Non-covalent Interactions in the Synthesis and Design of New Compounds -  - E-Book

Non-covalent Interactions in the Synthesis and Design of New Compounds E-Book

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This book aims to overview the role of non-covalent interactions, such as hydrogen and halogen bonding, pi-pi, pi-anion and electrostatic interactions, hydrophobic effects and van der Waals forces in the synthesis of organic and inorganic compounds, as well as in design of new crystals and function materials. The proposed book should allow to combine, in a systematic way, recent advances on the application of non-covalent interactions in synthesis and design of new compounds and functional materials with significance in Inorganic, Organic, Coordination, Organometallic, Pharmaceutical, Biological and Material Chemistries. Therefore, it should present a multi- and interdisciplinary character assuring a rather broad scope. We believe it will be of interest to a wide range of academic and research staff concerning the synthesis of new compounds, catalysis and materials. Each chapter will be written by authors who are well known experts in their respective fields.

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Table of Contents

COVER

TITLE PAGE

NOTES ON EDITORS

LIST OF CONTRIBUTORS

PREFACE

REFERENCES

PART I: ORGANIC SYNTHESIS

1 ACTIVATION OF COVALENT BONDS THROUGH NON-COVALENT INTERACTIONS

1.1 INTRODUCTION

1.2 EXAMPLES OF HYDROGEN BOND-ASSISTED ACTIVATIONS

1.3 HALOGEN BOND-ASSISTED ACTIVATIONS

1.4 OTHER TYPES OF NON-COVALENT INTERACTIONS AND PERSPECTIVES

1.5 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

2 BORON–NITROGEN BOND

2.1 INTRODUCTION

2.2 BN AROMATIC HETEROCYCLES

2.3 BN NONAROMATIC HETEROCYCLES

2.4 BN INTERACTION: SUPRAMOLECULAR ARCHITECTURES

2.5 BN INTERACTION: CHEMOSENSING

2.6 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

3 INFLUENCE OF STERIC, ELECTRONIC, AND MOLECULAR PREORGANIZATION EFFECTS IN THE REACTIVITY OF β-PHENYLETHYLAMINES WITH NONENOLIZABLE ALDEHYDES

3.1 INTRODUCTION

3.2 DOPAMINE REACTION WITH NONENOLIZABLE ALDEHYDES: THE PICTET–SPENGLER REACTION

3.3 TYROSINE DERIVATIVES REACTION WITH NONENOLIZABLE ALDEHYDES

3.4 NON-COVALENT INTERACTIONS REGARDING

L

-TYROSINE AND ITS TETRABUTYLAMMONIUM SALT

3.5 TYRAMINE AND β-PHENYLETHYLAMINE REACTION WITH FORMALDEHYDE

3.6 BENZYLAZACYCLOPHANE SYNTHESIS

3.7 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

4 NON-COVALENT INTERACTIONS IN THE SYNTHESIS OF MACROCYCLES

4.1 INTRODUCTION

4.2 ANION-TEMPLATED SYNTHESIS

4.3 CATION-TEMPLATED SYNTHESIS

4.4 HYDROGEN BOND-DIRECTED SYNTHESIS

4.5 OTHER MACROCYCLIZATIONS

4.6 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

PART II: INORGANIC, COORDINATION AND ORGANOMETALLIC SYNTHESES

5 NON-COVALENT INTERACTIONS OF WATER WITH METAL COMPLEXES IN SOLUTION

5.1 INTRODUCTION

5.2 HYDROGEN BONDING AND VAN DER WAALS INTERACTIONS

5.3 NEUTRON AND X-RAY METHODS TO INVESTIGATE STRUCTURAL ASPECTS OF METAL ION AND METAL COMPLEX SOLVATION AND THEIR SOLUTION STRUCTURE

5.4 WATER, METAL IONS, AND METAL COMPLEXES IN SOLUTION

5.5 FINAL COMMENTS

ACKNOWLEDGEMENTS

REFERENCES

6 π–π INTERACTION DIRECTED APPLICATIONs OF METAL COMPLEXES

6.1 INTRODUCTION

6.2 MODEL AND SOME RULES OF π–π STACKING

6.3 CATALYSIS

6.4 MAGNETISM

6.5 PHOTOPHYSICAL PROPERTIES

6.6 CONCLUSION

ACKNOWLEDGMENTS

REFERENCES

7 NON-COVALENT STABILIZATION IN TRANSITION METAL COORDINATION AND ORGANOMETALLIC COMPLEXES

7.1 INTRODUCTION

7.2 THEORETICAL CHALLENGES IN ADDRESSING NCIs AND DISPERSION IN TRANSITION METAL COMPLEXES

7.3 INTRAMOLECULAR NCIs AS A STABILIZING FACTOR

7.4 FACE-SELECTIVE METAL COORDINATION TO AROMATIC LIGANDS

7.5 INTERMOLECULAR NCIs IN METAL–METAL DA COMPLEXES AND OTHER AGGREGATES

7.6 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

8 HALOGEN BONDING IN THE SYNTHESIS AND DESIGN OF COORDINATION AND ORGANOMETALLIC COMPOUNDS

8.1 INTRODUCTION

8.2 HALOGEN–HALOGEN BONDING

8.3 HALOGEN–NITROGEN INTERACTIONS

8.4 HALOGEN–CHALCOGEN BONDING

8.5 HALOGEN BONDING IN ORGANOMETALLIC COMPOUNDS

8.6 FINAL REMARKS

ACKNOWLEDGMENTS

REFERENCES

9 THE INFLUENCE OF NON-COVALENT INTERACTIONS IN THE STRUCTURE AND DIMENSIONALITY OF HYBRID COMPOUNDS AND COORDINATION POLYMERS

9.1 INTRODUCTION

9.2 NON-COVALENT INTERACTIONS IN LAYERED AND 3D OPEN FRAMEWORK ZIRCONIUM AMINOPHOSPHONATES

9.3 THE ROLE OF π

π STACKING IN THE ASSEMBLY, DIMENSIONALITY, AND STABILITY OF CPs

9.4 SUPRAMOLECULAR INTERACTIONS AFFECTING THE METAL COORDINATION

9.5 THE RELATIONSHIP BETWEEN NETWORK DIMENSIONALITY AND CATION SIZE

9.6 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

PART III: CRYSTAL DESIGN AND HOST–GUEST COMPOUNDS

10 DIHALOGENS AS HALOGEN BOND DONORS

10.1 INTRODUCTION

10.2 TYPICAL HALOGEN BOND DONORS

10.3 TYPICAL HALOGEN BOND ACCEPTORS

10.4 BASIC FEATURES OF DIHALOGENS

10.5 CHARGE TRANSFER AND DIHALOGENS

10.6 CASE STUDIES

10.7 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

11 CONSTRUCTION OF SUPRAMOLECULAR ASSEMBLIES BASED ON ANION–π INTERACTIONS

11.1 INTRODUCTION

11.2 PHYSICAL NATURE

11.3 EXAMPLES OF SUPRAMOLECULAR ASSEMBLIES

11.4 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

12 ASYMMETRIC AZAMACROCYCLES AS CHIRAL SOLVATING AGENTS

12.1 INTRODUCTION

12.2 BINOL-BASED CHIRAL MACROCYCLIC AMINES

12.3 CHIRAL MACROCYCLIC AMIDES

12.4 CHIRAL MACROCYCLIC AMINES

12.5 CHIRAL AZA-CROWN MACROCYCLES

12.6 FINAL COMMENTS

REFERENCES

13 NEW STRATEGIES FOR THE DESIGN OF INCLUSION COMPOUNDS WITH CUCURBITURIL HOSTS

13.1 INTRODUCTION

13.2 PROMINENT FEATURES OF CB

n

FOR HOST–GUEST CHEMISTRY

13.3 STIMULI-RESPONSIVE SUPRAMOLECULAR NANOSTRUCTURES

13.4 CONCLUDING REMARKS

ACKNOWLEDGMENTS

REFERENCES

14 PARALLEL INTERACTIONS OF AROMATIC MOLECULES AT LARGE HORIZONTAL DISPLACEMENTS

14.1 INTRODUCTION

14.2 PARALLEL WATER–AROMATIC INTERACTIONS AT LARGE HORIZONTAL DISPLACEMENTS

14.3 PARALLEL INTERACTIONS BETWEEN AROMATIC RINGS AT LARGE HORIZONTAL DISPLACEMENTS

14.4 CONCLUSIONS

ACKNOWLEDGMENTS

REFERENCES

15 SELECTIVE MOLECULAR BINDING AND NANOSUPRAMOLECULAR ASSEMBLY OF

p

-SULFONATOCALIX[

n

]ARENES

15.1 INTRODUCTION

15.2 SELECTIVE MOLECULAR BINDING

15.3 NANOSUPRAMOLECULAR ASSEMBLY

15.4 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

16 SYNTHESIS, DESIGN, CHARACTERIZATION, AND APPLICATION OF METALLO-SUPRAMOLECULAR POLYMERS

16.1 INTRODUCTION

16.2 SYNTHESIS OF MSPs

16.3 DESIGN OF MSPs

16.4 APPLICATIONS OF MSPs

16.5 CONCLUSIONS

ACKNOWLEDGMENTS

REFERENCES

PART IV: CATALYSIS

17 CATALYTIC APPLICATIONS OF METAL COMPLEXES IMMOBILIZED BY NON-COVALENT INTERACTIONS ONTO CHEMICALLY DERIVED GRAPHENES AND RELATED MATERIALS

