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- Volume 1, 2008
Annual Review of Analytical Chemistry - Volume 1, 2008
Volume 1, 2008
- Preface
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A Personal Journey of Discovery: Developing Technology and Changing Biology
Vol. 1 (2008), pp. 1–43More LessThis autobiographical article describes my experiences in developing chemically based, biological technologies for deciphering biological information: DNA, RNA, proteins, interactions, and networks. The instruments developed include protein and DNA sequencers and synthesizers, as well as ink-jet technology for synthesizing DNA chips. Diverse new strategies for doing biology also arose from novel applications of these instruments. The functioning of these instruments can be integrated to generate powerful new approaches to cloning and characterizing genes from a small amount of protein sequence or to using gene sequences to synthesize peptide fragments so as to characterize various properties of the proteins. I also discuss the five paradigm changes in which I have participated: the development and integration of biological instrumentation; the human genome project; cross-disciplinary biology; systems biology; and predictive, personalized, preventive, and participatory (P4) medicine. Finally, I discuss the origins, the philosophy, some accomplishments, and the future trajectories of the Institute for Systems Biology.
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Spectroscopic and Statistical Techniques for Information Recovery in Metabonomics and Metabolomics
Vol. 1 (2008), pp. 45–69More LessMethods for generating and interpreting metabolic profiles based on nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and chemometric analysis methods are summarized and the relative strengths and weaknesses of NMR and chromatography-coupled MS approaches are discussed. Given that all data sets measured to date only probe subsets of complex metabolic profiles, we describe recent developments for enhanced information recovery from the resulting complex data sets, including integration of NMR- and MS-based metabonomic results and combination of metabonomic data with data from proteomics, transcriptomics, and genomics. We summarize the breadth of applications, highlight some current activities, discuss the issues relating to metabonomics, and identify future trends.
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Mass Spectrometry for Rapid Characterization of Microorganisms
Vol. 1 (2008), pp. 71–93More LessAdvances in instrumentation, proteomics, and bioinformatics have contributed to the successful applications of mass spectrometry (MS) for detection, identification, and classification of microorganisms. These MS applications are based on the detection of organism-specific biomarker molecules, which allow differentiation between organisms to be made. Intact proteins, their proteolytic peptides, and nonribosomal peptides have been successfully utilized as biomarkers. Sequence-specific fragments for biomarkers are generated by tandem MS of intact proteins or proteolytic peptides, obtained after, for instance, microwave-assisted acid hydrolysis. In combination with proteome database searching, individual biomarker proteins are unambiguously identified from their tandem mass spectra, and from there the source microorganism is also identified. Such top-down or bottom-up proteomics approaches permit rapid, sensitive, and confident characterization of individual microorganisms in mixtures and are reviewed here. Examples of MS-based functional assays for detection of targeted microorganisms, e.g., Bacillus anthracis, in environmental or clinically relevant backgrounds are also reviewed.
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Scanning Electrochemical Microscopy
Vol. 1 (2008), pp. 95–131More LessThis review describes work done in scanning electrochemical microscopy (SECM) since 2000 with an emphasis on new applications and important trends, such as nanometer-sized tips. SECM has been adapted to investigate charge transport across liquid/liquid interfaces and to probe charge transport in thin films and membranes. It has been used in biological systems like single cells to study ion transport in channels, as well as cellular and enzyme activity. It is also a powerful and useful tool for the evaluation of the electrocatalytic activities of different materials for useful reactions, such as oxygen reduction and hydrogen oxidation. SECM has also been used as an electrochemical tool for studies of the local properties and reactivity of a wide variety of materials, including metals, insulators, and semiconductors. Finally, SECM has been combined with several other nonelectrochemical techniques, such as atomic force microscopy, to enhance and complement the information available from SECM alone.
