Analogies and Metaphors
Instrumentation is used as an extension of the senses to "see" how atoms and molecules behave.
Using the "black box" activity as a class activity shows inductive reasoning as an analogy to what is done when using instrumentation. The "black box" in this case is a box that contains a single, simple object such as a cylinder, a ring, a cube, and soforth. The object is placed in the box and sealed with tape. The student's task is to build a model in terms of some object whose behavior is well understood as being an explanation of the behavior of the object in the box. The student is allowed any "experiment" that does not damage the box or its contents. (This activity is similar to the Obscertainer Kit activity in the Atomic Structure module.)
A systematic way to carry out this activity is to ask a question, design an "experiment" to answer the question, make the observation, and then formulate an assumption on the basis of the observation. For example, the question might be, "Does the object roll or slide?" The "experiment" then would be to carefully tilt the box in various directions while listening carefully. The next step is to record what is heard-either it rolls or slides or it may roll in one direction and slide in the perpendicular direction. The assumption then would be that the object rolls in all directions or rolls in one direction and slides in another, depending upon what is heard. After a series of such steps, the student should be able to describe an object that is a good model of the object in the box. Of course, intrinsic attributes such as color cannot be determined this way; however, using a magnet as an "instrument" would allow the decision about whether the object is magnetically susceptible or not.
CEPUP, Chemical Education for Public Understanding Program, developed by the Lawrence Hall of Science of the University of California at Berkeley, is a modular approach to developing scientific literacy in the general population. Although it is directed toward students in middle/junior high schools, there is an activity in the "Determining Threshold Limits" module that would be a good student activity to illustrate why instrumentation is essential to the chemist. The activity involves diluting food coloring until it is no longer visible to the unaided eye. Then, instrumentation must be used to detect the presence of the coloring material (refer to Equipment and Instrumentation for additional information).
The Basic Principle of Spectroscopy
The principle behind all absorption spectroscopic methods-microwave, ultraviolet, visible, infrared, NMR-is the same. It involves resonant absorption of energy by different systems. A good analogy is that of a small boat in water resonating to the frequency of a water wave that is related to the length (or beam width) of the boat. The small boat will rock most violently in response to a wave that is about the length of the boat. The length of the wave is determined by the wave's frequency.
What in a molecule absorbs energy? It depends upon the energy of the quanta being absorbed. Lower energy quanta affect the rotational motion of molecules as a whole. An HCl molecule, for example, will rotate about its center of mass upon absorbing a sufficiently energetic quantum of energy. But just like electronic energy, rotational energy is quantized, that is, there are only certain allowed rotational energy levels. Generally, rotational quanta have frequencies that fall in the microwave region of the electromagnetic spectrum. Molecules can also vibrate either by stretching or bending the bonds. Thus, molecules may absorb energy affecting these motions.
A good analogy for this vibration type is two spherical masses suspended by threads and connected together by springs. Consider two such spheres of equal mass. When connected together by a stiff spring, the masses vibrate at a greater frequency than when connected by a less stiff spring. Similarly, for the same spring, spheres with smaller masses will vibrate at a greater frequency than more massive spheres. The spring stiffness is analogous to the stiffness of a chemical bond.
Pictures in the Mind
How do scientists obtain knowledge of molecular structure details? The following brief descriptions of instrumental techniques, although not exhaustive, give some idea how this information is obtained. These techniques play a large role in developing "pictures in the mind" of molecular structure. Gas chromatography is discussed in Pictures in the Mind in the Separations module. Specific applications of several instrumental techniques are presented in Links and Connections in the Forensic Chemistry module.
Infrared Spectroscopy (IR)
"Pictures in the mind" are useful in understanding infrared spectroscopy. When ball-and- spring models are used to represent molecules, the spring is a good model for the behavior of the chemical bond between two atoms. Molecules absorb infrared radiation at wavelengths 1.5x10 4 to 2.5x10 3 nm. These wavelengths correspond to frequencies of 2x10 13 to 12x10 13 Hz. An analysis of the energy of the radiation shows that the absorptions are associated with the excitation of vibrational motions. These to and fro motions of atoms at opposite ends of a chemical bond occur at natural frequencies just like the natural frequency of a ball-and-spring model. The masses of the atoms in the molecule, the shape of the molecule, and the strengths of the chemical bonds fix the natural vibrational frequencies.
Knowing the molecular formula and analyzing frequencies, provides information about the molecular moments of inertia, the molecular geometry, and the chemical bonds. Infrared spectroscopy works with gaseous, liquid, and solid compounds. It may also be used to "identify" compounds. The IR spectrum of gaseous HBr and DBr (deuterium bromide with the H in HBr replaced with heavy hydrogen, D) is shown in Transparency Masters in the Appendix (see References , Pimentel, 1963, p. 249.) The only difference between the two spectra is that in DBr, the absorption is shifted to a higher frequency (shorter wavelength) due to the greater mass of the D atom. Otherwise, the absorption patterns are basically the same. More complicated molecules have more detailed spectra, but the spectrum for each molecule is so characteristic that it may be used to detect the presence of the particular substance.
Nuclear Magnetic Resonance Spectroscopy (NMR)
In 1945, Felix Block (Stanford University) and Edward M. Purcell (Harvard University) independently observed an interesting phenomenon concerning the magnetic moments of matter. When a magnetic field is applied to some types of matter, the atomic nuclei in the sample align their spin axes in certain definite orientations. Since that time the significance of Nuclear Magnetic Resonance (NMR) has reached extraordinary proportions. Because of its multiple roles in both chemical and biological sciences, NMR is one of the fastest growing and most widely used instrumental technologies.
