The nature of the hydrogen bond: outline of a comprehensive hydrogen bond theory
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford [u.a.]
Oxford Univ. Press
2009
|
| Ausgabe: | 1. publ. |
| Schriftenreihe: | IUCr monographs on crystallography
23 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Klappentext |
| Beschreibung: | XI, 317 S. graph. Darst. |
| ISBN: | 9780199673476 9780199558964 0199558965 |
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| 100 | 1 | |a Gilli, Gastone |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a The nature of the hydrogen bond |b outline of a comprehensive hydrogen bond theory |c Gastone Gilli and Paola Gilli |
| 250 | |a 1. publ. | ||
| 264 | 1 | |a Oxford [u.a.] |b Oxford Univ. Press |c 2009 | |
| 300 | |a XI, 317 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a IUCr monographs on crystallography |v 23 | |
| 650 | 4 | |a Hydrogen bonding | |
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| 830 | 0 | |a IUCr monographs on crystallography |v 23 |w (DE-604)BV005455767 |9 23 | |
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Datensatz im Suchindex
| _version_ | 1804138577154539520 |
|---|---|
| adam_text | CONTENTS
Introduction
A century of the hydrogen bond (H-bond)
6
1.1
The discovery of the H-bond
6
1.2
The theoretical understanding of the H-bond
7
1.3
The experimental approach to the H-bond
13
1.4
Significant books and reviews
19
Generalities, definitions and preliminary classification
23
2.1
Basic H-bond nomenclature
23
2.2
Formal H-bond definitions
23
2.3
The H-bond as a shared-proton interaction: A chemical
classification
28
2.4
Н
-bonds involving main-group elements (Class
1) 30
2.4.1
Conventional
Н
-bonds (Group
1.1) 31
2.4.2
Weak
Н
-bonds: General properties (Groups
1.2-4) 32
2.4.2.1
Treatment of
H
-А
contact distances
35
2.4.2.2
H-bond directionality
36
2.4.2.3
Importance of crystal-packing patterns
38
2.4.3
Weak H-bond donors (Group
1.2) 38
2.4.3.1
C
-Н···
bonds
40
2.4.3.2
S
-Н···
bonds
42
2.4.3.3
P
-Н···
bonds
42
2.4.3.4
Si-H,
As
-Н
and
Se
-Н···
bonds
43
2.4.4
Weak H-bond acceptors (Group
1.3) 44
2.4.4.1
С
-Hal
(Hal
=
F, Cl, Br)
as acceptors
44
2.4.4.2
S, Se
and
Te as
acceptors
44
2.4.4.3
P, As and Sb as acceptors
45
2.4.4.4
С
as acceptor
46
2.4.5
Weak ^acceptors (Group
1.4) 47
2.5
Н
-bonds involving metal centers (Class
2) 49
2.5.1
Metals as H-bond donors (Group
2.1) 50
2.5.2
Metals as H-bond acceptors (Group
2.2) 53
2.5.3
Metal hydrides as H-bond acceptors or dihydrogen
bond (DHB) (Group
2.3) 53
2.5.3.1
DHB to main-group hydrides
54
2.5.3.2
DHB to transition-metal hydrides
56
2.5.4
Metal ligands as H-bond donors or acceptors
(Groups
2.4-5) 56
Contents
2.6
H-bond
classification
by physical properties: Weak.
