Chemical Education Newsletter

Innovation with Integrity

Academics in Focus

Structural Characterization of Asprin with X-ray Crystallography

NMR Within Everyone’s Reach

Setting New Standards in Performance and Value for LC/MS

A Compact Benchtop FT-IR Spectrometer for The Academic Laboratory

Practical Powder Diffraction Teaching Program

Academics

4 NMR Within Everyone’s Reach

5 XRD for Everyone, Everywhere

6 Structural Characterization of Asprin; a very Familiar Organic Compound

9 Setting New Standards in Performance and Value for LC/MS

10 A Compact Benchtop FT-IR Spectrometer for the Academic Laboratory

12 Practical Powder Diffraction Teaching Program

In this issue:

2

Robust, High Performance and Easy-to-Use Systems, Ideally Suited for Academics

Over the past two centuries, chemistry has changed our daily lives more than any other scientific discipline. Chemistry makes our world more colorful, efficient, reliable and safe. We see Chemical Edu-cation as an important piece in creating tomorrow’s world; therefore developing and supporting analytical instruments for the academic environment has been a key focus of Bruker for many years. Today, Bruker delivers a series of power-ful, robust, yet easy to use analytical instruments, which are ideal for use by both students and experts in academic settings. Bruker is strongly committed to serving the needs of academia, and has recently launched a number of new instruments especially with academic laboratories in mind. Please take the opportunity to browse through this newsletter to learn more about the features and capabilities of these exciting new products for the aca-demic laboratory and see how they are being applied to student teaching. In addition, we have also recently expanded our product-line to offer

Gas Chromatography Systems (GC) Gas Chromatography-Mass

Spectrometers (GC/MS and GC/MS/MS) Inductively Coupled Plasma Mass

Spectrometers (ICP-MS)

These systems, previously known as Varian products, are well accepted and established market leaders that univer-sally deliver outstanding performance at a premium value. With the addition of these products, Bruker now has a more complete portfolio to address your challenging needs. Moreover, Bruker has retained former Varian key personnel to support these product lines worldwide. As we welcome our new colleagues into our growing family, we welcome the opportunity to be your partner. For more information, visit:

www.bruker.com/academics

3

Academics in Focus

Undergraduate students using ALPHA FT-IR spectrometers during a chemistry class at Loras College in Dubuque, IA. (Photograph courtesy of David Oostendorp, Ph.D., Professor of Chemistry, Loras College.)

Fourier 300

4

FT-NMR

NMR Within Everyone‘s Reach

Fourier 300 brings NMR within every-one’s reach. It delivers powerful perfor-mance at extremely compact size, low weight and most importantly, minimal cost. With its new Fourier probe tech-nology and a unique push-button, power on/off concept, ease of siting and handling is guaranteed. Designed and built by the world‘s NMR market leader, Fourier 300’s unique qualities include the industry standard operating software, TopSpin™. TopSpin’s various tools for exploring the world of NMR make Fourier 300 the ideal solution for chemistry education and routine analysis. Researchers have access to numerous pre-defined 1D and 2D experiments and interactive, automated processing tools help to transfer spectroscopic data into a corresponding report.

TopSpin

Fourier 300 runs NMR software TopSpin, offering various tools for exploring the world of NMR.

TopSpin provides numerous tools to support the interpretation and evaluation of spectra.

Ideal for the undergraduate NMR laboratory, the Fourier 300 will allow you to incorpo-rate new experiments into your curriculum. From simple 1D proton spectra to advanced proton-carbon correlation experiments, all are available with just a few mouse clicks. The Fourier 300 provides the essential tools for analytical instrumentation courses in organic chemistry labs. Whatever the goal—elucidate the structure of an organic molecule, or learn NMR as a method—the flexibility of Topspin software and its com-prehensive tutorials put both within easy reach of your students.

Fourier 300 is equipped with SampleX-press Lite™, Bruker’s entry system to NMR automation. It is a compact sample changer which can hold up to 16 samples. SampleX-press Lite is fully integrated with TopSpin™ for robust and easy to use automation. Very short gaps between experiments, together with access to any of the individual samples via the routine user interface IconNMR™, provide superior efficiency and flexibility.

Fourier 300’s full automation capabilities free the user from tedious calibration or optimization, enabling them to remain focused on their research goals. Users will immediately be comfortable with the familiar PC Windows environment, and will find Topspin’s user interface similar to many popular programs.

