Single molecule vibrational chemistry

Spectroscopies with SPMs are being developed rapidly. The ability to study isolated or small structures of adsorbates has allowed incredible insight into the rich chemistry of surfaces, particularly the defining roles that defect-sites play. The recent demonstrations of single molecule vibrational spectroscopies with the STM and NSOM have further opened up new avenues for investigation. 

Pascual JI, Lorente N, Song Z, Conrad H, Rust HP (2003) Selectivity in vibrationally mediated single-molecule chemistry. Nature 423 525... 

Keywords Vibrational spectroscopy scanning tunneling microscopy and spectroscopy conductance inelastic conductance single-molecule chemistry controlled manipulation mode-selective reactivity. 

In this chapter, we review important concepts regarding vibrational spectroscopy with the STM. First, the basis of the technique will be introduced, together with some of the most relevant results produced up to date. It will be followed by a short description of experimental issues. The third section introduces theoretical approaches employed to simulate the vibrational excitation and detection processes. The theory provides a molecular-scale view of excitation processes, and can foresee the role of various parameters such as molecular symmetry, adsorption properties, or electronic structure of the adsorbate. Finally, we will describe current approaches to understand quenching dynamics via internal molecular pathways, leading to several kinds of molecular evolution. This has been named single-molecule chemistry. 

The few experiments available to date about single-molecule chemistry have provided a different view of understanding the complexities behind excitation and relaxation of vibrational in adsorbates. Certainly, more than a tool for technological processing, it will develop concepts and strategies for selectively studying catalytic reactions. 

Part V focuses on single molecule chemistry at metal surfaces. Herein the chapter by S. W. Hla and K. Braun describes how the STM can be used to induce single molecule reactions, starting from bond breaking all the way to bond formation. The chapter by N. Lorente deals with atomic scale vibrational spectroscopy studies and how they allow to obtain chemical information on individual molecules. 

The level of theory necessary to correctly model vibrational spectra is a lively topic in modern ab initio chemistry and has been discussed on a number of occasions.The reader is referred to some of these papers for discussion of calculated spectra in single molecules. The present discussion focuses on application to H-bonded complexes. 

Shaul Mukamel, who is currently the C. E. Kenneth Mees Professor of Chemistry at the University of Rochester, received his Ph.D. in 1976 from Tel Aviv University, follot by postdoctoral appointments at MIT and the University of California at Berkeley and faculty positions at the Weizmann Institute and at Rice University. He has b n the recipient of the Sloan, Dreyfus, Guggenheim, and Alexander von Humboldt Senior Scientist awards. His research interests in theoretical chemical physics and biophysics include developing a density matrix Liouville-space approach to femtosecond spectroscopy and to many body theory of electronic and vibrational excitations of molecules and semiconductors multidimensional coherent spectroscopies of sbucture and folding dynamics of proteins nonlinear X-ray and single molecule spectroscopy electron transfer and energy ftrnneling in photosynthetic complexes and Dendrimers. He is the author of over 400 publications in scientific journals and of the textbook. Principles of Nonlinear OfMical Spectroscopy (Oxford University Press), 1995. 

Vibrational spectroscopy has been, and will continue to be, one of the most important teclmiques in physical chemistry. In fact, the vibrational absorption of a single acetylene molecule on a Cu(lOO) surface was recently reported [ ]. Its endurance is due to the fact that it provides detailed infonnation on structure, dynamics and enviromnent. It is employed in a wide variety of circumstances, from routine analytical applications, to identifying novel (often transient) species, to providing some of the most important data for advancing the understanding of intramolecular and intemiolecular interactions. 

The usefulness of quantum-chemical methods varies considerably depending on what sort of force field parameter is to be calculated (for a detailed discussion, see [46]). There are relatively few molecular properties which quantum chemistry can provide in such a way that they can be used directly and profitably in the construction of a force field. Quantum chemistry does very well for molecular bond lengths and bond angles. Even semiempirical methods can do a good job for standard organic molecules. However, in many cases, these are known with sufficient accuracy a C-C single bond is 1.53 A except under exotic circumstances. Similarly, vibrational force constants can often be transferred from similar molecules and need not be recalculated. 

Adenine as an isolated molecule has no symmetry elements and therefore might mathematically be considered chiral however, as in the case of glycine (Section 1.2.1), this description is not useful in chemistry since the enantiomers differ only by inversion through the weakly pyramidal nitrogen atom of the amine functionality, the main body of the molecule being planar. The inversion corresponds to a low-frequency vibration and a low-energy barrier such that single enantiomers... 

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