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Novel Detection Schemes of Nuclear Magnetic Resonance and Magnetic Resonance Imaging: Applications from Analytical Chemistry to Molecular Sensors
Vol. 1 (2008), pp. 133–163More LessNuclear magnetic resonance (NMR) is a well-established analytical technique in chemistry. The ability to precisely control the nuclear spin interactions that give rise to the NMR phenomenon has led to revolutionary advances in fields as diverse as protein structure determination and medical diagnosis. Here, we discuss methods for increasing the sensitivity of magnetic resonance experiments, moving away from the paradigm of traditional NMR by separating the encoding and detection steps of the experiment. This added flexibility allows for diverse applications ranging from lab-on-a-chip flow imaging and biological sensors to optical detection of magnetic resonance imaging at low magnetic fields. We aim to compare and discuss various approaches for a host of problems in material science, biology, and physics that differ from the high-field methods routinely used in analytical chemistry and medical imaging.
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Chemical Cytometry: Fluorescence-Based Single-Cell Analysis
Vol. 1 (2008), pp. 165–190More LessCytometry deals with the analysis of the composition of single cells. Flow and image cytometry employ antibody-based stains to characterize a handful of components in single cells. Chemical cytometry, in contrast, employs a suite of powerful analytical tools to characterize a large number of components. Tools have been developed to characterize nucleic acids, proteins, and metabolites in single cells. Whereas nucleic acid analysis employs powerful polymerase chain reaction–based amplification techniques, protein and metabolite analysis tends to employ capillary electrophoresis separation and ultrasensitive laser-induced fluorescence detection. It is now possible to detect yoctomole amounts of many analytes in single cells.
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Chemical Analysis of Single Cells
Vol. 1 (2008), pp. 191–227More LessChemical analysis of single cells requires methods for quickly and quantitatively detecting a diverse array of analytes from extremely small volumes (femtoliters to nanoliters) with very high sensitivity and selectivity. Microelectrophoretic separations, using both traditional capillary electrophoresis and emerging microfluidic methods, are well suited for handling the unique size of single cells and limited numbers of intracellular molecules. Numerous analytes, ranging from small molecules such as amino acids and neurotransmitters to large proteins and subcellular organelles, have been quantified in single cells using microelectrophoretic separation techniques. Microseparation techniques, coupled to varying detection schemes including absorbance and fluorescence detection, electrochemical detection, and mass spectrometry, have allowed researchers to examine a number of processes inside single cells. This review also touches on a promising direction in single cell cytometry: the development of microfluidics for integrated cellular manipulation, chemical processing, and separation of cellular contents.
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Ion Chemistry in the Interstellar Medium
Vol. 1 (2008), pp. 229–259More LessWe present an overview of the interstellar medium, including physical and chemical conditions, spectroscopic observations, and current challenges in characterizing interstellar chemistry. Laboratory studies of ion-atom reactions, including experimental approaches and instrumentation, are described. We also tabulate and discuss comprehensive summaries of ion-neutral reactions involving hydrogen, nitrogen, and oxygen atoms that have been studied since Sablier and Rolando's 1993 review.
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Plasma Diagnostics for Unraveling Process Chemistry
Vol. 1 (2008), pp. 261–291More LessThis review focuses on the use of diagnostic tools to examine plasma processing chemistry, primarily plasma species energetics, dynamics, and molecule-surface reactions. We describe the use of optical diagnostic tools, mass spectrometry, and Langmuir probes in measuring species densities, rotational and kinetic energies, and plasma-surface reactions. Molecule-surface interactions for MXn species (M = C, Si, N; X = H, F, Cl) are presented and interpreted with respect to the molecule's electronic configuration and dipole moments.
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Biomolecule Analysis by Ion Mobility Spectrometry
Vol. 1 (2008), pp. 293–327More LessAlthough nonnative protein conformations, including intermediates along the folding pathway and kinetically trapped misfolded species that disfavor the native state, are rarely isolated in the solution phase, they are often stable in the gas phase, where macromolecular ions from electrospray ionization can exist in varying charge states. Differences in the structures of nonnative conformations in the gas phase are often large enough to allow different shapes and charge states to be separated because of differences in their mobilities through a gas. Moreover, gentle collisional activation can be used to induce structural transformations. These new structures often have different mobilities. Thus, there is the possibility of developing a multidimensional separation that takes advantage of structural differences of multiple stable states. This review discusses how nonnative states differ in the gas phase compared with solution and presents an overview of early attempts to utilize and manipulate structures in order to develop ion mobility spectrometry as a rapid and sensitive technique for separating complex mixtures of biomolecules prior to mass spectrometry.