Spectra Evaluation

For more information, visit: www.bruker.com/fourier300

5

X-ray Diffraction

D2 PHASER Benchtop XRD

XRD for Everyone, Everywhere

The new D2 PHASER is the most compact and fastest, all-in-one crystal-line phase analysis tool available on the market.

The reinvention started right in the center of any diffractometer – the goniometer. As size always matters, the first step was to develop an ultra-compact goniom-eter in order to reduce the overall system dimensions. At the same time, that goni-ometer still needed the highest possible angular accuracy for the best analytical data. The solution our engineers came up with was so unique that we thought it would be worth filing a patent.

The key requirement for the new system was minimum installation requirements. So we decided to run it with a small internal cooling circuit only and to limit the power supply to that of a standard wall socket. The advantage is obvious: For the first time you can now put a dif-fractometer on the back of a truck, head for a remote camp, hook it up to a diesel generator and solve unknown structures right on the spot. Or if you are not so adventurous, you simply place it on a cart and steer it to your classroom.

Independent of where you use it, the new D2 PHASER needs less than 650 W of power and no cooling water, which make the system a green solution as well. A nice side effect of this low power operation is that the X-ray tube will last virtually forever.

Whenever you restrict your input power, people will tell you that you have to make compromises on either the speed of the analysis or the data quality. And they’re right, in a way. But what you can do is add a state-of-the-art one-dimensional detector. Our LYNXEYETM detector simultaneously captures a large angular range and radically reduces the measurement time: With a performance enhancement in terms of intensity of a factor of more than 150, the D2 PHASER is actually playing in the top of the class. Additionally, the LYNXEYE allows sup-pression of sample fluorescence, provid-ing an excellent peak-to-background ratio even for strongly fluorescent samples, eliminating any need for secondary monochromators.

When you complete the system with all the components for autonomous opera-tion, and package the whole configura-tion together with PC, monitor, keyboard and mouse, into a compact housing, you’ll end up with the most powerful and compact X-ray diffractometer in the world – the D2 PHASER.

For more information, visit: www.bruker.com/xrd

6

X-ray Crystallography

Structural Characterization of Aspirin; a very Familiar Organic Compound

The synthesis of aspirin is a part of many undergraduate organic synthesis laboratories. These courses teach synthesis and purification skills. With the SMART X2S benchtop system, undergraduate students can now employ X-ray crystallographic methods for 3-D structural characterization in an easy and intuitive way. Crystallography provides the most unambiguous structural information of all analytical methods and previously was only available to cutting edge research.

In this experiment, acetic anhydride is added to salicylic acid in the presence of a catalyst, phosphoric acid. The mixture is heated to form the acetylsalicylic

acid (Aspirin) and acetic acid. Water is added to destroy the excess acetic anhydride and cause the product to crystallize. Aspirin is then collected and re-crystallized from an ethanol water mixture. After successful synthesis and crystallization, course participants will learn to manipulate crystals under a microscope and choose crystals suitable for X-ray structure determination. Aspirin forms well-defined colorless monoclinic crystals which are solvent free, air stable and easy to manipulate with a preparation needle. Students will identify clear, nicely grown, isometric crystals for further preparation. An ideal crystal will have at least one edge with a length of about 700 micrometers.

Monoclinic Aspirin crystals are placed on Bruker‘s sample holder

Sample is inserted into the SMART X2S

The GUI guides the student through the experiment, providing easy to understand graphical feedback about the status and qual-ity of the structure determination process.

The system generates Archive CD with interactive report

Sample preparation is easy and straight forward: The crystal will be attached to the tip of a Bruker sample holder. The sample holder is pre-aligned and features a polyimide-film tip, which supports the crystal that is glued using an UV curable adhesive. The advantage of UV curable adhesive is that it leaves ample time for a student to manipulate the sample without the adhesive curing, yet it allows the crystal to be fixed in place within seconds by shining UV light on it. A protective cap is put onto the pin and the sample is ready for X-ray investigation. To start an experiment, students supply the sample and an empty CD ROM for data archiving. Basic information about the sample is provided for the report generation (Chemical formula, size and color of the crystal).

