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Design and characterization of tectones based on guanidinium-oxoanion interactions for the assembly in water [Elektronische Ressource] / Laxman H. Malge

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TECHNISCHE UNIVERSITÄT MÜNCHEN DEPARTMENT FÜR CHEMIE Design and Characterization of Tectones based on Guanidinium-Oxoanion Interactions for the Assembly in Water Laxman H. Malge Vollständiger Abdruck der von der Fakultät für Chemie der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. M. Schuster Prüfer der Dissertation: 1. Univ.-Prof. Dr. F. P. Schmidtchen 2. apl. Prof. Dr. P. Härter Die Dissertation wurde am 17.06.2010 bei der Technischen Universität München eingereicht und durch die Fakultät für Chemie am 14.07.2010 angenommen. To my parents Acknowledgements Work presented in this thesis was carried out from April 2006 to April 2010 in the Department of Organic Chemistry and Biochemistry at Technical University of Munich. I would like to thank Prof. Dr. F. P. Schmidtchen for his continuous encouragement and support. The work would not have been completed without his patience and understanding.

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Published 01 January 2010
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TECHNISCHE UNIVERSITÄT MÜNCHEN
DEPARTMENT FÜR CHEMIE


Design and Characterization of Tectones based on
Guanidinium-Oxoanion Interactions for the Assembly
in Water


Laxman H. Malge


Vollständiger Abdruck der von der Fakultät für Chemie der Technischen Universität München
zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften
genehmigten Dissertation.



Vorsitzender: Univ.-Prof. Dr. M. Schuster
Prüfer der Dissertation: 1. Univ.-Prof. Dr. F. P. Schmidtchen
2. apl. Prof. Dr. P. Härter


Die Dissertation wurde am 17.06.2010 bei der Technischen Universität München eingereicht
und durch die Fakultät für Chemie am 14.07.2010 angenommen.










































































To my parents
















































































Acknowledgements


Work presented in this thesis was carried out from April 2006 to April 2010 in the Department of
Organic Chemistry and Biochemistry at Technical University of Munich.

I would like to thank Prof. Dr. F. P. Schmidtchen for his continuous encouragement and support. The
work would not have been completed without his patience and understanding. His vast experience in
the field of organic and supramolecular chemistry helped me to overcome every obstacle during the
work. His timely advice during the difficult times helped me a lot to come out.

I would like to thank Prof. Vladimir Kral for fruitful discussions during his short visits to Munich.

My special thanks go to Dr. Tomas Briza, Dr. Robert Kaplanek and Dr. Bohumil Dolensky for the long
discussions held during their stay in the laboratory and outside.

I would like to thank Mrs. Otte, Mr. Kaviani and Mr. Cordes for providing me mass spectra of the
compounds prepared in this work. I would also be thankful to Dr. Bettina Bechlars for making available
the X-ray crystal structure.

I would take the opportunity to thank Dr. Vinod Jadhav and Dr. Wiebke Antonius for their continuous
help throughout these years. I wish to thank Ashish Tiwari for his help during the stay in laboratory.

I thank all my friends Dr. Sriram Kotkar, Dr. Nagendra Kondekar, Dr. Kulbhushan Durugkar, Dr.
Rameshwar Patil, Dr. Namdev Vatmurge, Dr. Amol Kendhale, Mr. Awadut Giri, Mr. Pandurang
Chouthaiwale and Mr. Ganesh Jogdand for their unwavering support extended to me since campus
days. I am indebted to my brother Mr. M. L. Chapale for his belief in my ability to do the Ph. D.

I would be grateful to my parents and family members for their love and constant encouragement
throughout my studies.