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In Vitro Electrochemistry of Biological Systems
Vol. 1 (2008), pp. 329–355More LessThis article reviews recent work involving electrochemical methods for in vitro analysis of biomolecules, with an emphasis on detection and manipulation at and of single cells and cultures of cells. The techniques discussed include constant potential amperometry, chronoamperometry, cellular electroporation, scanning electrochemical microscopy, and microfluidic platforms integrated with electrochemical detection. The principles of these methods are briefly described, followed in most cases with a short description of an analytical or biological application and its significance. The use of electrochemical methods to examine specific mechanistic issues in exocytosis is highlighted, as a great deal of recent work has been devoted to this application.
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Current Applications of Liquid Chromatography/Mass Spectrometry in Pharmaceutical Discovery After a Decade of Innovation
Vol. 1 (2008), pp. 357–396More LessCurrent drug discovery involves a highly iterative process pertaining to three core disciplines: biology, chemistry, and drug disposition. For most pharmaceutical companies the path to a drug candidate comprises similar stages: target identification, biological screening, lead generation, lead optimization, and candidate selection. Over the past decade, the overall efficiency of drug discovery has been greatly improved by a single instrumental technique, liquid chromatography/mass spectrometry (LC/MS). Transformed by the commercial introduction of the atmospheric pressure ionization interface in the mid-1990s, LC/MS has expanded into almost every area of drug discovery. In many cases, drug discovery workflow has been changed owing to vastly improved efficiency. This review examines recent trends for these three core disciplines and presents seminal examples where LC/MS has altered the current approach to drug discovery.
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Optical Probes for Molecular Processes in Live Cells
Vol. 1 (2008), pp. 397–421More LessIn this review, I summarize the development over the past several years of fluorescent and/or bioluminescent indicators to pinpoint cellular processes in living cells. These processes involve second messengers, protein phosphorylations, protein-protein interactions, protein-ligand interactions, nuclear receptor–coregulator interactions, nucleocytoplasmic trafficking of functional proteins, and protein localization.
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Cell Culture Models in Microfluidic Systems
Vol. 1 (2008), pp. 423–449More LessMicrofluidic technology holds great promise for the creation of advanced cell culture models. In this review, we discuss the characterization of cell culture in microfluidic systems, describe important biochemical and physical features of the cell microenvironment, and review studies of microfluidic cell manipulation in the context of these features. Finally, we consider the integration of analytical elements, ways to achieve high throughput, and the design constraints imposed by cell biology applications.
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Peptides in the Brain: Mass Spectrometry–Based Measurement Approaches and Challenges
Vol. 1 (2008), pp. 451–483More LessThe function and activity of almost every circuit in the human brain are modified by the signaling peptides (SPs) surrounding the neurons. As the complement of peptides can vary even in adjacent neurons and their physiological actions can occur over a broad range of concentrations, the required figures of merit for techniques to characterize SPs are surprisingly stringent. In this review, we describe the formation and catabolism of SPs and highlight a range of mass spectrometric techniques used to characterize SPs. Approaches that supply high chemical information content, direct tissue profiling, spatially resolved data, and temporal information on peptide release are also described. Because of advances in measurement technologies, our knowledge of SPs has greatly increased over the last decade, and SP discoveries will continue as the capabilities of modern measurement approaches improve.
