Molecular aggregation: structure analysis and molecular simulation of crystals and liquids
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford [u.a.]
Oxford Univ. Press
2007
|
| Ausgabe: | 1. publ. |
| Schriftenreihe: | International Union of Crystallography: IUCr monographs on crystallography
19 |
| Schlagworte: | |
| Online-Zugang: | Table of contents only Inhaltsverzeichnis |
| Beschreibung: | Hier auch später erschienene, unveränderte Nachdrucke Includes bibliographical references and index |
| Beschreibung: | XV, 425 S. Ill., graph. Darst. |
| ISBN: | 0198570805 9780198570806 9780199673650 |
Internformat
MARC
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| 100 | 1 | |a Gavezzotti, Angelo |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Molecular aggregation |b structure analysis and molecular simulation of crystals and liquids |c Angelo Gavezzotti |
| 250 | |a 1. publ. | ||
| 264 | 1 | |a Oxford [u.a.] |b Oxford Univ. Press |c 2007 | |
| 300 | |a XV, 425 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a International Union of Crystallography: IUCr monographs on crystallography |v 19 | |
| 500 | |a Hier auch später erschienene, unveränderte Nachdrucke | ||
| 500 | |a Includes bibliographical references and index | ||
| 650 | 4 | |a Chimie quantique - Simulation par ordinateur | |
| 650 | 7 | |a Computermodellen |2 gtt | |
| 650 | 4 | |a Cristallographie | |
| 650 | 4 | |a Cristaux | |
| 650 | 4 | |a Dynamique moléculaire - Simulation par ordinateur | |
| 650 | 4 | |a Forces intermoléculaires - Simulation par ordinateur | |
| 650 | 7 | |a Kristallen |2 gtt | |
| 650 | 7 | |a Kristallografie |2 gtt | |
| 650 | 7 | |a Kwantumchemie |2 gtt | |
| 650 | 4 | |a Liquides | |
| 650 | 7 | |a Moleculaire dynamica |2 gtt | |
| 650 | 7 | |a Simulatie |2 gtt | |
| 650 | 7 | |a Vloeistoffen |2 gtt | |
| 650 | 4 | |a Crystallographpy | |
| 650 | 4 | |a Intermolecular forces |x Computer simulation | |
| 650 | 4 | |a Molecular dynamics |x Computer simulation | |
| 650 | 4 | |a Quantum chemistry |x Computer simulation | |
| 650 | 4 | |a Crystals | |
| 650 | 4 | |a Liquids | |
| 650 | 0 | 7 | |a Computersimulation |0 (DE-588)4148259-1 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Zwischenmolekulare Kraft |0 (DE-588)4191346-2 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Organischer Festkörper |0 (DE-588)4172779-4 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Kondensierte Materie |0 (DE-588)4132810-3 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Organische Flüssigkeit |0 (DE-588)4172772-1 |2 gnd |9 rswk-swf |
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| 830 | 0 | |a International Union of Crystallography: IUCr monographs on crystallography |v 19 |w (DE-604)BV005455767 |9 19 | |
| 856 | 4 | |u http://www.loc.gov/catdir/toc/ecip0619/2006027156.html |3 Table of contents only | |
| 856 | 4 | 2 | |m Digitalisierung UB Bayreuth |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015489568&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-015489568 | ||
Datensatz im Suchindex
| _version_ | 1804136286999543808 |
|---|---|
| adam_text | Contents
PART I FUNDAMENTALS
1
The molecule: structure, size and shape
3
1.1
Atoms and bonds
3
1.2
Classification concepts in many particle systems
5
1.2.1
Structure
5
1.2.2
Symmetry
8
1.2.3
Order
9
1.2.4
Enthalpy and entropy
9
1.3
Must a molecule have a size?
10
1.3.1
Mass and length dimensions
10
1.3.2
Atomic radii
13
1.3.3
Molecular volume and surface
15
1.3.4
Size in terms of electron density
18
1.4
Must a molecule have a shape?
20
1.5
Historical portraits: a chemistry course in the early 1960 s
24
2
Molecular vibrations and molecular force fields
30
2.1
Vibrational modes and force constants
30
2.2
Molecular mechanics
35
2.3
Evolution of molecular force fields
39
2.4
Appendix: an example of coordinate transformation
43
2.5
Historical portraits: Got a force constant?