17.1 INTRODUCTION

17.2 PREPARATION OF CDGs

17.3 FUNCTIONALIZATION BY NON-COVALENT INTERACTIONS

17.4 CATALYTIC APPLICATIONS

17.5 PERSPECTIVES

ACKNOWLEDGMENTS

REFERENCES

18 COOPERATION OF NON-COVALENT INTERACTIONS AND COORDINATION IN CATALYSIS

18.1 INTRODUCTION

18.2 HYDROGEN BONDING COOPERATION WITH COORDINATION

18.3 HALOGEN BONDING COOPERATION WITH COORDINATION OR HYDROGEN BONDING

18.4 COOPERATION OF COORDINATION WITH OTHER TYPES OF NON-COVALENT INTERACTIONS

18.5 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

19 HYBRID ORDERED MESOPOROUS MATERIALS AS SUPPORTS FOR PERMANENT ENZYME IMMOBILIZATION THROUGH NON-COVALENT INTERACTIONS

19.1 INTRODUCTION

19.2 NON-COVALENT METHODS OF ENZYME IMMOBILIZATION

19.3 ORDERED MESOPOROUS MATERIALS

19.4 NON-COVALENT IMMOBILIZATION OF ENZYMES ON ORDERED MESOPOROUS MATERIALS

19.5 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

PART V: BIORELEVANT SYNTHESES

20 MODULATION OF BIORELEVANT RADICAL REACTIONS BY NON-COVALENT INTERACTIONS

20.1 INTRODUCTION

20.2 SOLVENT EFFECTS IN RADICAL REACTIONS

20.3 QUANTITATIVE TREATMENT OF H-BOND STRENGTH IN SOLUTION: ABRAHAM’S SOLVATOCHROMIC PARAMETERS

20.4 EFFECT OF NON-COVALENT INTERACTIONS ON REACTIONS OF PHENOLIC ANTIOXIDANTS WITH PEROXYL RADICALS

20.5 EFFECTS OF NON-COVALENT INTERACTIONS ON THE REACTIVITY OF PHENOXYL RADICALS

20.6 EFFECTS OF NON-COVALENT INTERACTIONS ON THE REACTIONS OF ALKOXYL RADICALS WITH AMINES OR AMIDES

20.7 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

21 CURRENT UNDERSTANDING OF π–π INTERACTIONS AND THE APPLICATIONS IN PROTEIN DESIGN

21.1 INTRODUCTION

21.2 SIGNIFICANCE OF π–π INTERACTIONS IN PROTEIN FOLDING

21.3 π–π INTERACTIONS IN PEPTIDE ASSEMBLY

21.4 π–π INTERACTIONS IN PEPTIDE THERAPEUTICS

21.5 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

22 NON-COVALENT INTERACTIONS FOR THE PREPARATION OF PSEUDOPEPTIDIC SYNTHETIC COMPOUNDS AND MATERIALS

22.1 INTRODUCTION

22.2 NON-COVALENT INTERACTIONS IN THE PREPARATION OF CYCLIC PSEUDOPEPTIDES

22.3 PSEUDOPEPTIDES IN DYNAMIC COVALENT CHEMISTRY

22.4 NON-COVALENT INTERACTIONS IN PEPTIDE-LIKE FOLDAMERS

22.5 SELF-ASSEMBLED PSEUDOPEPTIDES FOR THE PREPARATION OF NANOSTRUCTURES

22.6 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

PART VI: MATERIAL CHEMISTRY

23 NON-COVALENT EXFOLIATION OF GRAPHITE TO PRODUCE GRAPHENE

23.1 INTRODUCTION

23.2 SOLID-PHASE EXFOLIATION

23.3 LIQUID-PHASE EXFOLIATION

23.4 CONCLUSIONS AND OUTLOOK

ACKNOWLEDGEMENTS

REFERENCES

24 ELECTROSTATIC INTERACTIONS IN THE DESIGN OF POLYMERIC PRODUCTS

24.1 INTRODUCTION

24.2 SYNTHETIC STRATEGIES

24.3 PROPERTIES OF IONOMERS

24.4 PERSPECTIVE IN FUTURE RESEARCH

REFERENCES

25 SUPRAMOLECULAR STERIC HINDRANCE AT BULKY ORGANIC/POLYMER SEMICONDUCTORS AND DEVICES

25.1 INTRODUCTION

25.2 FOUR-ELEMENT DESIGN PRINCIPLE

25.3 SSH IN ORGANIC SEMICONDUCTORS

25.4 EXTENSION OF SSH CONCEPT TO POLYMER SEMICONDUCTORS

25.5 FINAL COMMENTS

ACKNOWLEDGMENTS

REFERENCES

INDEX

END USER LICENSE AGREEMENT

List of Tables

Chapter 04

Table 4.1 Effect of an Anion on the Product Distribution of the Reaction between Diamines 3 and 4 and Diisocyanates 5 and 6

Table 4.2 Reaction Yields in the Synthesis of 22 Templated by Different Anions

Table 4.3 Distribution of Cyclic Oligomers Obtained by Oligomerization of Ethylene Oxide in the Presence of Anhydrous Salts

Chapter 05

Table 5.1 Hydrogen Bonds According to Jeffrey

Chapter 07

Table 7.1 Reaction Energies (see Scheme 7.1) Computed at Various Levels of Theory

Table 7.2 Calculated Thermochemical Parameters for Various Combinations of Monomers, in the Gas Phase as well as with a COSMO Solvation Treatment (Basis Set Superposition Error Was not Accounted For)

Table 7.3 Estimate of the Thermochemical Parameters for the Inclusion of Pt2 and Pd11 into CB[7] in the Gas Phase (ZORA-BLYP-D3/All Electron TZP) and in Water (COSMO Geometries, Treated with COSMO-RS) (Energies in kcal/mol; in case of Δ

S

f

Energy is in cal/(K∙mol))

Chapter 09

Table 9.1 Empirical Atomic Radius in Å for Alkaline Earth Metals [22]

Table 9.2 Overview of the Results of the CSD Search Using as Query the Fragment Shown in Scheme 9.6

Chapter 12

Table 12.1 Binding Constants of Host (

R

)-1a and (

R

)-1b for Selected Guests [12]

Table 12.2 Chemical Shift Difference (ΔΔ

δ

) Between Enantiomers of

rac-

Alcohols (56–66) in the Presence of (

S,S,S,S,S,S

)-41 or (

S,S,S,S,S,S

)-43 in CDCl

3

Table 12.3 Absolute Configuration of Enantiomer Showing More Up-field Shift in the

1

H-NMR Spectra in the Presence of (

S,S,S,S,S,S

)-41 or (

S,S,S,S,S,S

)-43

Table 12.4 Partial

1

H-NMR Spectra of

rac-

Phenylacetic Acid Derivatives 3, 4, 18, 45 in the Presence of 0.25 eq. of 67 and 68

Table 12.5 Partial

1

H NMR Spectra of

rac-

Propionic Acid Derivatives 51a–c in the Presence of 0.25 eq. of 67 and 68

Table 12.6 Partial

1

H NMR Spectra of

rac

-α-Amino Acid Derivatives 69a–d, 70e–d, 71, 72, 73 in the Presence of 0.25 eq. of 67 and 68

Table 12.7 Measurement of

1

H Chemical Non-equivalencies (ΔΔ

δ

) of the Guests in the Presence of (

S,S,S,S,S,S

)-74 by

1

H NMR Spectroscopy (400 MHz) in CDCl

3

at 25°C

Table 12.8

1

H-NMR Chemical Shift Nonequivalences for Mandelic Acid Derivatives

a

Chapter 14

Table 14.1 Geometrical Parameters for OH/π, CH

O, Parallel Alignment, and Lone-Pair/π Interactions and Their Presence in Crystal Structures Found in the CSD

Table 14.2 Interaction Energies and Geometrical Parameters Calculated at Various Levels of Theory for Water–Benzene Parallel Alignment Interactions

Table 14.3 SAPT Interaction Energy Decomposition for Water–Benzene Parallel Alignment Interactions

Table 14.4 ETS/PBE-D3 Interaction Energy Decomposition Water–Benzene Parallel Alignment Interactions

Table 14.5 Influence of Parallel-Up Interaction on Other Water–Benzene Interactions

Table 14.6 Interaction Energies and Geometric Parameters of Parallel-Down Interactions of Benzene with Uncoordinated Water and Coordinated Water (Aqua Complexes of Different Charges)

Table 14.7 Interaction Energies Between Benzene Molecules with Different Interplanar Angles at Different Offsets

Table 14.8 Comparison of Energies of Benzene–Benzene, Pyridine–Pyridine, and Benzene–Pyridine Interactions at Different Horizontal Displacements

Chapter 15

Table 15.1 Complex Stability Constants (

K

S

/M), Standard Enthalpy (∆

H

°/(kJ/mol)), and Entropy Changes (

T∆S°

/(kJ mol)) for Intermolecular Complexation of Organic Ammonium Cations with SC

n

As in Aqueous Solution at 298.15 K [13]

Table 15.2 Complex Stability Constants (

K

S

/M), Standard Enthalpy (∆

H

°/(kJ/mol)), and Entropy Changes (

T∆S°

/(kJ/mol)) for Intermolecular Complexation of Aromatic Cationic Guests with SC

n

As in Aqueous Solution at 298.15 K [22, 23]

Table 15.3 Complex Stability Constants (

K

S

/M) for Intermolecular Complexation of Amino Acids with SC

n

As in Aqueous Solution at 298.15 K [11]

Chapter 16

Table 16.1 Binding Constants of Zn

II

, Fe

II

, and Co

II

Complexes with Different Types of Polypyridine Ligands

Table 16.2 Important 4′-Substituted TPY

Chapter 17

Table 17.1 General Properties of Graphene Materials

Chapter 19

Table 19.1 Immobilization of Lipase on Siliceous and Hybrid OMSM with Channel-Like Pores (Upper Part of Table), Amorphous Silica (Center), and OMSM with Cage-Like Pores (Bottom Part of the Table)

Table 19.2 Immobilization of Laccase on SBA-15 and Amorphous Silica Supports

Table 19.3 Laccase Immobilization on OMM Materials Functionalized with Amine Groups

Chapter 20

Table 20.1 Rate Constants for the Reaction between Phenols and Peroxyl Radicals in Two Solvents Having Different H-Bond Accepting Ability, as a Function of the H-Bond Donating Ability (

α

2

H

) of the Phenol

Table 20.2 Rate Constants for the Reaction with Alky Peroxyl Radicals at 30°C in Chlorobenzene and Strength of the Intramolecular H-Bond

Table 20.3 Equilibrium Constant for the H-Bond with 1,1,1,3,3,3-Hexafluoropropan-2-ol (HFP) and H-Bond Accepting Ability of Phenoxyl Radicals [42]

Table 20.4 Rate Constants for the Reaction of CumO∙ and Et

3

N Measured by the LFP Technique

List of Illustrations

Chapter 01

Scheme 1.1 Some modes of covalent bond activation by hydrogen bonds.

Scheme 1.2 C

C cleavage in 2-hydroxy-6-keto-6-phenyl-hexa-2,4-dienoic acid [10, 11].

Scheme 1.3 Acetylacetone dioxygenase (Dke1)-catalyzed oxidative C

C cleavage in acetylacetone (

retro

-Claisen reaction) (a) [9]; regioselective H-bond-assisted C

C cleavage in β-diketones (b) [12].

Scheme 1.4 Regioselective C

C cleavage in (

E

,

Z

)-2-(2-(4-substitutedphenyl) hydrazono)-4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione [13].

Scheme 1.5 Cope-type hydroamination of alkenes [14, 15].

Scheme 1.6 Asymmetric Michael reaction between chalcone and diethyl malonate [16].

Scheme 1.7 Hydrogen bond-assisted enantio- and diastereoselective synthesis of vinylcyclopropanes [18].