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Analysis of Atmospheric Aerosols
Vol. 1 (2008), pp. 485–514More LessAerosols represent an important component of the Earth's atmosphere. Because aerosols are composed of solid and liquid particles of varying chemical complexity, size, and phase, large challenges exist in understanding how they impact climate, health, and the chemistry of the atmosphere. Only through the integration of field, laboratory, and modeling analysis can we begin to unravel the roles atmospheric aerosols play in these global processes. In this article, we provide a brief review of the current state of the science in the analysis of atmospheric aerosols and some important challenges that need to be overcome before they can become fully integrated. It is clear that only when these areas are effectively bridged can we fully understand the impact that atmospheric aerosols have on our environment and the Earth's system at the level of scientific certainty necessary to design and implement sound environmental policies.
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Multiplexed Spectroscopic Detections
Vol. 1 (2008), pp. 515–547More LessThis review describes various platforms used for multiplexed spectroscopic analysis. We highlight the use of different types of spectroscopy for multiplexed detections, including Raman spectroscopy, surface-enhanced Raman spectroscopy, surface plasmon resonance, and fluorescence. This review also explores the use of cross-reactive sensors in combination with pattern-recognition algorithms to monitor multiple analytes in aqueous and vapor matrices. It also discusses applications of these techniques, paying special attention to their use in the detection of biologically relevant analytes.
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Terrestrial Analysis of the Organic Component of Comet Dust*
Vol. 1 (2008), pp. 549–578More LessThe nature of cometary organics is of great interest, both because these materials are thought to represent a reservoir of the original carbon-containing materials from which everything else in our solar system was made and because these materials may have played key roles in the origin of life on Earth. Because these organic materials are the products of a series of universal chemical processes expected to operate in the interstellar media and star-formation regions of all galaxies, the nature of cometary organics also provides information on the composition of organics in other planetary systems and, by extension, provides insights into the possible abundance of life elsewhere in the universe. Our current understanding of cometary organics represents a synthesis of information from telescopic and spacecraft observations of individual comets, the study of meteoritic materials, laboratory simulations, and, now, the study of samples collected directly from a comet, Comet P81/Wild 2.
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High-Resolution Mass Spectrometers
Vol. 1 (2008), pp. 579–599More LessOver the past decade, mass spectrometry has been revolutionized by access to instruments of increasingly high mass-resolving power. For small molecules up to ∼400 Da (e.g., drugs, metabolites, and various natural organic mixtures ranging from foods to petroleum), it is possible to determine elemental compositions (CcHhNnOoSsPp…) of thousands of chemical components simultaneously from accurate mass measurements (the same can be done up to 1000 Da if additional information is included). At higher mass, it becomes possible to identify proteins (including posttranslational modifications) from proteolytic peptides, as well as lipids, glycoconjugates, and other biological components. At even higher mass (∼100,000 Da or higher), it is possible to characterize posttranslational modifications of intact proteins and to map the binding surfaces of large biomolecule complexes. Here we review the principles and techniques of the highest-resolution analytical mass spectrometers (time-of-flight and Fourier transform ion cyclotron resonance and orbitrap mass analyzers) and describe some representative high-resolution applications.
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Surface-Enhanced Raman Spectroscopy
Vol. 1 (2008), pp. 601–626More LessThe ability to control the size, shape, and material of a surface has reinvigorated the field of surface-enhanced Raman spectroscopy (SERS). Because excitation of the localized surface plasmon resonance of a nanostructured surface or nanoparticle lies at the heart of SERS, the ability to reliably control the surface characteristics has taken SERS from an interesting surface phenomenon to a rapidly developing analytical tool. This article first explains many fundamental features of SERS and then describes the use of nanosphere lithography for the fabrication of highly reproducible and robust SERS substrates. In particular, we review metal film over nanosphere surfaces as excellent candidates for several experiments that were once impossible with more primitive SERS substrates (e.g., metal island films). The article also describes progress in applying SERS to the detection of chemical warfare agents and several biological molecules.
