The three main instruments are:

1. a Beckman XL-I analytical ultracentrifuge equipped with both scanning absorbance and interferrometric optics,
2. a SLM-Aminco 8000 T-format fluorescence spectrometer with polarizers, and
3. an Olis DSM-20 CD spectrometer with an auto-titrator attachment. We routinely use these instruments to measure thermal stability of proteins, molecular weight and oligomerization state, and macromolecule association constants.

The facility houses various supporting equipment including refractometers, a 5-digit picnometer, luminometers, balances, and a gel imaging system. The facility is directed and run by Dr. Chad K. Park and is used to advise and collaborate with scientists on all aspects of biophysics, from cloning, protein expression and purification, to assay development, data regression and analysis.

Initially, the laboratory was established to perform organic and inorganic syntheses published in the scientific literature; however, the service has evolved to where the CSF can perform limited original work. The main purpose is to serve the needs of clients with limited chemical synthesis resources. The CSF has expertise and equipment to perform on projects on small sub milligram to large hundred gram scale.

The area is a two person lab equipped with: three Rotovaps®; facilities to perform reactions under inert, anhydrous conditions; four vacuum pumps; chillers; and Flash chromatography glassware. The facility prepares small molecules such as sugars, nucleosides, biologically active materials, metabolites drug products and monomers of nano-materials.

Chemical Analyses available include the UA NMR Facility and the Mass Spectrometry and Proteomic Facility. The CSF is staffed by one PhD scientist (Dr. Ron Wysocki) and two to five undergraduates.

Tooling and capabilities for the clean room currently consist of the following tools:

• Laurell Technologies WS-650-23 Spin Processor
• Karl Suss MJB3 Mask Aligner/Exposure system (C.D. down to 1 um)
• Advanced Plasma Equipment (APE)
• Reactive Ion Etcher (RIE)
• Riegler and Kirstein Langmuir Blodgett Dipping Trough
• Jelight UV-Ozone Cleaner
• Harrick Oxygen Plasma Cleaner
• Exhausted Laminar flow benches (2)
• Chemical Hood
• Laminar flow bench (not exhausted)
   

Barnstead nanopure Ultrapure water system (18 M-ohm water system with Ultrafiltration) Garments are provided and the cost is included in the user fees.

New capabilities currently under construction in the clean room include:

• Organic Vapor Deposition (thermal)
• E-beam Deposition for metals and inorganics
• Thermal Evaporation (High Current Tungsten Boat system)
• MBraun Glovebox Device Fabrication system
• Solartron 1255 Frequency Response Analyzer
• Keithley Sourcemeter to measure device electrical properties
   

The Facility's purpose is to answer the need of the Department and the University faculty, as well as the outside academic and non-academic users, in state of the art continuous wave (CW) and pulsed EPR experiments. The latter include all kinds of electron spin echo envelope modulation (ESEEM), pulsed electron-nuclear double resonance (ENDOR), and pulsed electron-electron double resonance (ELDOR) measurements.

The typical spectroscopic problems addressed by the EPR Facility are related to identification of paramagnetic centers (e.g., transient radicals produced in chemical reactions) by CW EPR, solving the structure of paramagnetic centers (e.g., ligand structure of metal centers of enzymes) using ESEEM and pulsed ENDOR, and to distance measurements between paramagnetic centers (e.g., the distance between the electron transfer cofactors in biological systems) using pulsed ELDOR.

The Facility is currently equipped with a CW X-band EPR spectrometer Bruker ESP-300, which will be replaced by the new Bruker ELEXSYS E500 spectrometer in the near future. This new spectrometer will be equipped with a CW ENDOR system. The maximum magnetic field available in CW EPR experiments is about 1.4 T, and the accessible range of sample temperatures is from about 4 K to 600 K (the cryogenic temperatures are achieved using the Oxford ESR-900 gas flow cryostat). In addition, the Facility operates three homebuilt broadband pulsed EPR spectrometers covering the ranges of microwave frequencies from 2 to 8 GHz (S- and C-bands), 8 to 18 GHz (X- and Ku-band), and 26 to 40 GHz (Ka-band). These spectrometers are equipped with high-power traveling wave tube amplifiers (1 kW for the S- to Ku-bands and up to 350 W for the Ka-band), which makes them usable not only in pulsed ENDOR, but also in ESEEM and pulsed ELDOR experiments. The pulsed ENDOR accessory is based on the Amplifier Research 250L amplifier (250W in CW mode and up to 800 W in pulsed mode). The maximum magnetic field available in pulsed experiments is about 2 T, and the accessible range of the sample temperatures is from about 4 to 300 K (the cryogenic temperatures are achieved using the Oxford CF-935 gas flow cryostat).

