Biochemistry, California State University, Chico

16. Novel Application of Statistical Predictors: First Stage Calculation of Solvent Accessible Protein Residues…………………………….…..p.38 Reecha Nepal; Daniel Rose; Shabnam Gholizadeh; Robert Lau; Radhika Mishra; Kimberly Uweh and Brooke Lustig* Department of Chemistry, San José State University

17. An Analysis of the Structures of Phallotoxin Compounds Utilizing Molecular Modeling………………………………………………..………p.38 Christina McCulley; Stuart McDaniel and Robert Zoellner* Department of Chemistry and Biochemistry, California State University, Chico

18. Computational Analysis of Metal-Hydrosulfide Complexes Supported by a Novel Carbonic Anhydrase Biomimetic Ligand System………....p.39 Sylvanna Krawczyk; Benjamin F. Gherman* and Eric C. Brown* Department of Chemistry, California State University, Sacramento

28

19. Computational Study of the Cyclization Reactions of Quinoxaline-Based Enediynes……………………………………………………….….p.40 Ramiro Fernandez; Nadezhda Korovina; Benjamin F. Gherman* and John D. Spence* Department of Chemistry, California State University, Sacramento

20. Further progress towards the total enantioselective synthesis of the gallicynoic acids……………………………………………………...…….p.41 Brandon Tautges; Ryan Barnes and David Ball* Department of Chemistry and Biochemistry, California State University, Chico

21. Synthesis of Karrikin Analogues: Butenolide Derivatives that Play an Important Role in Post-Fire Seed Germination…………………...…….p.41 Victoria Johnson and Daniel Straus* Department of Chemistry, San José State University

22. Catalytic Enantioselective 1,4-Additions of Allyl Indium Reagents to α,β-Unsaturated Aldehydes………………………………………....…....p.42 Stella Plukchi; Diego Colorado and Claudia G. Lucero* Department of Chemistry, California State University, Sacramento

23. Approaches to the Synthesis of Optically Active 4-Amino-2,6-pyridinedicarboxylate Ligands by Catalytic Coupling Reactions…...…p.42 Jia Lu and Dan Straus* Department of Chemistry, San José State University

24. Total Synthesis of (+)-Tatarinoid C………………………........……p.43 Dimitar Panayotov; Maddy McCrea-Hendrick and Claudia Lucero* Department of Chemistry, California State University, Sacramento

25. Synthesis of Multivalent, Glycosylated Antiretrovirals………….....p.43 Careena Cary and Katherine McReynolds* Department of Chemistry, California State University, Sacramento

26. Radical Cyclization of Vinylcyclopropane to form Eight-Membered Rings…………………………………………………………………...……p.44 Krystle Merritt and James Miranda* Department of Chemistry, California State University, Sacramento

27. Effects of Trimethylamine N-oxide on the Solubility of Diketopiperazine……………………………………………………………p.44 Brian Castellano and Daryl K. Eggers* Department of Chemistry, San José State University

28. Alginate gel encapsulation of enzyme bromoperoxidase…..……..p.45 Bo Hwang; John H. Kim; Nikhita Tulsi; Daniel Pacheco and Roy K. Okuda* Department of Chemistry, San José State University

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29. Expression, Purification, and Characterization of Carnobacteriocin B2 Casee Barnes; Peter Arnold and Jennifer Lillig* Department of Chemistry, Sonoma State University

30. Modified Silica Glass Effects on Protein Adsorption and Structure Yamah Amiri and Daryl K. Eggers* Department of Chemistry, San José State University

31. Impact of Electrostatic Interactions on the Binding of Cationic Tricyclic Drugs to Model Membranes…………………………………....p.47 Katelyn Caslavka and Linda S. Brunauer* Department of Chemistry & Biochemistry, Santa Clara University

32. Surface Effects of Polar Organic Side Groups on Apomyoglobin Confined to a Silica Matrix……………………………………………..….p.47 Mitchell Chancellor; Phillip Calabretta and Daryl Eggers* Department of Chemistry, San José State University

33. Selectivity of Selected Aptamers Toward Multiple Variations of a VEGF Peptide………………………………………………………………p.48 Nicholas Giustini; Dustyn H. Uchiyama; Christopher M. Rose; Michael J. Hayes; Gregory R. Stettler; Trevor M. Axelrod; Scott F. Hickey and Steven W. Suljak* Department of Chemistry & Biochemistry, Santa Clara University

34. Toward an Understanding of the Role of Desolvation in Protein Folding: Changes in the Solubility of a Phenylalanine Derivative….…p.48 Tanya Ghaemmaghami; Melinda D. Mendolla and Daryl K. Eggers* Department of Chemistry, San José State University

35. Development of an Enzyme-Linked Detergent-Free Transphosphatidylation System for Microscale Synthesis of Phosphatidylserine…………………………………..………………....….p.49 Sandra McCaw and Linda S. Brunauer* Department of Chemistry & Biochemistry, Santa Clara University

36. Light Initiated Hydroxylation of Substrate C-H bonds using Hybrid P450 Enzymes………………………………………………....……….….p.49 Ngoc Huynh; Ngoc-Han Tran; Thuba Bui; Angelina Nguyen; Yen Nguyen; Jeremiah Heredia; Garrett Chavez and Lionel Cheruzel* Department of Chemistry, San José State University

37. Bulk Water Effects on Nucleoside Solubility as Probed with Salt Solutions…………………………………………………………………….p.50 Ishraq Sadhan; Elisa Aguilar and Daryl K. Eggers* Department of Chemistry, San José State University

38. Overexpression of HIV TAR RNA and Tat Peptides…...………....p.50 Tan Tran; Josh Sun and Elaine Collins* Department of Chemistry, San José State University

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Student Poster Abstracts

1. Synthesis of polymer nanocapsules by surface initiated polymerization from a nano-drop template

Emily Tran; Paul J. Henry; Lauren E. Tracy and Thorsteinn Adalsteinsson*

Department of Chemistry & Biochemistry, Santa Clara University Our goal is to produce bio-compatible sub-micron sized capsules for use as drug delivery vesicles, or vesicles to deliver ultra-small volumes of liquids. We are focusing on the preparation of capsules in an oil-in-water system in which the monomer is deposited from the continuous phase onto the outside of the emulsion particles to form the polymer capsule. This enables us to encapsulate oil solution droplets that may contain oil soluble, fragile, drug-type molecules. We have effectively produced particles with diameters ranging from 150 to 200 nanometer that are coated with a few nanometer thick poly(N-isopropyl acrylamide) and poly(methacrylamide) polymer layers. We demonstrate the polymer capsule formation by NMR spectroscopy, dynamic light scattering and SEM microscopy. This research is a step toward developing encapsulation methods, where oil solutions can be encapsulated in sub-nanoliter quantities. 2. Synthesis and Characterization of Microspherical Imprinted Polymers

as P450 Enzyme Mimic.