45
3
Quantum chemistry
53
3.1
Some fundamentals of quantum mechanics
53
3.1.1
Dynamic variables, wavefunctions, operators
54
3.1.2
The
Schrödinger
equation and stationary states
54
3.1.3
Linear momentum
56
3.1.4
Angular momentum
57
3.1.5
Spherical harmonics
59
3.1.6
The harmonic oscillator
60
3.2
The hydrogen atom and atomic
orbitais
61
3.3
Spin
63
3.4
Many-electron systems
65
3.5
Molecular
orbitais:
The Fock and Roothaan equations
67
3.5.1
The variational principle
69
3.5.2
Why do a molecular orbital calculation?
72
CONTENTS
3.6
Approximate
quantum
chemical methods: NDO and EHT
74
3.7
Evolution of quantum chemical calculations: Beyond
Hartree-Fock
76
3.7.1
Configuration interaction and MOller-Plesset
perturbation methods
77
3.7.2
Density functional theory (DFT) methods
78
3.7.3
Other beyond-Hartree-Fock methods
80
3.7.4
Ethylene
in perspective
81
3.8
Dimerization energies and basis set superposition error
81
3.9
Historical portraits: early experiences in quantum chemistry
82
The physical nature and the computer simulation of the
intermolecular
potential
87
4.1
Experimental facts and conceptual framework
87
4.2
The representation of the molecular charge distribution
and of the electric potential
89
4.2.1
Full electron density
89
4.2.2
Central multipoles
90
4.2.3
Distributed multipoles
92
4.2.4
Point charges
92
4.3
Coulombic potential energy
94
4.4
Polarization (electrostatic induction) energy
96
4.5
Dispersion energy
99
4.6 Pauli
(exchange) repulsion energy
101
4.7
Total energies versus partitioned energies
103
4.7.1
Pairwise additivity
103
4.7.2
Interpretation
104
4.8
Intermolecular hydrogen bonding
105
4.9
Simulation methods
106
4.9.1
The intermolecular atom-atom model for organic
crystals
106
4.9.2
Distributed multipole methods
110
4.9.3
Other density-based methods
111
4.10
Ad hoc or transferable? Force field fitting from
ab initio
calculations
112
Crystal symmetry and X-ray diffraction
120
5.1
A structural view of crystal symmetry: bottom-up
crystallography
120
5.2
Space group symmetry and its mathematical representation
127
5.3 von Laue s
idea,
1912 130
5.4
The structure factor
131
5.4.1
Scattering by one or two charge points
131
5.4.2
The atomic scattering factor
133
CONTENTS xi
5.4.3
The molecular structure factor
134
5.4.4
The structure factor for infinite periodic systems
135
5.5
Miller indices and Bragg s law
137
5.6
The electron density in a crystal
139
5.7
The atomic prejudice
139
5.8
Structure and X-ray diffraction: Some examples
140
5.9
Historical portraits: Training of a crystallographer in the
1960s 144
Periodic systems: Crystal
orbitais
and lattice dynamics
153
6.1
The mathematical description of crystal periodicity
153
6.1.1
Equivalent positions and systematic absences in
diffraction patterns
153
6.1.2
Reciprocal space, wave vector, Brillouin zone
155
6.1.3
Bloch functions
155
6.2
The electronic structure of solids
157
6.2.1
The crystal orbital approach
157
6.2.2
Band structures: Complicated but not difficult
158
6.2.3
Comparison with experiment; electronic density
of states
162
6.3
Lattice dynamics and lattice vibrations
163
6.3.1
Periodic vibrations in infinite crystals
163
6.3.2
Comparison with experiment; measuring
lattice-vibration frequencies
167
Molecular structure and macroscopic properties: Calorimetry
and thermodynamics
172
7.1
Molecules and macroscopic bodies
172
7.2
Energy
174
7.2.1
The partition function: Molecules
174
7.2.2
The partition function: Macroscopic systems
176
7.2.3
Internal energy I: From statistics and quantum
mechanics
177
7.2.4
Internal energy II: From thermal and mechanical
experiments
179
7.3
Heat capacity
179
7.4
Entropy
180
7.4.1
Classical entropy
181
7.4.2
Statistical entropy
182
7.4.3
The calculation of entropy for chemical systems
182
7.5
Free energy and chemical equilibrium
183
7.5.1
Chemical potential
183
7.5.2
Free energy
184
7.5.3
Chemical potentials in practice
184
7.6
Thermodynamic measurements
186
xii
CONTENTS
7.6.1
Heat capacity
186
7.6.2
Melting enthalpies
188
7.6.3
Sublimation enthalpies
190
7.7
Derivatives
193
8
Correlation studies in organic solids
196
8.1
The Cambridge Structural Database
(CSD)
of organic crystals
196
8.2
Structure correlation
198
8.3
Retrieval of molecular and crystal structures from the
CSD 199
8.4
The SubHeat database
201
8.5
The geometrical categorization of
intermolecular
bonding
202
8.6
Space analysis of molecular packing modes
203
8.6.1
Empty space versus filled space
203
8.6.2
Close packing in crystals
204
8.7
The calculation of
intermolecular
energies in crystals
207
8.7.1
Lattice energies: Some basic concepts
207
8.7.2
Convergence problems in lattice sums
212
8.7.3
Sublimation entropies and vapor pressures of crystals
213
8.8
General-purpose force fields for organic crystals
214
8.9
Accuracy and reproducibility
217
8.10
Correlation between molecular and crystal properties: Fact or
fiction?