moderate, and strong H-bonds
59
2.7
Correlation among physical descriptors: The problem of
the driving variable
60
Modelling the
Н
-bond
by crystallographic methods
65
3.1
Crystallographic databases and structural correlations
65
3.1.1
A survey of structural databases
65
3.1.2
Crystal-structure correlation (CSC) methods
68
3.1.3
Bond lengths, bond energies and bond-number
conservation rule
71
3.1.3.1
Bond lengths, energies and numbers
71
3.1.3.2
Bond-number conservation rule
72
3.1.3.3
The Lippincott and Schroeder H-bond
model (LS-HB)
75
3.2
A new class of H-bonds: The resonance-assisted
H-bond (RAHB)
81
3.2.1
Cooperative H-bonds: An introduction
81
3.2.2
Evidence for RAHB from CSC studies of
іЗ
-diketone
enols
84
3.2.2.1
A survey of CSC results
84
3.2.2.2
RAHB interpretation: The ionic model
89
3.2.2.3
RAHB interpretation: The resonant model
91
3.2.2.4
Appendix
ЗА:
RAHB as a cybernetic effector
100
3.2.2.5
Appendix 3B: RAHB as a state-correlation
diagram
100
3.2.2.6
Appendix 3C: RAHB electron effective-mass
model
103
3.2.3
RAHB generalization and systematics
108
3.2.3.1
RAHB generalization
108
3.2.3.2
Intra-
and
intermolecular
O-H-0
RAHB 111
3.2.3.3
Intramolecular N-H-N RAHB
121
3.2.3.4
Heteronuclear X-H-Y RAHB
122
3.3
Completing the
Н
-bond
classification: The chemical leitmotifs
147
3.3.1
A full
Н
-bond
classification from the systematic
analysis of the O-H-0 system
147
3.3.1.1
A full
CSD
analysis of the O-H-0 system
147
3.3.1.2
Interpreting the O-H-0 system: The
electrostatic-covalent
Н
-bond
model
155
3.3.1.3
Interpreting the O-H-0 system:
The PA/pir, equalization principle
159
3.3.2
CAHB generalization to other homonuclear
X-H-X bonds
161
3.3.3
CAHB generalization to heteronuclear
Х
-H—
Y
bonds
163
Contents ix
3.3.4
CAHB geometry-energy relationships
163
Modelling the
Н
-bond
by thermodynamic methods
168
4.1
Introduction
168
4.2
The use of
ΔΡΑ
and
ΔρΑ;
indicators in
Н
-bond
studies
168
4.2.1
PA and
pKñ
definitions
168
4.2.2
Proton-transfer and proton-sharing H-bonds
170
4.2.3
Computing
ΔΡΑ
and
ΑρΚΛ
values: The problem
of
ΔΡΑ
evaluation
171
4.2.4
The use of PA and
рКя
as predictors of the
Н
-bond
strength: A summary
173
4.3
Predicting (-)CAHB and (+)CAHB strengths from
enthalpy versus proton affinity correlations
174
4.3.1
ΔΗ°ΌΚ
against
ΔΡΑ
correlations
174
4.3.2
A verification of the PA equalization principle
175
4.4
Predicting
Н
-bond
strengths from crystal geometry
versus
рКл
correlations
177
4.4.1
рК.л
tables for the most common
Н
-bond
donors
and acceptors
177
4.4.2
The
рКл
slide rule
177
4.4.3
Two projects for validating the
рК.л
equalization
principle
180
4.4.3.1
First project. pKa equalization in CAHBs
with A.pKn near zero
180
4.4.3.2
Second project.
рКя
equalization in
the N-H-O/O-H- -N system
181
4.4.3.3
Conclusions
183
4.5
Appendix.
рК.л
tables arranged for chemical functionality
184
The empirical laws governing the
Н
-bond:
A summary
193
5.1
Summary of chemical leitmotifs (CLs): The three main
classes of H-bonds
193
5.2
Summary of VB methods: The electrostatic-covalent
Н
-bond
model (ECHBM)
196
5.3
Summary of the
ΡΑ/ρ/ζ,
equalization principle
199
5.4
On the chemical nature of the H-bond
200
Outline of a novel transition-state
Н
-bond
theory (TSHBT)
203
6.1
Empirical laws, models and scientific theories: An introduction
203
6.2
A new way of looking at the
Н
-bond:
The TSHBT
206
6.2.1
Introduction
206
6.2.2
Criteria for the choice of a suitable PT reaction
206
6.3
A practical verification of the TSHBT
208
6.3.1
A suitable reaction: The ketohydrazone ^± azoenol
system
208
Contents
6.3.2
Methods of study
208
6.3.3
Analysis of crystallographic results
210
6.3.4
DFT emulation
211
6.3.5
Marcus analysis of DFT data
213
6.3.6
Conclusions
220
The strength of the
Н
-bond:
Definitions and thermodynamics
222
7.1
The
Н
-bond
strength in gas-phase, non-polar solvents and
molecular crystals
222
7.1.1
Enthalpy-entropy compensation and its influence on
the
Н
-bond
strength
222
7.1.2
Н