Interaction with the SMART X2S is very user friendly. The system features a Kiosk style GUI with input through a touch screen interface. No crystallographic knowledge is required.The GUI is intuitive and will guide the student through the experiment, providing easy to understand graphical feedback about the status and quality of the structure determination process.

7

The SMART X2S

Aspirin recrystallized from ethanol/water

The synthesis of aspirin is a part of many undergraduate organic synthesis laboratories. These courses teach synthesis and purification skills. With the SMART X2S benchtop system, undergraduate students can now employ X-ray crystallographic methods for 3-D structural characterization in an easy and intuitive way.

Synthesis of Aspirin

The automation software combines an expert‘s knowledge of structural chemistry with the power of cutting edge data processing engines for structure solution and refinement used in research instrumentation at laboratories world-wide. The SMART X2S software automatically determines the structure of most routine organic and coordination compounds.

The system generates an interactive report in HTML format with an embedded molecule display that allows interaction with the molecule. The molecule viewer lets the student determine distances between atoms or calculate angles. The molecule can be rotated and displayed in various modes (Ball and stick, space filling CPK model, molecule surface, etc). The report will start automatically when the archive CD is inserted in any CD ROM drive. The Archive CD contains all data, from raw images to refined structure files. These data can be used in advanced crystallography courses and are fully compatible with Bruker’s suite of crystallographic research software.

8

X-ray Crystallography, cont‘d

Structure-Property Relationships of Stable Free Radicals: Verdazyls with Electron-Rich Aryl Substituents. Victoria Chemistruck, Dallas Chambers, and David J. R. Brook, J. Org. Chem. 2009, 74, 1850–1857

1,2-Dimethyl-4,5-diphe-nylbenzene determined on a Bruker SMART X2S benchtop crystallographic system. J. B. Briggs, M. D. Jazdzyk and G. P. Miller, Acta Cryst. (2009). E65, o1171

3(Bis(2-diphenylphosphi-noethyl) phenylphosphine)-chloro-platinium(II hexafluorophosphate. Scott A. Heston, Bruce C. Noll, Monte L. Helm, Acta Cryst. (2009). E65, m793

Publication Quality Data at Your Fingertips

The SMART X2S provides reports in a variety of formats. Crystallographic Information Framework (CIF) files for publication in various journals and HTML reports with embedded molecule graphics. These reports are available from the archive CD that is provided at the end of the experiment. This is important in cases where the instrument has collected data for manual processing, teaching of crystallographic methods or when a structure needs additional attention The embedded graphics of the HTML report allow interaction with the molecule – zoom, rotation, display of molecule surfaces, measuring of distances between atoms and much more. The graphics do not require any crystallographic software to be installed. The reports are ideal for easy dissemination of results and describe the experimental setup, software used during the structure elucidation, and provide tables with reliability criteria of the refined structure, as well as bond lengths and angles.

Detailed html reports and crystallographic information files (cif) facilitate the publication of results from x-ray crystallographic experiments.

For more information, visit: www.bruker.com/smartx2s

“We have successfully introduced the SMART X2S into an undergraduate organic labora-tory course. The instrument was used for the characterization of the crystallized sulfathiazole polymorphs and the structure determination of a tricyclic lactone, a product of the condensa-tion of citral and malonic acid that is difficult to characterize using physical methods like NMR and IR. Student response has been very enthusiastic!”

Prof. Nigam P. Rath, Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri - St. Louis

“The SMART X2S pushes X-ray crystallography into the realm of standard structure determina-tion tools that can be utilized on a daily basis, right alongside IR and NMR spectroscopy.”

Professor Glen Miller, Professor of Organic Chemistry and Materials Science at the University of New Hampshire

“We all are still surprised how seamless the automated integration software works. Even when we have to manually process the data set we are extremely satisfied with user-friendly APEX2 software package.”

Dr. Uwe Monkowius, Johannes Kepler University, Linz, Austria

“We now have instant access to this unam-biguous method and are able to determine 3D structures in our own lab within a few hours. The instrument delivers superb data and is very easy to use. The SMART X2S is absolutely vital to us!”