220
8.10.1
Divariate
analysis
220
8.10.2
Principal component analysis
223
8.11
Acceptable crystal structures
225
8.12
Historical portraits: Lattice energies and the phase problem
in the old days
225
9
The liquid state
230
9.1
Proper liquids
230
9.2
Molecular dynamics (MD)
230
9.2.1
Equations of motion
231
9.2.2
Temperature
232
9.2.3
Pressure
233
9.2.4
NPT and NVT simulations
234
9.2.5
Performance and constraints in molecular dynamics
simulations
235
9.3
The Monte Carlo
(MC)
method
236
9.4
Structural and dynamic descriptors for liquids
237
9.4.1
Radial distribution functions
238
9.4.2
Correlation functions
241
9.5
Physicochemical properties of liquids from MD or
MC
simulations
243
9.5.1
Enthalpy, heat capacity and density
243
CONTENTS xiii
9.5.2 The Jorgensen
school
244
9.5.3
Crystal and liquid equations of state
245
9.6
Polarizability and dielectric constants
246
9.7
Free energy simulations
247
9.8
A theme with variations
249
9.9
Water
249
10
Computers
254
10.1
Bits and pieces
254
10.2
Operating systems
256
10.3
Computer programming
258
10.4
Bugs and program checking and validation
260
10.5
Reproducibility
261
10.6
Because it s there ?
262
PARTII
THE FRONTIER
11
Structure-property and structure-activity relationships
269
11.1
Fundamental research and applied technology
269
11.2
The structure-activity dogma
270
11.3
Crystal dissolution
273
11.4
Thermal properties
275
11.4.1
Thermal expansion coefficients
275
11.4.2
Heat capacity and heat transport
277
11.5
Strain and stress, elastic and viscous properties
278
11.6
Optical, electric and magnetic properties
284
11.6.1
Color
284
11.6.2
Optical properties and the polar axis
289
11.6.3
Electric and magnetic properties
292
12
Intermolecular bonding
296
12.1
The decline of the intermolecular atom-atom bond
296
12.1.1
The Feynman-Ehrenfest chemical bond
296
12.1.2
More familiar models: distance-energy analyses
298
12.2
Full density models: the SCDS-Pixel method
304
12.2.1
Theory
304
12.2.2
Coulombic energy
305
12.2.3
Polarization energy
306
12.2.4
Dispersion energy
307
12.2.5
Repulsion energy
308
12.2.6
Total energies and parameters
308
12.2.7
The generation of crystal coordinates
309
12.2.8
Pixel calculations: General features
310
xiv CONTENTS
12.2.9 Pixel
theory: Pros and cons
314
12.3
Systematic application of the Pixel theory to
intermolecular bonding
315
12.3.1
A glossary of intermolecular recognition modes
315
12.3.1.1
Interactions not involving hydrogen
316
12.3.1.2
C-H·
■ ·
X interactions
318
12.3.1.3
The O-H·
· ·
X and N-H-
■ ·
X
hydrogen bond
319
12.3.1.4
π
-interactions
323
12.3.2
Crystal energies
325
12.4
Directed bonds versus diffuse bonding
326
13
Phase equilibria, phase changes, and mesophases:
Analysis and simulation
330
13.1
Things and molecules
330
13.2
Basic thermodynamic functions
331
13.3
Melting
332
13.4
Solid-liquid equilibrium and nucleation from the melt
338
13.5
Vapor-liquid and vapor-solid equilibrium
341
13.6
Glasses
342
13.7
Liquid crystals
345
13.8
Nucleation and growth from solution: Experiments
347
13.8.1
Overview
347
13.8.2
Light scattering, calorimetry
348
13.8.3
Chemical spectroscopy
349
13.8.4
X-ray scattering and diffraction
350
13.9
Crystal growth and morphology
351
13.9.1
Crystal faces, attachments energies, and morphology
prediction
351
13.9.2
Electron micrography and atomic force microscopy
(AFM)
355
13.10
Evolutionary molecular simulation
356
14
Crystal polymorphism and crystal structure prediction
367
14.1
A fundamental fact
367
14.2
What are crystal polymorphs?
