Spectroscopy and Computation of Hydrogen-Bonded Systems E-Book

• Herausgeber: Wiley-VCH GmbH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 983

Veröffentlichungsjahr: 2022

Beschreibung

Reflects the polymorphic nature of hydrogen bonding, having the advantage of bringing together the latest experimental and computional work in the field.

Leseprobe

Table of Contents

Cover

Title Page

Copyright

Part I: Theory

1 Linear Response Theory Applications to IR Spectra of H‐Bonded Cyclic Dimers Taking into Account the Surrounding. Updating Contributions Involving Davydov Coupling, Fermi Resonances and Electrical Anharmonicity

1.1 Introduction

1.2 Dimer Strong Anharmonic Coupling Theory

1.3 Comparison with Experiments

1.4 Conclusion

1.5 Acknowledgment

References

2 Dynamic Interactions Shaping Vibrational Spectra of Hydrogen‐Bonded Systems

2.1 Introduction

2.2 Theoretical Model of the Infrared Spectra of Gaseous (CH

3

)

2

O‐HCl and (CH

3

)

2

O‐HF Complexes

2.3 Simulation of the Cl–H(D) and F–H Stretching Bands in the DME‐H(D)Cl and DME‐HF Complexes

2.4 Methodology of Molecular Dynamics

2.5 Spectroscopic Study of Uracil, 1‐Methyluracil, and 1‐Methyl‐4‐thiouracil

2.6 Hydrogen Bond Interaction Dynamics in the Adenine and Thymine Crystals

2.7 Guanine and Cytosine Crystals

2.8 Spectroscopic Signature for Ferroelectric Ice

2.9 Conclusions

Acknowledgment

References

3 Trajectory On‐the‐Fly Molecular Dynamics Approach to Tunneling Splitting in the Electronic Ground and Excited States

3.1 Introduction

3.2 Semiclassical Tunneling Approach

3.3 Results and Discussion

3.4 Conclusions

Acknowledgments

References

Part II: Spectroscopy

4 Spectroscopic Signatures of Low‐Barrier Hydrogen Bonding in Neutral Species

4.1 Introduction

4.2 Spectroscopic Metrics for Hydrogen Bonding

4.3 Concluding Remarks

Acknowledgments

References

Note

5 Hydrogen‐Bonding Interactions Using Excess Spectroscopy

5.1 Introduction of Hydrogen Bond

5.2 Theory of Excess spectroscopy

5.3 Studies of Hydrogen Bonds by Excess IR

References

6 Intramolecular Hydrogen Bonding in Porphyrin Isomers

6.1 Introduction

6.2 H‐Bond Characteristics

6.3 Correlations Between Geometry and HB Strength

6.4 Parameters That Can Describe the HB Strength

6.5 Tautomerization Mechanisms

6.6 Summary

Acknowledgments

References

7 Isotope Effects in Hydrogen Bond Research

7.1 Introduction

7.2 Hydrogen Bond Potentials

7.3 Calculations

7.4 Hydrogen Bond Types

7.5 Deuterium Isotope Effects on Chemical Shifts

7.6 Intramolecular Hydrogen Bonds

7.7 Biological Systems

7.8 Intermolecular Hydrogen Bonds

7.9 Primary Isotope Effects

7.10 Isotope Effects and Acidity

7.11 Solvent Isotope Effects and Exchange Rates

7.12 Exchange in the Solid‐State

7.13 Hydrogen Bond Energies

7.14 Tautomerism

7.15 Solid‐State NMR

7.16 Conclusions

References

8 Intramolecular Hydrogen Bonding: Shaping Conformers' Structure and Stability

8.1 Introduction

8.2 The Halogen‐Substituted Acetic Acids CF

3

COOH, CCl

3

COOH, and CBr

3

OOH: Implications of IMHB on Structure and Conformers' Stabilities

8.3 The Significance of IMHB in the

ortho

Chloro‐ and Fluoro‐Substituted Benzoic Acids

8.4 IMHB in Thiotropolone: Sculpturing the Bidirectional Infrared‐Induced Bond‐Breaking/Bond‐Forming Tautomerization

8.5 Conclusion

Acknowledgments

References

9 Hydrogen Bonding from Perspective of Overtones and Combination Modes: Near‐Infrared Spectroscopic Study

9.1 Introduction

9.2 Investigation of Hydrogen Bonding of Water by NIR Spectroscopy

9.3 The Chain Length Effect on the Degree of Self‐association of 1‐Alcohols

9.4 Combined NIR and Dielectric Study on Association of 1‐Hexanol in

n

‐Hexane

9.5 NIR Studies of Microheterogeneity in Alcohol/Alcohol and Alcohol/Alkane Binary Mixtures

9.6 Overtones of

ν

C≡N Vibration as a Probe of Molecular Structure of Nitriles

9.7 Weak Hydrogen Bond in Poly(3‐Hydroxybutyrate) (PHB) Studied by NIR Spectroscopy

9.8 Studies of Hydrogen Bonding By Use of Higher Overtones

9.9 Comparison of Hydrogen Bonding Effects and Solvent Effects on Wave numbers and Intensities of the Fundamental and First Overtone of the N–H Stretching Mode of Pyrrole Studied By NIR/IR Spectroscopy and One‐Dimensional Vibrational Schrödinger Equation Approach

9.10 Summary

Acknowledgments

References

10 Direct Observation and Kinetic Mapping of Point‐to‐Point Proton Transfer of a Hydroxy‐Photoacid to Multiple (Competing) Intramolecular Protonation Sites

10.1 Introduction

10.2 From Intermolecular Proton Transfer to Solvent to Intramolecular Point‐to‐Point Transfer in 1 : 1 Hydrogen‐Bonding Complexes of Water with Bifunctional OH Photoacids

10.3 Water Is Able to Donate and Accept an H‐bond as Demonstrated by IR Absorption in 1 : 1 Water–(Acid or Base) Complexes

10.4 Proton Transfer Along with Water Bridges in Acetonitrile (ACN) Spanning the Distance Between an Acidic and a Basic Side Groups of Bifunctional Photoacids