Austin Roberts; Alvin Thai and Lionel Cheruzel*

Department of Chemistry, San José State University

Cytochrome P450s are heme-thiolate enzymes that play an important role in the biosynthesis and biodegradation of endogenous compounds. The classical P450 reaction is the regio and stereo selective introduction of an oxygen atom, derived from molecular oxygen, into a substrate unactivated carbon center. Over the years, great advances have been made in mimicking P450 reactivity by utilizing metal (Fe, Mn, Ru) porphyrins and single oxygen atom donors (iodosylbenzene, peracids, hydrogen and alkyl peroxides). However, these models still lack substrate recognition properties leading to regioselectivity of oxidation and control of electron-proton transfer steps when oxygen is used as oxidant. Our long-term goal is to encapsulate substrate bound metalated porphyrin complexes within a polymer framework using molecular imprinted polymer methodology. Molecular Imprinted Polymers (MIPs) are highly porous materials with template-shaped cavities. We will report

31

the synthesis and characterization of microspherical polymers encapsulating tetra-4-hydroxyphenylporphyrin (TPP-OH). Atomic Force Microscopy has been used to characterize the shape and surface morphology of the microspherical polymers.

3. Thermodynamic properties of encapsulated binary n-Hexadecane/1-Octanol solutions within poly(t-butyl methacrylate) nanocapsules

Vincent Nguyen; Kyle W. Tubbs; Paul J. Henry and Thorsteinn Adalsteinsson*

Department of Chemistry & Biochemistry, Santa Clara University Binary solutions of n-Hexadecane and 1-Octanol are encapsulated within sub-micron sized poly(t-butyl methacrylate) polymer capsules to study the phase transition behavior. The radius of the encapsulated oil droplet is systematically varied from 60 nm to 110 nm to observe how the increase in the particle surface to volume ratio affects the phase transition behavior of the oil. The synthetic handle of the polymer capsules also allows variations in the thickness of the encapsulating polymer film, and the chemical composition of the film.This allows for changes in the flexibility of the film, and the surface tension between the polymer and the oil. The phase transition of the encapsulated oil is investigated through differential scanning calorimetry and variable temperature NMR spectroscopy. This gives a broad experimental basis in observing the actual transition temperature, the enthalpy of the phase transition, the amount of oil that remains in liquid form (perceivably the surface-phase in the system) and how the composition of remaining encapsulated liquid changes during the freezing of the oil.The experiments show a dramatic change in the phase behavior and surface-liquid composition as a function of the size of the confinement. The onset of the phase transition is shifted toward lower temperatures as the confinement decreases in size, while simultaneously more liquid remains unfrozen after the main transition. The composition of the unfrozen liquid appears to be enriched in n-hexadecane, rather than 1-octanol.

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4. The Fabrication of Single Walled Carbon Nanotubes (SWCNT) in an Electrolyte Gate Field Effect Transistor (EGFET)

Khanh-Van Tu; Hsiao-Chu Lin; Cattien Nguyen; Roger H. Terrill* and Daniel Straus*

Department of Chemistry, San José State University The integral component of this research is the characterization of ultrathin films and monolayers of single walled carbon nanotube (SWCNT) conductivity in a field effect transistor (FET) configuration. Like SWCNT-FETs that have been reported in the literature, our design has a SWCNT channel layer contacted on each end by gold electrode that serve as source and drain respectively. However, in our EGFET design there is an extremely intimate contact between the gate and the SWCNT channel because the gate is an electrolyte solution rather than a SiO2 film. To our knowledge, no examples of SWCNT EGFET designs exist in the literature. The long term goal of the research is to use EGFETs as electrochemical sensors. Prior work that used thick SWCNT films showed some chemical sensitivity. The present technological hurdle being confronted is the preparation of SWCNT films. We have done chemical modifications of both the SWCNT sidewalls and the glass substrate surfaces and have produced much thinner and much higher conductivity SWCNT films. It is hoped that these may become the basis of a new nanosized biosensor. 5. Synthesis of polymer nanocapsules via surface initiation from mini-

emulsions.

Paul Henry; Emily M. Tran; Lauren E. Tracy and Thorsteinn Adalsteinsson*

Department of Chemistry & Biochemistry, Santa Clara University

We present an efficient encapsulation method to obtain sub-micron sized polymer capsules. The synthetic approach can be used to encapsulate otherwise chemically fragile molecules with a few nanometer thick polymer shell. The capsule diameter can be varied from 150 to 200 nanometers while keeping extremely low distribution in sizes. We have successfully deposited poly(N-isopropyl acrylamide) and poly(methacrylamide) polymers onto the oil droplets. This method has a potential for becoming useful in encapsulating dyes, contrast agents or drug molecules for extended delivery applications. Here we present NMR and dynamic light scattering data to support our synthesis.

