GUIDE TO THE ZARELAB October 2012 Department of Chemistry, Stanford

University

~Welcome to the ZARELAB~

This booklet has been prepared to make your

visit with us more rewarding by presenting a

survey of our recent research activities. Each

section was written by those members pursuing

the work described therein.

Please feel free to ask the members of my group

to discuss any project.

Enjoy your visit!

Stanford University

Department of Chemistry – Mudd Bldg.

333 Campus Drive – Room 133

Stanford, CA 94305

(650) 723-4313

Website:

http://www.stanford.edu/group/Zarelab/

~Inside this Guide~

Table of Contents 2

Research Activities 3

Cell Imprinting

Reaction Dynamics

Mass Spectroscopy

Nanoparticles

Selected Recent Publications 18

Group Members 20

Maps of Stanford Campus & Vicinity 22

Dick Zare and the rocket test.

2

TABLE OF CONTENTS

Cell Imprinting 3 Single-Cell Genetic Analysis on a Microfluidic Platform

- - - Eric Hall, Samuel Kim

4 New Diagnostic Technology Based on Cell-Imprinted

Polymer

- - - Kangning Ren, Li Zhang

5 Prototypic Microfluidic Device for an Antimicrobial

Susceptibility Test

- - - Keisuke Inoue, Samuel Kim

6 Detection of Pathogenic Microorganisms in Media Using a

Porous, Cell-Imprinted Sol-Gel Polymer

- - - Maria T. Dulay, Kangning Ren

Reaction Dynamics 7 Coherently Prepared Quantum States for Stereo-Chemistry

- - - Nandini Mukherjee, Wenrui Dong and

Richard N. Zare

8 State-to-State Reaction Dynamics

- - - Justin Jankunas

Mass Spectrometry 9 Using Desorption Electrospray Ionization Mass

Spectrometry to Detect Reaction Intermediates

on the Millisecond Timescale

- - - Cornelia Flender

10 Utilizing Gas-Phase Reactivity to Characterize

Solution-Phase Catalysis by ESI-MS

- - - Andrew Ingram

11 Desorption Electrospray Ionization Mass Spectrometry

(DESI-MS) Imaging in Biomedical Research

- - - Livia S. Eberlin

12 Mass Spectroscopic Characterization and Analysis of

Protein Modifications and Interactions: Application to

Photosynthesis Process

- - - Sam Kim, Jae Kyoo Lee

14 Capturing Transient Intermediates of Organic Reactions

with Short Time-Scale ESI Source

- - - Jialing Zhang

15 Two-Step Laser Mass Spectrometry of Terrestrial

and Extraterrestrial Materials

- - - Qinghao Wu

16 Monitoring Electrocatalytic Cycles on Electrode Surfaces

in Real-Time

- - - Tim Brown

Nanoparticles 17 Nanoparticle Formation Using Precipitation and Self-Assembly

- - - Marie Russo Selected Publications 18 Zare Group Contact List 20 Maps of Stanford & Vicinity 22

3

SINGLE-CELL GENETIC ANALYSIS ON A MICROFLUIDIC PLATFORM

Eric Hall, Samuel Kim

In the study of a biological population, how important is individuality? Are the members of the

population so similar that the average behavior can describe them all, or are deviations significant

enough to make this kind of description misleading? The conventional techniques in biology use a large

number of cells and generate the ensemble-averaged values to describe cellular characteristics. These

methods are fast and efficient ways of observation as long as the individual cells exhibit little deviation

from this average behavior. However, if the deviations are significant, the large-scale ensemble

averaging methods fail to give a proper picture of biological phenomena. A simple example will be the

case of a bimodal distribution, where the cells with an average behavior actually represent a smaller

fraction of the population.

Recent advances in microfluidics opened up a new possibility in single-cell biology by providing the

necessary toolkits for handling and analyzing individual cells. We believe that it is an opportune time to

apply microfluidic technologies to investigate individuality of cells because important information

relevant to the most pressing biological questions is very likely obfuscated by ensemble averaging

techniques. Our section develops techniques for performing single-cell analysis on a microfluidic

device, more commonly referred to as “lab-on-a-chip”. We have made pioneering contributions to the

field, including the development of a device capable of capturing a single cell and delivering precise

amounts of reagents,1 and an on-chip chemical cytometer integrated with a picoliter micropipette for

cell lysis and derivatization.2 More recently, we have extended this technology to study the

phycobilisome degradation process in individual cyanobacteria cells.3

The current goal of our section is to develop microfluidic protocols for amplifying and investigating the

genomes of biologically interesting cells at the single-cell level and determine the significance of their

genetic diversity. These projects use variations of a device capable of extracting and amplifying

sufficient DNA from a single cell for sequencing (Fig. 1). We are investigating genetic adaptation of

viral attack in Synechocystis cyanobacteria after successfully opening single-cell genetic amplification

to such organisms by expanding the range of sample preparation techniques.4

1. A.R. Wheeler, W.R. Throndset, R.J. Whelan, A.M. Leach, R.N. Zare, Y.H. Liao, K. Farrell, I.D. Manger,

A. Daridon, Anal. Chem. 75, 3581 (2003). 2. H. Wu, A.R. Wheeler, R.N. Zare, Proc. Natl. Acad. Sci. U.S.A. 101, 12809 (2004). 3. B. Huang, H. Wu, D. Bhaya, A.R. Grossman, S. Granier, B.K. Kobilka, R.N. Zare, Science 315, 81 (2007). 4. E. Hall, Ph.D. Dissertation, “Microfluidic Platforms for Single-Cell Analyses” (2012).