368
14.2.1
The taxonomy of organic crystals
368
14.2.2
Phenomenology of crystal polymorphism
369
14.2.3
Crystal structure fingerprints: Detecting real
polymorphism
375
14.2.4
Analysis of crystal polymorphism by Pixel and
quantum chemical calculations
379
14.3
The construction of crystal structures by computer
383
14.3.1
Brute force approach
384
CONTENTS xv
14.3.2
The Prom sequential approach
385
14.3.3
Molecular clusters with one symmetry operator
385
14.3.4
Combination of two or three symmetry operators
387
14.3.5
The translation search: Sorting and ranking
389
14.3.6
The Prom algorithm: Pros and cons
389
14.3.7
Some examples of crystal structure generation
390
14.4
Crystal structure prediction by computer
395
14.4.1
The aims
397
14.4.2
The tools
398
14.4.3
Are crystal structures predictable?
398
15
Epilogue: A theory of crystallization?
405
15.1
Laws and theories
405
15.2 Aggregationstages 406
15.2.1
Oligomers
407
15.2.2
Nanoparticles
407
15.2.3
Mesoparticles
410
15.3
Macroscopic crystals
410
15.4
Thermodynamics, kinetics, and symmetry
411
15.5
The language of the theory
416
Index
419
Supplementary material
OPiX, an open-code computer program package for crystal packing analysis, poly-
morph generation and prediction, and Pixel-SCDS calculation; manuals and source
codes
Other open-source program codes for the calculations described in the book
The SubHeat database (see in Section
8.4)
The polymorph database (see in Section
14.2)
Details of calculations (lists of atomic coordinates, etc.)
This material is available at the author s website: http://users.unimi.it/gavezzot
|
| adam_txt |
Contents
PART I FUNDAMENTALS
1
The molecule: structure, size and shape
3
1.1
Atoms and bonds
3
1.2
Classification concepts in many particle systems
5
1.2.1
Structure
5
1.2.2
Symmetry
8
1.2.3
Order
9
1.2.4
Enthalpy and entropy
9
1.3
Must a molecule have a size?
10
1.3.1
Mass and length dimensions
10
1.3.2
Atomic radii
13
1.3.3
Molecular volume and surface
15
1.3.4
Size in terms of electron density
18
1.4
Must a molecule have a shape?
20
1.5
Historical portraits: a chemistry course in the early 1960's
24
2
Molecular vibrations and molecular force fields
30
2.1
Vibrational modes and force constants
30
2.2
Molecular mechanics
35
2.3
Evolution of molecular force fields
39
2.4
Appendix: an example of coordinate transformation
43
2.5
Historical portraits: Got a force constant?
45
3
Quantum chemistry
53
3.1
Some fundamentals of quantum mechanics
53
3.1.1
Dynamic variables, wavefunctions, operators
54
3.1.2
The
Schrödinger
equation and stationary states
54
3.1.3
Linear momentum
56
3.1.4
Angular momentum
57
3.1.5
Spherical harmonics
59
3.1.6
The harmonic oscillator
60
3.2
The hydrogen atom and atomic
orbitais
61
3.3
Spin
63
3.4
Many-electron systems
65
3.5
Molecular
orbitais:
The Fock and Roothaan equations
67
3.5.1
The variational principle
69
3.5.2
Why do a molecular orbital calculation?