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6. Formation of Colored Solutes, Precipitates and Films by Reactions of Organics in Sulfuric Acid Particles in the Upper Troposphere/Lower

Stratosphere

Kieu Ha; Nathan Feick; Jeffrey Berry; Saul Perez Montano; Linda Leong; Hoang Le; Khaled Khaled; Riyanto Dwisaksono; Laura T. Iraci* and

Annalise Van Wyngarden*

Department of Chemistry, San José State University Atmospheric particles are important for climate because they absorb and/or scatter radiation which ultimately can cause cooling or warming of the climate depending on the chemical composition of the particles. They also act as cloud condensation nuclei or cloud seeds, and thereby influence cloud reflectivity and cloud lifetime. Particles in the upper troposphere and lower stratosphere (UT/LS) consist mostly of concentrated sulfuric acid (40-80 wt %) and water which are highly reflective. However, recent airborne measurements have shown that these particles also contain a significant amount of organic compounds [Murphy et al. J. Geophys. Res., 2007]. This organic material can affect the optical and cloud formation properties of the particles. Our experiments mimicking UT/LS conditions show that model organic compounds (propanal, glyoxal and methylglyoxal) react with sulfuric acid, producing colored solutions, precipitates and even surface films that continued to darken for months after mixing. Surface films would be expected to greatly alter the climate properties of aerosols, so the kinetics of film formation were examined to determine the effects of organic mixture, acidity, temperature and exposure to light. In addition, UV-vis absorption spectroscopy was used to investigate the optical properties of organic/sulfuric acid mixtures in order to assess their impact on the radiative properties of UT/LS aerosols.

7. Characterization of Metal-Binding Sites of Calmodulin Utilizing Europium (III)

Truman Jefferson; Farah Memom and Gilles Muller*

Department of Chemistry, San José State University Calmodulin (CaM) is a calcium-binding protein that mediates important biological functions within the bodies of both vertebrates and invertebrates. The main focus of this research project was to study which of the four binding sites of CaM contribute to the chiral functions of the protein. Luminescence and excitation spectroscopy involving Europium (III) (Eu(III)) have been particularly useful in studies aimed at determining the structure and speciation of solution complexes, since the sharp excitation and luminescence transitions may often be analyzed in terms

34

of specific solution species. We hypothesize that the replacement of Ca(II) by Eu(III) ions in the Ca(II)-binding CaM will result in the observation of the different types of binding sites present in this protein.

8. Photochemical Studies of Iron-Only Hydrogenase

Melinda Pope and Carmen Works*

Department of Chemistry, Sonoma State University Photochemical studies of an iron-only hydrogenase model compound, Fe2(SCH2CH2CH2S)(CO)6 (the model), was investigated. Photochemical reactivity was studied in various solvents and results are consistent with the loss of CO and the generation of a solvento species. Studies presented here are concerned with the determination of the quantum yield for the loss of CO and the formation of the solvento species. The goal is to determine both solvent and wavelength effects of the photochemical generation of CO.

9. Photophysical and Chiroptical Properties of Chiral Lanthanide(III) Complexes

Bao Le and Gilles Muller*

Department of Chemistry, San José State University The study of Lanthanides(III), namely Eu(III) and Tb(III), complexed to chiral terpyridine (TPY) derivative ligands is an ongoing search to better understand the complexation between the Ln(III) ions and these ligands, as well as to understand the photophysical and chiroptical properties. Various luminescence and optical spectroscopic measurements were conducted to investigate the photophysical and chiroptical properties of these complexes with the ligands 4,4,4-trifluoro-1-phenylbutane-1,3-dione (BTA) and chiral TPY. Of special importance we report on the efficiency of the energy transfer processes as well as the influence of the chiral information on the polarized emitted light. The circularly polarized luminescence (CPL) spectra were recorded to investigate the chiroptical properties. Lifetimes of the lanthanide(III) excited states were also reported.

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10. Using Solvatochromic Fluorophores to Study Peptoid Structure

Stanley Hiew; Frederick J. Seidl; Marisa A. Plescia and Amelia Fuller*

Department of Chemistry & Biochemistry, Santa Clara University Peptoids, oligomers of N-substituted glycine, mimic peptide structure and function and have advantageous biostability. They are resistant to proteolytic degradation and have excellent cell membrane permeability. In our research, we seek to develop new methods of characterizing peptoid structures by incorporating the environmentally sensitive dye 4-DMN (4-N,N-dimethylaminonapthalimide) or 4-DMAP (4-N,N-dimethylaminophthalimide) as a peptoid side chain. Because the fluorescence properties of these dyes depend strongly on the polarity of their local environment, we predict that they will act as sensitive conformational probes. We will describe our progress in applying these dyes to study structural features of peptoids that bear the 1-naphthylethyl side chain, which is predicted to promote helical secondary structures strongly. Additionally, we will explore the use of 4-DMN and/or 4-DMAP to probe intramolecular association of amphiphilic peptoid helices ligated via “click” chemistry to generate putative tertiary structures.

11. Investigation of fluorescent molecules from Naematoloma Fasciculare

Jeffery Verde; Rosie Geranio and Steve Farmer*

Department of Chemistry, Sonoma State University Fluorescent molecules are interesting because they have a wide variety of applications in the field of biotechnology. For decades they have been used as tags to stain biomolecules and enhance their imaging and detection. Natural fluorescent molecules are important because they tend to be less toxic, biodegradable, and environmentally friendly. Because of this, my research group is interested in locating and isolating fluorescent molecules from natural sources. In particular, the mushroom Naematoloma Fasciculare contains molecules which are highly fluorescent. Although extensive work has gone into characterizing various natural products from this mushroom, there have been no studies regarding molecules with fluorescent properties. Our current project will focus on isolating and characterizing the fluorescent molecules found in Naematoloma Fasciculare and to determine their ability to act as fluorescent tags.

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12. Factors Effecting the Chiral Recognition of Amino Acids

Jamie Lunkley; Brian T. Nguyen and Gilles Muller*

Department of Chemistry, San José State University Chirality is important when considering biological macromolecules like proteins which relay on amino acids as basic parts of their primary structure. Pharmaceuticals are also often based upon chiral molecules. With that, it is essential to identify chiral molecules with greater accuracy. Circularly polarized luminescence (CPL) spectroscopy shows promise in chiral recognition as it is highly sensitive to chiral environments. We utilized CPL to probe the perturbation of a lanthanide(III) complex existing as a racemic equilibrium in solution by the addition of a single amino acid or a mixture of two. We manipulated parameters such as pH and ionic strength to determine how these would effect the association of the amino acid to the lanthanide(III) complex and how they effect the magnitude of the CPL signal. This work has shown that many factors are important to the formation of the [(Tb(pyridine2,6-dicarboxylate = DPA)3]3-:amino acid adduct. The formation is influenced by parameters such as pH and ionic strength. These are important because they have a direct effect on the intermolecular interactions responsible for the stability of the [Tb(DPA)3]3-:amino acid adduct. The CPL signal is also directly effected when these parameters are altered. Based on this study, it appears CPL is well suited for projects aimed at probing specific chiral structural changes and/or for recognition of chiral biological molecules, because of high sensitivity to changes in the surrounding chiral environment. This study also helps us to better understand the association model and formation of the [Tb(DPA)3]3- :amino acid adduct.