Scheme 1.8 Enantioselective cyclization of acetylenic β-dicarbonyl compounds [21].

Scheme 1.9 Activation/isomerization of alkynoates [22].

Scheme 1.10 Polypeptide hydrolysis within aspartic proteases [24].

Scheme 1.11 Hydrolysis of nitriles with the Glu–Lys–Cys catalytic triad [25].

Scheme 1.12 Stereoselective synthesis of enantioenriched α,β-diamino acids via a chiral imine complex of Ni(II) with sulfones [28].

Scheme 1.13 Diastereoselective reduction of diaryl

N-tert

-butanesulfinylketimines to nonracemic 1,3-diamines [30].

Scheme 1.14 Proposed dual H-bond-assisted activation for the asymmetric aza-Henry reaction of nitroethane with ketimines [33].

Scheme 1.15 Regioselective activation of C≡N bonds in an arylhydrazone of malononitrile [36].

Scheme 1.16 Proposed [37] mechanism for the direct synthesis of tetrazoles.

Scheme 1.17 Possible ways for the 1,3-dipolar cycloaddition of nitrile oxides to acetonitrile [40].

Scheme 1.18 Reaction of

rac

-(1-naphthyl)(trifluoromethyl)

O

-carboxy-anhydride with (

R

)-

α

-methylbenzylamine [41].

Scheme 1.19 Hydrogen bonding in the hydrolysis of ethers [42].

Scheme 1.20 Proline-catalyzed asymmetric aldol reaction [45].

Scheme 1.21 C

H

O interaction-directed asymmetric Hajos–Parrish reaction [47].

Scheme 1.22 Synthesis of benzofurans based on non-covalent interactions of Brønsted acids with hexafluoroisopropanol [49].

Scheme 1.23 Hydrolysis of thioether to citrate in the Krebs cycle.

Scheme 1.24 Keto–enol tautomerism in 4-thioxopentan-2-one.

Scheme 1.25 Regioselective synthesis of (2

Z

,4

E

)-4-(2-phenylhydrazono)pent-2-en-2-ol [53].

Scheme 1.26 Synthesis of

N

-arylaziridine [55].

Scheme 1.27 Reduction of 2-phenylquinoline [56].

Scheme 1.28 Baylis–Hillman reaction [58].

Scheme 1.29 Synthesis of

N

-benzhydryl acetamide [59].

Scheme 1.30 Asymmetric Pummerer reaction [62].

Scheme 1.31 Selective synthesis of (

E

,

Z

)-

N

-(5-phenyl-3H-1,2-dithiol-3-ylidene)ethan-ethioamide (I) and its isomerization (II) [63, 64].

Chapter 02

Scheme 2.1 Ionization equilibrium of boronic acid in water.

Figure 2.1 Representation of benzene’s inorganic analogue borazine, 6, and the hybrid azaborines 7, 8, and 9.

Scheme 2.2 Borazine representation: bond lengths and resonance structures showing the delocalization of the nitrogen electrons.

Figure 2.2 Hexagonal multilayer structure of h-boron nitride; resembles graphite structure but with the added properties of the polarization of the BN bond.

Figure 2.3 Structure and detonation performance of diazidonitroamine borazines 11 and 12 in comparison to a standard explosive 10.

Scheme 2.3 First reported synthesis of a BN isostere of an aromatic compound.

Figure 2.4 Examples of biologically active boron compounds.

Figure 2.5 Library of aromatic analogues synthesized by Dewar

et al

. [42]

.

Figure 2.6 Electronic and optically active compounds comprising an azaborine moiety in their structure.

Figure 2.7 Protecting groups for boronic acids and benzoxaborole.

Figure 2.8 General structure of the possible products of the reaction between the salen tri- and tetradentate ligands and boronic acid.

Figure 2.9 Examples of bioactive BN heterocycles.

Figure 2.10 BN analogues of nucleic acid bases for application in BNCT.

Figure 2.11 Examples of BN frustrated Lewis pairs.

Figure 2.12 Heterocyclic borenium ion catalysts.

Figure 2.13 Boryl radicals 46 and 47 with benzoquinone and benzoyl peroxide.

Figure 2.14 General structures of BODIPYs and analogues [128].

Figure 2.15 General structure of boron subphthalocyanines 48 and examples of other luminescent BN heterocycles: boron porphyrin complex, 49, and 1,3,2-diazaboroline, 50.

Scheme 2.4 Hydrogen release conditions for 1,2-BN-cyclohexane (a) and 3-methyl-1,2-BN-cyclopentane (b).

Figure 2.16 BN macrocycles and cages 55–57.

Figure 2.17 Pentameric boroxine cage 58.

Scheme 2.5 Synthesis of macrocyclic boracycles 59 and 60.

Figure 2.18 BN polymers 61–64 and their applications.

Figure 2.19 BN polymers 65–67.

Figure 2.20 BN organogels 68–70.

Scheme 2.6 Construction of bioconjugates 71

via

an iminoboronate function.

Scheme 2.7 Folic acid modification with fluorescent boronic acids. Construction of BN-based cancer cell targeting fluorescent conjugates 72.

Scheme 2.8 Supramolecular protecting system for enzymes based on the reversible nature of the BA–SHA system.

Figure 2.21 Construction of bioconjugates 74 from immobilization of HRP or AP into a chromatographic support (sepharose).

Scheme 2.9 Complexation of the phenyldiboronic acid–PEG-linked peptide (CNGRC) and the salicylhydroxamate polyethylenimine/DNA-bgal vector to construct vector 75.

Scheme 2.10 Mechanisms for the fluorescence intensity changes for the amino anthracene fluorophore.

Figure 2.22 Wulff-type aza-crown ether boronic acids with specific fluorescence increase upon binding with

D

-glucosamine.

Figure 2.23 Wulff-type diboronic acids: compound 84, diboronic acid PET sensor chelating a glucose molecule; compound 85, metal-chelating diboronic PET sensor.

Figure 2.24 Compound 86,

D

-glucuronic acid-selective fluorescent system and metal chelate; compound 87, diboronic acid with a phenanthroline spacer.

Figure 2.25 Compound 88, two-dimensional PET sensor; compound 89, chiral recognition by a di-Wulff-type boronic acid.

Scheme 2.11 ROS detection based on the PET sensor.

Scheme 2.12 Water detection in organic solvents using a PET sensor.

Scheme 2.13 Dopamine detection using a PET sensor.

Scheme 2.14 Fluorescence intensity changes for the naphthalimide fluorophore.

Scheme 2.15 Wang

et al.

’s study of the naphthalimide fluorophore.

Figure 2.26 ICT sensor–aminocoumarin chromophore.

Figure 2.27 Colorimetric sensor based on ICT chromophore.

Scheme 2.16 Proposed equilibria for the ICT sensor.

Figure 2.28 Saccharide recognition–response ICT sensor in aqueous methanol at pH 8.

Scheme 2.17 Spirobenzopyran boronic acid colorimetric sensor.

Figure 2.29

Ortho

boronic acid-substituted azobenzene.

Figure 2.30 Compound 116, intermolecular BN interaction with a color change upon saccharide binding; compound 117, colorimetric sensor complex bearing a compound with a BN interaction and alizarin complexone.

Scheme 2.18 Interaction between the reported polymer 118 and saccharides in different pH environments.

Chapter 03

Scheme 3.1 β-phenylethylamines.

Scheme 3.2 The Pictet–Spengler reaction.

Scheme 3.3 Tetrahydroisoquinoline synthesis from dopamine.

Scheme 3.4 Reaction of 6,7-dimethoxiphenylethylamine with 3-nitrobenzaldehyde.

Scheme 3.5 Reaction of

m

-tyramine with aldehydes.

Scheme 3.6 Reaction of

L

-tyrosine ethyl ester with formaldehyde.

Scheme 3.7 Mannich-type reaction of

L

-tyrosine with formaldehyde in basic medium.

Scheme 3.8 Molecular preorganization by self-assembly of

L

-tyrosine derivatives via intermolecular hydrogen bonds.

Scheme 3.9 Hydrogen bonds for dimer formation.

Scheme 3.10 Crystal packing of

L

-tyrosine isopropyl ester. The O

H

N hydrogen bonds are shown as dashed green lines, and N

H

O hydrogen bonds are shown as dashed lines.

Scheme 3.11 Reaction of tyramine with formaldehyde.

Scheme 3.12 ORTEP diagram for tyramine.

Scheme 3.13 The extended hydrogen bond network in tyramine crystal structure. The O

H

N hydrogen bonds are shown as dashed lines, and N

H

O hydrogen bonds are shown as dashed yellow lines.

Scheme 3.14

L

-Tyrosine reaction with formaldehyde in basic medium.

Scheme 3.15

L

-Tyrosine behavior in basic aqueous medium.

Scheme 3.16

L

-Tyrosine tetrabutylammonium reaction with formaldehyde.

Scheme 3.17

L

-Tyrosine tetrabutylammonium behavior in acetonitrile.

Scheme 3.18 β-Phenylethylamine reaction with formaldehyde.

Scheme 3.19 β-Phenylethylamine reaction with aromatic aldehydes.

Scheme 3.20

N

-Benzylazacyclophane synthesis.

Scheme 3.21

N

-(3-Nitrobenzyl)tyramine reaction with formaldehyde.

Chapter 04

Scheme 4.1 Iodide-templated synthesis of Hg(II) complex 1 and the synthesis of cyclooctapyrrole 2 in the presence of sulfate anions.

Scheme 4.2 Synthesis of polyuria macrocycles 8–10.

Scheme 4.3 Structures of precursors for the chloride-templated synthesis of imidazoliophanes.

Scheme 4.4 Synthesis of macrocycles 21 and 22 and the proposed transition states.

Scheme 4.5 Synthesis of macrocycles 23, 26, and 27.

Scheme 4.6 Self-templating macrocyclization producing chloride complexes 30a and b.

Scheme 4.7 Formation of macrocycles 33 and 34 without and with the chloride anion, respectively. Structures of the proposed intermediates 35 and 36 are also shown.

Scheme 4.8 Synthesis of C5-symmetric cyanostar macrocycle 37.

Scheme 4.9 Synthesis and structure of receptors 40, 42, and 44.

Scheme 4.10 Synthesis and structures of bambusurils, which bind anions with high affinity.

Scheme 4.11 Proton-templated synthesis of macrocycles 48a–c.

Scheme 4.12 Synthesis of cyclopeptide 51.

Scheme 4.13 Synthesis of sugar-containing macrocycles 55 and 56.

Scheme 4.14 Reactions investigated to synthesize 58 and 59.

Scheme 4.15 Synthesis of sugar-containing macrocycle 63.