The Facility is supervised and maintained by Dr. Andrei Astashkin (Astachkine), a Ph. D. scientist with thirty years experience in the field of EPR.

The Center's technical expertise and research equipment is designed to foster student training and research collaborations throughout the College of Science, complementing existing research strengths in the areas of nano-science and nanotechnology including microfluidics, self-assembly, chemical patterning, optical and electronic devices, etc. The Center is housed on the first floor of the Chemical Sciences Building and is supervised by dedicated technical staff, Brooke Beam Ph.D., whose responsibilities include student training, instrument maintenance as well as experimental measurements. The Center is administered by the department of Chemistry and Biochemistry and is open to all University of Arizona research groups.

The Keck imaging facility currently houses three scanning probe microscopes (SPM); Agilent 5500, Veeco Multimode with a Nanoscope IIIa controller, and Veeco Dimension 3100 with a Nanoscope IV controller. The Agilent SPM can be coupled to an inverted optical microscope to take advantage of emerging complementary optical imaging techniques. Additionally, the Dimension 3100 has the ability to probe the electrical properties of surfaces with conductive tip, scanning spreading resistance, and scanning capacitance modules. A Confocal fluorescence microscope, a Total Internal Reflection Fluorescence (TIRF) microscope, a PTI Fluorometer, and a Scanning Electron Microscope (SEM) are located in the Keck imaging the facility. The SEM is equipped with a Thermo Noran System Six X-ray microanalysis system and a J.C. Nabity Nanometer Pattern Generation Sytem (NPGS). Finally, a Potential Modulation Attenuated Total Reflectance spectrometer (PMATR) is being assembled in the Keck imaging facility and will be available for use in late 2010.

The role of the facility is to assist students and researchers with crystallization, data collection and structure solution or perform the studies on a fee-for-service basis. Most users choose to do their own structural work. A great deal of macromolecular data collection now occurs at synchrotron sources. MCC personnel work with users to identify appropriate beam lines, obtain beam time, prepare and ship samples, and collect synchrotron data.

In addition to single-crystal experiments, Dr. Roberts has recently conducted solution small-angle x-rays scattering experiments (SAXS) at SSRL in conjunction with Dr. Montfort's research group. One of the MCC researchers, Dr. Andrzej Weichsel, teaches a 1 credit unit course, Biochemistry 587 entitled Practical Macromolecular Crystallography which is a companion course to Biochemistry 585, Biochemical Structure. Workshops covering topics such as structure validation and use of structural results in biological research are under development.

MCC Facility instrumentation includes:

• Single crystal data collection: Rigaku R-Axis IV++ imaging plate system mounted on a Rigaku RU-H3R rotating anode generator with Max-Flux confocal optics and an Oxford Cryosystems liquid nitrogen cold stream device.
• Crystallization: Art Robbins Instruments Phenix crystallization robot and CrysCam drop imager. Incubators, microscopes, inert-atmosphere glove box for crystallization, and a Xenon-chamber for heavy-atom derivatization. A Wyatt Nanostar DLS instrument and a single crystals microspectrometer are available for use courtesy of Dr. Montfort.
• Data analysis: Linux and Windows computers for stereographics, data reduction, and computation. MCC is managed by Dr. Sue A. Roberts and Dr. Andrzej Weichsel. Ms. Abreeza Zegeer is available part- time to assist with crystallization experiments. MCC is located on the 5th floor of the Bioscience West building. More information is available at: www/cbc.arizona.edu/xray/
   