13. Detailed Characterization of a Tridentate Ligand for Circularly Polarized Luminescent Ln(III)-Containing Probes

Andrew Ingram; Alexander Dunlap and Gilles Muller*


4-(2-methylbutyl)aminodipicolinic acid (H2MEBADPA) has been fully characterized in terms of aqueous phase protonation constants (pKas), photophysical measurements, and use as a ligand for circularly polarized luminescence active lanthanide(III) complexes. The pKas were determined by spectrophotometric titrations, utilizing a fully sealed titration system. Photophysical measurements consisted of room temperature fluorescence as well as quantum yield determinations at various pH’s which show that only fully deprotonated MEBADPA2- is appreciably fluorescent. The emission of MEBADPA2- has been determined to be quenched by hydroxide and methoxide anions, most

37

likely through base-catalyzed excited-state tautomerism or proton transfer. Relative stabilities of the europium(III) complexes (mono, bis, and tris) have been assessed by direct excitation of the Eu(III) cation and determination of the three formation constants (logb's) by luminescence titrations.

14. Determination of Stability Constants of Lanthanide(III)-Based Systems for Circularly Polarized Luminescence

Eliseo Quiroz; Andrew J. Ingram; Angela Tisch and Gilles Muller*

Department of Chemistry, San José State University Circularly Polarized Luminescence (CPL) spectroscopy is able to characterize enantiomeric mixtures for biological and pharmaceutical use where chirality is important, because it can sometimes determine the difference between an effective or ineffective drug. In CPL spectroscopy, a chiral molecule is probed with lanthanide(III) complexes. Determination of the stepwise stability constants for N,N'-(R,R-1-phenylethyl), N,N'-(S,S-1-phenylethyl)-, and N,N'-(R,S-1-phenylethyl)-2,6-pyridine dicarboxamide with Eu3+ to aid in our Pfeiffer effect studies. We hypothesize that the formation of stable 3:1, 2:1, and 1:1 (ligand:metal) complexes with the chiral ligands would be achieved, but will be difficult for the meso-ligand due to the opposite stereochemistry of each chiral carbon atom present in the meso-ligand (lead to steric hindrances upon complexation). In this study, a selection of lanthanide(III)-based systems were characterized in order to expand the tool set for CPL-based systems used as probes for biomolecules. Two different ligands were complexed with Eu3+ ion and fully characterized in terms of stability constants. This study also confirmed that the steric hindrances resulting from the helical wrapping of the meso-ligand molecules around the lanthanide dictate the formation of stable 1:3 species.

15. Computational Study of the Thermal Rearrangement of Allylic Sulfinates to Sulfones

Christina McCulley; Randy M. Miller and David B. Ball*

Department of Chemistry and Biochemistry, California State University, Chico

The experimental product distributions indicate that the rearrangement of allylic sulfinates to sulfones occurs via two competing pathways. The two theoretical pathways are believed to be a concerted 2, 3-sigmatropic rearrangement and an ionic process with an allylic carbocation ion-pair intermediate. We present a DFT computational study of the ground and

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transition state structures for the 2, 3-sigmatropic rearrangement pathway and a preliminary study of the ionic process. 16. Novel Application of Statistical Predictors: First Stage Calculation

of Solvent Accessible Protein Residues

Reecha Nepal; Daniel Rose; Shabnam Gholizadeh; Robert Lau; Radhika Mishra; Kimberly Uweh and Brooke Lustig*


A standard first-step in predicting three-dimensional protein structures involves the prediction of relative solvent accessibility (RSA). Here we have applied regression methods that include residue sequence homology values in conjunction with statistical predictors corresponding to each of the twenty canonical amino acids. Two major regions are observed with a variety of sequence homology parameters (including 20 and 6-term sequence entropy), for a 268-protein learning set, when plotted against inverse Calpha packing density. Region II with less than 11 Calpha per 9Å radius was noted to be essentially flat, and indicated significant exposure to solvent. Then we fit the 268-protein learning set with the relevant sequence homology terms and query residue statistical predictors. With key homology-based parameters, the addition of qualitative predictors (AA-set) that involve 20 query amino acid types improves the subsequent prediction of surface accessible residues for the 215-protein Manesh test set. No significant differences in accuracy are noted with respect to using BLAST as opposed PSI-BLAST homology-based parameters for RSA values normalized in the interval 0 to 1. Subsequent calculations, fitting the original RSA values and then generating estimated test set RSA values, indicated similar accuracies comparable to other first stage prediction methods. Development of a second stage methodology is of current interest.

17. An Analysis of the Structures of Phallotoxin Compounds Utilizing

Molecular Modeling

Christina McCulley; Stuart McDaniel and Robert Zoellner*


Seven phallotoxins were isolated and identified in 1937 from Amanita phalloides mushrooms, along with the better-known amatoxins. Both amatoxins and phallotoxins are poisonous but phallotoxins are not toxic when ingested because they are apparently not able to be absorbed through the lining of the intestine. To better understand the phallotoxins both structurally and energetically, computational methods were used to

