J. C. Dobrowolsk et al.
84
5.1 Introduction
Feynman, in his Lectures on Physics, invoked a poet’s metaphor that “The whole
universe is in a glass of wine” [1]; it would be organically self-evident, yet maybe
more prosaic, if he had added “and a piece of camembert”. A piece of camembert,
looked at closely enough, mirrors the universe’s age and the evolution of stars as
well as a glass of wine does, but the complexity of phase equilibria, fermentation, the
evolution of living creatures, and chirality—the mysterious source of life, would be
seen immediately. Also, the presence of mathematics in a piece of camembert is evident not only in Euclidean chirality, displayed by amino acids as a quaternary protein
structure, but also in the mathematical logic and combinatorics of primary protein
structure, the universal algebra of biochemical processes, and both the discrete and
continuous topology of molecular manifolds. here, we shall focus on the basis of
this diversity: the individual natural α-amino acids in a native, aqueous environment.
usually, the primary importance of amino acids is recognised in their role as the
building blocks of proteins fundamental to the cell structure and function of every
living organism. However, each free and single α-amino acid at the physiological pH
of an organism also plays a fundamental role in maintaining the vital functions of the
organism. the vibrational Circular dichroism (vCd) and Raman optical Activity
(ROA) spectroscopy of the α-amino acid molecules reviewed in this chapter refer
only to free and single amino acids in water at various ph levels. the purpose of this
review is to provide an up-to-date perspective on the capability of vCd and RoA to
solve the problems of structures for chiral molecules in the solution state. however, to
understand the implications of such studies for biology and medicine, we devote subchapter 2 to the role of free amino acids in an organism’s metabolism and physiology.
the presence of basic amino and acidic carboxy groups attached to the same
carbon atom in an α-amino acid molecule, after dissolution in water, results in the
dissociation of these groups and leads to the formation of a zwitterionic form which
usually predominates. however, the 20 amino acids encoded by the standard genetic code have a variety of side chains equipped with additional functional groups
that modify the amino acid character from acidic to basic and from hydrophilic to
hydrophobic. this makes the possible dissociation equilibria of amino acids dissolved in water very complex and dependent on several factors. this is why we
summarised information on dissociation constants, isoelectric points, and hydrophobicity parameters of α-amino acids in subchapter 3.
the conformational variety of structures is significant even for small amino acids. Indeed, for neutral valine, 19 structures have been found to be stable, yet, for
lysine and arginine, as many as 391 and 520 conformers have been found, respectively [2]. therefore, even for small amino acids, the interpretation of vibrational
spectra requires quantum chemical analysis. the complexity of interactions and
equilibria occurring for amino acids in aqueous solutions makes considering the
influence of the solution on structure and vibrational spectra absolutely necessary.
this is why we provide the reader with subchapter 4, describing elements of the
theory of chiroptical vibrational spectra and methods enabling solvent simulations.
having covered the general fundamentals of amino acids and vibrational spectroscopy, the focus of subchapter 5.5 shifts to vCd and RoA results for amino acids.
84
5.1 Introduction
Feynman, in his Lectures on Physics, invoked a poet’s metaphor that “The whole
universe is in a glass of wine” [1]; it would be organically self-evident, yet maybe
more prosaic, if he had added “and a piece of camembert”. A piece of camembert,
looked at closely enough, mirrors the universe’s age and the evolution of stars as
well as a glass of wine does, but the complexity of phase equilibria, fermentation, the
evolution of living creatures, and chirality—the mysterious source of life, would be
seen immediately. Also, the presence of mathematics in a piece of camembert is evident not only in Euclidean chirality, displayed by amino acids as a quaternary protein
structure, but also in the mathematical logic and combinatorics of primary protein
structure, the universal algebra of biochemical processes, and both the discrete and
continuous topology of molecular manifolds. here, we shall focus on the basis of
this diversity: the individual natural α-amino acids in a native, aqueous environment.
usually, the primary importance of amino acids is recognised in their role as the
building blocks of proteins fundamental to the cell structure and function of every
living organism. However, each free and single α-amino acid at the physiological pH
of an organism also plays a fundamental role in maintaining the vital functions of the
organism. the vibrational Circular dichroism (vCd) and Raman optical Activity
(ROA) spectroscopy of the α-amino acid molecules reviewed in this chapter refer
only to free and single amino acids in water at various ph levels. the purpose of this
review is to provide an up-to-date perspective on the capability of vCd and RoA to
solve the problems of structures for chiral molecules in the solution state. however, to
understand the implications of such studies for biology and medicine, we devote subchapter 2 to the role of free amino acids in an organism’s metabolism and physiology.
the presence of basic amino and acidic carboxy groups attached to the same
carbon atom in an α-amino acid molecule, after dissolution in water, results in the
dissociation of these groups and leads to the formation of a zwitterionic form which
usually predominates. however, the 20 amino acids encoded by the standard genetic code have a variety of side chains equipped with additional functional groups
that modify the amino acid character from acidic to basic and from hydrophilic to
hydrophobic. this makes the possible dissociation equilibria of amino acids dissolved in water very complex and dependent on several factors. this is why we
summarised information on dissociation constants, isoelectric points, and hydrophobicity parameters of α-amino acids in subchapter 3.
the conformational variety of structures is significant even for small amino acids. Indeed, for neutral valine, 19 structures have been found to be stable, yet, for
lysine and arginine, as many as 391 and 520 conformers have been found, respectively [2]. therefore, even for small amino acids, the interpretation of vibrational
spectra requires quantum chemical analysis. the complexity of interactions and
equilibria occurring for amino acids in aqueous solutions makes considering the
influence of the solution on structure and vibrational spectra absolutely necessary.
this is why we provide the reader with subchapter 4, describing elements of the
theory of chiroptical vibrational spectra and methods enabling solvent simulations.
having covered the general fundamentals of amino acids and vibrational spectroscopy, the focus of subchapter 5.5 shifts to vCd and RoA results for amino acids.