Mass spectrometry (MS) is a powerful tool in analytical and bioanalytical chemistry that provides detailed structural information on a wide variety of compounds (1-1,000,000 daltons) by using very small amounts of material (ng, pmol, fmol). Another important feature of MS is that it is easily and often coupled with separation techniques such as gas-chromatography (GC) and high performance liquid chromatography (HPLC). In a modern MS laboratory it is desirable to have many of these different techniques and options available. Our MSF has a wide variety of instrumentation and personal experience to provide high quality service for colleagues on campus and also for off-campus researchers (including international collaborations).

The MSF provides state-of-the-art support (teaching and research) in a wide variety of research areas campus wide and also for the local community. The MS Facility is extensively involved in national and international research collaborations which help to enhance the national reputation of the university in Chemistry and Biochemisty. Two permanent Ph. D. level staff scientists with many years of experience in mass spectrometry operate the facility (Drs. Somogyi and Shu). They are joined by two graduate students who work in the facility as research assistants on a year by year appointment.

The mass spectrometric and analytical services include molecular weight determinations, structure elucidations, and qualitative and quantitative analyses of organic, inorganic and biological compounds. Instrumentation includes a Micromass high resolution GCT GC/MS instrument, a Finnigan (Thermoelectron) LCQ HPLC/MS system, a Bruker Reflex III MALDI_TOF instrument, an IonSpec FT_ICR (4.7 T) instrument, a Bruker Ultraflex MALDI TOF-TOF and an Apex Qh FT-ICR (9.4 T) high resolution instrument equipped with a dual ESI/MALDI source. The Apex Qh FT-ICR instrument provides ultrahigh resolution (up to 900,000) and mass accuracy with a sub ppm level.

Our three main duties are “service, education, and research”. We provide MS service for a wide variety of samples submitted by researchers from 20-22 different Departments on campus. We also served the local community by analyzing samples using our state-of-the art mass spectrometers (e.g., the FT-ICR) that are not available in Southern Arizona. We are regularly and strongly involved in both undergraduate and graduate education on campus. We participate in different courses and provide help for several graduate students during their Ph.D. program. We regularly offer and teach a summer workshop on mass spectrometry and are involved in a “Tandem MS/MS” short course on the big annual ASMS (American Society of Mass Spectrometry) meeting. We collaborate with highly respected professors on and off-campus in different research area, including bio-analytical chemistry, transition metal chemistry, atmospheric science and astrobiology.

The laboratory is equipped with a Varian Inova 600 spectrometer with cryogenic probe and Bruker Avance DRX 600 MHz and 500 MHz spectrometers, all with the latest technology and capabilities for elucidation of structure and conformation of complex molecules in solution. All three instruments have pulsed-field gradients, shaped pulses, 3 or 4 RF channels and digital oversampling and filtering. A new 400 MHz Bruker Avance-III instrument was installed in November, 2009, with a 600-sample autosampler capable of remote operation via the web and a CP-MAS solids accessory. This instrument is operated during the week in a walk-up automation mode and on weekends for solid-state NMR. A Varian Unity 300 MHz with four-nucleus (CPHF) and inverse broadband probes is available, and a Varian Gemini 200 MHz instrument is used for undergraduate courses. All of the instruments are hands-on, with training provided in the form of intensive workshops and individual instruction as well as a formal graduate-level NMR course. A Quad-core Gateway 9515 Linux dataserver and compute engine equipped with software for processing and analysis of 2D and 3D NMR data is available and can be used over the network from a desktop or laptop. The NMR Facility has purchased a permanent campus-wide site license for the MestReNova NMR data processing software package, making desktop NMR data processing available to the entire campus community.

The facility houses two spectrometers that are capable of gas-phase UV photoelectron spectroscopy. One of the instruments has the dual capacity of running X-ray photoelectron spectroscopy. To our knowledge, this instrument is the only gas-phase X- ray photoelectron spectrometer in the world outside of a synchrotron facility. The instruments have the ability to analyze gaseous neutral molecules from gases, liquids, and solids that sublime up to 500°C.