Due to the properties of mass and charge, nuclei appear to behave as magnets. These nuclei are also spinning, and the spinning electric charges generate magnetic fields. When an external magnetic field is applied, interaction occurs with the nuclei. Hydrogen is such a nucleus.
There are two possible orientations for a spinning proton (H) in the nucleus of an atom; it may be aligned either with or against the external magnetic field. It is possible to measure the frequency of the electromagnetic radiation (radio waves) required to change the orientation of the proton from one magnetic dipole to another, resulting in a net absorption of energy by the hydrogen nuclei. When the energy absorbance is measured, an NMR spectrum of the sample can be obtained.
Since the magnetic field is held constant during NMR experiments, each nucleus requires a different radio frequency (called a chemical shift) for resonance to occur. Graphically, the x-axis of the NMR spectrum is the frequency difference between the unknown compound and a reference compound. The y-axis corresponds to the relative number of nuclei absorbing energy at a given radiofrequency.
The NMR spectrum in Transparency Masters in the Appendix was obtained for the compound (ethyl acetate) whose structural formula is shown.
The triplet peak (three-line group) is derived from the CH 3 group on the right of the molecule. The singlet peak is derived from the CH 3 group at the left side of the molecule, and the quartet peak (four-line group) is derived from the CH 2 group near the center of the molecule. If the functional groups present in the molecule are known, then the structure may be determined.
NMR spectroscopy is widely used in medicine. Magnetic Resonance Imaging (MRI) is the term used to describe the application of the principles of NMR spectroscopy to scan internal tissues of living organisms, including human beings. MRI can be done on almost any part of the body. Its applicability depends on the resonance of water molecules, and it can be used to determine the water content of tissue in the body. MRI is a nonintrusive procedure. It does not involve the use of harmful radiation such as X-rays, nor are dyes and pigments needed. MRI, by revealing the chemical composition and the density of tissues within the body, can allow physicians to diagnose any abnormalities that may be present in these tissues.
Perhaps the best application of MRI is for imaging parts of the nervous system. Lesions and tumors of the brain and spinal cord are shown with excellent resolution. MRI is also excellent in studying disorders of the circulatory system, eye, and musculo-skeletal system. One of the interesting facts is that prior to using MRI, it must be definitely established that there are no iron chips or splinters in the subject's eyes. If any iron fragments are present, then grave damage to the eye, even blindness, might occur. This would happen because the very strong magnetic field used with the technique would literally rip the iron fragment out of the eye. Depending upon the size of the fragment, it could simply puncture the eyeball or literally cause it to explode. The disadvantages of MRI are the costs of instrumentation, electrical energy used to run the instrument, and the training of the scientists to use it. MRI promises to be one of the most useful techniques for medicine in the future.
NMR is already an indispensable tool for scientists in chemistry, biology, and medicine. Its importance cannot be overemphasized. Applications of the technique by chemists have revolutionized chemistry. The technique is influencing research fields in biochemistry, materials research, geochemistry, botany, physiology, and medical sciences. Unfortunately, along with the improvement of NMR instrumentation, the cost of the increases in its utility have been almost exponential. In thirty years, the cost of commercial instruments has risen from about $55,000 to about $850,000.
X-ray Diffraction
X-rays have frequencies near 10 18 Hz and wavelengths near 10 -1 nm. X-rays can be deflected in regular patterns from parallel planes of a crystal with similar dimensions. The resulting pattern is either photographed or detected electronically. The pattern is determined by the spacing of the atoms or particles in the crystal and their spatialarrangement. X-rays are used since the scattering effects only occur when the wavelengths of the radiation are of similar dimensions to the particle separations within the crystal. The patterns produced are unique to the crystalline material being examined and thus serve as a tool for definitive identification and structure determination. Because of the complexity of X-ray data, the availability of computers has significantly facilitated their analysis.
Mass Spectrometry
In mass spectrometry, a gaseous ion is accelerated to a known kinetic energy by an electrical field. The ion's mass can be measured either by tracking its curved trajectory through a magnetic field or by its time of flight over a fixed distance to the detector. The production of molecular ions causes some fragmentation of molecules and gives a collection of ions. The masses of ions are determined by the structural units in the original molecule. A mass spectrum of CF 3 -CH 3 will include a mass peak for the parent ion (CF 3 -CH 3 ) + at 84 u. It also includes mass peaks at 15 u and 69 u due to (CH 3 ) + and (CF 3 ) + , respectively. These are logical structural subunits of the parent molecule. Thus, the mass spectrum gives more information than just the molar mass of the original molecule. (Actually, many more mass peaks would be observed due to other fragmentation patterns of the molecule; however, these were not mentioned for the sake of simplicity.)
Mass spectrometers are frequently coupled in tandem with other instruments, to obtain specific information about the components in mixtures. When coupled with a gas chromatograph, the mass spectrometer provides one of the best general purpose analytical instruments available. The combination has application in chemical, biological, geological, environmental, and crime laboratories.
An overhead transparency illustrating the operation of a mass spectrograph is included in the Appendix. The transparency shows the separation of neon into its three primary isotopes.
Other
There are other instrumental methods besides those previously discussed. Of particular note are lasers and computers coupled with instrumentation. Synchrotron light sources (X-rays), free-electron lasers, neutron diffraction, electron spin resonance, Raman spectra, electron diffraction, and other instrumental techniques also are widely used in chemical research. The electron and scanning electron microscope also play a role in chemical research. The newest microscope, scanning tunneling microscope (STM), is reported to be able to "see" and "feel" contours of atomic and molecular surfaces.
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