Figure 1. Cells are manipulated with microfluidic channels (black) and control valves (red) into chambers (blue) designed to deliver specific nanoliter volumes of reagents.

4

NEW DIAGNOSTIC TECHNOLOGY BASED ON CELL-IMPRINTED POLYMER

Kangning Ren, Li Zhang

Cell imprinting is a technology recently developed in the Zare laboratory which produces artificial receptors to cells of interest by template-induced assembly of functional groups on a polymer surface. These cell-imprinted polymers are used to selectively capture the target cells from a mixture. In this method, a prepolymer solution is contacted with a template made of the cells of interest. The prepolymer organizes about the cell template to mimic its shape and in a manner to form the strongest interaction. Subsequently, the polymer is fully cured and the template is removed, leaving imprints in the material which are ready to selectively capture cells of the same species as was on the template. We have proven that the capture mechanism is a combination of recognition of cell shape and chemical recognition of characteristic groups on the surface of the cell. We are applying this technology to developing diagnostic technology for bacteria infection. Infectious disease is one of the major causes of morbidity and mortality for humans. Quick and accurate diagnosis of infection is the prerequisite to choose proper treatment and to prevent the spreading of the disease. For some infectious diseases, the current diagnostic methods are either too slow or too expensive. We are developing a new diagnostic method based on cell-imprinted polymer film, which will capture the target bacteria in a liquid specimen on the designed spot of a device. With this method, we anticipate the power to selectively concentrate the suspected pathogen from a patient’s sample so that detection can be achieved without incubation, thereby greatly reducing the diagnosis time and cost. Besides patient specimen, the above mentioned strategy could also be applied to detecting the presence of certain microorganism in other samples. One significant application could be quick and low-cost on-site food safety test.

Figure 1. Cell-imprinting of a polymeric film on a microscope slide. Cells are pressed into a pre-polymer. Cavities of cell-imprints are left after peel the template and clean the surface. The inset at top centre is an AFM image of polydimethylsiloxane surface imprinted with M.smegmatis (M.smeg), a surrogate for M. tuberculosis.

The inset at top right is a microscopic image of the M. smeg captured on the imprinted surface. M. smeg were stained to be dark. REFERENCES 1. R. Schirhagl, E. W. Hall, I. Fuereder and R. N. Zare, Analyst 137, 1495-1499 (2012) 2. R. Schirhagl, K. Ren, and R. N. Zare, Science China Chemistry 55, 1-15 (2012) 3. K. Ren and R. N. Zare, ACS Nano 6, 4314–4318 (2012)

5

PROTOTYPIC MICROFLUIDIC DEVICE FOR A ANTIMICROBIAL SUSCEPTIBILITY TEST

Keisuke Inoue, Samuel Kim

Antimicrobial susceptibility test (AST) is typically performed in clinical microbiology labs to

confirm susceptibility of specific bacterial species/isolates to selected antibiotic treatments or

to detect drug resistance. The results of the test, in the form of minimal inhibitory

concentration (MIC) values or disk diffusion zone diameters, are interpreted and reported to a

patient’s physician to recommend drug concentrations and combinations for successful

eradication of bacteria. The possibility of acquired drug resistance requires constant

monitoring of such susceptibility data. Traditional methods require culturing that often takes

overnight. Faster AST results can be used to modify antimicrobial treatment in a more timely

fashion.

We are developing a microfluidic device that enables miniaturized AST. Serial dilution of

antibiotics concentrations, cell culture, and measurement of cell density will be integrated on a

single platform. It is expected that, with this device, the amount of reagents and the duration

of testing time be greatly reduced. Also, direct counting of cell numbers will allow more

accurate determination of drug resistance in bacteria.

6

DETECTION OF PATHOGENIC MICROORGANISMS IN MEDIA USING A POROUS, CELL-IMPRINTED SOL-GEL POLYMER

Maria T. Dulay, Kangning Ren

Evaluation of the microbial quality of media such as water and food, is an essential priority for

global health. Many microorganisms, such as bacteria and viruses, have important functions in

nature, however, certain potentially harmful microorganisms can have significantly adverse

effects on animals and humans, resulting in high rates of death and high costs to various

industries and consumers.

Current methods for the detection of microorganisms in water and food rely almost solely on

molecular methods that are either quantitative, giving absence or presence results, or

qualitative, providing enumeration of microorganism concentrations. The most widely used

molecular methods incorporate PCR for a more sensitive, rapid, quantitative and

immunological technique. These methods, however, can be time consuming, costly, and

sometimes lacking high specificity.

We are working towards the creation of a porous sol-gel-based material with micron-sized

through-pores that allow microorganisms, such as E. coli, to flow through the material and be

selectively captured in the polymer, containing cavities made by imprinting of the target

bacterial onto the polymer surface. This work is complementary to the work being done on

thin-film cell-imprinted sol-gel and PDMS polymers.

