Gastone Gilli and Paola Gilli
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780199558964
- eISBN:
- 9780191720949
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199558964.003.0009
- Subject:
- Physics, Crystallography: Physics
Functional H-bonds are H-bonds which are significantly stronger than the surrounding ones and, for this reason, can play a specific role in the mechanism of action of important chemical or ...
More
Functional H-bonds are H-bonds which are significantly stronger than the surrounding ones and, for this reason, can play a specific role in the mechanism of action of important chemical or biochemical processes. This chapter reports a preliminary collection of these bonds organized in a graphic gallery of cases with little discussion, a collection of themes which have already been, or deserve to be, investigated to unravel the true role played by the H-bond in natural systems. Themes treated include: RAHB-driven processes (prototropic tautomerism in heteroconjugated systems, secondary structure of proteins, and DNA base pairing); H-bond-controlled crystal packing; bistable H-bonds in functional molecular materials (ferro/antiferroelectric crystals, excited-state proton transfer); low-barrier charge-assisted H-bonds in enzymatic catalysis (the catalytic triad of serine proteases; and proton transmission in water chains (Grotthuss mechanism, gramicidine A channel, aquaporin channels).Less
Functional H-bonds are H-bonds which are significantly stronger than the surrounding ones and, for this reason, can play a specific role in the mechanism of action of important chemical or biochemical processes. This chapter reports a preliminary collection of these bonds organized in a graphic gallery of cases with little discussion, a collection of themes which have already been, or deserve to be, investigated to unravel the true role played by the H-bond in natural systems. Themes treated include: RAHB-driven processes (prototropic tautomerism in heteroconjugated systems, secondary structure of proteins, and DNA base pairing); H-bond-controlled crystal packing; bistable H-bonds in functional molecular materials (ferro/antiferroelectric crystals, excited-state proton transfer); low-barrier charge-assisted H-bonds in enzymatic catalysis (the catalytic triad of serine proteases; and proton transmission in water chains (Grotthuss mechanism, gramicidine A channel, aquaporin channels).
Gastone Gilli and Paola Gilli
- Published in print:
- 2009
- Published Online:
- September 2009
- ISBN:
- 9780199558964
- eISBN:
- 9780191720949
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199558964.001.0001
- Subject:
- Physics, Crystallography: Physics
Hydrogen bond (H-bond) effects are well known: it makes sea water liquid, joins cellulose microfibrils in sequoia trees, shapes DNA into chromosomes, and polypeptide chains into wool, hair, muscles, ...
More
Hydrogen bond (H-bond) effects are well known: it makes sea water liquid, joins cellulose microfibrils in sequoia trees, shapes DNA into chromosomes, and polypeptide chains into wool, hair, muscles, or enzymes. However, its very nature is much less known and we may still wonder why O-H···O energies range from less than 1 to more than 30 kcal/mol without evident reason. This H-bond puzzle is tackled here by a new approach aimed to obtain full rationalization and comprehensive interpretation of the H-bond in terms of classical chemical-bond theories starting from the very root of the problem, an extended compilation of H-bond energies and geometries derived from modern thermodynamic and structural databases. From this analysis new concepts emerge: new classes of systematically strong H-bonds (CAHBs and RAHBs: charge- and resonance-assisted H-bonds); full H-bond classification in six classes (the chemical leitmotifs); assessment of the covalent nature of all strong H-bonds. This finally leads to three distinct though inter-consistent theoretical models able to rationalize the H-bond and to predict its strength which are based on the classical VB theory (electrostatic-covalent H-bond model, ECHBM), the matching of donor-acceptor acid-base parameters (PA/pKa equalization principle), and the shape of the H-bond proton-transfer pathway (transition-state H-bond theory, TSHBT). A number of important chemical and biochemical systems where strong H-bonds play an important functional role are surveyed, such as enzymatic catalysis, ion-transport through cell membranes, crystal packing, prototropic tautomerism, and molecular mechanisms of functional materials. Particular attention is paid to the drug-receptor binding process and to the interpretation of the enthalpy-entropy compensation phenomenon.Less
Hydrogen bond (H-bond) effects are well known: it makes sea water liquid, joins cellulose microfibrils in sequoia trees, shapes DNA into chromosomes, and polypeptide chains into wool, hair, muscles, or enzymes. However, its very nature is much less known and we may still wonder why O-H···O energies range from less than 1 to more than 30 kcal/mol without evident reason. This H-bond puzzle is tackled here by a new approach aimed to obtain full rationalization and comprehensive interpretation of the H-bond in terms of classical chemical-bond theories starting from the very root of the problem, an extended compilation of H-bond energies and geometries derived from modern thermodynamic and structural databases. From this analysis new concepts emerge: new classes of systematically strong H-bonds (CAHBs and RAHBs: charge- and resonance-assisted H-bonds); full H-bond classification in six classes (the chemical leitmotifs); assessment of the covalent nature of all strong H-bonds. This finally leads to three distinct though inter-consistent theoretical models able to rationalize the H-bond and to predict its strength which are based on the classical VB theory (electrostatic-covalent H-bond model, ECHBM), the matching of donor-acceptor acid-base parameters (PA/pKa equalization principle), and the shape of the H-bond proton-transfer pathway (transition-state H-bond theory, TSHBT). A number of important chemical and biochemical systems where strong H-bonds play an important functional role are surveyed, such as enzymatic catalysis, ion-transport through cell membranes, crystal packing, prototropic tautomerism, and molecular mechanisms of functional materials. Particular attention is paid to the drug-receptor binding process and to the interpretation of the enthalpy-entropy compensation phenomenon.