Users within the university are trained to collect and analyze their own data, and facility staff performs experiments on submitted samples for outside users. We ask that users pay a small hourly fee to help cover the costs of instrument use. Since most users possess a limited amount of expertise in this area, research problems often require other services in addition to typical data collection and presentation of submitted samples. Literature searching to develop background on the research, computational modeling and electronic structure calculations, and experimental design are common services provided to aid in the detailed analysis of the data and its implications to the research problem. Finally, facility staff is largely responsible for composing major sections of collaborative publications.

In addition to collaborative research, the facility provides support to many teaching labs in the department. Currently, a few students each semester from the CHEM 412 course (inorganic laboratory course) work with graduate students on projects that involve data collection of several compounds. There are plans for next semester to institute a data collection component to at least one of the labs in this course so that all students will have experience collecting and analyzing data to understand basic inorganic principles. This introduction of a photoelectron spectroscopy component to a lab represents a first step towards a wider use of the facility in laboratory and teaching courses.

As an outreach activity, the facility has engaged participants of a summer program for minority high school students and teachers for the past 5 years. During a four week period, the participants synthesize, characterize, and collect photoelectron spectroscopy data on [FeFe]-hydrogenase active-site mimics. The conclusion of the four weeks requires a presentation detailing the chemistry and techniques learned. Arizona Proteomics Consortium The Department of Chemistry and Biochemistry has provided Proteomics Services to the University of Arizona for over 10 years. Various proteomics capabilities and core labs have been in operation on campus since 2000 and have grown substantially over the past decade in terms of hardware, software, personnel, and capabilities.

In 2006, we formed the Arizona Proteomics Consortium, an effort intended to increase our capacity to support sample analyses for principal investigators statewide. We routinely and successfully use mass spectrometry coupled to liquid hromatography to identify DNA or RNA bound proteins, secreted proteins, chemically-adducted proteins, and catalog proteins involved in whole system biology systems (using multidimensional protein identification technology, MudPIT), as well as those involved in protein-protein interactions.

Currently our facility is supported financially by the Southwest Environmental Health Sciences Center, the Arizona Cancer Center, The Department of Chemistry and Biochemistry and the Bio5 Institute. The facility is led by Dr. George Tsaprailis, Director (home department Center for Toxicology) and Dr. Linda Breci, Associate Director (home department Chemistry and Biochemistry), and has six additional Ph.D., M.S., and B.S. staff members.

Instrumentation is located in three laboratories across campus and includes two MALDI-TOF MS instruments, an ABI 4000 Qtrap, a Waters QTOF Premier with nanoAcquity HPLC, an ABI 3000 triple quadrupole, and Thermo Finnigan MS instruments including an LCQ Classic, two LCQ Deca XP’s, and two LTQ’s, each fronted by nano-HPLC-ESI systems. A Bruker MALDI-TOF/TOF and 9.4T FTICR with nano- HPLC are also available as a shared resource with the Dept. of Chemistry’s Mass Spectrometry Facility. In addition, we were recently awarded NIH/NCRR funding for an LTQ Velos Orbitrap mass spectrometer and nanoHPLC as well as an Advion NanoMate source (HEI grant to Dr. Tsaprailis, Director Arizona Proteomics Consortium) that was installed in September, 2010. The Orbitrap is equipped with alternative dissociation methods such as electron transfer dissociation (ETD) and higher energy collision dissociation (HCD). The former has been shown to unequivocally keep labile modifications intact, yielding c and z ions, which are used to sequence and map the modification first hand. The latter dissociation method can result in immonium ions that can confirm the presence of phosphotyrosine. Our laboratory is also equipped with DIGE imaging, 1D and 2D gel electrophoresis equipment, and a number of digestion and spot picking robotics. Data mining and protein identification is done using various licensed search algorithms (Sequest, MASCOT, Scaffold) or freeware (X!Tandem, OMSSA). We have also developed SALSA and P-mode software to identify protein posttranslational modifications. Scientists from the Proteomics group work closely with researchers to design experiments, monitor progress to optimize success and train researchers and students in proteomics techniques at all levels – undergraduate, graduate and post-doctoral. In addition, Drs. Tsaprailis and Breci teach a 2-day short course each year at the annual meeting of the American Society for Mass Spectrometry.