Two of the uses of such a device is in the purification of drinking water and the detection of

food-borne pathogens. This research involves different areas of chemistry, including organic

synthesis of the sol-gel polymers via sol-gel chemistry, which allows one to tweak the reaction

to create different types of sol-gel polymers, ranging from rigid, stand-alone bulk materials to

flexible ones with varying porosities and pore-size distributions.

7

COHERENTLY PREPARED QUANTUM STATES FOR STEREO-CHEMISTRY

Nandini Mukherjee, Wenrui Dong and Richard N. Zare

In order to understand how the molecular orientations (stereo-dynamic) and vibrational motions

(mode-selective) influence the reaction dynamics, we prepare molecules in well-defined rovibrational

eigenstates states (v, J, M) of the ground electronic surface using a recently introduced coherent

nonlinear optical techniques called Stark Induced Raman Adiabatic Passage (SARP)1,2. The spatial

orientation is determined by the direction of the angular momentum vector J specified by the M

quantum number. Complete population transfer to a desired rovibrational eigenstate (v, J, M) along

with orienting or aligning the angular momentum vector J in space is achieved using a sequence of

partially overlapping pump and stokes laser pulses with suitable polarizations and interpulse delay. In

our laboratory H2 (v=1, J=2, M=0) state is prepared using SARP with delayed green (532 nm, second

harmonic of Nd3+:YAG) and red (699 nm dye) single mode laser pulses. Quantum state prepared

molecules are probed using resonance enhanced multi-photon (2+1) ionization (REMPI) and detected

in a time of flight Mass spectrometer. Figure 1 below shows theoretical simulation results of complete

population transfer to H2 (v=1, J=2, M=0) using SARP. Figure 2 shows 60% depletion of experimental

2+1 REMPI signal as a result of population transfer from the supersonically cooled ground state

H2(v=0, J=0, M=0) to the excited vibrational state H2(v=1, J=2, M=0) in a high vacuum (~ 10-8 Torr)

reaction chamber. Our next phase of this research involves reactive collisions using H2 molecular

targets in coherent superposition of (v, J, M) quantum states.

REFERENCES 1. N. Mukherjee and R. N. Zare, “Can stimulated Raman pumping cause large population transfers in

isolated molecules?,” J. Chem. Phys. 135, 184202 (2011). 2. N. Mukherjee and R. N. Zare, “Stark-Induced Adiabatic Raman Passage (SARP) for Preparing

Polarized Molecules,” J. Chem. Phys. 135, 024201 (2011). 3. N. Mukherjee, Wenrui Dong, R. N. Zare, “Transfer of More than Half the Population to a Selected

Rovibrational M State of H2 by Stark-Induced Adiabatic Raman Passage,” to be submitted to Phys. Rev. Lett.

Figure 1. Theory: Complete population inversion to H2 (v =1) using SARP with delayed Stokes (ES) and Pump (EP) laser pulses.2

Figure 2. Experiment: 2+1 REMPI signal from H2(v=0, J=0, M=0) state; pump to Stokes pulse delay is 7ns. Pump and stokes laser pulses have durations of ~ 6 and 4.5 ns respectively. Pump to Stokes pulse energy ratio ~ 10. 3

8

STATE-TO-STATE REACTION DYNAMICS

Justin Jankunas and Mahima Sneha

The state-to-state reaction dynamics section in the Zarelab devotes its efforts to the experimental investigation of bimolecular reactions in the gas phase. We employ a PhotoLoc1 method using a three-dimensional ion imaging apparatus2 to record the three components of the molecular ion speed. The speed is then converted into the differential cross section (DCS). The H + H2 chemical reaction is of a particular interest to us. Fully dimensional quantum mechanical calculations are now available for this three-atom system which makes the comparison between theory and experiment especially insightful. Recently we have measured DCS for the H + D2 → HD (v' = 4, j') + D reaction at a collision energy of 1.97 eV (Figure 1)3,4. We explained this seemingly odd behavior of the DCS in terms of a centrifugal barrier in the exit channel of a reaction and suggested that it should be general and could be seen in other chemical reactions.

Another very exciting and long-awaited project we are involved in deals with the geometric phase effect in the H + H2 reaction. For example, the H + HD → HD (v', j') + H reaction can proceed via either an inelastic channel, where the incoming H atom does not exchange with the molecular H atom, and via a reactive scattering, where the two H atoms do exchange. The experimentally measured DCS will be a superposition of the amplitudes of these two processes and, as a result, oscillations are expected to be present for certain HD (v', j') states. The presence of the geometric phase would influence, in a predictable manner, the way the inelastic and reactive amplitudes interfere. Up to now the manifestation of the geometric phase in a reactive system has not been observed experimentally. We hope this would be the first such measurement.