Finally I would like to thank my wife Pallavi for her love, affection and unassuming support extended to
me during this work.
TABLE OF CONTENTS
1. Introduction .............................................................. 1
1.1. Intermolecular non-covalent interactions ...................................................1
1.1.1. Hydrogen bonding ............................................................................................................ 2
1.1.2. Hydrophobic effect............................................................................................................ 3
1.1.3. Van der Waals forces ....................................................................................................... 5
1.1.4. π-π interactions ................................................................................................................ 5
1.1.5. Electrostatic effects........................................................................................................... 6
1.2. Survey of artificial receptors for polar solvents...........................................7
2. Aim of this work..................................................... 20
3. Synthesis ................................................................24
3.1 Synthesis of the hydrophilic bicyclic guanidinium host 34 ...........................24
3.2 Synthesis of the hydrophilic bicyclic guanidinium host 51 ...........................25
3.3 Synthesis of the tetra-cyclic guanidinium host 68........................................32
3.4 Attempted synthesis of the lactone guest 36...............................................32
3.5 Synthesis of the aromatic phosphinate guest 37.........................................38
4. Results and discussion of binding studies ........47
4.1 ITC titrations in Water .................................................................................48
4.1.1 ITC titration of host 28 with guest 37 in Water ....................................................................... 48
4.1.2 ITC titration of host 28 with guest 119 in Water ..................................................................... 49
4.1.3 ITC titration of host 34 with guest 37 in Water ....................................................................... 50
4.2 ITC titrations in DMSO................................................................................51
4.2.1 ITC titration of host 28 with guest 37 in DMSO...................................................................... 51
4.2.2 ITC titration of host 34 with guest 37 in DMSO...................................................................... 53
4.2.3 ITC titration of host 51 with guest 37 in DMSO...................................................................... 53
4.2.4 ITC titration of host 51 with guest 119 in DMSO.................................................................... 54
4.3 MD simulations ...........................................................................................56
4.3.1 MD simulations in H O .......................................................................................................... 57 2
4.3.2 MD simulations in DMSO ...................................................................................................... 59
4.3.3 MD simulations in MeOH....................................................................................................... 61
4.3.4 MD simulations in CHCl ....................................................................................................... 63 35. Experimental Part .................................................. 66
5.1 Reagents, Methods and Materials ..............................................................66
5.2 Experimental Procedures............................................................................69
5.3 Experiments in-silico.................................................................................103
5.3.1 Topology file for guanidinium host 51.................................................................................. 103
5.3.2 Topology file for guanidinium host 34.................................................................................. 107
5.3.3 Topology file for guanidinium host 28.................................................................................. 109
5.3.4 Topology file for phosphinate guest 37................................................................................ 111
6. Summary...............................................................116
7. References............................................................119
Abbreviations
Ac Acetyl
AHP Anilinium hypophosphinate
Ala Alanine
AMBER Assisted Model Building with Energy Refinement
Arg Arginine
arom aromatic
Bn Benzyl
Boc tert-Butoxycarbonyl
bp Boiling Point
BTSA Bis(trimethylsilyl)acetamide
BTSP bis(trimethylsilyl)phosphonite
calc calculated
CFF Consistent Force Field
CHARMM Chemistry at Harvard Molecular Mechanics
chemical shift
d Dublett
DABAL Aluminium-1,4-Diazabicyclo[2.2.2]-octane
DABCO 1,4-Diazabicyclo[2.2.2]-octane
DCM Dichloromethane
de diastereomeric excess
DMF N,N-Dimethylformamide
DMSBT dimethylsilyl-bis (trifluoromethanesulfonate)
DMSO Dimethylsulfoxide
DNA Desoxyribonucleic acid
DPPA Diphenyl phosphoryl azide
dppf 1,1'-Bis(diphenylphosphino)ferrocene
dppp 1,3-bis(diphenylphosphino)propane
DVB Divinylbenzene
EDIPA Ethylenediisopropylamine
ESI Electrospray Ionization
Et Ethyl
Fig Figure
FT Fouriertransformation
GROMACS Groningen Machine for Chemical Simulations
HMDS Hexamethyldisilazane
HMPA Hexamethylphosphoramide
HPLC High Performance Liquid Chromatography
HRMS High Resolution Mass Spectrometry
IPP Thiamine diphosphate
IR Infrared
ITC Isothermal Titration Calorimetry
K Association Constant ass
LDA Lithiumdi-iso-propylamide
Lys Lysine
MD Molecular dynamics
dMe Methyl
MM Molecular Mechanics
MOM Methoxymethyl
mp Melting Point
MS Mass Spectroscopy
MTB Methyltributylammonium
MTBE Methyl tert.-butyl ether
+
NAD Nicotinamide adenine dinucleotide
NAMD Nanoscale Molecular Dynamics
NMR Nuclear Magnetic Resonance
NOE Nuclear Overhauser Effect
Nos Nosyl
OPLS Optimized Potential for Liquid Simulations
p Quintett
ppm parts per million
q Quartett
QM Quantum Mechanics
RCM Ring closing metathesis
RMSD Root-Mean-Square-Deviation
R Retention Time t
RT Room Temperature
s Singulett
SPE Solid Phase Extraction
T Temperature
t Triplet
TBDMS tert.-butyl dimethyl silane
TBDPS tert.-butyl diphenyl silane
t-Bu tert.-Butyl
TEA Triethyl amine
Tf Trifluormethansulfonyl
TFA Trifluoroacetic acid
THF Tetrahydrofuran
TLC Thin Layer Chromatography
TMA Tetramethylammonium
TMS trimethyl silane
Ts Tosyl
UV Ultraviolett
Val Valine
VIS Visible
AMP adenosine monophosphate
GMP guanosine monophosphate
UMP uridine monophosphate