Prof. William G. Bornmann, Director of the Transla-tional Chemistry Core facility, MD Anderson Cancer Center Houston, Texas

Customer Testimonials

9

Mass Spectrometry

Customer Testimonials Setting New Standards in Performance and Value for LC/MS

Bruker’s new amaZon SL Ion Trap Mass Spectrometer is designed to dramati-cally enhance the analytical capabilities and productivity of laboratories involved with the analysis of a wide range of molecules. The amaZon SL delivers superior sensitivity and unmatched data acquisitions speed in combination with class leading mass resolution and overall robust performance, all at a value price.

The amaZon SL incorporates a number of key features which enhance its capabili-ties and value. These features include:

Class leading levels of sensitivity and mass accuracy Highly automated and intuitive

software to provide quick answers. Optimal and consistent molecular

fragmentation to aid in definitive compound identification Fast data acquisition speed at full

isotopic resolution in both MS and MS/MS for use with UHPLC. Unprecedented on-the-fly polarity

switching for the rapid, efficient analysis of diverse sets of compounds. Options for the analysis of Liquid

or Solid Samples Exceedingly low maintenance

requirements

Ideal for use in an Analytical Chemistry or Biochemistry teaching laboratory, espe-cially for monitoring and assessing the products, yield, and purity of chemical reactions or for studying proteins or gly-coproteins. The amaZon SL is especially designed with a combination of powerful instrumentation and intuitive software to facilitate sophisticated sample analysis, even by novice users.

Complete, Accurate Analysis and Compound Identification

The amaZon SL can utilize fragmentation analysis (MSn) which allows for more comprehensive compound identification or even de novo elucidation of molecular structures. Compounds can easily be analyzed and identified by comparing results with reference spectra stored in MSn libraries.

Intuitive Instrument Operation Modes

The SmartLine software suite provides extremely quick and easy access to ana-lytical answers. Smart and intuitive automation routines

for system calibration, tuning and data processing. Simplified GUI enables smooth and

easy instrument control Compass™ OpenAccess enables use

of the amaZon SL by non-expert users by enabling non MS-experts to run samples or batches using predefined methods with automated sample analysis and reporting.

For more information, visit: www.bruker.com/amazon

Direct Analysis of Organic Synthesis Reaction by amaZon SL to confirm molecular identity

Automated Data Analysis of Chemical Reaction Monitoring utilizing amaZon SL and Compass OpenAccess

amaZon SL

Figure 1

Figure 2

Infrared Spectroscopy

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Wavenumber cm-1

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Gas phase spectrum of HCl measured with the

ALPHA FT - IR spectrometer

R(0) P(1)

R(6)

P(7)

The ro - vibrational lines are split due to the chlorine 35 and chlorine

37 natural isotopic ratio of 3 : 1

SAMPLE WAS CONTAINED IN A

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Gas phase spectrum of HCl measured with theALPHA FT - IR spectrometer

R(0) P(1)

R(6)

P(7)

The ro - vibrational lines are split due to the chlorine 35 and chlorine37 natural isotopic ratio of 3 : 1

SAMPLE WAS CONTAINED IN A GLASS CELL

REFERENCE WAS THE OPEN CHANNEL

BROAD GLASS ABSORPTION BAND IS SEEN AS WELL

Analysis of Hydrogen Chloride Measured with the ALPHA FT-IR Spectrometer

Figure 1Fourier transform infrared spectrometers (FT-IR) currently used in colleges and universities have several limitations. Their size and complexity limit the number of students that can be accommodated. The instruments are not always rugged enough to stand up to tough handling by students. System maintenance and vali-dation of functionality require time man-agement and resources. Bruker’s ALPHA FT-IR spectrometer was designed from the ground up to address these con-cerns. It occupies about the footprint of text book, less than half the size of current academic instruments. It is the first instrument targeted to the academic market to offer a permanently aligned interferometer with a wear-free bearing.

Infrared spectroscopy is predicated upon the interaction of infrared radiation with asymmetric modes of vibration of molecules. The vapor phase of most spe-cies produces a characteristic spectrum based on its unique physical properties. Infrared spectroscopy can be used to determine these physical properties, in particular, the molecular structure and force constants of the chemical bonds. The vapor phase spectrum of a heteronuclear diatomic molecule (e.g., HCl) provides an excellent example that can be used to demonstrate these principles to students. When infrared radiation absorbed by a liquid or solid is measured, well-defined and unique regions of absorption can be attributed to excitation from the ground state to the first excited state in the middle infrared, typically 400–4000 cm–1. Additionally, the IR spectra of molecules in the gas phase show absorption bands of greater definition.