72
CONTENTS
3.6
Approximate
quantum
chemical methods: NDO and EHT
74
3.7
Evolution of quantum chemical calculations: Beyond
Hartree-Fock
76
3.7.1
Configuration interaction and MOller-Plesset
perturbation methods
77
3.7.2
Density functional theory (DFT) methods
78
3.7.3
Other beyond-Hartree-Fock methods
80
3.7.4
Ethylene
in perspective
81
3.8
Dimerization energies and basis set superposition error
81
3.9
Historical portraits: early experiences in quantum chemistry
82
The physical nature and the computer simulation of the
intermolecular
potential
87
4.1
Experimental facts and conceptual framework
87
4.2
The representation of the molecular charge distribution
and of the electric potential
89
4.2.1
Full electron density
89
4.2.2
Central multipoles
90
4.2.3
Distributed multipoles
92
4.2.4
Point charges
92
4.3
Coulombic potential energy
94
4.4
Polarization (electrostatic induction) energy
96
4.5
Dispersion energy
99
4.6 Pauli
(exchange) repulsion energy
101
4.7
Total energies versus partitioned energies
103
4.7.1
Pairwise additivity
103
4.7.2
Interpretation
104
4.8
Intermolecular hydrogen bonding
105
4.9
Simulation methods
106
4.9.1
The intermolecular atom-atom model for organic
crystals
106
4.9.2
Distributed multipole methods
110
4.9.3
Other density-based methods
111
4.10
Ad hoc or transferable? Force field fitting from
ab initio
calculations
112
Crystal symmetry and X-ray diffraction
120
5.1
A structural view of crystal symmetry: bottom-up
crystallography
120
5.2
Space group symmetry and its mathematical representation
127
5.3 von Laue's
idea,
1912 130
5.4
The structure factor
131
5.4.1
Scattering by one or two charge points
131
5.4.2
The atomic scattering factor
133
CONTENTS xi
5.4.3
The molecular structure factor
134
5.4.4
The structure factor for infinite periodic systems
135
5.5
Miller indices and Bragg's law
137
5.6
The electron density in a crystal
139
5.7
The atomic prejudice
139
5.8
Structure and X-ray diffraction: Some examples
140
5.9
Historical portraits: Training of a crystallographer in the
1960s 144
Periodic systems: Crystal
orbitais
and lattice dynamics
153
6.1
The mathematical description of crystal periodicity
153
6.1.1
Equivalent positions and systematic absences in
diffraction patterns
153
6.1.2
Reciprocal space, wave vector, Brillouin zone
155
6.1.3
Bloch functions
155
6.2
The electronic structure of solids
157
6.2.1
The crystal orbital approach
157
6.2.2
Band structures: Complicated but not difficult
158
6.2.3
Comparison with experiment; electronic density
of states
162
6.3
Lattice dynamics and lattice vibrations
163
6.3.1
Periodic vibrations in infinite crystals
163
6.3.2
Comparison with experiment; measuring
lattice-vibration frequencies
167
Molecular structure and macroscopic properties: Calorimetry
and thermodynamics
172
7.1
Molecules and macroscopic bodies
172
7.2
Energy
174
7.2.1
The partition function: Molecules
174
7.2.2
The partition function: Macroscopic systems
176
7.2.3
Internal energy I: From statistics and quantum
mechanics
177
7.2.4
Internal energy II: From thermal and mechanical
experiments
179
7.3
Heat capacity
179
7.4
Entropy
180
7.4.1
Classical entropy
181
7.4.2
Statistical entropy
182
7.4.3
The calculation of entropy for chemical systems
182
7.5
Free energy and chemical equilibrium
183
7.5.1
Chemical potential
183
7.5.2
Free energy
184
7.5.3
Chemical potentials in practice
184
7.6
Thermodynamic measurements
186
xii
CONTENTS
7.6.1
Heat capacity
186
7.6.2
Melting enthalpies
188
7.6.3
Sublimation enthalpies
190
7.7
Derivatives
193
8
Correlation studies in organic solids
196
8.1
The Cambridge Structural Database
(CSD)
of organic crystals
196
8.2
Structure correlation
198
8.3
Retrieval of molecular and crystal structures from the
CSD 199
8.4
The SubHeat database
201
8.5
The geometrical categorization of
intermolecular
bonding
202
8.6
Space analysis of molecular packing modes
203
8.6.1
Empty space versus filled space
203
8.6.2
Close packing in crystals
204
8.7
The calculation of
intermolecular
energies in crystals
207
8.7.1
Lattice energies: Some basic concepts
207
8.7.2
Convergence problems in lattice sums
212
8.7.3
Sublimation entropies and vapor pressures of crystals
213
8.8
General-purpose force fields for organic crystals
214
8.9
Accuracy and reproducibility
217
8.10
Correlation between molecular and crystal properties: Fact or
fiction?