Scheme 4.16 Cyclo-oligomerization of amino acids 64 and 65.

Scheme 4.17 Synthesis of cyclic ureas 69–71.

Scheme 4.18 Hydrogen bond-directed synthesis of macrocycle 74.

Scheme 4.19 Reaction of monomers and dimers to form oligomers.

Scheme 4.20 Hydrogen bond-directed synthesis of macrocycles 86–89.

Scheme 4.21 Synthesis of rigid cyclic peptides.

Scheme 4.22 Synthesis of macrocycles 97, 98, and 101 from diacids and diamines.

Scheme 4.23 Proposed pathway for the formation of macrocycle 105.

Scheme 4.24 Synthesis of pillar[n]arenes and their interconversion under thermodynamic control.

Scheme 4.25 Amino acid-templated synthesis of macrocycle 111.

Chapter 05

Figure 5.1 Ordered ice-like structures for 2/3 ML of water on Pt(111). The left figure is the traditional bilayer structure (denoted as H-up bilayer) with half of the water parallel to the surface and bonded through the O lone pair directly to a Pt atom. The right figure shows the H-down bilayer structure in which the perpendicular waters (HOH) are in H-down configuration forming an agostic Pt

HOH bond.

Figure 5.2 Distance distribution from the central atom.

Figure 5.3 Water oxygen–cation–water oxygen bond angle distributions calculated for aqueous solutions of Rb

+

(0.1 M RbBr), Cu

2+

(0.5 M Cu(ClO

4

)

2

), Cr

3+

(1.0 M Cr(NO

3

)

3

), Y

3+

(1.0 M YCl

3

), and La

3+

(1.0 M LaCl

3

). These distributions correspond to hydration shells of no specific geometry for Rb

+

, tetrahedral (plus components of trigonal bipyramidal and distorted octahedral) geometry for Cu

2+

, octahedral geometry for Cr

3+

, square antiprism geometry for Y

3+

, and tricapped trigonal prism geometry for La

3+

.

Figure 5.4 Trigonal first-shell structure and mostly tetrahedral structure in the second shell and beyond. A limited number of waters drawn for clarity.

Figure 5.5 Spatial density functions highlighting the most probable regions around a water molecule to find an Rb

+

cation or a Br

anion in a 0.002 mole fraction aqueous solution of RbBr.

Scheme 5.1 Possible anionic and cationic interaction modes between a water molecule and a square-planar Pt

2+

center. Definition of the axial region used in the analysis.

Figure 5.6

cis

-[PtCl

2

(NH

3

)

2

]·H

2

O complex in the “H-ahead” orientation for d(Pt

O) = 3.4 Å.

Figure 5.7 Spatial distribution functions around the [Pd(OH

2

)

4

]

2+

. Pd (green sphere), coordinated oxygen atoms (blue spheres). Right, water oxygen atoms (red surfaces); left, perchlorate chlorine atoms (purple surfaces).

Scheme 5.2 Possible pathways for the H

H splitting mediated by [CpRu(PTA)

2

Cl].

Figure 5.8 Gibbs energy profile in water for the chloride by H

2

ligand exchange, starting from [CpRu(PTA)

2

Cl] and leading to the formation of the dihydrogen complex {[CpRu(PTA)

2

2

-H

2

)](H

2

O)

3

}.

Figure 5.9 Complex unit single crystal X-ray structure of [RuCp(PTA)

2

-μ-CN-1κ

C

:2κ

2

N

-RuCp(PTA)

2

]

+

, including the atomic labelling scheme. For clarity hydrogen atoms are not included.

Figure 5.10 Pair correlation functions extracted through EPSR simulation for water around [RuCp(PTA)

2

-μ-CN-1κ

C

:2κ

2

N

-RuCp(PTA)

2

]

+

. These functions express the probability of finding an atom at a given distance from another atom. Probability to find water oxygen (Ow, full line) or water hydrogen (Hw, dashed line) around three atoms belonging to [RuCp(PTA)

2

-μ-CN-1κ

C

:2κ

2

N

-RuCp(PTA)

2

]

+

, namely, H and C on the Cp ligand and N on the PTA ligand. Lines have been shifted vertically for clarity.

Figure 5.11 Spatial distribution functions for water molecules around cyclopentadiene ligand [107, 108]. The yellow cloud represents the region where the probability of finding a water molecule exceeds 50% (regardless of its orientation). The left panel is restricted to distance 3.5–4.5 Å from the central Ru atom, while the right-hand panel explores the region between 4.5 and 6.0 Å.

Figure 5.12 Experimental and TD-DFT UV-vis absorption spectra (5 × 10

−4

 M). The thin vertical lines represent the energies of the individual TD-DFT excitations.

Chapter 06

Figure 6.1 Electrostatic model of the quadrupole moments of benzene.

Figure 6.2 Stacking patterns in benzene rings: (a) face-to-face (sandwich), (b) edge-to-face (T-shaped), and (c) offset face-to-face (parallel-displaced).

Scheme 6.1 Synthesis of a pyrene-tagged ruthenium carbene complex 1 [42].

Scheme 6.2 Pyrene-tagged ruthenium carbene complex 1 anchored on the surface of SWCNTs via π–π interactions [42].

Scheme 6.3 Ring-closing metathesis reaction catalyzed by [email protected] [42].

Scheme 6.4 Synthesis of pyrene-modified pyrphos ligand 3 [43].

Scheme 6.5 Asymmetric hydrogenation of α-dehydroamino esters catalyzed by [Rh(COD)

2

]BF

4

@3 [43].

Scheme 6.6 Electrocatalytic oxidation of water by a monomeric ruthenium catalyst [email protected] [44].

Scheme 6.7 Edge-to-face aromatic π–π interaction in an optically active diruthenium–allenylidene complex 5 [45].

Scheme 6.8 Enantioselective propargylic substitution reactions of propargylic alcohols with nucleophiles catalyzed by Ru–Cat [45].

Scheme 6.9 Synthesis of a pyrene-tagged gold complex 6 [46].

Scheme 6.10 Cycloisomerization of enyne catalyzed by [email protected] [46].

Scheme 6.11 Ni(II) complexes 7 and 8 with pyrene-based ligand [47].

Figure 6.3 π–π stacking interaction between the adjacent pyridine rings in 9 [49].

Figure 6.4 π–π stacking interaction in 10 [50].

Scheme 6.12 Ligands used in the syntheses of Cu(II) complexes 11–17; (a) 1,10-phenanthrolin-2-ol (PhenOH) (b) 2-(1

H

-pyrazol-1-yl)-1,10-phenanthroline (PhenP) (c) 2-(1

H

-1,2,4-triazol-1-yl)-1,10-phenanthroline (PhenTA) (d) 2-(3-methyl-pyrazol-1

H

-yl)-1,10-phenanthroline (PhenMP) (e) 2-(3-amino-pyrazol-1

H

-yl)-1,10-phenanthroline (PhenAP) [55].

Figure 6.5 π–π stacking in mononuclear manganese(II) complex 18 [56].

Figure 6.6 π–π interaction and hydrogen bonding in a mononuclear manganese(III) complex 19 (solvent molecules are omitted) [57].

Figure 6.7 π–π interaction and hydrogen bonding in the binuclear manganese(III) complex 20 (perchlorate ions and solvent molecules are omitted) [57].

Figure 6.8 π–π interactions exhibited by [NiL

2

]·0.5Me

2

CO (21, solvent molecules are omitted) [58].

Figure 6.9 Intramolecular π–π stacking interaction in (a) complex 22, (b) complex 23, and (c) complex 24 (hexafluorophosphate anions are omitted) [66].

Figure 6.10 Intramolecular face-to-face π-stacking in (a) complex 25 and (b) complex 26 (hexafluorophosphate anions are omitted) [68].

Figure 6.11 Pt

Pt chain structures and π–π interactions in (a) complex 27 (H-atoms are omitted), (b) complex 28, and (c) complex 29 (H-atoms are omitted) [69].

Figure 6.12 Molecular structure of the platinum(II) complex 30 [70].

Figure 6.13 Molecular structure of the platinum(II) complex 31 [70].

Chapter 07

Scheme 7.1 Reaction of phosphanes with a μ-chloro-bridged palladacycle derived from 2-phenylpyridine [50].

Figure 7.1 Singlet ground state geometries (PBE-D3/def2-TZVP) of the palladacyclic dimer (a) and its associated phosphane adducts (b: R = Ph, c: R = Cy). Note that the dimer in the solvent cavity as well as in the gas phase is not planar at its energy minimum but slightly folded. (a) The starting dimer; (b) the PPh

3

adduct; (c) the PCy

3

adduct.

Figure 7.2 London dispersion contribution to the reaction energy (from TPSS-D3/TZVP [64]) with respect to the interatomic pair distance.

Scheme 7.2 The thermolythic treatment of azulene L1 leads to syn-facial complexes Mo1, Fe1, and Mn1.

Scheme 7.3 Thermolytic treatment of Mo2 with (Me

3

CN)

3

Cr(CO)

3

, [RhCl(CO)

2

]

2

, and Fe

2

(CO)

9

leads to syn-facial heterobimetallics Cr1, Rh1, and Fe1.

Scheme 7.4 The thermolytic treatment of Cr2 with various labile (MeCN)

3

M(CO)

3

complexes produces the syn-facial complexes Cr3 and Mo3.

Scheme 7.5 The thermolytic treatment of L2 produces the syn-facial homometallic complexes Co1 and Fe2.

Figure 7.3 ADFview2013 plots of non-covalent interaction (NCI) regions materialized by reduced density gradient isosurfaces (cutoff value

s

 = 0.02 a.u.,

ρ

 = 0.05 a.u.) colored according to the sign of the signed density

λ

2

ρ

(red and blue colors are associated to negatively and positively signed terms) for gas phase relaxed singlet ground state models of Rh1, Mo1, Cr1, Fe1, Mo4, Cr3. Calculations were performed with the gas phase singlet ground state geometry optimized at the ZORA-TPSS-D3(BJ)/all electron TZ2P level within the ADF2013 package [75a]. Experimental and computed intermetal distances are provided along with the computed Wiberg bond indices.

Figure 7.4 ADFview2013 plots of non-covalent interaction (NCI) regions materialized by reduced density gradient isosurfaces (cutoff value

s

 = 0.02 a.u.,

ρ

 = 0.05 a.u.) for gas phase relaxed singlet ground state models of Co1 and Co

2

(CO)

8

. Calculations were performed with the gas phase singlet ground state geometry optimized at the ZORA-TPSS-D3(BJ)/all electron TZ2P level within the ADF2013 package [75a]. Experimental and computed intermetal distances are provided along with the computed Wiberg bond indices.