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Time-Resolved Microdialysis for In Vivo Neurochemical Measurements and Other Applications
Vol. 1 (2008), pp. 627–661More LessMonitoring changes in chemical concentrations over time in complex environments is typically performed using sensors and spectroscopic techniques. Another approach is to couple sampling methods, such as microdialysis, with chromatographic, electrophoretic, or enzymatic assays. Recent advances of such coupling have enabled improvements in temporal resolution, multianalyte capability, and automation. In a sampling and analysis method, the temporal resolution is set by the mass sensitivity of the analytical method, analysis time, and zone dispersion during sampling. Coupling methods with high speed and mass sensitivity to microdialysis sampling help to reduce some of these contributions to yield methods with temporal resolution of seconds. These advances have been primarily used in monitoring neurotransmitters in vivo. This review covers the problems associated with chemical monitoring in the brain, recent advances in using microdialysis for time-resolved in vivo measurements, sample applications, and other potential applications of the technology such as determining reaction kinetics and process monitoring.
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Applications of Ultrafast Lasers for Optical Measurements in Combusting Flows*
Vol. 1 (2008), pp. 663–687More LessOptical measurement techniques are powerful tools for the detailed study of combustion chemistry and physics. Although traditional combustion diagnostics based on continuous-wave and nanosecond-pulsed lasers continue to dominate fundamental combustion studies and applications in reacting flows, revolutionary advances in the science and engineering of ultrafast (picosecond- and femtosecond-pulsed) lasers are driving the enhancement of existing diagnostic techniques and enabling the development of new measurement approaches. The ultrashort pulses afforded by these new laser systems provide unprecedented temporal resolution for studies of chemical kinetics and dynamics, freedom from collisional-quenching effects, and tremendous peak powers for broad spectral coverage and nonlinear signal generation. The high pulse-repetition rates of ultrafast oscillators and amplifiers allow previously unachievable data-acquisition bandwidths for the study of turbulence and combustion instabilities. We review applications of ultrafast lasers for optical measurements in combusting flows and sprays, emphasizing recent achievements and future opportunities.
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Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry for the Investigation of Proteins and Peptides
Vol. 1 (2008), pp. 689–705More LessMass spectrometry (MS) is an excellent technology for molecular imaging because of its high data dimensionality. MS can monitor thousands of individual molecular data channels measured as mass-to-charge (m/z). We describe the use of matrix-assisted laser desorption/ionization (MALDI) MS for the image analysis of proteins, peptides, lipids, drugs, and metabolites in tissues. We discuss the basic instrumentation and sample preparation methods needed to produce high-resolution images and high image reproducibility. Matrix-addition protocols are briefly discussed along with normal operating procedures, and selected biological and medical applications of MALDI imaging MS are described. We give examples of both two- and three-dimensional imaging, including normal mouse embryo implantation, sperm maturation in mouse epididymis, protein distributions in brain sections, protein alterations as a result of drug administration, and protein changes in brain due to neurodegeneration and tumor formation. Advantages of this technology and future challenges for its improvement are discussed.
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Formation and Characterization of Organic Monolayers on Semiconductor Surfaces
Vol. 1 (2008), pp. 707–736More LessOrganic-semiconductor interfaces are playing increasingly important roles in fields ranging from electronics to nanotechnology to biosensing. The continuing decrease in microelectronic device feature sizes is raising an especially great interest in understanding how to integrate molecular systems with conventional, inorganic microelectronic materials, particularly silicon. The explosion of interest in the biological sciences has provided further impetus for learning how to integrate biological molecules and systems with microelectronics to form true bioelectronic systems. Organic monolayers present an excellent opportunity for surmounting many of the practical barriers that have hindered the full integration of microelectronics technology with organic and biological systems. Of all the semiconductor materials, silicon and diamond stand out as unique. This review focuses upon the preparation and characterization of organic and biomolecular layers on semiconductor surfaces, with special emphasis on monolayers formed on silicon and diamond.
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Nanoscopic Porous Sensors
Vol. 1 (2008), pp. 737–766More LessThere are thousands of different nanometer-scale pores in biology, many of which act as sensors for specific chemical agents. Recent work suggests that protein and solid-state nanopores have many potential uses in a wide variety of analytical applications. In this review we survey this field of research and discuss the prospects for advances that could be made in the near future.