-bond
strength in the gas phase
223
7.1.3
Н
-bond
strength in non-polar solvents
224
7.1.4
Н
-bond
strength in molecular crystals
225
7.2
The
Н
-bond
strength in aqueous solutions
225
7.2.1
Introduction: Drug-receptor binding as a sample
system
225
7.2.2
Hydrophilic and hydrophobic contributions to
drug-receptor binding
226
7.2.3
Hydrophobic binding: Thermodynamics of the
steroid-nuclear receptor system
228
7.2.4
Hydrophilic-hydrophobic binding: Thermodynamics
of the adenosine Aj membrane receptor
232
7.2.5
Enthalpy-entropy compensation: A universal property
of drug-receptor binding
235
7.2.6
Solvent reorganization and enthalpy-entropy
compensation in drug-receptor binding:
The
Grunwald
and Steel model
238
7.2.7
Thermodynamic discrimination in ligand-gated
ion channels
241
7.2.8
Enthalpy-entropy compensation in
crown ethers and cryptands
242
The role of strong
Н
-bonds in nature: A gallery of functional
H-bonds
245
8.1
Introduction
245
8.1.1
Detecting strong H-bonds
245
8.1.2
The concept of functional H-bonds
245
8.2
RAHB-driven prototropic tautomerism
247
8.2.1
RAHB-activation of the carbon in
q
to a carbonyl
247
8.2.2
RAHB-induced enolization in keto-enol tautomerism
248
8.2.3
RAHB-induced tautomerism in heteroconjugated
systems
248
8.2.4
RAHB cooperativity and anticooperativity in
more complex cases
249
Contents xi
8.3
H-bond-controlled crystal packing
251
8.3.1
The crystal packing of squaric acid and its anions
251
8.4
Bistable
Н
-bonds in functional molecular materials
253
8.4.1
Generalities
253
8.4.2
RAHB and ferro/antiferroelectric behavior
254
8.4.3
RAHB and excited-state proton transfer (ESPT)
258
8.5
Functional
Н
-bonds in biological systems
260
8.5.1
RAHB in the secondary structure of proteins and in
DNA
base pairing
260
8.5.2
Charge-assisted
Н
-bonds in enzymatic catalysis
261
8.5.2.1
Generalities
261
8.5.2.2
The catalytic triad of
serine
proteases
263
8.5.2.3
A5-3-Ketosteroid isomerase
266
8.5.2.4
An aspartic protease: HIV-1 protease
267
8.6
Σ
-bond
cooperativity and anticooperativity in PAHBs
269
8.6.1
Cooperative and
anticooperative
water chains
269
8.6.2
An example of cooperativity: The
gramicidine A
channel
272
8.6.3
An example of anticooperativity: Water-without-proton
transmission in aquaporin channels
275
References
277
Index
315
Hydrogen bond
ι Η
bond
)
effects are known: it makes sea water liquid, joins cellulose
microfibrils in trees, shapes
DNA
into genes and
poh
peptide
chains into wool, hair, muscles
or enzymes. Its true nature is less know
η
and we may still
w
onder
why OH
· ■ ■
О
bond
energies range from less than
1
to more than
30 kcal
mol
without apparent reason.
This
Η
bond puzzle is re-examined here from its very beginning on the ground of an
inclusive compilation of experimental
Η
bond energies and geometries.
New concepts emerge from this analysis: new classes of systematically strong
Η
bonds
iCAHBsand RAHBs: charge and resonance-assisted
Η
bonds); full
Η
bond classification
in six classes
ι
the six chemical leitmotifs
);
and assessment of the co
aient
nature of strong
Н
-bonds. This leads to three distinct but inter-consistent models able to rationalize the
H
bond and predict its strength, based on classical YB theory, matching of donor acceptor
acid-base parameters
(
PA or
рКл
),
or shape of the
Н
-bond
proton-transfer pathway.
Applications survey a number of systems where strong
Н
-bonds play an important functional
role, namely drug receptor binding, enzymatic catalysis, ion transport through cell membranes
This book is addressed to researchers, lecturers, and postgraduates in crystallography,
chemistry, molecular biology and pharmacology, molecular material sciences, and
solid state physics.
Castone Gilli
is Professor of Physical Chemistry and Director of the Centre for Structural
Diffractometry at the University of
Ferrara,
Italy.
Paola
Gilli is Researcher of Physical Chemistry at the Department of Chemistry of the
University ot Fcrrara, Italv.