Figure 1. DCS for HD (v' = 4, j' = 2 and 6) at a collision energy of 1.97 eV. It has been a common wisdom that as the rotational excitation of HD increases the peak of the DCS shifts to a more forward direction, i.e. smaller angles on the x-axis. These two DCS clearly display an opposite trend. We suggest that this behavior will be present whenever a large fraction of the total energy is tied up as the internal energy of a product. As a consequence, little energy is left for the translational energy of the separating products. The centrifugal barrier in the exit channel associated with greater impact parameters (higher-order partial waves) cannot be overcome by such slower-moving products. As a result, lower impact parameters result in a more backward-scattered products, in accord with the experimental observations. REFERENCES 1. N. E. Schafer, A. J. Orr-Ewing, W. R. Simpson, H. Xu and R. N. Zare, Chem. Phys. Lett. 212, 155 (1993). 2. K. Koszinowski, N. T. Goldberg, A. E. Pomerantz and R. N. Zare, J. Chem. Phys. 125, 133503 (2006). 3. J. Jankunas, R. N. Zare, F. Bouakline, S. C. Althorpe, D. Herraez-Aguilar and F. J. Aoiz, Science 336, 1687 (2012). 4. J. Aldegunde, D. Herraez-Aguilar, P. G. Jambrina, F. J. Aoiz, J. Jankunas and R. N. Zare, J. Phys. Chem. Lett. 3, 2959 (2012).

9

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MS

Reagents

Catalyst

USING DESORPTION ELECTROSPRAY IONIZATION MASS SPECTROMETRY TO DETECT REACTION INTERMEDIATES ON THE MILLISECOND TIMESCALE

Cornelia Flender

Catalyzed C-H amination and hydroxylation reactions are important in that they provide new ways to synthesize pharmaceuticals. In this interdisciplinary project, we collaborate with the DuBois group from Stanford University to monitor reactions using a new mass spectrometry based technique, called desorption electrospray ionization (DESI)1,2. The DuBois group has developed technologies for C–H hydroxylation and amination3,4. These transformations are difficult to study because they include short-lived intermediates, and reaction efficiencies are limited by catalyst arrest. The objective of this project is to develop a method, based on DESI-MS, to facilitate characterization and enable improvement of catalytic methods for selective C–H functionalization. It is likely that novel catalysts will be constructed in the course of these investigations. The catalyst is placed on a glass or paper surfacein front of the inlet of the mass spectrometer (MS). The catalytic reaction is induced by directing charged droplets of the reagent-containing solution onto the catalyst (see Figure). The charged droplets are produced by applying a voltage to the solvent capillary and directing a nebulizing gas (N2) into the solvent stream. As the droplets hit the catalyst, ions are released from the sample in secondary microdroplets which are intercepted by the inlet of the MS. The catalytic reaction takes place inside these microdroplets and is quenched by evaporation of the droplets. The method offers the exceptional possibility to detect early reaction intermediates, because the detection in the MS takes place only milliseconds after the initiation of the reaction on the paper surface.

Figure 1. DESI-MS setup for the detection of reaction intermediates

A greater understanding of reaction intermediates and insight into catalyst arrest will enable development of more robust protocols for amination and hydroxylation. The study will lead to improvements in the efficiency of next generation catalytic systems. REFERENCES 1. R. H. Perry, K. R. Brownell, K. Chingin, T. J. Cahill, R. M. Waymouth, R. N. Zare, “Transient Ru-Methyl Formate

Intermediates Generated with Bifunctional Transfer Hydrogenation Catalysts,” Proc. Nat. Ac. Sci. 109, 2246-2250 (2012).

2. T. J. Cahill, R. H. Perry, R. H. Roizen, J. Du Bois, R. N. Zare, “Capturing Fleeting Intermediates in a Catalytic

C-H Amination Reaction Cycle,” Proc. Nat. Ac. Sci. (2012, accepted).

3. E. McNeill, J. Du Bois, “Catalytic C-H Oxidation by a Triazamacrocyclic Ruthenium Complex,” Chem. Sci. 3, 1810-1813

(2012).

4. M. E. Harvey, D. G. Musaev, J. Du Bois, “A Diruthenium Catalyst for Selective, Intramolecular Allylic C-H Amination:

Reaction Development and Mechanistic Insight Gained through Experiment and Theory,” J. Am. Chem. Soc. 133, 17207-

17216 (2011).

10

UTILIZING GAS-PHASE REACTIVITY TO CHARACTERIZE SOLUTION-PHASE CATALYSIS BY ESI-MS

Andrew Ingram

The ability of mass spectrometry to isolate ionic species of interest from complicated reaction

mixtures presents a unique opportunity to characterize intermediates in a catalytic cycle. The

ion control capabilities of ion trap mass analyzers make it possible to probe the gas-phase

reactivity of specific ions to characterize or discover catalytic cycles.1 Currently in our lab, gas-

phase ions are generated and transferred to a mass spectrometer using traditional electrospray

ionization (ESI) (Scheme 1). Upon entering the mass spectrometer, ions of interest are mass

selected and then allowed to react with a gaseous reagent in the ion trap. Products of these

gas-phase reactions are then mass analyzed and detected. Using this technique, we are able to

study the reactivity of specific catalytic intermediates.

