7 Biologically Relevant Molecules Studied in Low Temperature Inert Matrices
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many biosynthetic mechanisms, including that of AtP [8]. Protein folding is also
controlled by the conformations of the constituting amino acids.
ultimately, the energetically-accessible spatial arrangements of the atoms in the
molecules (or, in other terms, the conformations assumed by the molecules), determine the physical and chemical properties of substances and their biological functions. the many structural and conformational studies already performed on small
molecules constitute nowadays a basis for the understanding of the conformational
behavior of the complex biomolecular systems. this fact also stresses the relevance
of such studies, in particular when they focus on molecules that are building blocks
of biological macromolecules ( e.g., amino acids, nucleic acids bases) and can be
performed under precisely controlled conditions, such as those achievable for a
molecule isolated in a low temperature inert matrix.
7.2 The Matrix Isolation Method
matrix isolation is a technique where gaseous atoms and molecules are trapped
in an environment of solidified inert gases at temperatures close to absolute zero.
the method was originally used to study free radicals and other short-lived chemical reaction intermediates, but receives nowadays many other uses. By combining
this trapping technique with different spectroscopic detection methods a powerful
research tool has evolved, which is being applied in many laboratories worldwide
in a large number of research areas.
the matrix isolation method was first developed almost simultaneously by the
groups of Pimentel, at Berkeley (uSA), and Porter, at Cambridge (uK) [9, 10]. the
name of the method was coined in the historical paper by Pimentel, Whittle and
dows “Matrix Isolation Method for the Experimental Study of Unstable Species”,
a single-page paper which appeared in the Journal of Chemical Physics, in 1954
[9]. very interestingly, matrix isolation only started to become popular among
organic chemists almost 20 years later, after publication of 3 papers, nearly at
the same time, by three different groups, where the experimental observation of
the hitherto elusive cyclobutadiene was reported. Cyclobutadiene was produced
photochemically in situ in inert argon matrices containing the precursor α-pyrone
[11–13]. α-Pyrone was found to undergo a fast photoequilibration with its isomeric
open-ring aldehyde-ketene and a much slower ring closure to a bicyclo β-lactone
(the α-pyrone Dewar isomer), which in turn eliminated CO 2 to give cyclobutadiene
(Fig. 7.1). As mentioned above, at that time cyclobutadiene had never been experimentally characterized, and these studies received great impact among the scientific
community.
though matrix isolation was invented as a tool for studies of reactive species,
the method has also some advantages over other techniques for the study of stable
molecules, and has been used extensively for this purpose too. In general, matrix
isolation is useful when we are interested (i) to observe directly and characterize
181
many biosynthetic mechanisms, including that of AtP [8]. Protein folding is also
controlled by the conformations of the constituting amino acids.
ultimately, the energetically-accessible spatial arrangements of the atoms in the
molecules (or, in other terms, the conformations assumed by the molecules), determine the physical and chemical properties of substances and their biological functions. the many structural and conformational studies already performed on small
molecules constitute nowadays a basis for the understanding of the conformational
behavior of the complex biomolecular systems. this fact also stresses the relevance
of such studies, in particular when they focus on molecules that are building blocks
of biological macromolecules ( e.g., amino acids, nucleic acids bases) and can be
performed under precisely controlled conditions, such as those achievable for a
molecule isolated in a low temperature inert matrix.
7.2 The Matrix Isolation Method
matrix isolation is a technique where gaseous atoms and molecules are trapped
in an environment of solidified inert gases at temperatures close to absolute zero.
the method was originally used to study free radicals and other short-lived chemical reaction intermediates, but receives nowadays many other uses. By combining
this trapping technique with different spectroscopic detection methods a powerful
research tool has evolved, which is being applied in many laboratories worldwide
in a large number of research areas.
the matrix isolation method was first developed almost simultaneously by the
groups of Pimentel, at Berkeley (uSA), and Porter, at Cambridge (uK) [9, 10]. the
name of the method was coined in the historical paper by Pimentel, Whittle and
dows “Matrix Isolation Method for the Experimental Study of Unstable Species”,
a single-page paper which appeared in the Journal of Chemical Physics, in 1954
[9]. very interestingly, matrix isolation only started to become popular among
organic chemists almost 20 years later, after publication of 3 papers, nearly at
the same time, by three different groups, where the experimental observation of
the hitherto elusive cyclobutadiene was reported. Cyclobutadiene was produced
photochemically in situ in inert argon matrices containing the precursor α-pyrone
[11–13]. α-Pyrone was found to undergo a fast photoequilibration with its isomeric
open-ring aldehyde-ketene and a much slower ring closure to a bicyclo β-lactone
(the α-pyrone Dewar isomer), which in turn eliminated CO 2 to give cyclobutadiene
(Fig. 7.1). As mentioned above, at that time cyclobutadiene had never been experimentally characterized, and these studies received great impact among the scientific
community.
though matrix isolation was invented as a tool for studies of reactive species,
the method has also some advantages over other techniques for the study of stable
molecules, and has been used extensively for this purpose too. In general, matrix
isolation is useful when we are interested (i) to observe directly and characterize