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model the phallotoxins beginning with initial trial geometries that incorporated different torsion angles at the peptide bond to determine the lowest energy structures for the molecules. The molecular modeling programs Gaussian 03W and PC Spartan Pro were used, and the molecules were investigated at Hartree-Fock and density functional levels of theory. 18. Computational Analysis of Metal-Hydrosulfide Complexes Supported

by a Novel Carbonic Anhydrase Biomimetic Ligand System

Sylvanna Krawczyk; Benjamin F. Gherman* and Eric C. Brown*

Department of Chemistry, California State University, Sacramento Carbonic Anhydrase (CA) is a class of metalloenzyme most commonly known for its role as a pH regulator in living organisms. In plant life, this enzyme exhibits chemical activity by sequestering environmentally detrimental heterocumulenes (e.g., carbon dioxide and hydrogen sulfide) from the atmosphere and fixing them to the tissues of the plant. This makes CA an ideal model for the development of environmentally relevant biomimetic catalysts for use in industry. The active site of CA in vivo contains a zinc(II) hydrosulfide complex supported by a neutral ligand system consisting of three histidine side chains. However, previous studies have stipulated that neutral ligand systems were incapable of supporting such complexes in solution, requiring instead an anionic ligand such as the hydrotris(pyrazolyl)borate (Tp) ligand. This work employs computational methodology, specifically density functional theory (DFT), to investigate the ability of a neutral synthetic CA-mimetic ligand, tris(2-pyridylmethyl)amine (tpa), to stabilize the zinc hydrosulfide moiety. Several criteria contributing to the stability of the neutral-ligand complex relative to the Tp-ligand complex of past studies are assessed. Additionally, utilizing the tpa ligand, four precursory complexes using zinc(II) and analogous cadmium(II) cations as metal centers have been computationally modeled and their energies calculated in order to explore the likelihood they will undergo a hydrolysis reaction (similar to that which occurs in the CA catalytic cycle) yielding the metal-SH complex (see figure below).

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19. Computational Study of the Cyclization Reactions of Quinoxaline-Based Enediynes

Ramiro Fernandez; Nadezhda Korovina; Benjamin F. Gherman* and John D. Spence*

Department of Chemistry, California State University, Sacramento Enediynes compounds, upon exposure to heat or light, can form diradicals via the Bergman cyclization. The diradicals are able to extract hydrogen atoms from the sugar backbone of DNA, leading to strand scission and cell death. While this makes enediynes useful as a potential anticancer treatment, the utility of these compounds can be significantly increased if the wavelength of light required for excitation leading to cyclization could be increased from the UV region into the visible region. Possibilities to this end include extending the length of conjugation in the enediyne supporting unit and adding naphthyl substituents to the enediynes. The increased steric bulk from the enediyne substituents can allow for a C1-C5 pathway for cyclization to become competitive with the Bergman C1-C6 pathway. Computational methods have been applied here to study the cyclization of naphthyl-substituted enediynes supported by quinoxalines of varying size. Using ! density functional theory (DFT) calculations, the kinetics and thermodynamics of the C1-C5 and C1-C6 cyclization reactions have been computed for enediynes 1-3 (see figure). Introduction of the quinoxaline supporting groups appears to increase the favorability (both kinetic and thermodynamic) of the C1-C5 thermal cyclization pathway. In addition, time-dependent DFT (TD-DFT) calculations have been used to compute and assign UV-Vis spectra for the enediynes. Results confirm that λmax does increase with increased conjugation, shifting the wavelength of maximum absorption from the UV region into the visible region.

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20. Further progress towards the total enantioselective synthesis of the gallicynoic acids.

Brandon Tautges; Ryan Barnes and David Ball*


Recently a series of nine structurally related acetylenic carboxylic acids, gallicynoic acids, have been isolated from basiomycete Coriolopsis gallica. Some of these acetylenic metabolites exhibit diverse bioactivities, including cytotoxic, antimicrobial, enzyme-inhibitory, and anti-HIV activities. We have modified our previous synthetic schemes in our attempts to produce these acetylenic acids in a racemic fashion. Our first scheme featured ruthenium catalytic conjugate addition of terminal acetylenes and Sonogashira cross-coupling of terminal acetylenes to unactivated alkyl bromides and iodides that failed to produce the desired hetero-coupled products. Our second synthetic scheme failed in our attempts to de-protect an acetal in conjugation with an alkyne in the presence of a tert-butylsilyl protecting group. Our revamped synthetic scheme giving our desired racemic products will be presented. We are currently devising enantioselective an acetylide/aldehyde process that will lead to non- racemic gallicynoic acids with the desired stereochemistry. 21. Synthesis of Karrikin Analogues: Butenolide Derivatives that Play an

Important Role in Post-Fire Seed Germination.

Victoria Johnson and Daniel Straus*

Department of Chemistry, San José State University Derived from an indigenous Australian word for smoke, karrikins are chemical compounds produced from burning plant matter. They are strong stimulants of germination, helping to restore plant populations in newly burned areas. We recently synthesized several karrikin analogues, following several published protocols. Their effects on stimulating germination were tested on Arabidopsis thaliana, as well as Emmenanthe penduliflora, a wildflower that typically grows in recently burned grasslands. Both plants showed an increase in germination response after exposure to various levels of karrikin. Effects on flowering response were also tested in both the laboratory and field, with mixed results.

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22. Catalytic Enantioselective 1,4-Additions of Allyl Indium Reagents to α,β-Unsaturated Aldehydes

Stella Plukchi; Diego Colorado and Claudia G. Lucero*

Department of Chemistry, California State University, Sacramento The enantioselective conjugate allylation of α,β-unsaturated aldehydes will be investigated. The addition of nucleophiles to α,β-unsaturated aldehydes prefers to proceed in a 1,2- fashion rather than in a 1,4-fashion. Activation of the α,β-unsaturated aldehydes with chiral imidazolidinones, however, has proven to be successful in directing the addition in a 1,4-fashion. The 1,4-addition of organometallic reagents to α,β-unsaturated carbonyl compounds is one of the most useful and reliable methods for C-C bond formation. It is our goal to introduce the first enantioselective conjugate allylation of α,β-unsaturated aldehydes using substituted allyl indium reagents. This asymmetric approach will allow access to a wide range of useful building blocks that can be further functionalized to a variety of biologically active natural products.

23. Approaches to the Synthesis of Optically Active 4-Amino-2,6-pyridinedicarboxylate Ligands by Catalytic Coupling Reactions.