10.5 Time‐Resolved Fluorescence Measurements of Proton Transfer along with Water Bridges

10.6 Isotope D/H Effect

10.7 Insights into the Mechanism of Proton Transfer Through One‐Water Bridge in Bifunctional 2‐Naphthols

10.8 Summary

Acknowledgments

References

Note

11 Spectroscopic Determination of Hydrogen Bond Energies

11.1 Introduction

11.2 Binding Energy Measurement Involving Infrared (IR) Excitation

11.3 Determination of the Binding Energy of H‐Bonded Complexes Using Spectroscopic Techniques Involving Electronic Excitation

11.4 Estimation of the Well Depth of H‐Bonding Interactions Through Microwave Spectroscopy

11.5 Conclusion

References

12 IR and NMR Spectral Diagnostics of Hydrogen Bond Energy and Geometry

12.1 Introduction

12.2 Spectral Characterization of Hydrogen Bond Geometry

12.3 Spectral Markers for Hydrogen Bond Energy

References

13 ATR‐Far‐Ultraviolet Spectroscopy Holds Unique Advantages for Investigating Hydrogen Bondings and Intermolecular Interactions of Molecules in Condensed Phase

13.1 Introduction

13.2 Characteristics and Advantages of FUV Spectroscopy for the Studies of Liquids and Solids

13.3 FUV Spectroscopic Studies of Hydrogen Bonds and Hydration Structures of Electrolyte Aqueous Solutions

13.4 Quantum Chemical Calculations of the

Transition of Hydrated Group I Cations

13.5 Hydrogen Bonding States of Interfacial Water Adsorbed on an Alumina Surface Studied by Variable Angle‐ATR‐FUV Spectroscopy

13.6 ATR‐FUV and Quantum Chemical Calculation Studies of Hydrogen Bondings in Amides

13.7 ATR‐FUV and Quantum Chemical Calculation Studies of Hydrogen Bondings in Nylons

13.8 An ATR‐FUV Study for Poly(ethylene glycol) (PEG) and Its Complex with Lithium Ion (Li

+

)

13.9 Summary and Perspective

References

14 Water–Hydrogen‐Bond Network and Hydrophobic Effect

14.1 Introduction

14.2 Bulk Water

14.3 Water Near Fully Hydrophobic Solutes

14.4 IR Spectroscopy of the Water Hydrogen Bonding in the Alcohol–Water Systems

14.5 Epilogue

Acknowledgments

References

15 Hydrogen Bond Chains in Foldamers and Dynamic Foldamers

15.1 Hydrogen‐Bonded Foldamers

15.2 Hydrogen‐Bonded Dynamic Foldamers

15.3 Reversible Hydrogen‐Bond Directionality in Dynamic Foldamers

15.4 Cyclic Hydrogen Bond Chains

References

Index

End User License Agreement

List of Tables

Chapter 1

Table 1.1 Different sorts of Hamiltonians.

Table 1.2 Symmetrized coordinates.

Table 1.3 Parameters used for fitting the experimental lineshapes of Figure...

Table 1.4 Parameters used for fitting the experimental lineshapes of acetic...

Table 1.5 Parameters used for fitting the experimental lineshapes of Figure...

Table 1.6 Parameters used for fitting the experimental lineshapes of crystal...

Table 1.7a Parameters used for fitting the experimental lineshapes of Figure...

Table 1.7b Fermi resonances parameters for crystalline adipic acid in presen...

Table 1.8 Parameters used for fitting the experimental lineshapes of Figure ...

Table 1.9a Parameters used for fitting the experimental lineshapes of crysta...

Table 1.9b (continued). Fermi resonances parameters for crystalline glutaric...

Table 1.10 Parameters used for fitting the experimental lineshapes of the 3...

Table 1.11 Parameters used for fitting the experimental lineshapes of the cr...

Table 1.12 Parameters used to fit experimental H/D‐2‐NA spectra.

Table 1.13 Values of Fermi coupling parameters used for fitting experimental...

Table 1.14 Parameters used for fitting experimental Aspirin‐H and Aspirin‐D ...

Table 1.15 Theoretical parameters used for the fitting of the experimental l...

Table 1.16 Parameters used in the theoretical fitting of formic acid species...

Table 1.17 Fermi resonances parameters for crystalline glutaric acid (cf. Fi...

Table 1.18 Parameters involved for fitting the experimental spectra of 2‐fur...

Table 1.19 Fermi coupling parameters (in cm

) used for fitting experimental ...

Table 1.20 Parameters used for fitting the experimental line shapes of the

Table 1.21a Parameters used for fitting the experimental lineshapes of

and...

Table 1.21b Fermi resonance parameters for used for fitting the experimental...

Table 1.22 Parameters used in the theoretical lineshape of Figure 1.28.

Table 1.23 Parameters used for fitting the lineshapes of gaseous (CH3)

O

HC...

Chapter 3

Table 3.1 Calculated [27] and experimental [36] values of tunneling splittin...

Table 3.2 Calculated [27] and experimental [40] tunneling splitting due to i...

Chapter 4

Table 4.1 Electronic structure predictions for ground‐state potential surfa...

Table 4.2 Electronic structure predictions for excited‐state potential surf...

Chapter 5

Table 5.1 van der Waals radii (in Å) of selected atoms.

Table 5.2 Classification of interactions [1, 21].

Chapter 6

Table 6.1 Calculated relative energies (kcal mol

−1

) of the lowest ene...

Table 6.2 HB characteristics of tautomers of

1

and their isotopologues.

Table 6.3 HB characteristics of tautomers of

2

and their isotopologues.

Table 6.4 HB characteristics of tautomers of

3

and their isotopologues.

Table 6.5 HB characteristics of tautomers of

4

and their isotopologues.

Table 6.6 HB characteristics of tautomers of

5

and their isotopologues.

Table 6.7 HB characteristics of tautomers of

6

and their isotopologues.

Table 6.8 HB characteristics of tautomers of

7

and their isotopologues.