Scheme 7.6 Synthesis of Ceccon’s heterobimetallic complexes Rh2–5 from Cr4.

Scheme 7.7 Ligand exchange at Rh6 that leads to Rh3 upon isomerization.

Scheme 7.8 Proposed mechanism of isomerization of complex Rh7 into Rh4 catalyzed by Lewis acidic rhodium(I) and iridium(I) salts.

Scheme 7.9 The treatment of Ir1 at room temperature with (MeCN)

3

Cr(CO)

3

affords syn-facial complex Ir2.

Figure 7.5 ADFview2013 plot of non-covalent interaction (NCI) regions materialized by reduced density gradient isosurfaces (cutoff value

s

 = 0.02 a.u.,

ρ

 = 0.05 a.u.) for gas phase relaxed singlet ground state models of Rh8. Calculations were performed with the gas phase singlet ground state geometry optimized at the ZORA-TPSS-D3(BJ)/all electron TZP level within the ADF2013 package [75a]. Experimental and computed intermetal distances are provided along with the computed Wiberg bond indices.

Figure 7.6 (a) Schematic definition of the concept of hemichelation; (b) the stabilizing non-covalent interactions in hemichelates based on the tricarbonyl(η

6

-benzyl)chromium anion operate in solution as well as in the solid state mostly through the support of attractive coulombic interactions.

Scheme 7.10 Kalinin’s synthesis of syn-facial complexes Pd1 and Pd2 from Zn1 and Zn2, respectively [98].

Scheme 7.11 Synthesis of hemichelates Pd3–5 from the reaction of anion Cr5 with μ-chlorido-bridged palladium(II) allyl complexes [100].

Scheme 7.12 Synthesis of hemichelates Pd6–10 and Pt1 from anion Cr5 and a range of μ-chlorido-bridged pallada- and platinacycles [96].

Scheme 7.13 The acidic demetallation of fast exchanging Pd8 produces enantioenriched Cr6, of which the enantiomeric excess is temperature dependent [96].

Scheme 7.14 Synthesis of Rh(I) hemichelates Rh9 and Rh10 from the reaction of anion Cr7 with [(NBD)RhCl]

2

and [(CO)

3

RhCl]

2

, respectively [95].

Scheme 7.15 Synthesis of Mn(I) hemichelates Mn6–7 by the derivation of tetracarbonyl manganacycle derived from 2-phenylpyridine Mn2 by insertion of a Fischer-type carbene into the C

Ar

Mn bond.

Scheme 7.16 The electron-unsaturated complex Mn8 equilibrates with complex Mn9 in solution.

Figure 7.7 ADFview2013 plot of non-covalent interaction (NCI) regions materialized by reduced density gradient isosurfaces (cutoff value

s

 = 0.02 a.u.,

ρ

 = 0.05 a.u.) for gas phase relaxed singlet ground state models of Mn10. Calculations were performed with the gas phase singlet ground state geometry optimized at the ZORA-TPSS-D3(BJ)/all electron TZP level within the ADF2013 package [75a]. Experimental and computed intermetal distances are provided along with the computed Wiberg bond indices.

Scheme 7.17 Synthesis of Ru and Os complexes with M

E dative bond; M = Ru, Os; E = P, Sb, As.

Scheme 7.18 Possible mechanism of (PPh

3

)(CO)

4

Os

Os(Cl)(CO)

3

GeCl

3

complex formation.

Scheme 7.19 Synthesis of Pomeroy’s compounds with formation of dative Os

M bond; M = Re, Cr, W.

Scheme 7.20 Synthesis of (η

5

-C

5

Me

5

)(CO)

2

Ir-W(CO)

5

complex Ir3.

Figure 7.8 (a) ADFview2008 drawings of interacting resulting bonding HOMO Kohn–Sham orbitals of Os–Cr complex Os1. Orbitals related to the complex are depicted here with an isosurface contour value of 0.04 e bohr

−3

(ZORA-BP-D2/all electron TZP level) [119]. (b–d) ADFview2013 [75a] plots of non-covalent interaction (NCI) regions materialized by reduced density gradient isosurfaces (cutoff value

s

 = 0.02 a.u.,

ρ

 = 0.05 a.u.) colored according to the sign of the signed density

λ

2

ρ

(red and blue colors are associated to negatively and positively signed terms) for gas phase relaxed singlet ground state ZORA-TPSS-D3(BJ)/all electron TZ2P level models of Os1 (b), Os2 (c), and Ir3 (d). Experimental and computed intermetal distances are provided along with the computed Wiberg bond indices.

Scheme 7.21 Formation of the oligomers in the Rh(I) square-planar complexes.

Figure 7.9 Optimized singlet ground state structures for the three conformers (a–c) of [Rh11]

2

2+

[24e].

Figure 7.10 Singlet ground state DFT geometries of [Rh11]

2

2+

computed with (a) and without (b) dispersion correction [24e].

Figure 7.11 Formulas of complexes Pt2 (oxaliplatin), Pd11, and Pt3 (carboplatin).

Figure 7.12 (a) Relative total bonding energies for

α

,

β

, and

γ

geometries of dimers of Pt2, Pd11, and Pt3. (b) Explicit geometries of

α

,

β

, and

γ

arrangements for [Pt2]

2

.

Figure 7.13 (a) NOCV deformation density Δ

ρ

1

(left—Δ

ε

orb

 = −5.84 kcal/mol and

ω

 = 15%), Δ

ρ

2

(right—Δ

ε

orb

 = −4.07 kcal/mol;

ω

 = 11%); Δ

E

orb

—orbital stabilization energy for corresponding deformation density Δ

E

torb

—energy of total orbital interactions in the corresponding dimer

ω

—percentage of Δ

E

orb

in the Δ

E

torb

. (b) ADFview2013 plots of non-covalent interaction (NCI) regions indicated by

reduced density gradient

isosurfaces (cutoff value

s

 = 0.02 a.u.,

ρ

 = 0.05 a.u.) colored according to the sign of the signed density

λ

2

ρ

(red and blue colors are associated to negatively and positively signed terms) for the gas phase relaxed singlet ground state model of Pt-containing complexes β-[Pt2]

2

. All calculations were performed with gas phase singlet ground state optimized geometries at the ZORA-BLYP-D3/all electron TZP level. Non-covalent N

H

O bonds are materialized by attractive non-covalent red-colored isosurfaces. Blue isosurfaces are assigned to van der Waals interactions or to Pauli repulsion.

Chapter 08

Scheme 8.1 Schematic description of the electron density distribution of covalently bound halogens (a) and the expected halogen bonding intermolecular interactions (b) [6].

Scheme 8.2 Synthesis of halogen bond-assisted adduct and its hydrolysis [10].

Scheme 8.3 Formation of 1D infinite networks through halogen bonding-driven self-assembly [11].

Scheme 8.4 Halogen bond-assisted synthesis of 5a; multiple halogen bond interactions in 5b.

Scheme 8.5 Comparison of enthalpies and entropies of formation of C

I

F

Ni halogen and N

H

F

Ni hydrogen bonds determined by NMR titration in solution [16].

Scheme 8.6 Synthesis and synthon interactions in 6–10 [18].

Scheme 8.7 Cooperation of coordination, hydrogen, and halogen bonding, in the synthesis of 10–12 [12].

Scheme 8.8 Cl

Cl interactions in 11–13; DMSO molecules are omitted for clarity [12].

Scheme 8.9 Coordination, hydrogen, and halogen bond-assisted synthesis of 14–16 [21].

Scheme 8.10 Halogen bonding in 17–19 [22].

Scheme 8.11 Supramolecular chains in 20 consisting of

N

-methyl-3,5-diiodopyridinium cations and [Ru(bipy)(CN)

4

]

2−

anions connected by C–I

N(cyano) halogen bonds [24].

Scheme 8.12 Synthesis and structure of 21 showing C

Br

N and C

Br

O halogen bonds [25].

Scheme 8.13 Synthesis of coordination polymers 22 and 23 [26, 27].

Scheme 8.14 Halogen bonding in 24 and 25 [28].

Scheme 8.15 (a) Schematic representation of the self-assembly of TFDIB with [Fe(acacPy)

3

] and [Al(acacPy)

3

]·3H

2

O; (b) Shortest intermolecular contacts in 27 are due to hydrogen bonds (A) and O

I (B) and N

I (C) interactions [29].

Scheme 8.16 Synthesis and supramolecular chains in the structure of 28 formed through C

Br

SCN halogen bonds [30].

Scheme 8.17 Synthesis of hydrogen and halogen bond-assisted supramolecular networks in 29 and 30 [31].

Scheme 8.18 Synthesis of 31–34, and halogen bonding pairs in their supramolecular structures. A Cl

O

C halogen bond with a molecule of acetone is also shown in 32 [32].

Scheme 8.19 Halogen bonding in the structure of 35. Both C

I

O (carboxylato) and C

I

O (ether) act in pairs. The noncoordinated molecules of 1,4-dioxane as well as hydrogen atoms have been omitted for clarity [33].

Scheme 8.20 Synthesis of 36 and 37 under hydrothermal conditions [34].

Scheme 8.21 Halogen and hydrogen bonding in the structure of 38 [36].

Scheme 8.22 Cl

N halogen bonding in the crystal structure of [AlCl

3

(C

3

N

3

Cl

3

)], 39 [37].

Scheme 8.23 Synthesis (a) and halogen bonding in the structures of 40 and 41 (b) [38].

Scheme 8.24 Halogen-bonded zigzag chains in the structures of 42 and 43 [39].

Scheme 8.25 Synthesis of 44 and 45 (a); C

I

F halogen bonding between the BF

4

anion and [Ru(

C

CHI)(Ph

2

PCH

2

CH

2

PPh

2

)(Cp

*

)]

+

cation (b) [40].

Scheme 8.26 Synthesis of 46 (a); 1D arrangement in 46 through halogen bonding Mg─Cl⋯I─C interactions (b) [41].

Chapter 09

Scheme 9.1 The six classes of dynamic coordination polymers.

Figure 9.1 Polyhedral representation of α-zirconium phenylphosphonate (a) and representation of the layer surface in α-type zirconium phosphonates (b).

Figure 9.2 Scheme of a layered diphosphonate in which both phosphonic groups are bonded to the same face of the inorganic layer and the organic pendants occupy the interlayer space.

Figure 9.3 Polyhedral structure of C5 viewed along the

b

-axis.

Figure 9.4 Layer framework found for layered zirconium biphosphonates, in which the zwitterionic character of the diphosphonate moiety and the non-covalent interactions are shown.

Figure 9.5 Polyhedral representation of the structure of Zr bisphosphonate containing alcoholic, carboxylic, and benzylic groups in the interlayer region.