We are in the process of applying these methods to study selective ethylene oligomerization, a

commercial process in which cationic chromium complexes convert C2H4(g) into commodity

chemicals such as 1-hexene and 1-octene with greater than 80% selectivity.2 This unique

selectivity is proposed to arise from metallocycle intermediates 3, 4, and 5 (Scheme 2)

however, the precise composition, oxidation states, and reactivity of these species have never

been conclusively determined. Key determinations we hope to make across various catalytic

systems are: (a) the chemical composition of metallacycle intermediates, (b) the relative rate of

ethylene insertion versus olefin elimination for each metallacycle as function of size, and

(c) the feasibility of bimetallic pathways as a route to selectively generate 1-octene.

Scheme 1. Flow System for Solution Phase Scheme 2. Proposed ethylene

ESI-MS/MS. oligomerization mechanism.

REFERENCES

1. C. Adlhart, P. Chen, "Fishing for Catalysts: Mechanism-Based Probes for Active Species in

Solution," Helvetica Chimica Acta 83, 2192–2196 (2000).

2. D.S. McGuinness, "Olefin Oligomerization via Metallacycles: Dimerization, Trimerization,

Tetramerization, and Beyond," Chemical Reviews 111, 2321–41 (2011).

11

DESORPTION ELECTROSPRAY IONIZATION MASS SPECTROMETRY (DESI-MS) IMAGING IN BIOMEDICAL RESEARCH

Livia S. Eberlin

Molecular imaging by mass spectrometry (MS) has been increasingly explored in many different fields of science due to its outstanding capability of providing spatial information on the distribution of a multitude of molecules with the specificity and the sensitivity that are characteristic of MS analysis, and without the need of fluorescent or radioactive labeling. Desorption electrospray ionization (DESI-MS) is one of a recently developed group of ambient ionization techniques in mass spectrometry in which samples are directly examined in the ambient environment with minimal pretreatment. It employs a spray of charged droplets which impact the sample surface, extracting chemical compounds into secondary droplets that are then analyze by the mass spectrometer. With DESI-MS imaging, tissue sections can be directly imaged with no need for sample preparation, yielding rich chemical information in less than one second per pixel. DESI has been especially useful in the analysis of lipids from different biological samples, although analysis of many other molecules such as small metabolites, hormones, natural products and exogenous drugs have been performed from different samples and substrates. One of the main applications of DESI-MS for tissue imaging has been in the area of cancer diagnosis. In our group, we are using DESI-MS imaging in collaborative projects to investigate fundamental questions in biomedical research and also in translational, patient-oriented medical projects. In collaboration with Prof. Dean Felsher, we are answering fundamental questions in cancer research by applying DESI-MS imaging to investigate the changes in lipid and metabolites profiles that occur in tissue with activation and inactivation of the MYC oncogene in animal models (Figure). In collaboration with Prof. Justin Du Bois, we are evaluating the potential usefulness of DESI-MS imaging in pain research for investigating the penetration behavior and biochemical effect of different saxitoxins in skin tissue samples. Together with a team of surgeons and pathologists led by Dr. George Poultsides at Stanford Medical School, we are also currently exploring DESI as a tool for gastrointestinal tumor margin assessment.

Figure 1. (a) DESI-MSI experimental setup for detecting lipid species in carcinomas (red) and in the adjacent tissue (blue). The tissue section is present on a glass slide that is mounted on an x-y translation stage in front of the mass spectrometer. The impacting spray solvent (black dot) desorbs lipid species from the tissue into the mass spectrometer for analysis. (b) DESI-MS imaging of liver tissue sections from conditional MYC transgenic mice. DESI-MS ion images of m/z 771.5208 are shown from left to right for wild type; MYC activated for 2 months (MYC ON/2); MYC activated for 4 months (MYC ON/4); and MYC activated for 4 months and then deactivated for 3 months (MYC ON/4-OFF/3) and well H&E stains of serial.1

REFERENCE 1. H. R. Perry, D. I. Bellovin, E. H. Shroff, A. I. Ismail, T. Zabuawala, D. W. Felsher, R. N. Zare,

"Micrometer-Scale Chemical Map of MYC-Controlled Tumor Progression and Regression," in preparation, (2012).

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12

MASS SECTROSCOPIC CHARACTERIZATION AND ANAYSIS OF PROTEIN MODIFICATIONS AND INTERACTIONS:

APPLICATION TO PHOTOSYNTHESIS PROCESS

Sam Kim, Jae Kyoo Lee

Identification and understanding of the protein-protein interaction and the modifications of proteins are essential for understanding almost all the biological events from development to death of an organism. Mass spectrometry has been extensively used to address the fundamental questions related to protein modifications and interactions because it enables precise determination of molecular masses of peptides and proteins with high sensitivity, and therefore unambiguous identification and sequencing of proteins. Here, we develop various mass spectrometry techniques for more sensitive and effective protein analysis. We integrate chemical crosslinking techniques with mass spectrometry, which allows for the detection of transient non-covalent interactions between proteins through the formation of stable chemical bonds between them. Crosslinking patterns combined with x-ray crystallographic structural data can be used to identify the binding domains for a protein complex. We also introduce a new ambient mass spectrometry named Laser Desorption/Ionization Droplet Delivery (LDIDD) mass spectrometry (MS). It utilizes a pulsed laser for desorption/ionization within a liquid droplet in contact with the surface containing molecules to be mass spectrometrically analyzed while liquid droplet serves as the ion carrier and delivers the desorbed and ionized species to the inlet of a mass spectrometer. There mass spectrometric methods are used for studying protein-protein interactions and modifications. At its core, photosynthesis is a chemical process converting light energy into chemical energy through a number of complex processes including photon absorption, electronic energy transfer, water splitting, etc. The very early process of photon abortion is assisted by the antenna proteins called light harvesting complexes (LHCs) surrounding the reaction center photosystems (PSs), where the actual water splitting occurs. The LHC and PS form a highly ordered structure that is strongly coupled to its function, i.e. efficient absorption of photons and energy transfer. Upon the environmental changes such as low or high level of light illumination, photosynthetic complexes undergo organizational/distributional changes to achieve maximum utilization of available light energy and/or protection of the photosynthetic complexes (Fig. 1). Here, we employ the aforementioned mass spectrometric tools for protein analysis for studying this early photosynthetic process, especially focusing on the interactions between protein complexes of LHC and PS under different light conditions. The crosslinking of the LHCs and PSs will be conducted to capture transient weak interactions between them. The binding between LHC and PS will also be studied in their intact states with Desorption Electrospray Ionization (DESI) and Laser Desorption/Ionization Droplet Delivery (LDIDD) mass spectrometry (MS) for more effective and high-throughput analysis of the interactions and spatial organization of the protein complexes in plant leaf samples under localized light stress conditions (Fig. 1B).

13

Figure 1. (A) Schematic representation of reorganization of photosynthetic complexes of light harvesting complex (LHC) and photosystem (PS) under varying light conditions. (B) Mass spectrometric measurement and imaging of post-translational modifications of proteins and protein-protein interactions with Desorption Electrospray Ionization (DESI) and Laser Desorption/Ionization Droplet Delivery (LDIDD) mass spectrometry.

14

CAPTURING TRANSIENT INTERMEDIATES OF ORGANIC REACTIONS WITH SHORT TIME-SCALE ESI SOURCE

Jialing Zhang

The Zare group has set up a DESI-MS system and use it in characterization of catalytic reaction intermediates, to enable greater insight into catalyst arrest and provide new strategies for fine chemical synthesis. However, in certain reactions, lifetime of the intermediates might be too short to detect even for DESI-MS setup which has a sub-millisecond time-scale. In order to capture intermediates with shorter lifetime, modification of DESI-MS device or some new ideas will be needed. We are preparing to test two new reaction systems: 1, two reactants are pumped separately into two coaxial tubes, and reactions happen immediately when reactants flow out of the tubes (as shown in Fig. 1); 2, when three reactants are involved, the first two reactants can be pre-mixed by the coaxial tubes and then interact with the third one (as shown in Fig. 2).

Fig 1. Proposed schematic view of reaction system 1

Fig 2. Proposed schematic view of reaction system 2

15

TWO-STEP LASER MASS SPECTROMETRY OF TERRESTRIAL AND EXTRATERRESTRIAL MATERIALS

Qinghao Wu

Microprobe laser-desorption laser-ionization mass spectrometry (μL2MS) is a powerful and versatile microanalytical technique that is used to study organic molecules in situ in a wide range of terrestrial and extraterrestrial materials. The combination of focused laser-assisted thermal desorption and ultrasensitive laser ionization provides sensitivity, selectivity, and spatial resolution capabilities that are unmatched by traditional methods of analysis. Over the past decade, this laboratory has developed and applied the μL2MS technique in a number of different research projects. Some areas that we are currently focusing on are:

Instrument Development: To enhance the analytical ability of the μL2MS technique we are actively pursuing instrument developments. Our plans include: installation of a dye laser to allow adjustment of the ionization laser wavelength; installation of a high power IR laser to study the spectra characters of molecules ionized by IR laser; the addition of sample heating parts to study the pyrolysis process of the complex mixtures, such as asphaltene, kerogen and polymers.

Meteoritics: Analysis of polycyclic aromatic hydrocarbons (PAHs) in meteorites, meteoritic acid residues and interplanetary dust particles.

Petroleomics: This instrument has provided strong proofs for the controversy over the typical molecular structures in asphaltenes, a fraction of heavy oil consisting of highly polar and aromatic molecules. Currently, we are comparing the spectra of asphaltene in various locations. The purpose is hopefully to obtain the information about past environments, climates and biota.

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MONITORING ELECTROCATALYTIC CYCLES ON ELECTRODE SURFACES IN REAL-TIME

Tim Brown

Utilizing the sensitivity and selectivity of mass spectrometry, this research will try to combine it with electrochemistry to analyze both the non-volatile and the volatile species in a sample. The combination of electrochemistry and mass spectrometry through various means has been important to the study of oxidation-reduction reactions through potential structural determination of intermediates and products of electrochemical reactions.1 One form of ambient mass spectrometry, desorption electrospray ionization (DESI2) will be modified (Fig. 1) to be used at the surface of a 3-electrode setup, utilizing nano electrospray ionization (nano-ESI). By placing reactants in the electrolyte solution and applying a potential, oxidation-reduction reactions will take place and potential electrocatalysts will be activated. The primary microdroplets from the nano-ESI will desorb the electrolyte surface, forming secondary microdroplets containing reactants, intermediates, and products. The secondary microdroplets evaporate, isolating each species to be detected by the mass spectrometer.