220
8.10.1
Divariate
analysis
220
8.10.2
Principal component analysis
223
8.11
Acceptable crystal structures
225
8.12
Historical portraits: Lattice energies and the phase problem
in the old days
225
9
The liquid state
230
9.1
Proper liquids
230
9.2
Molecular dynamics (MD)
230
9.2.1
Equations of motion
231
9.2.2
Temperature
232
9.2.3
Pressure
233
9.2.4
NPT and NVT simulations
234
9.2.5
Performance and constraints in molecular dynamics
simulations
235
9.3
The Monte Carlo
(MC)
method
236
9.4
Structural and dynamic descriptors for liquids
237
9.4.1
Radial distribution functions
238
9.4.2
Correlation functions
241
9.5
Physicochemical properties of liquids from MD or
MC
simulations
243
9.5.1
Enthalpy, heat capacity and density
243
CONTENTS xiii
9.5.2 The Jorgensen
school
244
9.5.3
Crystal and liquid equations of state
245
9.6
Polarizability and dielectric constants
246
9.7
Free energy simulations
247
9.8
A theme with variations
249
9.9
Water
249
10
Computers
254
10.1
Bits and pieces
254
10.2
Operating systems
256
10.3
Computer programming
258
10.4
Bugs and program checking and validation
260
10.5
Reproducibility
261
10.6
"Because it's there"?
262
PARTII
THE FRONTIER
11
Structure-property and structure-activity relationships
269
11.1
Fundamental research and applied technology
269
11.2
The structure-activity dogma
270
11.3
Crystal dissolution
273
11.4
Thermal properties
275
11.4.1
Thermal expansion coefficients
275
11.4.2
Heat capacity and heat transport
277
11.5
Strain and stress, elastic and viscous properties
278
11.6
Optical, electric and magnetic properties
284
11.6.1
Color
284
11.6.2
Optical properties and the polar axis
289
11.6.3
Electric and magnetic properties
292
12
Intermolecular bonding
296
12.1
The decline of the intermolecular atom-atom bond
296
12.1.1
The Feynman-Ehrenfest chemical bond
296
12.1.2
More familiar models: distance-energy analyses
298
12.2
Full density models: the SCDS-Pixel method
304
12.2.1
Theory
304
12.2.2
Coulombic energy
305
12.2.3
Polarization energy
306
12.2.4
Dispersion energy
307
12.2.5
Repulsion energy
308
12.2.6
Total energies and parameters
308
12.2.7
The generation of crystal coordinates
309
12.2.8
Pixel calculations: General features
310
xiv CONTENTS
12.2.9 Pixel
theory: Pros and cons
314
12.3
Systematic application of the Pixel theory to
intermolecular bonding
315
12.3.1
A glossary of intermolecular recognition modes
315
12.3.1.1
Interactions not involving hydrogen
316
12.3.1.2
C-H·
■ ·
X interactions
318
12.3.1.3
The O-H·
· ·
X and N-H-
■ ·
X
hydrogen bond
319
12.3.1.4
π
-interactions
323
12.3.2
Crystal energies
325
12.4
Directed bonds versus diffuse bonding
326
13
Phase equilibria, phase changes, and mesophases:
Analysis and simulation
330
13.1
Things and molecules
330
13.2
Basic thermodynamic functions
331
13.3
Melting
332
13.4
Solid-liquid equilibrium and nucleation from the melt
338
13.5
Vapor-liquid and vapor-solid equilibrium
341
13.6
Glasses
342
13.7
Liquid crystals
345
13.8
Nucleation and growth from solution: Experiments
347
13.8.1
Overview
347
13.8.2
Light scattering, calorimetry
348
13.8.3
Chemical spectroscopy
349
13.8.4
X-ray scattering and diffraction
350
13.9
Crystal growth and morphology
351
13.9.1
Crystal faces, attachments energies, and morphology
prediction
351
13.9.2
Electron micrography and atomic force microscopy
(AFM)
355
13.10
Evolutionary molecular simulation
356
14
Crystal polymorphism and crystal structure prediction
367
14.1
A fundamental fact
367
14.2
What are crystal polymorphs?