Jia Lu and Dan Straus*

Department of Chemistry, San José State University 4-(N-2-methylbutyl)amino-2,6-pyridinedicarboxylic acid has been prepared in low yield by direct nucleophilic substitution of the corresponding chloropyridine derivative. However, the yield based on (excess) amine used is low, and the cost is prohibitive toward use of these ligands for CPL studies. We have undertaken attempts at using Buchwald’s catalytic coupling methodology. Catalytic Pd(II) acetate with BINAP ligand plus stoichiometric base in tetrahydrofuran or toluene proved adequate for the model reaction of 4-bromopyridine to afford 4-(N-2-methylbutyl)aminopyridine. However, these conditions did not prove conducive for coupling of diethyl 4-bromo-2,6-pyridinedicarboxylate or a similar chlorodiester with the amine of interest. Recently, the Buchwald group has provided us with a sample of a new precatalyst that has yielded encouraging results when used with cesium carbonate base in tert-butanol. Hydrolysis of the products appears to be a problem, and will be addressed as we optimize this coupling process.

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24. Total Synthesis of (+)-Tatarinoid C

Dimitar Panayotov; Maddy McCrea-Hendrick and Claudia Lucero*

Department of Chemistry, California State University, Sacramento The total synthesis of the enantiomer of the natural product, (+)-tatarinoid C is described in as few as 4 steps. (-)-Tatarinoid C is one of 19 compounds isolated from the rhizome of Acorus Tatarinowii, used in the treatment of central nervous system related diseases. Currently there is no reported synthesis of (-)-Tatarinoid C. As a result, it is our goal to accomplish the first synthesis of this bioactive molecule and its enantiomer. The precursors used in the synthesis are ethyl-L-lactate and 1,2,4-trimethoyxybenzene. Halogenation of the trimethoxy benzene and treatment with nBuLi allows for the di addition of the aromatic nucleophile to the silyl protected ethyl lactate in a high yield. Subsequent deoxygenation and removal of the protecting group yields the enantiomer of Tatarinoid C. It is our goal to optimize the synthetic route developed and apply the synthesis to the actual bioactive compound, (-)-Tatarinoid C.

25. Synthesis of Multivalent, Glycosylated Antiretrovirals

Careena Cary and Katherine McReynolds*

Department of Chemistry, California State University, Sacramento Drug resistance is of great concern in our evolving society. Designing novel pharmaceuticals is thus a current topic of interest. Glycodendrimers offer many prospects, especially with regards to antiretrovirals. The multivalent character of glycodendrimers is responsible for this. The sugar moieties on the periphery of these globular molecules are thought to mimic receptors on the outer cellular membrane of target cells. If a glycodendrimer were made to have a stronger binding affinity to the virus than the cell’s receptor, the viral adhesion event may be altogether avoided. Divergent synthesis of an amine core dendrimer was conducted. The synthesis began with the extension of a trivalent molecule, previously synthesized in our group. The beginning core, with three terminal carboxylic acids, was deprotonated and reacted with 1-3,diaminepropane for five days. The resulting amine terminated core was purified by HPLC producing a 19 % yield. Branching of the core was accomplished by following a procedure

44

from Jayamurgan et al. Methanol and t-butyl acrylate were added and stirred at room temperature for 72 hours. The branched core was extracted in the organic layer and deprotected with addition of TFA. The deprotected dendrimer was then purified by extraction and HPLC resulting in a 24 % yield. All molecules were assessed for purity by NMR. Optimization of the synthesis of the branched core is currently underway. Future work entails amide coupling of sugars to the six ends. Other possible directions include additional branching of the dendrimer and antiviral assaying.

26. Radical Cyclization of Vinylcyclopropane to form Eight-Membered Rings

Krystle Merritt and James Miranda*

Department of Chemistry, California State University, Sacramento

27. Effects of Trimethylamine N-oxide on the Solubility of Diketopiperazine

Brian Castellano and Daryl K. Eggers*

Department of Chemistry, San José State University Trimethylamine N-oxide, also known as TMAO, is an osmolyte found in marine organisms. TMAO is known to relieve osmotic stress while combating the denaturing effects of a natural waste product, urea. Most commonly, TMAO’s effects are attributed to its direct binding to protein structures and, thereby, to removal of binding sites for urea. In contrast, we hypothesize that TMAO reduces the free energy of the solvent, water, and counteracts the unfavorable effects of urea without a necessity for protein binding. This study employs diketopiperazine (DKP) as an amide-containing model compound. DKP solubility was measured with a density meter as a function of TMAO concentration and pH. The results show that DKP solubility decreases with increasing concentrations of TMAO. Also, the effect of TMAO is weakened at lower pH values which we interpret as a weaker solute effect on bulk water upon protonation of TMAO. These findings are consistent with the idea that TMAO lowers the free energy of the bulk water and disfavors solvation of molecules like DKP. Since DKP is a model compound for the backbone of all proteins, and because the backbone is not typically exposed to water in the folded conformation, the observed changes in DKP solubility agree with the known effects of TMAO on protein structure. Future work in our laboratory will aim to quantify the thermodynamic effects of TMAO on water and to relate this information to biological equilibria, in general.

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28. Alginate gel encapsulation of enzyme bromoperoxidase

Bo Hwang; John H. Kim; Nikhita Tulsi; Daniel Pacheco and Roy K. Okuda*

Department of Chemistry, San José State University In organic chemistry, enzymatic reactions are becoming more popular due to their sometimes unique properties as catalysts. However, enzymes are a limited resource especially when extracted from a living organism. Enzyme encapsulation in a solid matrix is a useful technique that allows for enzyme reutilization. In this project, sodium alginate was used to encapsulate Corallina vancouveriens acetone powder (CVAP), which contains a bromoperoxidase. Qualitative and quantitative analysis of the bromoperoxidase enzymatic activity were tested using phenol red and monochlorodimedone (MCD) assay, respectively. The rate of bromination of MCD showed a 64.9% decrease in alginate encapsulated CVAP for the first run and a 83.2% decrease in the fourth run when compared to the unencapsulated CVAP. 29. Expression, Purification, and Characterization of Carnobacteriocin B2