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Combining Self-Assembled Monolayers and Mass Spectrometry for Applications in Biochips
Vol. 1 (2008), pp. 767–800More LessBiochip arrays have enabled the massively parallel analysis of genomic DNA and hold great promise for application to the analysis of proteins, carbohydrates, and small molecules. Surface chemistry plays an intrinsic role in the preparation and analysis of biochips by providing functional groups for immobilization of ligands, providing an environment that maintains activity of the immobilized molecules, controlling nonspecific interactions of analytes with the surface, and enabling detection methods. This review describes recent advances in surface chemistry that enable quantitative assays of a broad range of biochemical activities. The discussion emphasizes the use of self-assembled monolayers of alkanethiolates on gold as a structurally well-defined and synthetically flexible platform for controlling the immobilization and activity of molecules in an array. The review also surveys recent methods of performing label-free assays, and emphasizes the use of matrix-assisted laser desorption/ionization mass spectrometry to directly observe molecules attached to the self-assembled monolayers.
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Liposomes: Technologies and Analytical Applications
Aldo Jesorka, and Owe OrwarVol. 1 (2008), pp. 801–832More LessLiposomes are structurally and functionally some of the most versatile supramolecular assemblies in existence. Since the beginning of active research on lipid vesicles in 1965, the field has progressed enormously and applications are well established in several areas, such as drug and gene delivery. In the analytical sciences, liposomes serve a dual purpose: Either they are analytes, typically in quality-assessment procedures of liposome preparations, or they are functional components in a variety of new analytical systems. Liposome immunoassays, for example, benefit greatly from the amplification provided by encapsulated markers, and nanotube-interconnected liposome networks have emerged as ultrasmall-scale analytical devices. This review provides information about new developments in some of the most actively researched liposome-related topics.
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Fundamentals of Protein Separations: 50 Years of Nanotechnology, and Growing
Vol. 1 (2008), pp. 833–855More LessThe separation of proteins in biology samples has long been recognized as an important and daunting endeavor that continues to have enormous impact on human health. Today's technology for protein separations has its origins in the early nanotechnology of the 1950s and 1960s, and the methods include immunoassays and other affinity extractions, electrophoresis, and chromatography. What is different today is the need to resolve and identify many low-abundance proteins within complex biological matrices. Multidimensional separations are the rule, high speed is needed, and the separations must be able to work with mass spectrometry for protein identification. Hybrid approaches that combine disparate separation tools (including recognition, electrophoresis, and chromatography) take advantage of the fact that no single class of separation can resolve the proteins in a biological matrix. Protein separations represent a developing area technologically, and understanding the principles of protein separations from a molecular and nanoscale viewpoint will enable today's researchers to invent tomorrow's technology.
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Functional and Spectroscopic Measurements with Scanning Tunneling Microscopy
Vol. 1 (2008), pp. 857–882More LessInvented as a surface analytical technique capable of imaging individual atoms and molecules in real space, scanning tunneling microscopy (STM) has developed and advanced into a technique able to measure a variety of structural, functional, and spectroscopic properties and relationships at the single-molecule level. Here, we review basic STM operation and image interpretation, techniques developed to manipulate single atoms and molecules with the STM to measure functional properties of surfaces, local spectroscopies used to characterize atoms and molecules at the single-molecule level, and surface perturbations affecting surface coverage and surface reactions. Each section focuses on determining the identity and function of chemical species so as to elucidate information beyond topography with STM.
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Coherent Anti-Stokes Raman Scattering Microscopy: Chemical Imaging for Biology and Medicine
Vol. 1 (2008), pp. 883–909More LessCoherent anti-Stokes Raman scattering (CARS) microscopy is a label-free imaging technique that is capable of real-time, nonperturbative examination of living cells and organisms based on molecular vibrational spectroscopy. Recent advances in detection schemes, understanding of contrast mechanisms, and developments of laser sources have enabled superb sensitivity and high time resolution. Emerging applications, such as metabolite and drug imaging and tumor identification, raise many exciting new possibilities for biology and medicine.
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