368
14.2.1
The taxonomy of organic crystals
368
14.2.2
Phenomenology of crystal polymorphism
369
14.2.3
Crystal structure fingerprints: Detecting real
polymorphism
375
14.2.4
Analysis of crystal polymorphism by Pixel and
quantum chemical calculations
379
14.3
The construction of crystal structures by computer
383
14.3.1
"Brute force" approach
384
CONTENTS xv
14.3.2
The "Prom" sequential approach
385
14.3.3
Molecular clusters with one symmetry operator
385
14.3.4
Combination of two or three symmetry operators
387
14.3.5
The translation search: Sorting and ranking
389
14.3.6
The Prom algorithm: Pros and cons
389
14.3.7
Some examples of crystal structure generation
390
14.4
Crystal structure prediction by computer
395
14.4.1
The aims
397
14.4.2
The tools
398
14.4.3
Are crystal structures predictable?
398
15
Epilogue: A theory of crystallization?
405
15.1
Laws and theories
405
15.2 Aggregationstages 406
15.2.1
Oligomers
407
15.2.2
Nanoparticles
407
15.2.3
Mesoparticles
410
15.3
Macroscopic crystals
410
15.4
Thermodynamics, kinetics, and symmetry
411
15.5
The language of the theory
416
Index
419
Supplementary material
OPiX, an open-code computer program package for crystal packing analysis, poly-
morph generation and prediction, and Pixel-SCDS calculation; manuals and source
codes
Other open-source program codes for the calculations described in the book
The SubHeat database (see in Section
8.4)
The polymorph database (see in Section
14.2)
Details of calculations (lists of atomic coordinates, etc.)
This material is available at the author's website: http://users.unimi.it/gavezzot |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author | Gavezzotti, Angelo |
| author_facet | Gavezzotti, Angelo |
| author_role | aut |
| author_sort | Gavezzotti, Angelo |
| author_variant | a g ag |
| building | Verbundindex |
| bvnumber | BV022279227 |
| callnumber-first | Q - Science |
| callnumber-label | QD921 |
| callnumber-raw | QD921 |
| callnumber-search | QD921 |
| callnumber-sort | QD 3921 |
| callnumber-subject | QD - Chemistry |
| classification_rvk | UQ 3200 |
| classification_tum | CHE 606f GEO 420f CHE 138f CHE 133f |
| ctrlnum | (OCoLC)71006745 (DE-599)BVBBV022279227 |
| dewey-full | 548 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 548 - Crystallography |
| dewey-raw | 548 |
| dewey-search | 548 |
| dewey-sort | 3548 |
| dewey-tens | 540 - Chemistry and allied sciences |
| discipline | Chemie / Pharmazie Geowissenschaften Physik Chemie |
| discipline_str_mv | Chemie / Pharmazie Geowissenschaften Physik Chemie |
| edition | 1. publ. |
| format | Book |
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| id | DE-604.BV022279227 |
| illustrated | Illustrated |
| index_date | 2024-07-02T16:48:49Z |
| indexdate | 2024-07-09T20:54:00Z |
| institution | BVB |
| isbn | 0198570805 9780198570806 9780199673650 |
| language | English |
| lccn | 2006027156 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-015489568 |
| oclc_num | 71006745 |
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| owner | DE-91G DE-BY-TUM DE-703 |
| owner_facet | DE-91G DE-BY-TUM DE-703 |
| physical | XV, 425 S. Ill., graph. Darst. |
| publishDate | 2007 |
| publishDateSearch | 2007 |
| publishDateSort | 2007 |
| publisher | Oxford Univ. Press |
| record_format | marc |
| series | International Union of Crystallography: IUCr monographs on crystallography |
| series2 | International Union of Crystallography: IUCr monographs on crystallography |
| spelling | Gavezzotti, Angelo Verfasser aut Molecular aggregation structure analysis and molecular simulation of crystals and liquids Angelo Gavezzotti 1. publ. Oxford [u.a.] Oxford Univ. Press 2007 XV, 425 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier International Union of Crystallography: IUCr monographs on crystallography 19 Hier auch später erschienene, unveränderte Nachdrucke Includes bibliographical references and index Chimie quantique - Simulation par ordinateur Computermodellen gtt Cristallographie Cristaux Dynamique moléculaire - Simulation par ordinateur Forces intermoléculaires - Simulation par ordinateur Kristallen gtt Kristallografie gtt Kwantumchemie gtt Liquides Moleculaire dynamica gtt Simulatie gtt Vloeistoffen gtt Crystallographpy Intermolecular forces Computer simulation Molecular dynamics Computer simulation Quantum chemistry Computer simulation Crystals Liquids Computersimulation (DE-588)4148259-1 gnd rswk-swf Zwischenmolekulare Kraft (DE-588)4191346-2 gnd rswk-swf Organischer Festkörper (DE-588)4172779-4 gnd rswk-swf Kondensierte Materie (DE-588)4132810-3 gnd rswk-swf Organische Flüssigkeit (DE-588)4172772-1 gnd rswk-swf Organische Flüssigkeit (DE-588)4172772-1 s Computersimulation (DE-588)4148259-1 s DE-604 Organischer Festkörper (DE-588)4172779-4 s Kondensierte Materie (DE-588)4132810-3 s Zwischenmolekulare Kraft (DE-588)4191346-2 s International Union of Crystallography: IUCr monographs on crystallography 19 (DE-604)BV005455767 19 http://www.loc.gov/catdir/toc/ecip0619/2006027156.html Table of contents only Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015489568&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Gavezzotti, Angelo Molecular aggregation structure analysis and molecular simulation of crystals and liquids International Union of Crystallography: IUCr monographs on crystallography Chimie quantique - Simulation par ordinateur Computermodellen gtt Cristallographie Cristaux Dynamique moléculaire - Simulation par ordinateur Forces intermoléculaires - Simulation par ordinateur Kristallen gtt Kristallografie gtt Kwantumchemie gtt Liquides Moleculaire dynamica gtt Simulatie gtt Vloeistoffen gtt Crystallographpy Intermolecular forces Computer simulation Molecular dynamics Computer simulation Quantum chemistry Computer simulation Crystals Liquids Computersimulation (DE-588)4148259-1 gnd Zwischenmolekulare Kraft (DE-588)4191346-2 gnd Organischer Festkörper (DE-588)4172779-4 gnd Kondensierte Materie (DE-588)4132810-3 gnd Organische Flüssigkeit (DE-588)4172772-1 gnd |
| subject_GND | (DE-588)4148259-1 (DE-588)4191346-2 (DE-588)4172779-4 (DE-588)4132810-3 (DE-588)4172772-1 |
| title | Molecular aggregation structure analysis and molecular simulation of crystals and liquids |
| title_auth | Molecular aggregation structure analysis and molecular simulation of crystals and liquids |
| title_exact_search | Molecular aggregation structure analysis and molecular simulation of crystals and liquids |
| title_exact_search_txtP | Molecular aggregation structure analysis and molecular simulation of crystals and liquids |
| title_full | Molecular aggregation structure analysis and molecular simulation of crystals and liquids Angelo Gavezzotti |
| title_fullStr | Molecular aggregation structure analysis and molecular simulation of crystals and liquids Angelo Gavezzotti |
| title_full_unstemmed | Molecular aggregation structure analysis and molecular simulation of crystals and liquids Angelo Gavezzotti |
| title_short | Molecular aggregation |
| title_sort | molecular aggregation structure analysis and molecular simulation of crystals and liquids |
| title_sub | structure analysis and molecular simulation of crystals and liquids |
| topic | Chimie quantique - Simulation par ordinateur Computermodellen gtt Cristallographie Cristaux Dynamique moléculaire - Simulation par ordinateur Forces intermoléculaires - Simulation par ordinateur Kristallen gtt Kristallografie gtt Kwantumchemie gtt Liquides Moleculaire dynamica gtt Simulatie gtt Vloeistoffen gtt Crystallographpy Intermolecular forces Computer simulation Molecular dynamics Computer simulation Quantum chemistry Computer simulation Crystals Liquids Computersimulation (DE-588)4148259-1 gnd Zwischenmolekulare Kraft (DE-588)4191346-2 gnd Organischer Festkörper (DE-588)4172779-4 gnd Kondensierte Materie (DE-588)4132810-3 gnd Organische Flüssigkeit (DE-588)4172772-1 gnd |
| topic_facet | Chimie quantique - Simulation par ordinateur Computermodellen Cristallographie Cristaux Dynamique moléculaire - Simulation par ordinateur Forces intermoléculaires - Simulation par ordinateur Kristallen Kristallografie Kwantumchemie Liquides Moleculaire dynamica Simulatie Vloeistoffen Crystallographpy Intermolecular forces Computer simulation Molecular dynamics Computer simulation Quantum chemistry Computer simulation Crystals Liquids Computersimulation Zwischenmolekulare Kraft Organischer Festkörper Kondensierte Materie Organische Flüssigkeit |
| url | http://www.loc.gov/catdir/toc/ecip0619/2006027156.html http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015489568&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV005455767 |
| work_keys_str_mv | AT gavezzottiangelo molecularaggregationstructureanalysisandmolecularsimulationofcrystalsandliquids |