Journal of Computational Chemistry & Molecular Modeling (JCCMM)
Proton Transfer Processes in Biological Reactions: A Computational ApproachSubmit Manuscript on this topic
Proton transfer (PT) reactions, in particular single (SPT), double (DPT) or multiple (MPT), are widespread phenomena in many branches of the life sciences. These reactions proceed through the transfer of the proton between donor and acceptor atoms, in some cases catalyzed by water molecules acting as a connector between these donor and acceptor atoms.
PT reactions are governed by the transition state (TS), a stationary point on the potential energy surface with one imaginary frequency that connects reagent and product. Notably, the position of the TS on the potential energy surface is the point most responsible for the definition of the pathway of the PT reaction. While PT reactions usually proceed over the activation barrier, it can be also possible to proceed under the barrier of the reaction: only through tunneling, when the proton energy levels for the initial and final states become equal. The activation barrier of the PT reaction thus defines the tautomeric equilibria and kinetic parameters, e.g. lifetime and rate constants.
It has been reliably found that the necessary and sufficient conditions for the successful tautomerization of the H-bonded complexes are:
• the presence of a local minimum on the surface of the potential (electronic) energy corresponding to the tautomerized complex;
• when the dynamic stability of the tautomerized complex, e.g. zero-point energy of the corresponding stretching vibration (whose frequency becomes imaginary in the TS of tautomerization) is less than the value of the reverse electronic barrier.
An investigation of PT processes and their different physico-chemical parameters, such as energetic (e.g., electronic and Gibbs free energies), geometric (e.g., distances and angles), polar (e.g., dipole moment), electron-topological (e.g., electron density or Laplacian of the electron density), and charge-based (e.g., NBO charges), are of utmost importance to better understand their internal essence. Moreover, this obtained data may be intensively applied to future scientific investigations into PT processes in the H-bonded complexes of any type and structure.
The elucidation of the height and shape of the PT energy barrier is also of great interest, as this data enables us to drive the PT processes or to predict their outcomes. As such, this Research Topic will thoroughly outline investigations into proton transfer processes in biologically significant reactions.
We welcome the submission of Original Articles, Reviews, or Perspectives on themes including, but not limited to:
• Theoretical (quantum-chemical calculations, Car-Parinello molecular dynamics etc.) or experimental (NMR, mass spectrometry, infrared spectroscopy etc.) investigation of PT reactions in diverse biomolecular systems (nucleic acids, DNA or RNA base pairs, biological membranes and membrane proteins, proteins, protein–DNA complexes, etc.) in different environments (aqueous media, biomolecular systems, materials, etc.);
• PT assisted by water molecules or coordinated by different chemical compounds, e.g., cisplatin etc.;
• Role of PT processes in the formation of the tautomers;
• Influence of the medium (e.g., hydration, solvation etc.) and physical fields (e.g., electric or magnetic etc.) on the PT processes;
• Quantum effects (e.g. proton tunneling) in the PT reactions.