Casee Barnes; Peter Arnold and Jennifer Lillig*

Department of Chemistry, Sonoma State University Background: Carnobacteriocin B2 (Cbn2) is a bacteriocin produced by Carnobacterium piscicola and exhibits non-specific binding to Listeria monocytogenes, a food-borne pathogen. The aim of this project is to express, purify, and characterize this peptide. Methods: A recombinant plasmid with the Cbn2 gene was transformed in E. coli and then expression of the peptide was induced using IPTG. Cbn2 was purified using affinity chromatography with chitin resin, and eluted through the addition of dithiothreitol (DTT). Spin filtration further purified the samples, and the final product was freeze-dried for storage. Efficiency of expression and purification was assessed using SDS PAGE. Results: LB Ampicillin broth was inoculated with a single colony of transformed E. coli. Optimal moment of IPTG addition was when the absorbance of the inoculated broth was between 0.4 and 0.5 at 600 nm, and optimal time for induction was for 12 hours at 25°C. Optimal elution occurred after incubation of the column-bound construct with DTT at 25°C for 40 hours. SDS PAGE showed that large contaminants remained in the elutant, and therefore spin-filtration was used to further purify the product. Conclusion: Carnobacteriocin B2 was successfully expressed and purified in E. coli. Future work includes the continuation of these

46

methods to produce more of the peptide and substituting F33 with other amino acids via mutagenesis. This particular amino acid was shown to be essential for the targeting, binding, and lysing of Listeria; preparing mutants and testing their lethality will provide further evidence of the residue’s role in Cbn2’s anti-microbial properties.

30. Modified Silica Glass Effects on Protein Adsorption and Structure

Yamah Amiri and Daryl K. Eggers*

Department of Chemistry, San José State University In this project, we investigate the extent of protein adsorption to modified silica glasses in hopes of defining surface chemistries that lead to low adsorption. The glasses are made by the sol–gel technique using tetramethoxysilane (TMOS) as the key reagent. The three model proteins employed in this study are apomyoglobin, lysozyme and α-lactalbumin. Each protein has a different overall charge; apomyoglobin is almost neutral, lysozyme has a +7 charge, and α-lactalbumin has a 5 charge. The glasses were made also to vary in charge by selecting modifying reagents that contain negative, positive, or neutral but polar functional groups; we hypothesize that a positively-charged glass will have more adsorption with a negatively-charged protein, and vice versa, if electrostatics are a major driving force for binding. In order to analyze the amount of adsorption that has occurred between a specific glass and protein solution, circular dichroism spectroscopy (CD) was used to track changes in protein concentration and to monitor changes in protein structure upon adsorption. CD data in the far-UV region provide a signal that, after conversion to units of molar ellipticity, detects changes in the secondary structure of each protein. For example, preliminary results indicate that lysozyme adsorbs considerably to a glass containing 5% of the neutral modifying reagent 3-glycidoxypropyl–trimethoxysilane, whereas other proteins bind less strongly to the same glass. This research may result in improved materials for applications in biomedical engineering, biocatalyst and biosensor development, food manufacture, and protein separation techniques.

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31. Impact of Electrostatic Interactions on the Binding of Cationic Tricyclic Drugs to Model Membranes

Katelyn Caslavka and Linda S. Brunauer*

Department of Chemistry & Biochemistry, Santa Clara University The exact mechanism(s) by which cationic tricyclic psychoactive drugs elicit their pharmacological effects is incompletely understood. Previous work in our laboratory has implicated both electrostatic and hydrophobic interactions in the associations of such drugs with natural as well as model membrane systems. In the current study we expand upon this work to further explore the importance of electrostatic interactions upon binding of a variety of tricyclic drugs as well as their quaternary ammonium derivatives.

32. Surface Effects of Polar Organic Side Groups on Apomyoglobin Confined to a Silica Matrix

Mitchell Chancellor; Phillip Calabretta and Daryl Eggers*

Department of Chemistry, San José State University Encapsulation in silica by the sol-gel technique is a useful method for preparing immobilized proteins for analysis by spectroscopic methods, including circular dichroism spectroscopy (CD) which we use to monitor changes in secondary structure. Previously, our laboratory demonstrated that a standard silica gel destabilizes the structure of our favorite reporter protein, apomyoglobin (apoMb), and that changing the surface chemistry of the silica can alter the helical content of the protein. In the current project, we incorporate various polar organic modifiers into the silica matrix to search for a more “biocompatible” composition that retains the native structure of apoMb in phosphate buffer. By altering the amount (percent based on ratio of silica to modifier) and type of each modifier (positive, negative or neutral charge), we observe a large range of effects on the structure of confined apoMb. The CD results indicate that non-polar modifiers increase helical structure with increasing content, whereas polar modifiers yield the best results at lower contents. Our current focus is on hydrophilic glasses made with low percentages of modifiers (2.5% to 5.0 %) that incorporate glycidoxypropyl, propylsulfonate(-), or trimethylammonium-propyl(+) functional groups into the silica and to characterize the effect of each modified glass on apoMb structure. We conclude that protein structure in silica glass is a complex function of silica surface chemistry, protein surface chemistry, and the conditions of glass formation. This work may someday lead to the development of new biomaterials for applications in biosensors, biocatalysis, and medical implants.

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33. Selectivity of Selected Aptamers Toward Multiple Variations of a VEGF Peptide

Nicholas Giustini; Dustyn H. Uchiyama; Christopher M. Rose; Michael J. Hayes; Gregory R. Stettler; Trevor M. Axelrod; Scott F. Hickey and

Steven W. Suljak*

Department of Chemistry & Biochemistry, Santa Clara University Aptamers have gained increasing attention as bioaffinity reagents for a wide array of target molecules. Through a modified form of CE-SELEX, we have recently identified a set of DNA aptamers that selectively bind a glycosylated 32-residue fragment of vascular endothelial growth factor but show little affinity for the non-glycosylated peptide. Here, we report the characterization of selectivity of these aptamers toward a number of similar control glycopeptides. The demonstrated selectivity of the candidate sequences illustrates the effectiveness of our selection strategy in isolating highly specific aptamers for a unique glycoform of the target molecule. Such aptamers offer potential in monitoring changing glycosylation patterns of glycoproteins in the progression of disease states.