Figure 9.6 Close-packed arrangement of benzyl groups, viewed along the

c

-axis, in the structure of zirconium derivative containing benzyl groups.

Figure 9.7 Representation of C1 ((a) polyhedral and (b) schematic) and C2 ((c) viewed along the

a

-axis and (d) viewed along the

c

-axis) structures.

Figure 9.8 Polyhedral representation of the hydrophobic cavities in C2, viewed along the

c

-axis (a) and along the [210] vector (b).

Figure 9.9 Analogies among amphiphilic systems and zirconium phosphonates with different alkyl chain lengths: (a) C1 and nonaggregated units, (b) C2 and direct micelle arrangement, (c) C5 and bilayer arrangement.

Figure 9.10 Polyhedral representation of the structures of Zpip1 (1) and Zpip2 (2).

Figure 9.11 FT-IR spectra of Zpip1 (a) and Zpip2 (b).

Figure 9.12 Polyhedral representation of the structure of (a, b) and Znic (c, d).

Figure 9.13 Temperature-induced transformation of the structure of Zison into ZisonA.

Figure 9.14 FT-IR spectra of compounds Zison (a), ZisonA (b), and Znic (c).

Figure 9.15 The

1

H MAS spectra of Zison (a), ZisonA (b), and Znic (c). The spectra were recorded at a MAS spinning frequency of 22 kHz.

Figure 9.16 View of a single layer of Cu-mxyl-bypi.

Figure 9.17 View of a single layer of Cu-pxyl-bypi.

Figure 9.18 Ball-and-stick representation of the Cu-pxyl-phen1 (a), Cu-pxyl-phen2 (b), and Cu-pxyl-phen3 (c) structures.

Figure 9.19 Representation of the structure of Cu-pxylp-bypi (c) in comparison with those of Cu-mxyl-bypi (a) and Cu-pxyl-bypi (b).

Figure 9.20 Structural representation packing of MONT1 and MONT2.

Figure 9.21 Ball-and-stick representation of the STRIP phase viewed perpendicularly to the

c

(a) and the

a

(b) axes.

Figure 9.22 Detail of the transformation of the MONT2 phase into the STRIP phase.

Figure 9.23 Comparison of the structure of STRIP phase (a) with those of Co–pcp–bipy (b) and Co–pcp–bpye (c) and a hypothetic STRIP phase without a water molecule (d).

Scheme 9.2 Reactions of [Mn(tda)(H

2

O)]

n

with different bipyridines.

Figure 9.24 Drawing of the polymeric chain of [Mn(tda)(2,2′-bipy)]

n

along the

a

-axis. The hydrogen atoms have been omitted for clarity. The view was chosen in order to highlight the local trigonal prismatic coordination of the Mn atoms.

Figure 9.25 The 2D slabs formed by 1D polymeric chains of [Mn(tda)(2,2′-bipy)]

n

, thanks to the perfect interpenetration of the 2,2-bipy ligands. The 2,2-bipy ligands of the central chain were drawn using the van der Waals surfaces in order to highlight the supramolecular non-covalent interactions.

Figure 9.26 Drawing of the polymeric chain of [{Mn(4,4′Me

2

bipy)}

2

(μ-H

2

O)(μ-tda)

2

] along the crystallographic axis

a

. The hydrogen atoms have been omitted for clarity, and dashed lines represent the hydrogen bonds between the water molecule and the uncoordinated carboxylate oxygen atoms.

Figure 9.27 Comparison of the coordination modes of [Mn (tda)(2,2′-bipy)]

n

and [{Mn(4,4′Me

2

bipy)}

2

(μ-H

2

O)(μ-tda)

2

].

Figure 9.28 The 2D slabs formed by 1D polymeric chains of [{Mn(4,4′Me

2

bipy)}

2

(μ-H

2

O)(μ-tda)

2

]. The 4,4′Me

2

bipy ligands of the central chain were drawn using the van der Waals surfaces.

Figure 9.29 The different stacking of three consecutive bipy ligands in [Mn(tda)(2,2′-bipy)]

n

(left) and [{Mn(4,4′Me

2

bipy)}

2

(μ-H

2

O)(μ-tda)

2

] (right).

Figure 9.30 Drawing of three units of [Mn(tda){(MeO)

2

bipy}·2H

2

O]

n

.

Scheme 9.3 Schematic representation of 4,5-dihydroxybenzene-1,3-disulfonate (dSC).

Figure 9.31 Packing diagram of [Mg(H

2

O)

6

] (dSC) 3H

2

O.

Figure 9.32 View perpendicular (left) and along (right) elongation axis of the Ca dSC 1D polymer.

Figure 9.33 View of the 2D [[Sr(dSC)(H

2

O)

4

]H

2

O]

n

layered structure.

Figure 9.34 Two views of the 3D [[Ba(dSC)(H

2

O)

4

] H

2

O]

n

network.

Scheme 9.4 Schematic representation of 2,5 thiazole [5,4-d] thiazoledicarboxylate (Thz

2−

).

Figure 9.35 Comparison of the 1D polymers based on Mn (a), Ca (b), and Sr (c).

Figure 9.36 Two views of the 2D [Ba(Thz)(H

2

O)

7

]

n

coordination polymer.

Scheme 9.5 Schematic representation of methylenediisophthalic acid (H

4

MDIP).

Scheme 9.6 Skeleton of the structure used as query in the CSD.

Chapter 10

Figure 10.1 Left: a true halogen bond involving halogen as XB donor and a heteroatom as halogen bond acceptor. Up right: type I halogen contact between two halogen atoms. Down right: type II halogen bond between two halogen atoms. Only type II is considered as a true halogen bond [4–6].

Figure 10.2 (a) A schematic representation of a polarized halogen atom in a R

1

X molecule. (b) Type II halogen bond between two halogen atoms.

Figure 10.3 (a) Halogen bonds involving metal-coordinated thiocyanate. S

1

I

1

: 2.836(3) Å, S

1

I

3

: 3.531(2) Å, S

2

I

4

: 2.954(3) Å, I

1

I

2

: 2.777(1) Å, I

3

I

4

: 2.7669(9) Å, I

1

S

1

I

3

78.31(6)° [36]. (b) Halogen bonds between [Fe(CN)

6

]

3−

and

N

-methyl-3,5-diiodopyridinium cation [35].

Figure 10.4 Laplacian of the electron density in dihalogens Cl

2

, Br

2

, and I

2

according to the Quantum Theory of Atoms in Molecules (QTAIM) [38]. The wavefunctions were calculated at the PBE0/def2-TZVPPD level of theory [39, 40]. Calculated X

X distances are 1.981, 2.279, and 2.654 Å for Cl

2

, Br

2

, and I

2

, respectively.

Figure 10.5 Laplacian of the electron density in interhalogens IBr and ICl according to the Quantum Theory of Atoms in Molecules (QTAIM) [38]. Wavefunctions were calculated at the PBE0/def2-TZVPPD level of theory [39, 40].

Scheme 10.1 Impact of a strong charge transfer on charge distribution of homonuclear X

2

molecule (see the text for details).

Figure 10.6 Crystal structure of Py

I

2

adduct (a) [52] and the cationic [I(py)

2

]

+

(b). The structure of [I(py)

2

]

+

was taken from Ref. [53]. The N

I distances in this crystal structure range from 2.255(3) Å to 2.261(3) Å and the N

I

N angle from 177.66(12)° to 180°. The counteranion BF

4

is omitted for clarity.

Figure 10.7 I

+

bridging two 2-imidazolidinethione units [41]. The counteranions (I

and I

3

) have been omitted for clarity.

Figure 10.8 Structure of [(

N

-methylbenzothiazole-2-thione)Br

2

]. The asymmetric unit contains two independent [(

N

-methylbenzothiazole-2-thione)Br

2

] systems. The slight differences are due to the packing. The chloroform of crystallization has been omitted for clarity [75]. S

1

Br

1

: 2.3244(8) Å, Br

1

Br

2

: 2.6673(4) Å, S

1

Br

1

Br

2

174.54(2)°, S

2

Br

3

: 2.2931(7) Å, Br

3

Br

4

: 2.7504(4) Å, S

2

Br

3

Br

4

178.39(2)°.

Figure 10.9 The halogen bond contacts in [(2(3

H

)-benzothiazolethione)Br

2

] (a) and [(2-benzimidazolethione)Br][I

3

] (b). (a) S

Br

1

: 2.2827(13) Å, Br

1

Br

2

: 2.8141(7) Å. (b) S

Br

1

: 2.1824(7) Å, Br

1

Br

3

: 3.2395(4) Å [75].

Figure 10.10 Ethylenethiourea with I

+

and I

3

[76].

Figure 10.11 Packing of [(

N

-methylbenzothiazole-2-thione)Br

2

] (a) and [(2(3H)-benzothiazolethione)Br

2

] (b) [75].

Figure 10.12 Partial charges on [(mbtt)ICl] and [(mbtt)IBr] [77].

Figure 10.13 Halogen bonds between [RuI

2

(H

2

dcbpy)(CO)

2

] and I

2

[93].

Figure 10.14 The symmetrical halogen bonds between [RuCl

2

(bpy)(CO)

2

] and I

2

. The Cl

I distance is 3.0421(3) Å and the I

I bond 2.7317(2)Å. I

I

Cl and Ru

Cl

I angles are 174.566(8)° and 115.76(1)°, respectively [94]. The partial charges are estimated by topological QTAIM analysis.

Figure 10.15 The halogen bonds and weak hydrogen bond interactions between [RuBr

2

(bpy)(CO)

2

] and I

2

. The structure has been solved in the chiral space group P2

1

. The solvent of crystallization (CHCl

3

) has been omitted for clarity. The shorter Br

1

I

1

(corresponds to the Ru

Br

I

A

distance) is 3.2938(4) Å, the longer Br

2

I

2

(corresponds to the Ru

Br

I

B

distance) is 3.3627(3) Å, and the I

I bond is 2.7212(3) Å. The I

2

I

1

Br

1

, I

1

I

2

Br

2

and Ru

Br

1

I

1

and Ru

Br

2

I

2

angles are 170.28(1)°, 173.80(1)°, 101.30(1)°, and 102.27(1)° [94].

Figure 10.16 The halogen bond contacts in the crystal structures of [RuI

2

(bpy)(CO)

2

]

I

2

solved in space group P-1. The shorter I

1

I

2

(corresponds to the Ru

I

I

A

distance) is 3.2553(13) Å, the longer I

3

I

4

(corresponds to the Ru

I

I

B

distance) 3.4108(15) and the I

I bond 2.7572(12) Å. The I

3

I

2

I

1

, I

2

I

3

I

1

and Ru

I

1

I

2

and Ru

I

4

I

3

angles are 172.75(2)°, 166.50(2)°, 97.81(2)°, and 98.90(2)°. The charges have been calculated by computational QTAIM analysis [94].