The facility is administered by a Staff Scientist, Dr. Ken Nebesny, an Associate Staff Scientist, Mr. Paul Lee, and a student Research Associate chosen yearly from a competitive pool of graduate students. LESSA is closely aligned scientifically with the Keck Nano-Imaging and Clean Room facilities and the three units often provide complimentary support and expertise to the same research programs and projects in both the department and across campus.

Current capabilities in the facility include a Kratos Axis 165 Ultra X-ray Photoelectron Spectrometer which is fitted with monochromatic (Al) and dual (Mg, Al) x-ray sources for X-Ray Photoelectron Spectroscopy (XPS), a high intensity ultra-violet source for Ultra-violet Photoelectron Spectroscopy (UPS), photoelectron imaging with spatial resolutions in the 1-2 um range, argon sputter ion cleaning and depth profiling, and in-situ sample heating and cooling. Recently the instrument underwent a significant upgrade with regards to the electron detector. An older multi-channeltron detection system was replaced with a state-of-the-art delay line detector (DLD) with a resulting order of magnitude increase in count rates. Lastly, the instrument also configured for fast sample introduction and storage for normal analytical use. We have additionally modified the system to mate with custom designed and in-house constructed vacuum deposition chambers so that pristine samples can be prepared and studied in situ, away from deleterious atmospheric effects. The additions include a specialized transfer system to mate with the original spectrometer sample handler configuration, an isolatable pumping system to maintain spectrometer pressures in the low 10 -9 torr range, and an inert atmosphere glove box permanently mated with capabilities for clean, ex situ sample introduction, manipulation and large scale testing. One of the additional chambers also has Low Energy Electron Diffraction (LEED) capabilities for fundamental single crystal studies.

In addition to the main facility instrumentation, LESSA designs, constructs and maintains various deposition chambers that are used to support the thin film research platforms in the department. The lab also has expertise in electron optics design, photon and electron counting techniques, vacuum system design and construction, electron analyzer design, construction, and repair.

LESSA is active in the education of the department and university community in the fields of surface analysis and surface science through individual training on facility equipment, seminars and invited special topic course lectures, and workshops.

It is staffed by a full time scientist, with students from this department, Pharmacy and Materials Science & Engineering, carrying out their own experimental work. The Facility has formal, actively publishing collaborations with primarily undergraduate institutions Northern Arizona University and Millersville University, and we benefit from regular access to beamline 11.3.1 of the Advanced Light Source for carrying out experiments on very weakly diffracting crystals.

Single crystal experiments are carried out on a Bruker Kappa APEXII DUO diffractometer with co- mounted molybdenum and copper X-ray sources. Now considered a standard setup, this was the second such instrumentation in the United States. Generally molybdenum radiation is used as the standard X- ray source suitable for most types of compound, particularly organometallic and coordination compounds and those which diffract well to a high resolution. Switching to copper radiation takes around two minutes is used primarily for light atom chiral compounds. With molybdenum radiation as close to a complete Ewald sphere of data as possible, with multiple redundancy and to a resolution of 0.75 Å, can be collected in around 12 hours; this can, however, be as quick as one hour depending on experimental setup. With copper radiation the resolution is limited by hardware to 0.82 Å and a typical dataset from a monoclinic crystal can be completed in 16–20 hours. All crystals are face-indexed for absorption corrections and data can be collected in the temperature range 80–400K.

Powder diffraction measurements are made on a PANalytical X’Pert MPD Pro diffractometer capable of measuring powder diffraction patterns in the temperature range 298–500K. Common uses are phase analysis of samples with unknown, or partially known, composition; diffraction measurements from thin films; variable-temperature studies of solid-state transformations. The diffractometer is also capable of X-ray reflectivity measurements from thin film samples, using X-ray mirror optics and a gas proportional detector, to measure film thickness.

