The Nature of the Hydrogen Bond Outline of a Comprehensive Hydrogen Bond Theory

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ISBN: 9780199558964 | 0199558965
Cover: Hardcover
Copyright: 8/25/2009

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Hydrogen bond (H-bond) effects are known: it makes sea water iquid, joins cellulose microfibrils in trees, shapes DNA nto genes and polypeptide chains into wool, hair, muscles or enzymes. Its true nature is less known and we may still wonder why O-H...O bond energies range from less than 1 to more than 30 kcal/mol without apparent reason. This H-bond puzzle is re-examined here from its very beginning and presented as an inclusive compilation of experimental H-bond energies and geometries. New concepts emerge from this analysis: new classes of systematically strong H-bonds (CAHBs and RAHBs: charge- and resonance-assisted H-bonds); full H-bond classification in six classes (the six chemical leitmotifs); and assessment of the covalent nature of strong H-bonds. This leads to three distinct but inter-consistent models able to rationalize the H-bond and predict its strength, based on classical VB theory, matching of donor-acceptor acid-base parameters (PA or pKa), or shape of the H-bond proton-transfer pathway. Applications survey a number of systems where strong H-bonds play an important functional role, namely drug-receptor binding, enzymatic catalysis, ion-transport through cell membranes, crystal design and molecular mechanisms of functional materials.

