REVIEW Mass Spectrometry of Self-Assembled Monolayers: A New Tool for Molecular Surface Science Milan Mrksich* Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60521 he scientific and engineering disci- T plines have developed sophisti- ABSTRACT Most reactions can be performed in solution and on a surface, yet the challenges faced in applying cated toolboxes for making mat- known reactions or in developing entirely new reactions for modifying surfaces remain formidable. The products ter—including examples from organic of many reactions performed in solution can be characterized in minutes, and even products having complex chemistry to create small molecules with structures can be characterized in hours. When performed on surfaces, even the most basic reactions require a virtually unlimited complexity, molecular bi- ology to prepare macromolecules with a substantial effort—requiring several weeks—to characterize the yields and structures of the products. This precise arrangement of amino acids and a contrast stems from the lack of convenient analytical tools that provide rapid information on the structures of defined tertiary structure, and lithographic molecules attached to a surface. This review describes recent work that has established mass spectrometry as a methods to fashion inorganic and metallic powerful method for developing and characterizing a broad range of chemical reactions of molecules attached to materials into integrated circuits and de- self-assembled monolayers of alkanethiolates on gold. The SAMDI-TOF mass spectrometry technique will enable a vices. Each of these approaches is based on next generation of applications of molecularly defined surfaces to problems in chemistry and biology. distinct methods for assembling matter, and each relies on analytical methods that KEYWORDS: biochip · interfacial reactions · label-free · self-assembled can characterize the structures that they monolayer · SAMDI-TOF mass spectrometry generate. In the bottom-up approaches common to synthetic chemistry, a range of methods including NMR and X-ray diffrac- tion are used to delineate the connectivity layer membranes.3 This review deals with of atoms within molecules. The biopolymers the analogous challenge of characterizing created using enzyme-mediated conver- the molecular structures of organic surfaces. sions are characterized using electro- The development of self-assembled mono- phoretic methods and high-resolution mass layers (SAMs) has, in principle, made it spectrometry, while integrated circuits are straightforward to functionalize surfaces characterized with electron microscopy, with a broad range of molecular composi- Downloaded via NORTHWESTERN UNIV on June 24, 2020 at 21:00:34 (UTC). scanning probe tools, and sensitive spec- tions to enable applications in biology and troscopies. The tools remain fundamental chemistry.4 Yet, the common methods used to each of these areas, enabling further ad- See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles. in surface analysis do not have the resolu- vances in the preparation of their respective tion and sensitivity required to analyze targets. complex molecular compositions and, in The pursuit of structures with at least turn, have limited efforts to pursue the de- one dimension sized between 1 and 100 sign and application of surfaces to these ar- nm—which underlies the nanoscience and eas. In this review, the recent development technology discipline that has grown over of mass spectrometric methods that are en- the past decade—is likewise dependent on abling applications of surface science in analytical methods, and in several cases it chemistry and biology is described. The re- *Address correspondence to has been hampered by a lack of methods view begins with an overview of the current [email protected]. 1 having appropriate performance. For ex- methods that are broadly available, a de- Received for review December 10, 2007 ample, it remains difficult to characterize scription of recent work that expands the and accepted December 17, 2007. the products resulting from treatment of scope of surfaces that can be analyzed, and Published online January 22, 2008. proteins or carbon nanotubes with organic provides examples that illustrate the im- 10.1021/nn7004156 CCC: $40.75 reagents,2 and it is still difficult to character- pact that these methods are having in the ize the dynamic structures of lipid rafts in bi- biological and chemical sciences. © 2008 American Chemical Society www.acsnano.org VOL. 2 ▪ NO. 1 ▪ 7–18 ▪ 2008 7 ANALYTICAL METHODS IN SURFACE SCIENCE molecules in a monolayer.9 Yet, the skills and facili- Atomic Composition—The UHV Toolbox. Several surface ties required to perform these measurements limit analytical techniques have been developed and now their use to a relatively small number of aficionados. provide a remarkable set of tools for the analysis of me- Atomic and lateral force microscopies that use a tallic and inorganic surfaces; these were recently high- scanning probe to image the forces with a substrate lighted with the award of the 2007 Nobel Prize in Chem- are now widely available and provide straightfor- istry to Gerhard Ertl. These methods offer exceptional ward characterization of the shapes, sizes, and sensitivity in characterizing the atomic composition and chemical properties of patterned nanostructures.10 structure of clean substrates and in turn have been criti- The extension of these methods with scanning REVIEW cal to developing materials and probes that are functionalized with chemical or bio- processes in semiconductor fab- logical molecules are enabling unprecedented stud- VOCABULARY: mass spectrometry –an rication—in part for their high ies of the properties of individual proteins with new analytical technique that measures the mass- sensitivity in measuring the insights into the roles of force in biology.11,12 Clearly, to-charge ratio of ions; a means of detecting densities of impurities and these methods have provided powerful tools for molecules according to their molecular weight dopants—and to understand- characterizing the shapes, mechanics, and proper- • self-assembled monolayer – a nanoscale ing the mechanisms of hetero- ties of nanoscale structures, but they do not provide two-dimensional structure consisting of a geneous catalytic processes.5,6 general routes for the molecular characterization of single layer of molecules on a substrate; An excellent survey of these complex interfaces. important for modifying the physical methods is provided in the text Molecular Structure—The Chemistry Toolbox. The introduc- 7 properties of a surface • biochip –anarrayof by Adamson and Gast. In- tion of SAMs—including alkylsiloxanes on oxide sub- peptides, proteins, or other molecules that can cluded is X-ray photoelectron strates and alkanethiolates on the coinage metals— be treated with samples to identify spectroscopy (XPS), where a made it possible to display organic molecules and carry protein–protein interactions and enzyme monoenergetic X-ray source is out reactions of those molecules at surfaces.13,14 These activities • SAMDI – the combination of self- used to eject inner-shell elec- advances gave way to a substantial body of work that assembled monolayers and matrix-assisted trons that are then analyzed to emphasized the need for surface analytical methods laser desorption/ionization mass spectrometry, quantitatively identify the com- that could provide information on the molecular struc- which permits rapid characterization of the position of elements comprising ture—in contrast to information on elemental composi- masses of alkanethiolates in a monolayer; a surface. Electron diffraction tion described above—of monolayers. Several meth- useful for characterizing chemical and and ion scattering methods are ods have been important to identifying molecular biochemical reactions at surfaces powerful methods for charac- fragments, or functional groups, including grazing terizing the structures of or- angle infrared spectroscopy and secondary-ion mass dered surfaces. A variety of optical methods—includ- spectroscopy (SIMS). The latter identifies masses of mo- ing ellipsometry and surface plasmon resonance (SPR) lecular fragments that derive from the high-energy spectroscopy—measure changes in refractive index to photodissociation of molecules at the surface. The data provide information on the amount of molecules local- can be analyzed to derive important information on ized at the interface. the molecular surface structure, but they are compli- It is clear that these methods were and remain criti- cated, and the technique is not routinely applied by the cal to the physics and fabrication of electronic struc- non-expert.15 tures and to surfaces used in catalysis—which have Needs in Molecular Surface Science. The preceding discus- relatively simple elemental structure and oftentimes sion points to a clear disconnection between current rely on dopants present at low concentrations. Yet, they surface analysis tools and applications in the chemical are less valuable for analyzing surfaces that are func- and biological sciences. Whereas the bulk characteriza- tionalized with complex chemical or biopolymeric tion of organic and biological macromolecules is now structures. In these cases, it is the connectivity of the at- routine, these methods cannot be applied to the small oms into molecules, and changes in this