Figure 1. The proposed setup for coupling electrochemistry and ambient mass spectrometry.

Our lab seeks to optimize the proposed setup to explore electrocatalytic cycles. The first electrocatalyst we will investigate is copper(II) tris(2-pyridylmethyl)amine (CuTPA). CuTPA is an known oxygen activator to convert oxygen to water that proceeds through a bridged peroxo species3 (Fig. 2). Each species is charged throughout the cycle, making it possible for all known species to be detected with mass our modified DESI setup. This research will increase fundamental understanding of electrochemical processes and provide insights for development of improved electrocatalysts.

Figure 2. Two known species present in the oxygen activation of CuTPA

REFERENCES 1. K. J. Volk, R. A. Yost, A. Brajter-Toth, "Electrochemistry on Line with Mass Spectrometry, Insight into Biological Redox

Reactions," Anal. Chem. 64, 21A–33A (1992). 2. Z. Takáts, J. M. Wiseman, B. Gologan, R. G. Cooks, "Mass Spectrometry Sampling Under Ambient Conditions with

Desorption Electrospray Ionization," Science 306, 471–473 (2004). 3. S. Fukuzumi, H. Kotani, H. R. Lucas, K. Doi, T. Suenobu, R. L. Peterson, K. D. Karlin, "Mononuclear Copper Complex-

Catalyzed Four-Electron Reduction of Oxygen," J. Am. Chem. Soc. 132, 6874–6875 (2010).

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NANOPARTICLE FORMATION USING PRECIPITATION AND SELF-ASSEMBLY

Marie Russo We are interested in preparing nanoparticles of consistent size using a simple precipitation procedure.

The efficacy of therapeutically important drugs can be increased by optimizing target specificity,

cellular uptake and circulation time. Encapsulating a drug within a nanoparticle has the potential to

improve the physical and chemical stability of the drug and decrease the dosage amount, which can

lessen or eliminate side effects.

We have been able to successfully encapsulate small interfering RNA (siRNA) within solid lipids

nanoparticles (SLNs), nanoemulsions and polymeric nanoparticles. SLNs are made from lipids, such as

tristearin and stearic acid, that remain solid at body temperature. Nanoemulsions can be made from

any type of oil, including the oil from human adipose tissue and vegetable oil. Polymer nanoparticles

can be made from many biocompatible polymers, including a copolymer of lactic and glycolic acid. The

aforementioned nanoparticles are stabilized by lipids, such as cholesterol and polyethylene-glycosylated

lipids. Furthermore, we have complexed siRNA to the cationic lipid, 1,2-dioleoyl-3-

trimethylammonium-propane (DOTAP), in order to successfully encapsulate the negatively-charged

siRNA within the nanoparticles.1

We have used fluorescently-labeled transfer RNA (tRNA) as a drug model for siRNA in order to show

sustained oligomer release from the particles. We have been able to prepare nanoemulsions and

polymer particles that release tRNA over a period of 7 days. The SLN preparation has a longer release

period, shown in Figure 2.

REFERENCE

1. T. Lobovkina, G. B. Jacobson; E. Gonzalez-Gonzalez; R. P. Hickerson; D. Leake; R. L. Kaspar; C. H. Contag;

R. N. Zare, “In Vivo Sustained Release of siRNA from Solid Lipid Nanoparticles,” ACS Nano. 12, 9977-9983

(2011).

Figure 2. Cumulative release of tRNA from SLN in PBS solution

Figure 1. Nanoprecipitation procedure1

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SOME SELECTED RECENT PUBLICATIONS

CELL-IMPRINTING 1. R. Schirhagl, E. W. Hall, I. Fuereder and R. N. Zare, "Separation of Bacteria with Imprinted

Polymeric Films," Analyst 137, 1495-1499 (2012). 2. K. Ren and R. N. Zare, "Chemical Recognition in Cell-Imprinted Polymers," ACS Nano 6,

4314-4318 (2012).

REACTION DYNAMICS 1. J. Jankunas, N. C.-M. Bartlett, R. N. Zare, L. Liu, X. Xu, and D. H. Zhang, "D + C(CH3)4→

HD (v', j') + C(CH3)3CH2: Possible Concerted Flow of Vibration Energy into Translation," Mol. Phys. 110, 1713-1720 (2012).

2. J. Jankunas, R. N. Zare, F. Bouakline, S. C. Althorpe, D.Herráez-Aguilar, and F. J. Aoiz,

"Seemingly Anomalous Angular Distributions in H + D2 Reactive Scattering," Science 336, 1687-1690 (2012).

3. R. N. Zare, "Reaction Dynamics: Concluding Remarks," Faraday Discussions 157, 501-504

(2012).