Figure 10.17 Crystal structures of [RuI

2

(bpy)(CO)

2

]

I

2

adducts solved in space group P2

1

2

1

2. The shorter I

1

I

2

(corresponds to the Ru

I

I

A

distance) is 3.1984(2) Å, the longer I

3

I

4

(corresponds to the Ru

I

I

B

distance) is 3.7984(3), and the I

I bond is 2.7554(2) Å. The I

3

I

2

I

1

, I

2

I

3

I

1

and Ru

I

1

I

2

and Ru

I

4

I

3

angles are 177.941(7)°, 152.083(6)°, 97.91(1)°, and 104.26(7)°. The charges have been calculated by computational QTAIM analysis [94].

Chapter 11

Figure 11.1 (a) Molecular electrostatic potential of benzene and hexafluorobenzene. (b) Schematic representation of the ion-induced dipole.

Figure 11.2 Interaction energies of pyrazine (a) and triazine (b) anion–π complexes from Refs. [79, 80].

Figure 11.3 Fragments of the X-ray crystal structures containing μ

4

-coordination of 1,2,4,5-tetrazine [79]. The relevant anion–π interactions are indicated by dashed lines (distances in Å). The CCDC reference codes are indicated.

Figure 11.4 X-ray structures of organometallic calixarenes with included iodide (left) and bisulfate (right). The CCDC reference codes are indicated. Hydrogen atoms have been omitted for clarity.

Figure 11.5 X-ray structure of [HAT(CN)

6

]

2

[Br

]

3

. The CCDC reference code is indicated.

Figure 11.6 Interaction energies of Cl

–π complexes of pyridazino[4,5-

d

]pyridazine and related rings [96].

Figure 11.7 Fragments of the X-ray crystal structures containing μ

2

- and μ

4

-coordination of pyridazino[4,5-

d

]pyridazine [95]. The relevant anion–π interactions are indicated by dashed lines (distances in Å). The CSD reference codes are indicated.

Figure 11.8 X-ray crystal structures of the molecular squares and pentagons constructed by Fe

II

and 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine [104]. The CSD reference codes are indicated.

Figure 11.9 X-ray crystal structures of TIVTAV and TIVTEZ [105]. The CSD reference codes are indicated. Distances in Å.

Figure 11.10 X-ray crystal structure of LOXFEL [107]. The CSD reference code is indicated. Distance in Å.

Figure 11.11 X-ray crystal structures of LODHUJ and LODJAR [108]. The CSD reference codes are indicated. Distances in Å.

Figure 11.12 X-ray crystal structures of YOGJIP and YOGKAI [110]. The CSD reference codes are indicated. Distances in Å.

Figure 11.13 X-ray crystal structure of ROSJOA [111]. The CSD reference code is indicated. Distances in Å.

Figure 11.14 X-ray crystal structure of XOTHUL [112]. The CSD reference code is indicated.

Figure 11.15 X-ray crystal structures of BEWHUI, BEWHES, and BEWHOC [113]. The CSD reference codes are indicated. Distances in Å.

Figure 11.16 X-ray crystal structures of XIVJIX, XIVJET, and XIVJOD [114]. The CSD reference codes are indicated. Distances in Å.

Figure 11.17 The X-ray crystal structure of HIRKUQ [116]. The CSD reference code is indicated. H-atoms are omitted for clarity.

Figure 11.18 (a) Crystal structure of [(NDI

•+

)BPh

4

]. H-atoms are omitted for clarity. (b) Partial view of the crystal structure of [(NDI

2+

)2BF

4

]; only one anion is shown. H-atoms are omitted for clarity.

Figure 11.19 The X-ray crystal structure of COVYUJ00 [118]. The CSD reference code is indicated. Distances in Å.

Figure 11.20 X-ray crystal structures of FOQHOK and FOQJAY [110]. The CSD reference codes are indicated. Distances in Å. H-atoms omitted for clarity.

Figure 11.21 X-ray crystal structure of CIQJIX [126]. The CSD reference code is indicated. Distances in Å. H-atoms omitted for clarity.

Chapter 12

Scheme 12.1 BINOL-based chiral macrocyclic amines.

Scheme 12.2 Guest compounds.

Scheme 12.3 Chiral macrocyclic amides.

Scheme 12.4 Guest compounds.

Scheme 12.5 Chiral macrocyclic amines.

Scheme 12.6 Guest compounds.

Scheme 12.7 Chiral rhombamine macrocycles.

Figure 12.1 Ortep drawing of (

R,R,R,R

)-67a molecule. Thermal displacement ellipsoids are drawn at the 50% probability level. H atoms are represented by spheres. Intramolecular hydrogen bonds are represented as broken lines.

Figure 12.2 ORTEP drawing of 1 : 4 complex of (

R,R,R,R

)-68a with 1,4-dioxane.

Figure 12.3 Variations in part of 400 MHz

1

H-NMR spectrum corresponding to the benzylic C

H resonance of

rac

- mandelic acid (4, 20.0 mM in CDCl

3

) upon increasing (

R,R,R,R

)-68a content.

Scheme 12.8 Amino acid derivatives.

Figure 12.4 Selected region of the 400 MHz NMR spectra of

rac

-4 of various enantiomeric purities in the presence of 0.25 eq. of (

R,R,R,R

)-67a.

Figure 12.5 Correlation between theoretical and observed % ee values of 4.

Figure 12.6 Selected region of the 2D NOESY spectra (400 MHz in CDCl

3

) of (

R

)-4a in the presence of 0.25 eq. of (

R,R,R,R

)-67a.

Scheme 12.9 Calixarene-like chiral macrocyclic amines.

Figure 12.7 Job plot of (

S,S,S,S,S,S

)-74 with (

R

)- and (

S

)-34. Δ

δ

stands for chemical shift change of the CH proton of 34 in the presence of (

S,S,S,S,S,S

)-74.

X

stands for mole fraction of host, (

X

 = [(

S,S,S,S,S,S

)-74]/[(

S,S,S,S,S,S

)-74] + [34]). Total concentration is 40 mM.

Figure 12.8 Fluorescence spectra of (

S,S,S,S,S,S

)-75d (1.0 × 10

−4

 M in CHCl

3

,

λ

ex

 = 460 nm) with and without (

R

)- and (

S

)-mandelic acid 4 (3.0 × 10

−3

 M).

Scheme 12.10 Chiral aza-crown macrocycles.

Chapter 13

Scheme 13.1 Chemical structures for cucurbit[

n

]uril macrocycles (CB7 and CB8).

Figure 13.1 Guest competition gold nanoparticles triggered by 1-adamantylamine (ADA) .

Figure 13.2 Isolation of plasma membrane proteins triggered by ferrocene derivatives. 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC),

N

-hydroxysuccimidyl Sepharose (NHS).

Figure 13.3 (a) Light-stimulated ternary complex formation between MV,

trans

azo, and CB8; (b) Photoresponsive hybrid raspberry-like colloids (HRCs) prepared by the host–guest chemistry of CB8.

Figure 13.4 Heat-responsive cellulosic hydrogel in the presence of CB8 .

Figure 13.5 Controlled release of DOX from supramolecular prodrug micelles triggered by endo-/lysosomal pH .

Figure 13.6 (a) Colloidosome formation/dissociation triggered by adamantylamine (ADA); (b) ternary supramolecular complex formation between PS-MV,

p

-Np, and CB8. (c) The molecular structure of CB8.

Figure 13.7 (a) CB8-based ternary complex for peptide trapping and electrochemical release. Fluorescence microscopy images of (b) the original peptide array, (c) no pattern after the reduction and washing of the substrate, and (d) the recovered peptide array .

Figure 13.8 (a) Redox-responsive gold nanoparticles; (b) normalized projected cell area for different functionalized slides. Bright field images of cells before (c) and after (d) electrochemical activation .

Figure 13.9 Calixarene-based supramolecular polymers controlled by the addition of CB[8] .

Figure 13.10 Redox-controlled reversible sequestering of 1-(anthracen-2-ylmethyl)pyridinium bromide (AnPy) in CB8, and schematic representation of layer-by-layer assembly of the PMVC

n

H

2

n

+1

-CB8 complex and PAA-N

3

.

Figure 13.11 (a) Light-switchable mechanized MSNs using CB7 and their release profiles upon (b) continuous light and (c) pulsed light irradiation .

Figure 13.12 Dual-controlled systems consisting of (a) base-responsive nanovalves (raising pH) and azobenzene stalks and (b) acid-responsive nanovalves (lowing pH) and azobenzene stalks .

Chapter 14

Figure 14.1 Offsets of benzene carbon atoms and benzene hydrogen atoms relative to center of benzene ring, since

r

C

 ≈ 1.4 Å and

r

H

 ≈ 2.5 Å.

Figure 14.2 Geometrical parameters that define water–phenyl interactions: Ω is the center of phenyl ring, H

1

is water hydrogen atom closer to this center, O is water oxygen and O

p

is the projection of water oxygen on the average phenyl ring plane, and X is any atom or group; β is the angle between Ω

H

1

and normal of the ring plane,

d

O

is the distance between water oxygen and phenyl ring center,

r

O

is the displacement (offset) of

O

p

, and

R

O

is the shortest (normal) distance between water oxygen and average ring plane; Θ is O

p

O

H

1

angle.

Figure 14.3 Oxygen normal distance (

R

O

) versus offset (

r

O

) plot for water–phenyl contacts found in the CSD with

d

O

distance shorter than 6.0 Å.

Figure 14.4 Density plots of oxygen normal distance (

R

O

) versus oxygen offset (

r

O

) for water–phenyl interactions found in PDB (uncorrected (a), area corrected (b)) and CSD crystal structures (uncorrected (c), area corrected (d)).

Figure 14.5 Oxygen normal distance (

R

O

) versus oxygen offset (

r

O

) plot for parallel alignment interactions between water and phenyl ring in the CSD crystal structures.

Figure 14.6 Geometric parameters of parallel alignment interactions of water and C

6

-aromatic rings. Ω is aromatic ring center;

d

H1

is the distance between Ω and H

1

;

R

H1

is normal distance between H

1

and mean plane of the phenyl ring; horizontal displacement (offset)

r

H1

is the distance from Ω to the projection of H

1p

of H

1

atom on the mean plane of the phenyl ring; S

1

to S

6

is any atom or group.

Figure 14.7 Parallel-up, parallel-down, and all-parallel interactions between water and C

6

-aromatic ring.