Introduction	p. 1
A Century of the hydrogen bond (H-bond)	p. 6
The discovery of the H-bond	p. 6
The theoretical understanding of the H-bond	p. 7
The experimental approach to the H-bond	p. 13
Significant books and reviews	p. 19
Generalities, definitions and preliminary classification	p. 23
Basic H-bond nomenclature	p. 23
Formal H-bond definitions	p. 23
The H-bond as a shared-proton interaction: A Chemical classification	p. 28
H-bonds involving main-group elements (Class 1)	p. 30
Conventional H-bonds (Groups 1.1)	p. 31
Weak H-bonds: General properties (Groups 1.2-4)	p. 32)
Treatment of H...A contact distances	p. 35
H-bond directionality	p. 36
Importance of crystal-packing patterns	p. 38
Weak H-bond donors (Group 1.2)	p. 38
C-H... bonds	p. 40
S-H... bonds	p. 42
P-H... bonds	p. 42
Si-H, As-H and Se-H... bonds	p. 43
Weak H-bond acceptors (Group 1.3)	p. 44
C-Hal (Hal=F, Cl, Br) as acceptors	p. 44
S, Se and Te as acceptors	p. 44
P, As and Sb as acceptors	p. 45
C as acceptor	p. 46
Weak acceptors (Group 1.4)	p. 47)
H-bonds involving metal centers (Class 2)	p. 49
Metals as H-bond donors (Group 2.1)	p. 50
Metals as H-bond acceptors (Group 2.2)	p. 53
Metal hydrides as H-bond acceptors or dihydrogen bond (DHB) (Group 2.3)	p. 53
DHB to main-group hydrides	p. 54
DHB to transition-metal hydrides	p. 56
Metal ligands as H-bond donors or acceptors (Groups 2.4-5)	p. 56
H-bond classification by physical properties: Weak, moderate, and strong H-bonds	p. 59
Correlation among physical descriptors: The Problem of the driving variable	p. 60
Modelling the H-bond by Crystallographic methods	p. 65
Crystallographic databases and structural correlation	p. 65
A survey of structural databases	p. 65
Crystal-structure correlation (CSC) methods	p. 68
Bond lengths, bond energies and bond-number conservation rule	p. 71
Bond lengths, energies and numbers	p. 71
Bond-number conservation rule	p. 72
The Lippincott and Schroeder H-bond model (LS-HB)	p. 75
A new class of H-bonds: An introduction	p. 81
Cooperative H-bonds: An Introduction	p. 81
Evidence for RAHB from CSC studies of ?-diketone enols	p. 84
A survey of CSC results	p. 84
RAHB interpretation: The ionic model	p. 89
RAHB interpretation: The resonant model	p. 91
Appendix 3A: RAHB as a cybernetic effector	p. 100
Apendix 3B: RAHB as a state-correlation diagram	p. 100
Appendix 3C: RAHB electron effective-mass model	p. 103
RAHB generalization and systematics	p. 108
RAHB generalization	p. 108
Intra-and intermolecular O-H...O RAHB	p. 111
Intramolecular N-H...N RAHB	p. 121
Heteronuclear X-H...y RAHB	p. 122
Completing the H-bond classification: The Chemical leitmotifs analysis of the O-H...O system	p. 147
A full H-bond classification from the systematic analysis of the O-H...O system	p. 147
A full CSD analysis of the O-H...O System	p. 147
Interpreting the O-H...O system: The electrostatic-covalent H-bond model	p. 155
Interpreting the O-H...O system: The PA/PKa equalization principle	p. 159
CAHB generalization to other homnuclear X-H...X bonds	p. 161
CAHB generalization to heteronuclear X-H...Y bonds	p. 163
CAHB geometry-energy relationships	p. 163
Modelling the H-bond by thermodynamic methods	p. 168
Introduction	p. 168
The use of ?PA and?OKa indicators in H-bond studies	p. 168
PA and PKa definitions	p. 168
Proton-transfer and proton-sharing H-bonds	p. 170
Computing ?PA and ?PKa values: The problem of ?PA evaluation	p. 171
The use of PA and PKa as predictors of the H-bond strength: A summary	p. 173
Predicting (-)CAHB and (+)CAHB strengths from enthaply versus proton affinity correlations	p. 174
?H°DIS against ?PA correlations	p. 174
A Verification of the PA equalization principle	p. 175
Predicting H-bond strengths from crystal geometry versus PKa correlations	p. 177
PKa tables for the most common H-bond donors and acceptors	p. 177
The PKa slide rule	p. 177
Two projects for validating the PKa equalization principle	p. 180
First project. PKa equalization in CAHBs with ?PKa near zero	p. 180
Second project. PKa equalization in the N-H-...O/O-H system	p. 183
Conclusions	p. 184
Appendix. PKa tables arranged for chemical funtionality	p. 184
The empirical laws governing the H-bonds: A summary	p. 193
Summary of chemical leitmotifs (CLs): The three main classes of H-bonds	p. 193
Summary of VB methods: The electrostatic-covalent H-bond model (ECHBM)	p. 196
Summary of the PA/Pka equalization principle	p. 199
On the chemical nature of the h-bond	p. 200
Outline a novel transition-state H-bond theory (TSHBT)	p. 203
Empirical laws, models and scietific theories: An introduction	p. 203
A new way of looking at the H-bond: The TSHBT	p. 206
Introduction	p. 206
Criteria for the choice of a suitable PT reaction	p. 206
A practical verification of the TSHBT	p. 208
A suitable reaction: The ketohydrazone?azoenol system	p. 208
Methods of study	p. 208
Analysis of crystallographic results	p. 210
DFT emulation	p. 211
Marcus analysis of DFT data	p. 213
Conclusions	p. 220
The Strength of the H-bond: Definitions and thermodynamics	p. 222
The H-bond strength in gas-phase, non-polar solvents and molecular Crystals	p. 222
Enthalphy-entrophy compensation and its influence on the H-bond strength	p. 222
H-bond strength in the gas phase	p. 223
H-bond strength in polar solvents	p. 224
H-bond strength in molecular crystals	p. 225
The H-bond strength in aqueous soulutions	p. 225
Introduction: Drug-receptor binding as a sample system	p. 225
Hydrophilic and Hydrophobic contributins to drug-receptor binding	p. 226
Hydrophobic binding: Thermodynamics of the steriod-nuclear receptor system	p. 228
Hydrophilic-hydrophobic binding: Thermodynamics of the adenosine A1 membrane receptor	p. 232
Enthalphy-entropy compensation: A universal property of drug-receptor binding	p. 235
Solvent reorganization and enthalpy-entrophy compensation in drug-receptor binging: The Grunward and Steel model	p. 238
Thermodynamic discrimination in ligand-gated ion channels	p. 241
Enthalpy-entrophy compensation in crown ethers and cryptands	p. 242
The role of strong H-bonds in nature: A gallery of functional H-bonds	p. 245
Introductin	p. 245
Detecting strong H-bonds	p. 245
The concept of 'functional H-bonds'	p. 245
RAHB-driven prototropic tautomerism	p. 247
RAHB-activation of the carbon in? to a carbonyl	p. 247
RAHB-induced enolization in keto-enol tautomerism	p. 248
RAHB-induced tautomerism in heterconjugated systems	p. 248
RAHB cooperativity and anticooperativity in more complex cases	p. 249
H-bond-controlled crystal packing	p. 251
The crystal packing of squaric acid and its anions	p. 251
Bistable H-bonds in fuctional molecular materials	p. 253
Generalities	p. 253
RAHB and ferro/antiferroelectric behavior	p. 254
RAHB and excited-state proton transfer (ESPT)	p. 258
Functional H-bonds in biological systems	p. 260
RAHB in the secondary structure of protiens and in DNA base pairing	p. 260
Charge-assisted H-bonds in enzumatic catalysis	p. 261
Generalities	p. 261
The catalytic triad of serine proteases	p. 263
?5-3-Ketosteroid isomerase	p. 266
An aspartic protease: HIV-1 Protease	p. 267
?-bond cooperativity and anticooperative in PAHBs	p. 269
Cooperative and anticooperative water chains	p. 269
An example of cooperativity: The gramicidline A channel	p. 272
An example of anticooperativity: Water-without-proton transmission in aquaporin channels	p. 275
References	p. 277
Index	p. 315
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The Nature of the Hydrogen Bond Outline of a Comprehensive Hydrogen Bond Theory

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