34. Toward an Understanding of the Role of Desolvation in Protein Folding: Changes in the Solubility of a Phenylalanine Derivative

Tanya Ghaemmaghami; Melinda D. Mendolla and Daryl K. Eggers*

Department of Chemistry, San José State University Our laboratory is developing a bulk-water-dependent desolvation energy model that includes the contribution of water in protein folding and provides a context for explaining the effects of secondary solutes on folding equilibria. By testing the solubility of nonpolar amino acids, our laboratory aims to quantify the desolvation component of the hydrophobic effect, a major driving force in protein folding. Because nonpolar amino acids are usually buried in the core of a folded protein, desolvation of the free amino acid upon precipitation is analogous to the change in hydration of the amino acid residue when a protein folds. In this particular study, our focus is on a derivative of the aromatic amino acid phenylalanine, Ac-Phe-NH2. The N-acetylated and C-amidated modifications remove the zwitterion character and provide a better model of the amino acid residue within a real protein. The solubility of this compound was measured in molar salt solutions co! ntaining chloride or acetate anions paired with Li+, K+, Cs+, and N(CH3)4+. Solubility was determined from the absorption value of Phe-saturated solutions at 258 nm. The results are similar to previous studies with other amino acids in our laboratory. In general, chloride

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solutions were found to yield a higher solubility than acetate solutions paired with the same cation, and N(CH3)4

+ was found to yield a higher solubility than the other three cations tested. In the future, these results will be combined with other experiments to back out the desolvation energy of this and other model compounds.

35. Development of an Enzyme-Linked Detergent-Free Transphosphatidylation System for Microscale Synthesis of

Phosphatidylserine

Sandra McCaw and Linda S. Brunauer*

Department of Chemistry & Biochemistry, Santa Clara University The enzyme phospholipase D may be utilized to accomplish the conversion of one glycerophospholipid, such as phosphatidylcholine, into a related one, such as phosphatidylserine. Such transphosphatidylations generally require either a two-phase ether/aqueous synthesis system that is difficult to control at the microscale or a single-phase system requiring detergent, which must subsequently be removed prior to use of the product. In the current study we report on progress made towards the development of a true microscale one-pot synthesis of dilauroylphosphatidylserine that may be accomplished in the absence of detergent.

36. Light Initiated Hydroxylation of Substrate C-H bonds using Hybrid P450 Enzymes

Ngoc Huynh; Ngoc-Han Tran; Thuba Bui; Angelina Nguyen; Yen Nguyen; Jeremiah Heredia; Garrett Chavez and Lionel Cheruzel*

Department of Chemistry, San José State University The specific and selective oxidation of an unactivated C-H bond remains one of the most challenging reactions in organic chemistry. Cytochrome P450, heme-thiolate enzymes, catalyze the insertion of an oxygen atom, derived from molecular dioxygen, into a C-H bond of a variety of substrates, often with high degrees of regio- and stereoselectivity. Recent interests in these proteins arise from the desire to harness their synthetic potential for biotechnological applications. The main challenge in utilizing P450s as biocatalysts has been in the control of the electron delivery to the buried active site of the enzymes while preventing protein deactivation by reactive oxygen species. We have developed hybrid enzymes constituted of a photosensitizer covalently attached to the heme domain of P450 BM3 mutants. These enzymes have been characterized by UV-Vis and fluorescence spectroscopies, and mass spectrometry. Our preliminary results in

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hydroxylating lauric acid under constant visible light irradiation will be presented.

37. Bulk Water Effects on Nucleoside Solubility as Probed with Salt

Solutions

Ishraq Sadhan; Elisa Aguilar and Daryl K. Eggers*

Department of Chemistry, San José State University The desolvation of nucleoside bases may be an important driving force in the formation of double-stranded DNA and RNA molecules. Our laboratory is developing a model to calculate desolvation energies from changes in the solubility of the individual nucleosides. Solubility can be determined precisely by measuring the absorbance of a nucleoside at saturation. In the current study, solubilities of two model compounds, guanosine and deoxyguanosine, were determined at room temperature in salt solutions of varying concentration. Salts were chosen from the Hofmeister series, a ranking of ions that tends to influence biological equilibria in the same relative order. Certain salts, such as lithium chloride (LiCl) and lithium acetate (LiOAc), were found to increase nucleoside solubility as salt concentration increased. Other salts resulted in a decrease in solubility with increasing salt concentration, whereas a third category of salts resulted in a minimum in solubility with increasing salt concentration. This last observation suggests to us that two different phenomena are influencing nucleoside solubility: (1) salt effects on the free energy of bulk water, and (2) direct binding of ions to nucleoside bases at high salt concentrations. Future studies will examine nucleoside solubility in other solutions and will attempt to relate the solubility data to the desolvation energy of each nucleoside. This research complements other studies in our laboratory aimed at understanding how changes in the thermodynamic properties of bulk water influence binding and conformational equilibria, in general.

38. Overexpression of HIV TAR RNA and Tat Peptides

Tan Tran; Josh Sun and Elaine Collins*

Department of Chemistry, San José State University The trans-activation of transcription (Tat) peptide and its binding to the trans-activating response element (TAR) RNA are observable in both the human immunodeficiency virus (HIV) and the bovine immunodeficiency virus (BIV). The interaction between the TAR RNA and the Tat peptide vastly increases the transcription efficiency of HIV thereby causing HIV to rapidly accumulate. Optimal binding of Tat to TAR requires the presence of a host protein, cyclin T1. To study the interaction between

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trans-activation of transcription (Tat) peptide and the trans-activating response element (TAR) RNA of HIV, the cDNA for a fusion of the Tat peptide with a cyclin T1 peptide (Tat-Cyc) and TAR RNA were both cloned separately by PCR-assisted gene assembly using overlapping primers. The PCR products were initially ligated into the pGEM-T vector (Promega). The cDNA for the TAR RNA will then be subcloned into the BamHI and EcoRI restriction sites of vector pUC18. The TAR R! NA will be transcribed with T7 RNA polymerase. The Tat-cyc peptide will be subcloned into the expression vector pSUMO-Star (LifeSensors) at the BsaI and Xba I restriction sites. Once both the TAR RNA and Tat-cyc peptides have been purified, the binding characteristics of the two will be analyzed and observed using Isothermal Titration Calorimetry (ITC). In the future, these studies will help design therapeutic agents to block or inhibit the viral activation and transcription of HIV.

american chemical society 23rd annual northern california ... · chemistry, 1997-2002; journal of...

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