Table 6.9 HB characteristics of tautomers of

8

and their isotopologues.

Table 6.10 HB characteristics of tautomers of

9

and their isotopologues.

Table 6.11 HB characteristics of tautomers of

10

and their isotopologues.

Chapter 7

Table 7.1 Deuterium isotope effects on

13

C chemical shifts in ppb of a and ...

Table 7.2 Quantum–mechanical calculations for

1

ΔN(D) of

N

‐formylglycineamid...

Chapter 10

Table 10.1 List of

σ

p

[36, 37] values of relevant protonatable side gr...

Table 10.2 Best‐fit parameters used in generating the simulated decay curve...

Table 10.3 The calculated p

values of the functional groups in different c...

Table 10.4 Time constants of R*OH, R*OH–water complex and the ESPT reaction...

Table 10.5 The ratio between [ROH]

free

and ROH–water complex in ACN as foun...

Table 10.6 Time constants of R*OH, R*OH–water complex and the ESPT reaction...

Table 10.7 Excited‐state lifetimes parameters for deuterated 2N8S and its i...

Table 10.8 Kinetic parameters used in generating the simulated decay curves...

Table 10.9 Calculated isotope effects for 2N8S in H

2

O/D

2

O for processes inv...

Chapter 11

Table 11.1 Experimental (determined via optothermal bolometric detection or...

Table 11.2 Room temperature free energy of formation Δ

G

obs

(cm

−1

Table 11.3 The stretching force constant (

k

s

) for several H‐bonded complexe...

Chapter 12

Table 12.1 Parameters of linear correlations between H‐bond energies and br...

Table 12.2 Coefficients

a

and

b

for Badger–Bauer equation (12.39).

Chapter 13

Table 13.1 Excitation energies (eV) of the center of balance of the absorpt...

Table 13.2 Excitation energies (eV) of the π–π* transition of FA, NMF, NMA,...

Table 13.3 Excitation energies (eV) of the π–π* transition of FA, NMF, NMA,...

Chapter 14

Table 14.1 Summarized recording and spectral parameters of the OD‐stretchin...

Table 14.2 Brief literature review of IR spectroscopic methods used to stud...

List of Illustrations

Chapter 1

Figure 1.1 (a) H‐bond monomer and the coordinates. (b) H‐bond dimer and the ...

Figure 1.2 Connections between the present theory and different older models...

Figure 1.3 Coordinates of single H‐bonded system.

Figure 1.4 Physics of the absorption mechanism. The ground state of the slow...

Figure 1.5 Fermi resonances interaction coupling parameters

between two si...

Figure 1.6 Davydov coupling interactions.

Figure 1.7 Action of the

operator on coordinates and eigenstates.

Figure 1.8 Davydov coupling with an unique Fermi resonance.

Figure 1.9 IR

lineshapes of gaseous cyclic acetic acid CD

CO

H/D dimers at...

Figure 1.10 Gas and liquid

lineshapes of

H at room temperature. Compariso...

Figure 1.11 Gaseous acrylic (a) and propynoic acids. Comparisons of experime...

Figure 1.12 Effects of temperature, isotopic substitution, and

parameter o...

Figure 1.13 Temperature and isotopic substitution effects at different polar...

Figure 1.14 Temperature and isotopic substitution effects at different polar...

Figure 1.15 Crystalline H(D)‐3‐thiophenacrylic acid experimental (H‐3TAcetic...

Figure 1.16 Crystalline H(D)‐3‐thiophenacrylic acid experimental (black line...

Figure 1.17 2‐Naphtylacetic Acid (2‐NA). Comparison of experimental lineshap...

Figure 1.18 Comparison between the experimental (grayed) and theoretical (da...

Figure 1.19 Structure of the superdimer and definition of the eight vibratio...

Figure 1.20 Crytalline phthalic (PAC) and terephthalic (TAC) acids at 77 and...

Figure 1.21 Liquid formic acid mixing of monomer and dimer of several H/D sp...

Figure 1.22 Lineshapes of polarized 2‐furoic acid when the Fermi resonances ...

Figure 1.23 Lineshapes of polarized 2‐furoic acid when there are three Fermi...

Figure 1.24 The two forms of oxindol.

Figure 1.25 Lineshapes of (

)‐hydrogenated and (

)‐deuterated oxindole comp...

Figure 1.26 Dimer of phosphinic acid.

Figure 1.27 Comparison between experimental (grayed) and theoretical linesha...

Figure 1.28 (CH

)

O

HCl complex in gas phase at 226

.

Figure 1.29 Gaseous (C

)

O

HCl complex. Effect of the

electrical anharmon...

Chapter 2

Figure 2.1 Equilibrium structure of the DME‐HCl complex with

C

s

symmetry, op...

Figure 2.2 Theoretical absorption bands (solid lines) for the Cl–H stretchin...

Figure 2.3 Purely vibrational transitions with labeling of the most intensiv...

Figure 2.4 Uracil (panel a), 1‐methyluracil (panel b), and 1‐methyl‐4‐thiour...

Figure 2.5 Analysis of the deformation densities, Δ

ρ

for the cluster of...

Figure 2.6 Analysis of the deformation densities for the cluster of 27 molec...

Figure 2.7 The five unit cells (A–E) with eight water molecules chosen for t...

Figure 2.8 Comparison between theoretical IR spectrum of ice Ih calculated a...

Figure 2.9 Comparison between librational spectra of ice Ih calculated at 60...

Chapter 3

Figure 3.1 Schematic illustration of (a) the umbrella inversion of ammonia, ...

Figure 3.2 Schematic view of the tunneling path.

Figure 3.3 (a)

p

‐Dependence of tunneling splitting and (b) bath mode energy ...

Figure 3.4 Changes in (a) tunneling amplitude, (b) barrier height, and (c) t...

Figure 3.5 (a)

p

‐Dependence of the number of tunneling events in 100 traject...

Chapter 4

Figure 4.1

Continuum of hydrogen‐bonding motifs

. The progression of hy...