A Compact Benchtop FT-IR Spectrometer for the Academic Laboratory

The fine structure of these absorption bands can be attributed to changes in the rotational energy of the molecule accompanying the transition, as shown in Figure 1 for HCl. The quantum mechani-cal description of the harmonic oscillator can be used to approximate the mode of vibration for a heteronuclear diatomic molecule. For excitation in the mid-infrared, vibration transitions usually take place from the ground state (v = 0) to the first excited state (v = 1), where this simple model predicts just one vibration band for HCl. Additional energy levels in the gas phase are due to the rotational substructure and a quantum number J for the rotational energy is introduced. J takes integer values starting from 0, as shown in Figure 2. Thus, each vibration level has a manifold of rotational levels and transitions occur from v = 0 to v = 1 with J changing by +1 (so-called R branch lines) and J changing by –1 (so-called P branch lines). The rotational energies are given by BJ (J + 1), where B is the rota-tional constant. The determination of B yields molecular structure information or, in this simple case, the bond length.

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V=1

V=0

J=4

J=3

J=2

J=1

J=0

J=4

J=3

J=2

J=1

J=0

V=1

V=0

J=4

J=3

J=2

J=1

J=0

J=4

J=3

J=2

J=1

J=0

Figure 2

Vibrational and rotational energy levels for a diatomic molecule such as HCl. The spacing between V=0 and V=1 is much more than depicted. The R branch ro-vibrational lines are shown on the left and the P branch ro-vibrational lines are shown on the right. Only the first few J levels are shown.

ALPHAWorld‘s Smallest Laboratory FT-IR

Spectrometer

ALPHA with QuickSnap™ Accessories

ALPHA’s user exchangeable QuickSnap™ sampling modules allow the analysis of almost any kind of sample (e.g. solids, liquids or gases).

With a touch of a button, the accessory module can be dismounted from the instrument, without the need for any tools. The pre-aligned accessories can easily be connected to the ALPHA, and automatically be recognized.

Bruker offers various transmission, attenuated total reflection (ATR), external and diffuse reflection FT-IR sampling accessories.

These excellent experimental results are possible because of good line shape, signal-to-noise ratio, and precise fre-quency registration of the ALPHA FTIR spectrometer. The compactness, robust-ness, and ease of use of the spectrom-eter enable laboratories to teach more students the fundamentals of FTIR spec-trometry in less time than ever before. The economical FTIR spectrometer deliv-ers performance and repeatable results in an instrument that is designed to meet the needs of the academic market.

For more information, visit: ww.bruker.com/alpha

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www.bruker.com/academics

The development of a comprehensive college level course for implementa-tion into a curriculum is a labor intensive and difficult task to undertake. Couple this with the pressures of performing research, publishing papers, teaching existing classes, and in some cases vying for tenure, and the development of a new course becomes an almost insurmount-able task. Bruker has solved this problem with a complete college level course called Practical Powder Diffraction, based on our D2 PHASER desktop X-ray dif-fractometer.

The course comes with over 11 hours of course material, ranging from basic his-tory and applications of powder diffrac-tion through essential theory and finally hands-on experience with a real system! The syllabus is completely set up for the professor including time for each lecture and material. The course provides all of the slides needed to teach the course, as well as notes for the professor explaining the concepts to be taught on each slide. All content is professionally created and includes detailed diagrams and videos on theory, sample preparation, instrument operation and more.

However, a powder X-ray diffractioncourse without hands-on experience is not of much benefit. That is why Bruker has also included eight laboratory sessions with this course. These ses-sions span over 40 hours of intensive lab instruction covering basics, such as phase identification, as well as advanced analysis, such as structure refinement and solution. Bruker AXS provides all of the powder samples needed for the class as well! These powders come with full MSDS sheets and with enough material to cover at least three years of labs.

The ease of use of the system and soft-ware makes it ideal for teaching purposesand the data quality make it a research quality system as well. If you have ever wanted to teach a course in powder X-ray diffraction but just didn’t have the time to develop the course material, then the Practical Powder Diffraction course from Bruker is your answer.

For more information, visit: www.bruker.com/xrd

Practical Powder DiffractionTeaching Program

The Practical Powder Diffraction teaching program kit includes everything you need to teach three years of courses, all in a handy carrying case.