4. R. N. Zare, "The Hydrogen Games and Other Adventures in Chemistry," Annu. Rev. Phys. Chem. 64, 1-19 (2013).

5. J. Aldegunde, D. Herráez-Aguilar, P. G. Jambrina, F. J. Aoiz, J. Jankunas, and R. N. Zare,

"H + D2 Reaction Dynamics in the Limit of the Low Product Recoil Energy," Journal of Physical Chemistry Letters (in press).

MASS SPECTROMETRY 1. O. C. Mullins, H. Sabbah, J. Eyssautier, A. E. Pomerantz, L. Barre, A. B. Andrews, Y. Ruiz-

Morales, F. Mostowfi, R. McFarlane, L. Goual, R. Lepkowicz, T. Cooper, J. Orbulescu, R. M. Leblanc, J. Edwards, and R. N. Zare, "Advances in Asphaltene Science and the Yen-Mullins Model," Energy & Fuels dx.doi.org/10.1021/ef300185p.

2. H. Sabbah, A. E. Pomerantz, M. Wagner, K. Mullen, and R. N. Zare, "Laser Desorption

Single-Photon Ionization of Asphaltenes: Mass Range, Compound Sensitivity, and Matrix Effects," Energy & Fuels 26, 3521-3526 (2012).

3. M. Eftekhari, A. I. Ismail, and R. N. Zare, "Isomeric Differentiation of Polycyclic Aromatic

Hydrocarbons Using Silver Nitrate Reactive Desorption Electrospray Ionization Mass Spectrometry," Rapid Commun. Mass Spectrom. 26, 1985–1992 (2012).

4. R. H. Perry, T. J. Cahill III, J. L. Roizen, J. Du Bois, and R. N. Zare, "Capturing Fleeting Intermediates in a Catalytic C-H Amination Reaction Cycle," Proc. Natl. Acad. Sci. USA (in press).

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NANOPARTICLES 1. J. Ge. J. Lei, and R. N. Zare, "Protein–Inorganic Hybrid Nanoflowers," Nature Nanotech.

7, 428-432 (2012). 2. J. Ge, E. Nyofytou, J. Lei, and R. N. Zare, "Protein-Polymer Hybrid Nanoparticles for Drug

Delivery," Small (in press).

3. P. Guo, T. M. Hsu, Y. Zhao, C. R. Martin, and R. N. Zare, "Preparing Amorphous Hydrophobic Drug Nanoparticles by Nanoporous Membrane Extrusion," Nanomedicine (in press).

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ZARELAB CONTACT LIST

OFFICE

LAB MEMBER PHONE OFFICE EMAIL NAME TITLE

Tim BROWN (650) 723-4334 017B timbrown@stanford.edu GS

Wenrui DONG (650) 723-4335 017A wrdong@stanford.edu PD

Maria DULAY (650) 723-8280 CLARK E250 mdulay@stanford.edu VS

Livia EBERLIN (650) 723-4334 017B liviase@stanford.edu PD

Conny FLENDER (650) 723-4334 017B cflender@stanford.edu PD

Eric HALL (650) 723-8280 CLARK E250 erichall@stanford.edu GS

Andrew INGRAM (650) 723-8029STAUFFER 1 -

ROOM 208 ajingram@stanford.edu GS

Keisuke INOUE (650) 723-8280 CLARK E250 keisuke7@stanford.edu VS

Justin JANKUNAS (650) 725-2983 315B jankunas@stanford.edu GS

Sam KIM (650) 723-8280 CLARK E250 slkim@stanford.edu PD

Jae Kyoo LEE (650) 723-8280 CLARK E250 jaeklee@stanford.edu PD

Barb MARCH (650) 723-4313 133 march1@stanford.edu ADMIN

Nandini MUKHERJEE (650) 723-4393 131 nmukherj@stanford.edu RA

Kangning REN (650) 723-8280 CLARK E250 kangning@stanford.edu PD

Marie RUSSO (650) 723-8280 CLARK E250 mrusso@stanford.edu GS

Qinghao WU (650) 723-4334 017C qhwu@stanford.edu PD

Dick ZARE (650) 723-3062 133 zare@stanford.edu PROF

Jialing ZHANG (650) 723-4334 017B jlzhang@stanford.eu VR

Li ZHANG (650) 723-8280 CLARK E250 zhlily77@stanford.edu VS

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THE ZARELAB

Richard Zare

Timothy Brown

Graduate Student

Wenrui Dong

Postdoc

Maria Dulay

Visiting Scholar

Livia Eberlin

Postdoc

Conny Flender

Postdoc

Eric Hall Graduate Student

Andrew Ingram

Graduate Student

Keisuke Inoue

Visiting Scholar

Justin Jankunas

Graduate Student

Sam Kim Postdoc

Jae Kyoo Lee

Postdoc

Barb March

Admin

Nandini

Mukherjee Senior Research

Scientist

Kangning Ren

Postdoc

Marie Russo

Graduate Student

Qinghao Wu

Postdoc

Jialing Zhang

Visiting Researcher

Li Zhang

Visiting Scholar

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STANFORD CAMPUS MAP

ZARELAB

Mudd Chemistry Bldg

333 Campus Drive

ZARELAB (West)

J.H. Clark Center

318 Campus Drive

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STANFORD VICINITY http://stanford.edu/home/visitors/vicinity.html

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NOTES