Figure 4.2

Predicted reaction coordinates for ground‐state TrOH and HFF

...

Figure 4.3

Fluorescence‐based spectroscopic probes

. The techniques of ...

Figure 4.4

Fluorescence excitation spectra of HFF isotopologs

. The initial p...

Figure 4.5

Allowed

vibronic transitions in HFF

. Schematic energy‐level diag...

Figure 4.6

Dispersed fluorescence spectra of HFF isotopologs

. The initial po...

Figure 4.7

Predicted reaction coordinate for electronically excited HFF

. The...

Chapter 5

Figure 5.1 AFM measurements of 8‐hydroxyquinoline assembled clusters on the ...

Figure 5.2 A schematic illustration of excess spectroscopy. In each panel, t...

Figure 5.3 (a) IR and (b) excess IR spectra in the O—H stretching region of

Figure 5.4 The excess IR spectra of (a) CH

3

OH‐H

2

O and (b) CD

3

OH‐H

2

O systems....

Figure 5.5 (a) IR and (b) excess IR spectra of the DMSO–methanol binary syst...

Figure 5.6 Schematic presentation of the direction of charge transfer from t...

Figure 5.7 (a) IR and (b) excess IR spectra of ETH‐CH

3

CN system in the

υ

...

Figure 5.8 Optimized structures and interaction energies of (a, b) ChCl, (c–...

Figure 5.9 (a) IR and (b) excess IR spectra of [C

2

OHMIM][BF

4

]‐CH

3

CN system i...

Figure 5.10 Optimized structures and the respective interaction energies of ...

Figure 5.11 The (a, c) IR and (b, d) excess IR spectra of (a, b) NMF‐DMSO‐

d

6

Figure 5.12 Calculated average relative hydrogen bond energies

E

and configu...

Figure 5.13 (a, b) IR and (c, d) excess IR spectra of (a, c) [Bmim][BF

4

]‐CH

3

Figure 5.14 (a) Deconvoluted IR spectrum in the aromatic C—H stretching regi...

Figure 5.15 (a) IR and (b) excess IR spectra of

tert

‐butanol‐CCl

4

system in ...

Figure 5.16 Optimized structures of (a)

tert

‐butanol monomer, (b)

tert

‐butan...

Chapter 6

Scheme 6.1 Free‐base porphyrin (porphine,

1

) and its isomers: porphycene (

2

)...

Figure 6.1 Trans and cis tautomers of

1

and the calculated relative energies...

Figure 6.2 Trans and cis tautomers of

2

and their relative energies.

Figure 6.3 Trans and cis tautomers of

3

and their relative energies.

Figure 6.4 Trans and cis tautomers of

4

and their relative energies.

Figure 6.5 Trans and cis tautomers of

5

and their relative energies.

Figure 6.6 Trans and cis tautomers of

6

and the relative energies.

Figure 6.7 Trans and cis tautomers of

7

and the relative energies.

Figure 6.8 Trans and cis tautomers of

8

and the relative energies.

Figure 6.9 Trans and cis tautomers of

9

and the relative energies.

Figure 6.10 Tautomers of

10

and the relative energies.

Figure 6.11 (a) Plot of the calculated NH‐stretching frequencies vs. the cor...

Figure 6.12 Correlation between the proton chemical shift and the NH‐stretch...

Figure 6.13 Correlation between the out‐of‐plane NH‐bending and the NH‐stret...

Chapter 7

Figure 7.1 Hydrogen bond potentials. A more complete potential is seen in Fi...

Figure 7.2 Hydrogen bond potential for picolinic acid

N

‐oxide in chloroform....

Figure 7.3 Structure of

k

‐H

3

(Cat EDT‐ST)

2

.

Figure 7.4 Intramolecular hydrogen bonds of RAHB type in aromatic systems.

Figure 7.5 Intramolecular hydrogen bonds in systems having a NH donor (the d...

Figure 7.6 Typical non‐RAHB types of intramolecular hydrogen bonds. The NH

2

C...

Figure 7.7 Two‐bond deuterium isotope effects on

13

C chemical shifts given i...

Figure 7.8 Resonance forms of 5‐nitrosalicylaldehyde.

Figure 7.9 Deuterium isotope effects on

13

C chemical shifts in ppm. Data for...

Figure 7.10 Deuterium isotope effects at

13

C chemical shifts of

o

‐hydroxythi...

Figure 7.11 Phenylenediamine derivatives of dehydracetic acid.

Figure 7.12 Deuterium isotope effects on

13

C chemical shifts in ppm of an en...

Figure 7.13 Deuterium isotope effects on

13

C chemical shifts in ppm. Left ma...

Figure 7.14 Resonance and tautomeric forms of thiophenoxyketenimines.

Figure 7.15 Deuterium isotope effects at the aldehyde proton chemical shift ...

Figure 7.16 Adenine and thymine with hydrogen bond.

Figure 7.17

N

‐Formylglycineamide with water attached.

Figure 7.18 Plot of predicted one‐bond deuterium isotope effects on

15

N chem...

Figure 7.19 Intermolecular hydrogen bond motifs.

Figure 7.20 (a) Diisopropylamine‐formate system.

Figure 7.21 Plot of primary deuterium isotope effects vs. OH chemical shifts...

Figure 7.22 Primary deuterium isotope effects vs. NH chemical shifts.

Figure 7.23 (

a

) 2,3‐Dipyrrol‐2‐ylquinoxalines. R and R1 are H,H; H,NO

2

, and ...

Figure 7.24 Primary deuterium isotope effects vs. C=OO

H

chemical shifts. Ser...

Figure 7.25 Two‐bond deuterium isotope effects of

o

‐hydroxy aromatic aldehyd...

Figure 7.26 Schiff bases with a carboxylic acid group in ortho position.

Figure 7.27 Example of a Schiff base modified to contain an amino acid.

Figure 7.28 Tautomerism of piroxicam.

Figure 7.29 Tautomeric equilibria of 3‐acyltetronic acid.

Figure 7.30 Deuterium isotope on

13

C chemical shifts in ppm of 3‐acyltetroni...