The Facility is able to troubleshoot and repair a wide variety of electronic equipment in use throughout the department, saving research groups from having to purchase expensive new products. We are also here to work on new electronic designs that can complement research groups' projects. The ChIEF staff has experience with High Voltage Power Supplies and Systems, Radio Frequency Equipment, Image Intensifiers, Microchannel Plates (MCPs), Photomultiplier Tubes (PMTs), Charged Coupled Device Imagers (CCDs), Cryogenic Systems, Motion Control Programmable Interrupt Controller (PIC) embedded systems, Programmable Gate Arrays (PGA), Digital Signal Processing (DSP), and other contemporary electronics.

The variety and breadth of equipment available allow us to power, troubleshoot, and repair a variety of applications. For example, our mixed signal oscilloscope allows simultaneous measurement and display of 16 digital channels and/or analog signals. It can be directly connected to the internet for remote data collection, or data can be saved on USB memory sticks. It is an essential piece of equipment for troubleshooting complex systems. ChIEF also has other equipment useful for troubleshooting and diagnostics, which can be checked out for short periods of time by research groups and graduate students. Examples include adjustable power supplies, multimeters, signal generators, counters, and other benchtop equipment.

The ChIEF staff has extensive experience in trouble shooting and repair of advanced research equipment. We have moved away from repair of small items that can be readily replaced (stirrers, heaters, etc) and are concentrating on saving research groups from having to replace expensive experimental equipment when possible.

Education and safety is an important component of ChIEF's operation. During the summer, ChIEF typically offers an electronics class to graduate students to teach them electronics and basic soldering techniques. In addition, when there is a potential safety concern, we identify the problem and suggest ways to correct it. Finally, there are numerous activities throughout the department that ChIEF has involvement in, such as the Lab Monitor Safety Meetings and departmental emergency response training.

ChIEF is staffed by two professional electrical engineers: Dr. Kevin Bao and Mike Reed

The Facility also offers a (for credit) scientific glassblowing class (Scientific Glassblowing 302A) for science majors and graduate students in both the fall and spring semesters. The shop is staffed by two master scientific glassblowers.

The glassblowing facility has, on-hand, virtually all sizes of borosilicate (Pyrex, Kimax) glass tubing ranging in size from 2 millimeter up to 178 millimeter in diameter. All sizes of commonly used ground glass joints, and a large selection of both glass and Teflon stopcocks are maintained in a large inventory.

The following techniques are routinely used: bench, lathe and stationary rack work: graded seals , glass to metal seals, oil diffusion pumps , quartz dewars (window and finger), glass to ceramic, quartz UV optical cells. In addition, the shop specializes in high vacuum techniques and has a working knowledge of vacuum gauges, leak detection techniques, vacuum rack designing, and applications of glass to metal couplings.

The machine shop is a research support component of the Department of Chemistry and Biochemistry at The University of Arizona. The shop also performs work for other university departments as well.

Services and Design The Machine Shop provides a variety of services and materials including:

• Precision machining of metals, plastics, and ceramics
• The design and construction of scientific instruments
• Project consultation
• Raw materials for do-it-yourself projects
• Machine shop training and use of a student shop
• Welding, High vacuum welding, brazing and soldering
• A small inventory of assorted hardware
   

The machine shop is staffed by two instrument makers with over 40 years of combined experience. The CBC instrument makers are skilled at helping researchers to develop ideas into complete designs and ultimately into working instruments. Depending on the needs of the client, the instrument makers can produce simple sketches, mechanical drawings or AutoCAD drawings. They routinely design simple parts and/or entire systems. The shop is equipped with manual milling machines, lathes, band saws, drill presses, welding equipment, sheet metal and surface grinding equipment.

Student Services: The Student Machine Shop is available 24/7 to qualified CBC students and researchers. It is equipped with a knee mill, lathe, band saw, drill press and pedestal grinder. Instruction and project consultation is available from the shop personnel. The machine shop staff teach the skills necessary for the proper and safe use of the student machine shop equipment through a course in machine shop practices.