The cover illustration shows a layer of the antiferroelectric crystal of squaric acid built up of
two intercrossing diagonal chains of resonance assisted
H
-bonds | RAHBs
ι
marked by darker
or lighter shadines.
FROM THE SAME SERIES
The Weak Hydrogen Bond
C R.
Desirajii,
T.
Steiner
Crystalline Molecular Complexes and Compounds: Structure and Principles
F. H. Herbstein
Molecular Aggregation: Structure Analysis and Molecular Simulation of
Crystals and Liquids
Aperiodic Crystals: From Modulated Phases to Quasicrystals
T.
Janssen,
G. C
hapuis,
M. de
Botateti
Structural
Crystallography of Inorganic Oxysalts
S. Y. Krivovicho
|
| any_adam_object | 1 |
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| author_facet | Gilli, Gastone |
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| classification_rvk | VE 5300 |
| classification_tum | CHE 134f |
| ctrlnum | (OCoLC)244766758 (DE-599)GBV581075544 |
| dewey-full | 546.2 541/.226 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 546 - Inorganic chemistry 541 - Physical chemistry |
| dewey-raw | 546.2 541/.226 |
| dewey-search | 546.2 541/.226 |
| dewey-sort | 3546.2 |
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| discipline | Chemie / Pharmazie Physik Chemie |
| edition | 1. publ. |
| format | Book |
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| id | DE-604.BV035283641 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T21:30:24Z |
| institution | BVB |
| isbn | 9780199673476 9780199558964 0199558965 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-017088816 |
| oclc_num | 244766758 |
| open_access_boolean | |
| owner | DE-703 DE-19 DE-BY-UBM DE-11 DE-91G DE-BY-TUM |
| owner_facet | DE-703 DE-19 DE-BY-UBM DE-11 DE-91G DE-BY-TUM |
| physical | XI, 317 S. graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Oxford Univ. Press |
| record_format | marc |
| series | IUCr monographs on crystallography |
| series2 | IUCr monographs on crystallography |
| spelling | Gilli, Gastone Verfasser aut The nature of the hydrogen bond outline of a comprehensive hydrogen bond theory Gastone Gilli and Paola Gilli 1. publ. Oxford [u.a.] Oxford Univ. Press 2009 XI, 317 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier IUCr monographs on crystallography 23 Hydrogen bonding Wasserstoffbrückenbindung (DE-588)4064787-0 gnd rswk-swf Wasserstoffbrückenbindung (DE-588)4064787-0 s DE-604 Gilli, Paola Sonstige oth IUCr monographs on crystallography 23 (DE-604)BV005455767 23 Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017088816&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017088816&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext |
| spellingShingle | Gilli, Gastone The nature of the hydrogen bond outline of a comprehensive hydrogen bond theory IUCr monographs on crystallography Hydrogen bonding Wasserstoffbrückenbindung (DE-588)4064787-0 gnd |
| subject_GND | (DE-588)4064787-0 |
| title | The nature of the hydrogen bond outline of a comprehensive hydrogen bond theory |
| title_auth | The nature of the hydrogen bond outline of a comprehensive hydrogen bond theory |
| title_exact_search | The nature of the hydrogen bond outline of a comprehensive hydrogen bond theory |
| title_full | The nature of the hydrogen bond outline of a comprehensive hydrogen bond theory Gastone Gilli and Paola Gilli |
| title_fullStr | The nature of the hydrogen bond outline of a comprehensive hydrogen bond theory Gastone Gilli and Paola Gilli |
| title_full_unstemmed | The nature of the hydrogen bond outline of a comprehensive hydrogen bond theory Gastone Gilli and Paola Gilli |
| title_short | The nature of the hydrogen bond |
| title_sort | the nature of the hydrogen bond outline of a comprehensive hydrogen bond theory |
| title_sub | outline of a comprehensive hydrogen bond theory |
| topic | Hydrogen bonding Wasserstoffbrückenbindung (DE-588)4064787-0 gnd |
| topic_facet | Hydrogen bonding Wasserstoffbrückenbindung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017088816&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017088816&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV005455767 |
| work_keys_str_mv | AT gilligastone thenatureofthehydrogenbondoutlineofacomprehensivehydrogenbondtheory AT gillipaola thenatureofthehydrogenbondoutlineofacomprehensivehydrogenbondtheory |