Figure 7.31 Dicarboxylic acid anion. The broken line indicates that this cou...

Figure 7.32 Tetraethylammonium (TEA) hydrogen succinate (

1

), tetramethylammo...

Figure 7.33 (

a

) β‐Diketone. (

b

) Nitromalonamide.

Figure 7.34 Equilibrium of thiodibenzoylmethane.

Figure 7.35 Plot of

4

ΔCS(OD) vs. the R1‐R2 distance for a series of

o

‐hydrox...

Figure 7.36 Equilibrium of 2‐acetyl‐1,8‐dihydroxy‐3,6‐dimethylnaphthalene.

Figure 7.37 The sum of one‐bond deuterium isotope effects on

15

N chemical sh...

Figure 7.38 Tautomeric equilibrium for Schiff bases of 2‐hydroxynaphthalene....

Figure 7.39 Plot of

1

ΔN(D) vs. the mole fraction for

o

‐hydroxy Schiff bases ...

Figure 7.40 Quinoline derivative showing bifurcated hydrogen bonds.

Figure 7.41 Double Schiff bases.

Figure 7.42 Tautomeric scheme of Schiff bases

N

‐(pyridoxylidene)tolylamine a...

Chapter 8

Figure 8.1 Experimentally observed low‐energy intramolecularly hydrogen‐bond...

Figure 8.2 General mechanism for vibrationally induced selective conformatio...

Figure 8.3 Conformers of TFA, TCA, and TBA.

Figure 8.4 B3LYP/6‐311++G(d,p) calculated minimum energy structures of benzo...

Figure 8.5 B3LYP/6‐311++G(d,p) calculated minimum energy structures of 2,6‐d...

Figure 8.6 B3LYP/6‐311++G(d,p) calculated potential energy profiles for inte...

Figure 8.7 Tautomers of thiotropolone and its conformers, with their B3LYP/6...

Figure 8.8 Experimental difference

infrared

(

IR

) spectrum (spectrum after ma...

Figure 8.9 B3LYP/6‐311+G(2d,p) computed

intrinsic reaction coordinate

(

IRC

) ...

Chapter 9

Figure 9.1 IR (a) and NIR (b) spectra of methanol in CCl

4

in the 3800–3000 c...

Figure 9.2 NIR spectra of water in the 12 000–4000 cm

−1

region measure...

Figure 9.3 (a) Temperature‐dependent NIR spectra of water from 5 to 85 °C. (...

Figure 9.4 Pure component NIR spectra (a) and concentrations (b) of two kind...

Figure 9.5 Contribution (a) and spectral (b) profiles determined from MCR of...

Figure 9.6 Synchronous 2DCOS spectrum constructed from NIR spectra of alcoho...

Figure 9.7 Synchronous 2D hetero‐correlation spectrum constructed from MIR a...

Figure 9.8 Relationship between the mole fraction of 1‐hexanol (

X

1‐hexanol

...

Figure 9.9 Contribution profiles (in mole fractions) obtained from MCR of co...

Figure 9.10 Composition‐mean excess NIR absorption spectra of methanol/ethan...

Figure 9.11 Contribution profiles (in mole fractions) obtained from MCR of c...

Figure 9.12 Composition‐mean excess NIR absorption spectra of 1‐hexanol/

n

‐he...

Figure 9.13 NIR spectra of CH

3

CN (solid), CD

3

CN (dashed), and CCl

3

CN (dash d...

Figure 9.14 NIR spectra of CH

3

CN (solid), CD

3

CN (dashed), and CCl

3

CN (dash d...

Figure 9.15 Chemical and lamellar structures of PHB. (a) Time‐dependent vari...

Figure 9.16 (a) Time‐dependent variations in NIR spectra in the 6050–5650 cm

Figure 9.17 (a) Time‐dependent variations in the NIR spectra in the 5200–506...

Figure 9.18 Vis/NIR/IR spectra in the OH stretching band region of phenol, 2...

Figure 9.19 Relative intensities of the OH stretching band of phenol, 2,6‐di...

Figure 9.20 FT‐NIR/IR spectra of (a) pyrrole, (b) pyridine, and (c) pyrrole ...

Figure 9.21 FT‐NIR spectra in the NH stretching overtone region of (a) pyrro...

Figure 9.22 Vibrational wave functions and dipole moment functions along pot...

Figure 9.23 Solvent dependence of absorption intensities and wave numbers of...

Figure 9.24 (a) Dependences on

ɛ

of the potential energy curve, dipole ...

Chapter 10

Figure 10.1 (a) Time‐resolved fluorescence of HPTS in water measured at 420 ...

Figure 10.2 (a) Dissociation profiles of 6‐carboxy 2‐naphthol showing the th...

Figure 10.3 p

K

a

0

(balls) and p

K

a

*

(squares) [27–35] values vs. Hammett's...

Figure 10.4 (a) Oscillations are evident in the fluorescence intensity of 2‐...

Figure 10.5 TCSPC‐normalized fluorescence of the R

*

OH form of 2N8S in ne...

Figure 10.6 Comparison between the numeric solutions of SSDP‐SB and SSDP‐DB ...

Figure 10.7 Time‐resolved fluorescence decay of 2N8S after lifetime correcti...

Figure 10.8 A demonstration of the strong hydrogen bond, which is formed in ...

Figure 10.9 (a) Fluorescence of HPTA and HPTA–DMSO complex in DCM. (b) Trans...

Figure 10.10 Correlation between the change in the IR absorption of the stre...

Figure 10.11 (a) IR spectra of H

2

O + DMSO complexes in DCM: 0.1 M H

2

O in DCM...

Figure 10.12 A pictorial sketch of the one‐ (a) and two‐ (b) water‐bridge ar...

Figure 10.13 UV absorption of 2N8S in pure water (gray full line), ACN (dash...

Figure 10.14 (a) Fluorescence emission spectra of 2N8S in pure ACN (359.5 nm...

Figure 10.15 Fluorescence spectra of 2N8S in ACN (full line), in ACN with 0....

