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.
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/9780199558964.003.0004
- Subject:
- Physics, Crystallography: Physics
Crystallographic databases collect some 300,000 structures, tens of thousands including one or more H-bonds. This impressive archive take in all varieties of inter- and intra-molecular H-bonds of any ...
More
Crystallographic databases collect some 300,000 structures, tens of thousands including one or more H-bonds. This impressive archive take in all varieties of inter- and intra-molecular H-bonds of any strength made by all possible atoms and can be asked any question on the H-bond nature provided we know how to do it. This chapter selects appropriate methods (crystal-structure correlations, Pauling's bond number, bond-number conservation, and Lippincott and Schroeder's method) and applies them to large sets of structural data representative of the most important H-bond classes. Particular attention is paid to strong O-H···O, N-H···N, and N-H···O/O-H···N resonance-assisted H-bonds (RAHBs) and their interpretation by different theoretical models. Three other classes of strong charge-assisted H-bonds (CAHBs) are identified and the H-bond classification is completed in six classes (the chemical leitmotifs). Results are interpreted in terms of electrostatic-covalent H-bond model (ECHBM) and PA/pKa equalization principle. A general equation linking H-bond energies and geometries is attempted.Less
Crystallographic databases collect some 300,000 structures, tens of thousands including one or more H-bonds. This impressive archive take in all varieties of inter- and intra-molecular H-bonds of any strength made by all possible atoms and can be asked any question on the H-bond nature provided we know how to do it. This chapter selects appropriate methods (crystal-structure correlations, Pauling's bond number, bond-number conservation, and Lippincott and Schroeder's method) and applies them to large sets of structural data representative of the most important H-bond classes. Particular attention is paid to strong O-H···O, N-H···N, and N-H···O/O-H···N resonance-assisted H-bonds (RAHBs) and their interpretation by different theoretical models. Three other classes of strong charge-assisted H-bonds (CAHBs) are identified and the H-bond classification is completed in six classes (the chemical leitmotifs). Results are interpreted in terms of electrostatic-covalent H-bond model (ECHBM) and PA/pKa equalization principle. A general equation linking H-bond energies and geometries is attempted.
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/9780199558964.003.0006
- Subject:
- Physics, Crystallography: Physics
The analysis performed in Chapters 3 and 4 leads to formulate a number of rules which can be considered the empirical laws governing the H-bond. The first is that H-bonds are not an undifferentiated ...
More
The analysis performed in Chapters 3 and 4 leads to formulate a number of rules which can be considered the empirical laws governing the H-bond. The first is that H-bonds are not an undifferentiated group but, conversely, need to be divided in classes according to their strength, mechanism of action, and modes of proton-exchange, acid-base association, and PA/pKa matching, the most important subdivision remaining that in six chemical leitmotifs (CLs), four of which collect all strong H-bonds known in nature. It is eventually concluded that the H-bond behaves as an interaction having a twofold nature (electrostatic and covalent) and a dual logic (two bonds formed by a same proton with two lone-pair donors) which, for these very reasons, is fully interpreted and rationalized in terms of VB theory (the electrostatic-covalent H-bond model) or general acid-base theory (the PA/pKa equalization principle).Less
The analysis performed in Chapters 3 and 4 leads to formulate a number of rules which can be considered the empirical laws governing the H-bond. The first is that H-bonds are not an undifferentiated group but, conversely, need to be divided in classes according to their strength, mechanism of action, and modes of proton-exchange, acid-base association, and PA/pKa matching, the most important subdivision remaining that in six chemical leitmotifs (CLs), four of which collect all strong H-bonds known in nature. It is eventually concluded that the H-bond behaves as an interaction having a twofold nature (electrostatic and covalent) and a dual logic (two bonds formed by a same proton with two lone-pair donors) which, for these very reasons, is fully interpreted and rationalized in terms of VB theory (the electrostatic-covalent H-bond model) or general acid-base theory (the PA/pKa equalization principle).
