developed to attain this knowledge by obtaining three dimensional structures. These
techniques, however, do not provide a direct view of the molecules in real space. To
overcome this drawback, atomic force microscope and inelastic tunneling probe
based on the scanning tunneling microscope are used to obtain real-space images of
the molecular structures and chemical bonds of mostly planar molecules [1, 2], and
absorbed molecules [3, 4], respectively. Very recently, Bredtmann et al. [5]
demonstrate how the chemically active valence electron densities can be directly
accessed from the full scattering patterns in order to reach information of how a
chemical reaction takes place and hence electronic bond-to-bond fluxes. The
degenerate Cope rearrangement of semibullvalene is selected as a working example. In addition, Kössl et al. [6] have followed the progress of the alcoholysis
reaction of phenylisocyanate with cyclohexanol and of 2,4-toluene-diisocyanate
with chloraldhydrate, by means of infrared absorption spectroscopy in combination
with anharmonic frequency calculations using density functional theory. The
measured infrared marker bands in the isocyanate NCO and alcohol OH stretching
region have been employed to in situ characterization of these reactions and in
particular for determination of Arrhenius activation energies. Bratos et al. [7],
describe the X-ray filming of the I 2 re-association in CCl 4 , comparing the experimental data with standard reaction rate theories. These authors emphasized that the
atomic motions must be followed even after the first “touch” of the reacting atoms
must, and by studying the earliest stages of a reaction process, designated collectively by the generic term “elementary chemical act”, is definitely becoming possible. Very recently, an international team, involving experimental and theoretical
researchers, has reported what it believes are the first direct measurements of
transition states where separate atoms can form a bond. In this work, fired X-rays at
molecules and atoms adsorbed onto a surface in a vacuum chamber are used, and
from the energy of a select portion of the X-rays scattered back, it is possible to
track how the electronic structure of each adsorbed atom changed as the reaction
progressed. The authors studied carbon monoxide oxidation on ruthenium as a well
known chemical reaction taking place in automobile catalytic converters [8]. In
addition, another team have also directly observed the formation of chemical bonds
using a femtosecond X-ray laser. The group used similar techniques to study the
formation of a gold trimer complex ([Au(CN) 2
−
] 3 ) from dissolving Au(CN) 2
− in
water. Both sets of researchers believe that analysing chemical bonds on such small
timescales will provide scientists with a tool to study the dynamics of complex
chemical and biological systems [9].
From the theoretical point of view, the emergence of molecular structure from
the complete molecular Hamiltonian is a very complex topic and interesting papers
on this subject have been published [10–16]. It is, with our present mathematical
understanding of quantum mechanics, impossible to solve any system which is
more complex than the hydrogen atom analytically in the sense of Schrödinger’s
quantum theory. Slightly larger systems may be solved to numerical accuracy, but
there is no hope to obtain the complete wave function for a chemically relevant
molecule. The problem of solving the quantum mechanical description of a number
258
J. Andrés et al.
techniques, however, do not provide a direct view of the molecules in real space. To
overcome this drawback, atomic force microscope and inelastic tunneling probe
based on the scanning tunneling microscope are used to obtain real-space images of
the molecular structures and chemical bonds of mostly planar molecules [1, 2], and
absorbed molecules [3, 4], respectively. Very recently, Bredtmann et al. [5]
demonstrate how the chemically active valence electron densities can be directly
accessed from the full scattering patterns in order to reach information of how a
chemical reaction takes place and hence electronic bond-to-bond fluxes. The
degenerate Cope rearrangement of semibullvalene is selected as a working example. In addition, Kössl et al. [6] have followed the progress of the alcoholysis
reaction of phenylisocyanate with cyclohexanol and of 2,4-toluene-diisocyanate
with chloraldhydrate, by means of infrared absorption spectroscopy in combination
with anharmonic frequency calculations using density functional theory. The
measured infrared marker bands in the isocyanate NCO and alcohol OH stretching
region have been employed to in situ characterization of these reactions and in
particular for determination of Arrhenius activation energies. Bratos et al. [7],
describe the X-ray filming of the I 2 re-association in CCl 4 , comparing the experimental data with standard reaction rate theories. These authors emphasized that the
atomic motions must be followed even after the first “touch” of the reacting atoms
must, and by studying the earliest stages of a reaction process, designated collectively by the generic term “elementary chemical act”, is definitely becoming possible. Very recently, an international team, involving experimental and theoretical
researchers, has reported what it believes are the first direct measurements of
transition states where separate atoms can form a bond. In this work, fired X-rays at
molecules and atoms adsorbed onto a surface in a vacuum chamber are used, and
from the energy of a select portion of the X-rays scattered back, it is possible to
track how the electronic structure of each adsorbed atom changed as the reaction
progressed. The authors studied carbon monoxide oxidation on ruthenium as a well
known chemical reaction taking place in automobile catalytic converters [8]. In
addition, another team have also directly observed the formation of chemical bonds
using a femtosecond X-ray laser. The group used similar techniques to study the
formation of a gold trimer complex ([Au(CN) 2
−
] 3 ) from dissolving Au(CN) 2
− in
water. Both sets of researchers believe that analysing chemical bonds on such small
timescales will provide scientists with a tool to study the dynamics of complex
chemical and biological systems [9].
From the theoretical point of view, the emergence of molecular structure from
the complete molecular Hamiltonian is a very complex topic and interesting papers
on this subject have been published [10–16]. It is, with our present mathematical
understanding of quantum mechanics, impossible to solve any system which is
more complex than the hydrogen atom analytically in the sense of Schrödinger’s
quantum theory. Slightly larger systems may be solved to numerical accuracy, but
there is no hope to obtain the complete wave function for a chemically relevant
molecule. The problem of solving the quantum mechanical description of a number
258
J. Andrés et al.