Figure 10.16 (a) TCSPC‐normalized fluorescence of the R

*

OH form of 2N8S ...

Figure 10.17 TCSPC‐normalized fluorescence of the R

*

OH and proton‐transf...

Figure 10.18 Plot of the data of Table 10.5. The slope of the linear correla...

Figure 10.19 (a) TCSPC‐normalized fluorescence of the R

*

OH form of 2N8S ...

Figure 10.20 TCSPC‐normalized fluorescence of the R*OH (squares) and proton‐...

Figure 10.21 (a) UV absorption spectra of 2N8S with up to 0.28M D

2

O (up to 0...

Figure 10.22 TCSPC‐normalized fluorescence of the R*OD and deuteron‐transfer...

Figure 10.23 (a) Comparison between the numeric solutions of SSDP‐SB and SSD...

Figure 10.24 Scheme of the step‐wise double‐ESPT reaction, which we envision...

Figure 10.25 Intramolecular sequential proton transfer through one‐water bri...

Chapter 11

Figure 11.1 Schematic showing

D

e

(equilibrium dissociation energy) and

D

0

fo...

Figure 11.2 Schematic showing the effect of zero‐point motion on a H‐bonded ...

Figure 11.3 Schematic of the experimental setup for VMI measurement.

Figure 11.4 Structure of water dimer.

Figure 11.5 Infrared spectrum of (H

2

O)

2

recorded while monitoring the

1

B

1

(...

Figure 11.6 Experimental velocity distributions (in red) of H

2

O and D

2

O phot...

Figure 11.7 Low lying stationary points of (H

2

O)

3

.

Figure 11.8 Schematic depicting the higher density of states for the dimer p...

Figure 11.9 Water complexes with dimethylamine (DMA) and trimethylamine (TMA...

Figure 11.10 Room temperature infrared spectrum of H

2

O⋯(CH

3

)

3

N (water⋯TMA) o...

Figure 11.11 Linear dependence of the calculated integrated absorbance on th...

Figure 11.12 REMPI spectrum of 9HFCA monomer. The signals were collected aft...

Figure 11.13 (a) Partially corrected multiphoton mass spectrum of (C

6

H

6

)

n

sh...

Figure 11.14 Plot showing the experimental signal intensity (points) of C

6

H

6

Figure 11.15 Schematic showing the relation between the appearance energy (2

Figure 11.16 Experimental schematic used for the determination of

D

0

of C

6

H

5

Figure 11.17 Mass‐selected two‐color multi‐photon ionization spectrum of C

6

H

Figure 11.18 (a) MATI spectrum recorded for the benzene monomer excited via ...

Figure 11.19 An extended ZEKE spectrum of

p

‐fluorophenol⋯H

2

S complex showing...

Figure 11.20 The Birge–Sponer extrapolation plot for fluorophenol⋯H

2

S in the...

Figure 11.21 SEP‐REMPI experimental scheme for the determination of

D

0

for M...

Figure 11.22 The hot‐band SEP spectra and the fluorescence spectra of 1‐naph...

Figure 11.23 Plot of equilibrium dissociation energy (

D

e

) vs. the stretching...

Chapter 12

Figure 12.1 Schematic representation and selected examples of two types of s...

Figure 12.2 (a, b) Parameters that describe hydrogen bond geometry: (a) thre...

Figure 12.3 Schematic representation of proton distribution functions in cas...

Figure 12.4 Schematic representation of proton distribution function includi...

Figure 12.5 Two forms of proton transfer pathway. (a) “Classical” shift of t...

Figure 12.6 Dependence of OHO bridging chemical shift on hydrogen bond geome...

Figure 12.7 (a, b) Relative contribution of substituent effects (green) and ...

Figure 12.8 Complexes were studied to establish a Δ

δ

C(H/D) − 

q

1

correla...

Figure 12.9 H‐bonded complexes are formed by (a) phosphinic and phosphoric a...

Figure 12.10 Schematic representation of the main factors influencing the

31

Figure 12.11 Intermolecular complexes with OHN hydrogen bonds: (a) benzoic a...

Figure 12.12 Some examples of NHN‐bonded systems. (a) Anionic —C≡NH⋯

−

N...

Figure 12.13 Complexes with FHF hydrogen bonds. (a) Schematic structures of ...

Figure 12.14 Complexes of acetic acid with fluoride anion, studied in Ref. [...

Figure 12.15 Structures of 1 : 1, 2 : 1, 3 : 1, and 1 : 2 complexes of FH wi...

Figure 12.16 Vicinal H/D isotope effects on

1

H NMR chemical shifts in system...

Figure 12.17 Complexes for which vicinal H/D isotope effects on

1

H NMR chemi...

Figure 12.18 Major vibration with participation of atoms forming hydrogen bo...

Figure 12.19 Schematic representation of evolution of a XH band shape upon h...

Figure 12.20 H‐bonded systems that require different definitions of H‐bond e...

Chapter 13

Figure 13.1 (a) ATR–FUV spectra of pure water and 1 M alkali metal cation ni...

Figure 13.2 Ground (bottom) and excited state (top) orbitals of the first sh...

Figure 13.3 Ground (bottom) and excited state (top) orbitals of the second s...

Figure 13.4 The energy and oscillator strength per water molecule of calcula...

Figure 13.5 (a) FUV spectra of the M+(H2O)6 clusters calculated with the EOM...

Figure 13.6 Ground and excited state energies of the first (right) and secon...

Figure 13.7 FUV absorption spectra of H

2

O on the aluminum with incident angl...

Figure 13.8 Optimum spectra of the bulk and interfacial phases calculated wi...

Figure 13.9 (a) ATR‐FUV spectra of FA, NMF, NMA, NdMF, and NdMA in the liqui...

Figure 13.10 Theoretical spectra of the amides (a) in vacuum calculated by T...

Figure 13.11 (a) The optimized structure of dimers for five kinds of amides ...

Figure 13.12 Chemical structures of (a) nylon 6, (b) nylon 11, (c) nylon 12,...

