Bio-active molecules in the gas phase

It should not be necessary to explain to living creatures the motivation for studying the structures and dynamics of bio-active molecules—as T. H. Huxley observed in 1860, ‘Vital forces are molecular forces’. Some of the more sceptical however, particularly those working in the life sciences, might query the rationale for their study in the gas phase—often at temperatures (and pressures) far below those of any viable metabolic system. So why choose the gas phase? Quite simply, because it allows ‘disaggregation’—the perturbations introduced by the local environment and experienced by the biomolecule can first be eliminated altogether and then controlled, and manipulated, for example through control of the number of bound water molecules, or selected metal ions, or protons, or other biomolecules. By adopting a reductionist approach, carefully designed experiments can be used to build up systematically, a picture of the relative importance of all the factors, both intra- and inter-, which affect biomolecular conformation, shape, molecular interactions, dynamics and ultimately, function, to provide key information through which their structure and function in the condensed phase, and eventually in biomolecular assemblies and in vivo, can be understood.

Not too many years ago, the idea of exploring the structure and dynamics of the molecules and molecular complexes involved in the biochemistry and biophysics of living organisms—hormones and neurotransmitters; amino acids, peptides and proteins; DNA bases, nucleosides and nucleic acids; sugars, oligosaccharides and glycoconjugates—isolated in the gas phase, was at best, an exotic notion. Now it has become anything but exotic and the volume of published experimental and computational research is growing at an ever-increasing rate. Its rapidly accelerating expansion has been fuelled by its relationship to pharmaceutical science, molecular biology and molecular medicine and aided by many technological developments. These include, for example:

 • increasingly selective, mostly laser-based spectroscopic strategies which lead to the structural assignment of individually resolved molecular conformers and complexes and very recently, to the experimental determination of the energy barriers that separate them;

 • ultra-fast kinetic spectroscopic strategies which enable determination of the rates of intramolecular decay processes, or of proton, electron or energy transfer;

 • Fourier transform ion cyclotron resonance mass spectroscopy, which allows measurements to be made at unprecedented levels of mass resolution and enables the study of peptide sequences and protein equilibria;

 • most important of all, is the advent of reliable (Nobel winning) methods which allow the ready transfer of ‘robust’ and ‘fragile’ biomolecules, both large and small, and their molecular complexes to be made almost routinely from the condensed (solid or solution) phase into the gas phase (even complete viruses!), while avoiding massive fragmentation.

The smaller molecules (typically <1 kDa), such as neurotransmitters, or protein receptor site blockers, or the ‘building blocks’ of the much larger biopolymer systems-peptides and proteins, nucleic acids, polysaccharides, glycopeptides and glycolipids—can be seeded into cold, free jet expansions as neutral molecules or molecular or hydrated complexes, using laser evaporation or micro-oven sources. Ionisation, proton transfer and ion trapping techniques are also available now, for their generation and concentration into sufficient number densities to allow their spectroscopic detection as cationic, protonated or cationised ions, or of valence or dipole bound anions.

Large (≥1 kDa) singly and multiply charged protonated, or cationised biopolymers, as well as their complexes and hydrated clusters can be transferred directly into the gas phase, using matrix assisted laser desorption/ionization (MALDI) or electrospray ionization (ESI) sources, to create populations of free or hydrated molecular ions or complexes, subsequently analysed using high resolution mass spectroscopy. Their overall shapes (collision cross-sections) and binding energies can be determined through ion mobility and ion equilibria measurements (in temperature controlled drift tubes); H/D exchange and black body infrared radiative dissociation (BIRD) measurements can provide indirect structural information.

The increasing availability of ever more powerful theoretical approaches, computer codes and computer hardware to run them, which has developed (and continues to develop) in parallel with each of these instrumental developments, has promoted a synergistic interaction between experimental measurement and ab initio (or molecular mechanics) calculation. Each one supports the other to allow quantitative interpretation of grossly under-determined experimental information.

New developments in the optical spectroscopy of molecular ions in the gas phase, particularly the use of ion traps and storage rings, are beginning to provide a bridge linking the fields of mass spectrometry (and the study of biopolymers and much higher molecular masses) and optical spectroscopy. The range of actual, or possible optical spectroscopic measurements now runs from the ultra-violet and visible, through the near, mid- and far infrared regions, into the THz region, where structural studies and the dynamics of co-operative motions in large molecules meet, and for small molecules, into the millimetre and microwave region. The first efforts at linking experimental measurements of isolated, clustered and solvated bioactive molecules in the gas phase, to their structure and physical behaviour in the condensed phase, are just beginning to appear. The following collection of Special Issue articles provides a flavour of the new set of links developing at the interface between the physical, computational and bio-sciences, and some of the excitement that is being generated by the intense and competitive pace of this lively field of research.

J. P. Simons, University of Oxford

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