Figure 14.8 Correlation of normal distance

R

H1

and offset

r

H1

for all-parallel (a) and parallel-up water–aromatic interactions (b).

Figure 14.9 Normal distance

R

H1

versus offset

r

H1

plot for parallel-down interactions of water and C

6

-aromatic ring for crystal structures found in the CSD.

Figure 14.10 Model systems used for calculations of interactions energies for all-parallel (A

1

, A

2

, A

3

) and parallel-up (B

1

, B

2

) interactions of water and benzene.

Figure 14.11 Model system used for calculations of parallel-down interactions between water and benzene; the most stable geometries with offsets of

r

H1

 = 0.0 Å and

r

H1

 = 3.0 Å are presented.

Figure 14.12 Model systems used for the evaluation of influence of parallel-up interactions on other attractive water–benzene interactions; parallel-up interaction is B/W2; the other interactions, OH/π, CH

O, parallel-up, or lone-pair/π interaction are B/W1.

Figure 14.13 Comparison of strength and abundance in crystal structures for attractive water–benzene interactions.

Figure 14.14 In crystal structure SENRUZ (4,4-azodibenzoic acid dihydrate) [46], water molecule forms parallel-up interaction at large horizontal displacement (

r

H1

 = 2.83 Å) with aromatic ring with two substituents (a); as a consequence of this parallel interaction at large horizontal displacement, water molecule forms additional hydrogen bonds and aromatic ring forms additional stacking interactions with surrounding molecules (b).

Figure 14.15 The normal distance

R

H1

versus offset

r

H1

plot for parallel-up (a) and parallel-down (b) interactions of coordinated water with C

6

-aromatic ring in crystal structures found in the CSD.

Figure 14.16 Model systems used for calculations of interaction energies for parallel-down interactions of coordinated water with benzene; aqua complexes with different charges were neutral [ZnCl

2

(H

2

O)

4

], positive [ZnCl(H

2

O)

5

]

+

, and double positive [Zn(H

2

O)

6

]

2+

; geometries in this figure are with

r

H1

 = 3.0 Å.

Figure 14.17 In crystal structure CAGHUO (tetraaqua-bis(4-cyanopyridine)nickel(II)-bis(tetraphenylborate)-4-cyanopyridine solvate tetrahydrate) [50], coordinated water molecule forms parallel-down interaction at large horizontal displacement (

r

H1

 = 2.62 Å) with phenyl ring (a); this large horizontal displacement enables coordinated water to form hydrogen bonds with cyano group of another aromatic ring and uncoordinated water molecule, while phenyl ring can form OH/π interaction with the same uncoordinated water (b).

Figure 14.18 Geometrical parameters of parallel benzene–benzene interactions;

d

is the distance between the centers (Ω and Ω′) of benzene molecules;

R

is the normal distance between the planes of interacting rings; Ω

p

is the projection of the center of one ring to the plane of the other ring;

r

is horizontal displacement (offset) the distance from Ω′ to Ω

p

; the angle between benzene planes is smaller than 10°; in this figure, geometry with

r

 = 5.0 Å is presented.

Figure 14.19 The distribution of offset values (

r

) for parallel interactions of benzene molecules in CSD crystal structures.

Figure 14.20 Normal distances (

R

) versus offset values (

r

) plot for parallel interactions between benzene molecules in CSD crystal structures.

Figure 14.21 The distribution of offset values (

r

) for parallel interactions between phenylalanine side chains in PDB crystal structures.

Figure 14.22 Normal distances (

R

) versus offset values (

r

) plot for parallel interactions between phenylalanine side chains in PDB crystal structures.

Figure 14.23 Three model systems used for calculations of energies of parallel interactions between benzene molecules; the presented geometries are with horizontal displacements of 5.0 Å.

Figure 14.24 Interaction energies (Δ

E

) for parallel interactions of benzene molecules (model systems A, B, and C, Fig. 14.23) for offset values from 0.0 to 6.0 Å (a) and plot of normal distances (

R

) versus offsets (

r

) for geometries with these energies (b).

Figure 14.25 Model system for calculations of benzene–benzene interaction energies for interplanar angles of 20° and 40°; geometries with

r

 = 3.5 Å are presented.

Figure 14.26 Curves of interaction energies between benzene molecules with interplanar angles of 0°, 20°, 40°, 60°, and 90°, calculated at B2PLYP-D2/def2-TZVP level.

Figure 14.27 Parallel benzene–benzene interaction at large horizontal displacement (

r

 = 5.10 Å) in crystal structure CENNUE (syncarpurea benzene solvate) (a); both benzene molecules form additional aromatic CH/π interactions with surrounding benzene molecules, CH/π interactions with syncarpurea molecules, and CH/O interactions with O atoms of syncarpurea molecules (b).

Figure 14.28 Geometrical parameters of parallel pyridine–pyridine interactions;

d

is the distance between the centers (Ω and Ω′) of pyridine molecules;

R

is the normal distance between the planes of interacting rings; Ω

p

is the projection of the center of one ring to the plane of the other ring;

r

is horizontal displacement (offset) the distance from Ω′ to Ω

p

; torsion angle T is N–Ω–Ω′–N′ torsion angle; the angle between pyridine planes is smaller than 10°.

Figure 14.29 The distribution of offset values (a) and normal distances versus offset values plot (b) for parallel interactions of pyridine molecules in CSD crystal structures.

Figure 14.30 Top view of parallel pyridine–pyridine orientations used for calculations of interaction energies; geometries with positive (+) and negative (−) offset values of 5.0 Å are presented.

Figure 14.31 Interaction energies (Δ

E

) for parallel interactions of pyridine molecules (model systems A, B, and C, Fig. 14.29) for offset values from −6.0 to 0.0 Å and from 0.0 to 6.0 Å (a) and plot of normal distances (

R

) versus offsets (

r

) for geometries with these energies (b).

Figure 14.32 Parallel pyridine–pyridine interaction in crystal structure KINLIC (dibromo-(dimethylamino(thiocarbonyl)thiamin,S)-dipyridyl-titanium(IV) pyridine solvate) [60] with large horizontal displacement (

r

 = 4.29 Å) (a); as a consequence of these pyridines being at large offsets, both pyridine molecules can form two additional CH/π interactions with ligands of surrounding titanium(IV) complex (b).

Figure 14.33 Top view of parallel benzene–pyridine orientations used for calculations of interaction energies; geometries with positive (+) and negative (−) offset values of 5.0 Å are presented.

Figure 14.34 Interaction energies (Δ

E

) for parallel benzene–pyridine molecules (model systems A, B, and C, Fig. 14.33) for offset values from −6.0 to 0.0 Å and from 0.0 to 6.0 Å (a) and plot of normal distances (

R

) versus offsets (

r

) for geometries with these energies (b).

Chapter 15

Scheme 15.1 Structures of four common

p

-sulfonatocalixarenes.

Scheme 15.2 Structures of organic ammonium guests G1–G19.

Scheme 15.3 Structures of aromatic cationic guests G20–G32.

Scheme 15.4 Deduced binding manners of (a) SC4A and (b) SC5A with G28 [23].

Scheme 15.5 Structures and biochemical mechanism of viologen toxicity and detoxification by complexation with SC5A (HWR, Haber–Weiss reaction; HMP, hexose monophosphate pathway) [27].

Scheme 15.6 Schematic illustration of post-translational modifications (e.g., lysine methylation) on unstructured protein tails, which serve as recruitment sites for protein–protein interactions (PPIs), and the disruption of the PPI via a competition from SC4A [46].

Scheme 15.7 Structures of some pharmic guests.

Scheme 15.8 Possible binding modes of (a) SC4A–TPT [51] and (b) SC4A–CPT-11 [52] complexes.

Scheme 15.9 The deduced binding geometries of (a, b) SC4A and (c, d) SC5A with metformin and phenformin according to NMR spectral analyses [53].

Scheme 15.10 The deduced binding equilibriums of SC4A with (a) dibucaine and (b) SC4A with tetracaine under acidic conditions [55].

Scheme 15.11 Structures of three bis-SC

n

As.

Scheme 15.12 Schematic representation of the construction of supramolecular 2D network and 1D linear polymers based on the complexation of the ditopic host bis-SC5A with tetracationic and dicationic porphyrin guests [66].

Scheme 15.13 Chemical structures of CB[8], EBV

4+

, and HBV

4+

and cartoon illustration of supramolecular binary polymer, cyclic oligomer, and ternary polymer formed by bis-SC4A upon complexation with EBV

4+

, HBV

4+

, and HBV

4+

⊄CB[8] [2]pseudorotaxane [68, 69].

Scheme 15.14 Structural illustration of the building blocks and schematic representation of the enzyme-responsive supramolecular polymers [73].

Scheme 15.15 Structural illustration of the reversible assembly/disassembly process of supramolecular polymer based on bis-SC4A and heteroditopic guest induced by the respective stimuli of protonation/deprotonation and electrochemical redox [75].

Scheme 15.16 Structural illustration of bis-SC4A and AzobPy and schematic of the morphological conversion between linear supramolecular polymer and spherical nanoparticle based on the

trans–cis

photoisomerization of AzobPy induced by light stimulus [77].

Scheme 15.17 Schematic description of the self-assembly process for forming α-CD-based pseudo[3]rotaxane ([email protected]), the supramolecular polymer with azobenzene in the

trans

configuration, and the corresponding UV-irradiated polymer containing

cis

-azobenzene [79].

Scheme 15.18 Schematic representation of the morphology transition from spherical micelles to the amorphous worm-like network and then the linear polymer, regulated by host–guest interactions [80].

Scheme 15.19 Chemical structures of guest molecules used for CIA.

Scheme 15.20 Schematic illustration of CIA with dicationic perylene bisimide as the guest [89].

Scheme 15.21 Different architectures of PMA aggregates in the presence of SC

n

As or bis-SC

n

As [94, 95].

Scheme 15.22 Formation of a multistimulus-responsive supramolecular binary vesicle composed of SC4A and an asymmetric viologen [103].

Scheme 15.23 Enzymatic responsiveness of amphiphilic assemblies of myristoylcholine fabricated in the absence or presence of SC4A [100].

Scheme 15.24 Formation of supramolecular binary vesicle composed of SC4A and nonamphiphilic polycations [72, 107].

Scheme 15.25 Schematic illustration of the photocyclization of free QA-TPE and the SC4A–QA-TPE nanoparticles [96].

Chapter 16

Scheme 16.1 Schematic representation of the topological structures of one-dimensional linear MSPs.

Scheme 16.2 Schematic representation of the synthesis routes of type I.

Scheme 16.3 Schematic representation of the synthesis routes of type II.