Figure 13.13 (a) ATR‐FUV spectra of nylon 6, nylon 11, nylon 12, nylon 6/6, ...

Figure 13.14 Calculated spectra of model compounds of nylon 6, nylon 11, and...

Figure 13.15 Computational trimer models of hydrogen‐bonded systems for (a) ...

Figure 13.16 (a)ATR‐FUV spectra in the 145–200 nm region for DG, TG, DGDM, D...

Figure 13.17 Dependence of absorbance on the concentration of Li

+

for mi...

Figure 13.18 (a) Wavelength shift (

δλ

) of three bands at 155, 163,...

Figure 13.19 The complex structure models; (a) Int 1, (b) Int 2, (c) Int 3....

Figure 13.20 Simulation spectra of neat PEG and complexes (Int 1, Int 2, and...

Chapter 14

Figure 14.1 The infrared spectra of pure D

2

O (red line), mixture of 1.4% D

2

O...

Figure 14.2 Infrared spectra of bulk water as a function of temperature and ...

Figure 14.3 The spectral components computed by the multivariant curve resol...

Figure 14.4 Schematic presentation of transmission high‐pressure cell.

Figure 14.5 Schematic representation of the subtraction procedure: 0.5 M sol...

Figure 14.6 OD stretching of subtracted spectrum of 0.03 M NaCl solution in ...

Figure 14.7 Difference spectra of methanol dissolved in 2.8 % HDO in H

2

O aft...

Figure 14.8 Infrared spectra of OD‐stretching band ν

OD

of the mixture of 2.8...

Figure 14.9 Infrared spectra of the OD‐stretching mode of clathrates. (a) Me...

Figure 14.10 The halfwidths of OD stretching of methane, ethane, xenon, and ...

Figure 14.11 The resulting spectra after subtraction procedure applied to th...

Figure 14.12 The normalized spectra of the decoupled OD‐stretching bands of ...

Figure 14.13 Experimentally determined vibrational spectra of 10 vol% MeOH s...

Figure 14.14 HOH‐bending mode frequency,

δ

HOH

, obtained from the SC and...

Figure 14.15 Number of perturbed H

2

O molecules per one molecule of alcohol c...

Figure 14.16 CH‐stretching mode frequency,

ν

CH

, obtained from the SC an...

Figure 14.17 CO‐stretching mode frequency,

ν

CO

, obtained from the SC an...

Chapter 15

Figure 15.1

N

,

N

‐Diarylformamide balances for the quantifying hydrogen‐bond c...

Figure 15.2 ACHC‐ and ACPC‐derived foldamers (arrows indicate the atoms betw...

Figure 15.3 Variations of residue and hydrogen‐bonding group from the amide ...

Figure 15.4 Helical aromatic oligoamide foldamers.

Figure 15.5 Foldamers aggregated by π‐stacking interactions.

Figure 15.6 Foldamers exploiting repulsive interactions: (a) Aggarwal's poly...

Figure 15.7 β‐Hairpin‐mimetic trimeric MAMBA foldamers.

Figure 15.8 β‐Sheet‐mimetic oligourea foldamers.

Figure 15.9 Accessible conformations of ethylene‐bridged triureas.

Figure 15.10 Control of topology in 2,6‐bis(

N

‐imidazolidin‐2‐onyl)pyridine o...

Figure 15.11 Determination of helical excess using VT NMR in (a) a configura...

Figure 15.12 Screw‐sense preference of a 3

10

helix induced by

L

‐α‐methylvali...

Figure 15.13 Binding of chiral Brønsted acids with a configurationally achir...

Figure 15.14 Regulation of screw‐sense preference by temperature‐dependent b...

Figure 15.15 Screw‐sense induction by association of a chiral ligand to a Cu...

Figure 15.16 Reversal of screw‐sense preference in DOPC‐derived vesicles....

Figure 15.17 Light‐modulated screw‐sense induction in phospholipid bilayers....

Figure 15.18 Tendril perversions in Aib foldamers.

Figure 15.19 (a) Deleted hydrogen bonds in tendril perversions and (b) γ‐tur...

Figure 15.20 Symmetry elements in dual hydrogen‐bond donor/acceptor monomers...

Figure 15.21 Hydrogen‐bond directionality reversal in helical oligoureas (2

1

...

Figure 15.22 Helical oligoureas as a molecular spring torsion balance.

Figure 15.23 Hydrogen‐bond directionality reversibility in ethylene‐bridged ...

Figure 15.24 Hydrogen‐bonding additives associating with ethylene‐bridged ol...

Figure 15.25 pH‐modulated hydrogen‐bond directionality switching in ethylene...

Figure 15.26 Remote fluorescence response from communication of protonation ...

Figure 15.27 Tautomerism in campestarenes.

Figure 15.28 Hydrogen‐bond directionality in amide‐appended corannulenes.

Figure 15.29 Cyclic hydrogen bond networks in alleno‐acetylenic cages.

Figure 15.30 The “open” and “closed” form of the AAC.

Figure 15.31 Chirality arising from a dissymmetric cyclic hydrogen bond netw...

Guide

Cover

Table of Contents

Title Page

Copyright

Begin Reading

Index

End User License Agreement

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Spectroscopy and Computation of Hydrogen‐Bonded Systems

Edited by Marek J. Wójcik and Yukihiro Ozaki

Editors

Prof. Marek J. WójcikJagiellonian UniversityFaculty of ChemistryGronostajowa 230‐387 KrakowPoland

Prof. em. Yukihiro OzakiKwansei Gakuin UniversityDepartment of Chemistry2‐1 GakuenKobe Sanda Campus669‐1337 Sanda, HyogoJapan

Cover Image: © Emre Terim/Shutterstock

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Print ISBN: 978‐3‐527‐34972‐2ePDF ISBN: 978‐3‐527‐83489‐1ePub ISBN: 978‐3‐527‐83490‐7oBook ISBN: 978‐3‐527‐83491‐4

Part ITheory

1Linear Response Theory Applications to IR Spectra of H‐Bonded Cyclic Dimers Taking into Account the Surrounding. Updating Contributions Involving Davydov Coupling, Fermi Resonances and Electrical Anharmonicity

Paul Blaise and Olivier Henri‐Rousseau

Laboratory of Mathematics and Physics, 52 Av. Paul Alduy, 66100 Perpignan, France

1.1 Introduction

This chapter is devoted to the application of the Henri‐Rousseau and Blaise model [1] which has incorporated quantum mechanically the damping of the H‐bond bridge into the Maréchal and Witkowski model [2] to the experimental infrared (IR) lineshapes of cyclic centrosymmetric dimers. In Figure 1.1, are depicted for example linear and cyclic H‐bonded carboxylic acids.

