NMR Calculation by Quantum Espresso (QE)

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Table of contents

Abstract
1. Chapter Ⅰ : Origins of Life
I.1 Origin of small biomolecules; amino acids
I.1.1 The origins of Amino Acids
I.1.2 The ‘RNA World’ and the origins of nucleotides
I.1.3 Other primordial biomolecules : lipids
I.2 The next step: formation of biopolymers, towards peptides and proteins
I.2.1 Temperature increase
I.2.2 “Polymerization on the rocks”
I.3 Mineral surfaces at the origins of life
I.3.1 Clay Minerals
I.3.2 Pyrite and other sulfides
I.3.3 Chirality of the surface
I.4 Amino Acid polymerization on oxide surfaces
I.5 Molecular-level characterization of adsorbed biomolecules
I.5.1 Solid state NMR spectroscopy
I.5.2 Study of Organic/Inorganic interactions by ss-NMR spectroscopy
I.5.3 Literature examples of NMR investigation of amino acid adsorption on mineral surfaces
I.5.4 Some general conclusions on NMR studies
I.6 IR Spectroscopy
I.6.1 Significance of the vibrational spectroscopy of amino acids
I.6.2 Literature on vibrational spectroscopy of amino acids on silica
I.7 Other experimental techniques
I.7.1 X-Ray Diffraction
I.8 Computational Modeling
I.8.1 Theoretical Method
I.8.2 Principles of periodic DFT simulation
I.8.3 Principles of ab-initio geometry optimization
I.8.4 Description of the silica surface
I.8.5 DFT modeling of amino acid adsorption on mineral (mainly silica) surface
I.8.6 NMR Calculations
2. Chapter Ⅱ Materials and Methods
II.1 Materials
II.3 Experimental
II.3.1 Experimental approach
II.5 Molecular modeling methods
II.5.1 Structural Models
II.5.2 NMR Calculation by Quantum Espresso (QE)
3. Chapter Ⅲ: Investigation of Leucine adsorption on Silica
III.1 Introduction
III.2 Macroscopic Characterization
III.2.1 X-Ray Diffraction
III.2.2 Thermogravimetric Analysis
III.3 Spectroscopic Characterization
III.3.1 Infrared Spectroscopy
III.3.2 Solid-state NMR spectroscopy
III.4 Computational approach
III.4.1 Adsorption Energies and molecular configurations
III.5 Conclusions on the Leu/SiO2 system
4. Chapter Ⅳ: Investigation of Glutamic acid adsorption on Silica
IV.1 Introduction
IV.2 Macroscopic Characterization
IV.2.1 X-ray Diffraction
IV.2.2 Thermogravimetric Analysis
IV.3 Spectroscopic Characterization
IV.3.1 Infrared Spectroscopy
IV.3.2 Solid State Nuclear Magnetic Resonance Spectroscopy
IV.4 Computational Approach
IV.4.1 Adsorption energies and molecular configurations
IV.4.2 Calculation of NMR chemical shift values
IV.5 Conclusions on the Glu/SiO2 system
5. Chapter Ⅴ: Thermal activation of amino acids on the SiO2 surface
V.1 Thermal activation of Leu/SiO2
V.1.1 IR study of the activation of a low-loading 1% Leu/SiO2
V.1.2 IR study of the rehydration of activated forms
V.1.3 Deuterium and thermal activation
V.1.4 13C NMR of thermally activated samples
V.1.5 Activating the linear dimer H-Leu-Leu-OH on silica
V.2 Thermal activation of Glutamic acid on SiO2
V.2.1 IR study of the activation of a low-loading 1% Glu/SiO2
V.2.2 IR study of PyroGlu/SiO2
V.2.3 IR study of H-Glu-Glu-OH/SiO2
V.3 Thermal treatment of co-adsorbed systems: Glu+Leu/SiO2
V.3.1 IR study of the activation of 3%Glu+Leu/SiO2
V.4 13C solid-state NMR of co-adsorbed systems (Glu+Leu)/SiO2
V.4.1 13C NMR
V.4.2 15N NMR
V.4.3 1H – 13C 2D HETCOR
V.4.4 1H – 15N 2D HETCOR
V.5 Conclusion and perspectives
General Conclusion
Annexes
References