One may distinguish the length of O—H bond and one of the H‐bond. In Figure 1.2 are recapitulated the connections between the present applied theory and diverse older ones.

1.2 Dimer Strong Anharmonic Coupling Theory

1.2.1 Different Theoretical Situations

1.2.1.1 Strong Anharmonic Coupling Within Adiabatic Approximation For Monomer

Let us consider a single H‐bonded system where and are nucleophilic substituents such as oxygen or nitrogen (See Figure 1.3). Define and as the operators corresponding to the lengths of X–H and X–Y bonds. Besides, both these lengths are oscillating, the first one at high frequency and the last one H‐bond bridge at low frequency.

Now suppose that a strong anharmonic coupling may occur between the X‐H high‐frequency mode and the XY low‐frequency mode .

Within the strong anharmonic coupling theory, it is assumed a linear dependence of the high‐frequency mode on the H‐bond bridge coordinate , according to:

(1.1)

where is the angular frequency of a isolated X–H bond and some parameter.

Figure 1.1 (a) H‐bond monomer and the coordinates. (b) H‐bond dimer and the coordinates.

Figure 1.2 Connections between the present theory and different older models.

The full Hamiltonian may be partitioned as follows:

(1.2)

The Hamiltonian of the slow mode may be viewed as either harmonic or anharmonic (Morse‐like)

Here, is the momentum coordinate of the slow mode of reduced mass and angular frequency , whereas is the dissociation energy of the Morse curve.

The Hamiltonian is corresponding to the (X–H) high‐frequency mode. Within the harmonic approximation and strong anharmonic coupling theory, it is:

(1.3)

whereas is the momentum coordinates for the fast mode.

The eigenvalue equations of the fast and slow harmonic modes are given respectively, neglecting the zero‐point energy of the fast mode by:

(1.4)

Within the adiabatic approximation the full Hamiltonian becomes simply:

where

(1.5)

Figure 1.4 represents the absorption mechanism generating a coherent state.

It is possible to generalize the above approach by introducing together with the coupling of the fast mode to the H‐bond bridge, another coupling of the fast mode with some bending mode according to:

with, by taking the H‐bond bridge potential as Morse‐like (See Table 1.1).

Figure 1.3 Coordinates of single H‐bonded system.

Figure 1.4 Physics of the absorption mechanism. The ground state of the slow mode H‐bond bridge (corresponding to the ground state situation of the fast mode) becomes a coherent state after excitation towards the first excited state of the fast mode.

Table 1.1 Different sorts of Hamiltonians.

where and are respectively the position and momentum coordinates of the bending mode having as angular frequency and as reduced mass.

1.2.1.2 Introduction of Fermi Resonances

Now, there is the possibility to introduce Fermi resonance [11] in this physical model as it is illustrated in Figure 1.5.

There is a coupling characterized by the parameter between the two situations evoked in Figure 1.5.

In the absence of damping, the full Hamiltonian involving Fermi resonances is:

(1.6)

Here, the three first right‐hand side Hamiltonians are the components of the bare H‐bond Hamiltonians without Fermi resonance given respectively by equations given in Table 1.1. Besides, the Hamiltonian corresponding to the bending mode and the interaction between the fast and bending modes are respectively:

(1.7)

Figure 1.5 Fermi resonances interaction coupling parameters between two situations of the fast, slow, and bending modes.

Source: Henri‐Rousseau and Blaise 2008 [18]/John Wiley & Sons.

where and are respectively the position and momentum coordinates of the bending mode of reduced mass and its angular frequency, whereas is the coupling parameter between the fast and bending modes. The eigenvalue equations of the harmonic Hamiltonians corresponding respectively to the fast and slow modes are respectively given by equations given by Eqs. (1.4) whereas that dealing with the bending modes is, ignoring the zero‐point energy:

(1.8)

Now, within the adiabatic approximation. The Hamiltonian (1.6) becomes:

(1.9)

The different Hamiltonians are given as follows:

Here, is the anharmonic coupling parameter involved in the Fermi resonance which is a function of .

As a consequence of the above equations, the full Hamiltonian describing the fast mode coupled to the H‐bond bridge (via the strong anharmonic coupling theory) and the bending mode (via the Fermi resonance process) may be written within the tensorial basis (1.10) according to [12]:

(1.10)

(1.11)

1.2.1.3 H‐Bonded Centrosymmetric Dimer

Now, look at an H‐bonded dimer. It will take place in a Davydov coupling [13]. Within the anharmonic coupling, the physics of the system may be viewed in Figure 1.6.

It may be observed that because of the symmetry of the dimer, there is a operator (with ), which exchanges the coordinates of the two slow modes H‐bond bridges of the cyclic dimer according to:

(1.12)

Ignoring for the present time the interaction between the two moieties and assuming that, within each moiety, the adiabatic approximation may be performed as for a single H‐bond, the Hamiltonian of the symmetric dimer embedded in the thermal bath, is:

Figure 1.6 Davydov coupling interactions.

Source: Henri‐Rousseau and Blaise 2008 [18]/John Wiley & Sons.

(1.13)

In Eq. 1.13, the two first right‐hand side terms are the adiabatic Hamiltonians of each moiety. They are given by an expression of the same form which is:

are the eigenkets of the Hamiltonians of the fast modes harmonic oscillators, whereas the Hamiltonians of each moiety are respectively: