Calculations of Prebiotic Molecules Formed from O(1D) Insertion Reactions Open Access

Anderson, Thomas Andrew (2010)

Permanent URL: https://etd.library.emory.edu/concern/etds/kk91fm28g?locale=en
Published

Abstract

Abstract

Calculations of Prebiotic Molecules Formed from O(1D)
Insertion Reactions
By Thomas Anderson
This work explores the stationary points on the potential energy surface for the
reactive organic molecules methanediol, methoxymethanol, and aminomethanol. These
molecules are predicted by astrochemical models to be the small molecular precursors to
larger, biologically-relevant molecules such as sugars and amino acids in interstellar
environments. These three molecules are highly unstable and therefore very short-lived
under regular laboratory conditions. Yet many such molecules are present in interstellar
clouds, often at high abundance because their lifetimes are significantly increased at the
low pressures and temperatures of interstellar environments. To identify a molecule in
space, a rotational spectrum must be taken in the laboratory and compared to
observational spectra. Due to the reactivity and instability of these prebiotic precursors,
however, the gas phase spectra are not easily obtained, and efficient laboratory
production mechanisms must be explored. O(1D) insertion reactions into C-H bonds of
stable organic molecular precursors are one possible production route for these molecules
because these reactions are highly exothermic, and therefore highly efficient. To
examine the feasibility of such reactions for laboratory production of these molecules, the
energies and structures of the singlet and triplet state minima and transition states for
these three molecules were calculated at the MP2/Aug-cc-pVTZ level of theory. These
results will serve as a starting-point for higher-level calculations of the full potential
energy surface. In addition to the target molecules, the starting material for each insertion
reaction as well as other potential molecular products were investigated.

Table of Contents


Table of Contents

Chapter 1 Background
1

1.1
Introduction ..................................................................................................1
1.2
Atomic Oxygen ............................................................................................2
1.3
Methanediol and Methoxymethanol ............................................................4
1.4
Aminomethanol and N-Methylhydroxylamine ............................................5
1.5
Calculations..................................................................................................6

Chapter 2 Starting Materials
7

2.1
Introduction ..................................................................................................7
2.2
Atomic Oxygen ............................................................................................8
2.3
Methanol ......................................................................................................8
2.4
Dimethyl Ether ...........................................................................................10
2.5
Methylamine ..............................................................................................11

Chapter 3 Singlet Optimizations
13

3.1
Introductions ..............................................................................................13
3.2
Methanediol ...............................................................................................14
3.3
Methoxymethanol ......................................................................................16


3.4
Aminomethanol..........................................................................................21
3.5
N-Methylhydroxylamine............................................................................24

Chapter 4 Triplet Optimizations
28

4.1
Introductions ..............................................................................................28
4.2
Methanediol ...............................................................................................29
4.3
Methoxymethanol ......................................................................................32
4.4
Aminomethanol..........................................................................................34
4.5
N-Methylhydroxylamine............................................................................37


Chapter 4 Disscussion and Conclusions
41

5.1
Introductions ..............................................................................................41
5.2
Methanediol ...............................................................................................42
5.3
Methoxymethanol ......................................................................................43
5.4
Aminomethanol and N-Methylhydroxylamine ..........................................43
5.5
Summary ....................................................................................................44

Appendix A Starting Materials
46

Appendix B Singlet Molecules
47



B.1
Singlet Methanediol ...................................................................................47
B.2
Singlet Methoxymethanol ..........................................................................48
B.3
Singlet Aminomethanol .............................................................................52
B.4
Singlet N-Methylhydroxylamine ...............................................................55


Appendix C Triplet Structures
57

C.1
Triplet Methanediol ...................................................................................57
C.2
Triplet Aminomethanol ..............................................................................57

Bibliography
59



List of Figures


2.01
MP2/Aug-cc-pVTZ optimized structure of methanol..................................9

2.02
MP2/Aug-cc-pVTZ optimized structure of dimethyl ether. ......................10

2.03
MP2/Aug-cc-pVTZ optimized structure of methylamine..........................12

3.01
Structures of the two methanediol singlet conformations..........................13

3.02
Transition states of methanediol at the following relative energies. .........15

3.03
Relative energies of the methanediol conformers and internal motion
transition states.......................................................................................................16

3.04
Structures of the three methoxymethanol singlet conformations at the
following relative energies. ....................................................................................18

3.05
Structures of the five methoxymethanol singlet transition states
determined by QST2 optimization. ........................................................................19

3.06
energies of the stationary points for singlet methoxymethanol. ................20


3.07
Structures of the four aminomethanol singlet conformations. ...................22

3.08
Structures of the four aminomethanol singlet transition states
determined by QST3 optimization. ........................................................................23

3.09
Relative energies of the stationary points for singlet aminomethanol .......24

3.10
The two stable structures of N-methylhydroxylamine singlet
conformations. .......................................................................................................25

3.11
Transition states of N-methylhydroxylamine at the following relative
energies ..................................................................................................................26

3.12
Relative energies of the stationary points for singlet
N-methylhydroxylamine. .......................................................................................26

4.01
Triplet structures of methanediol. ..............................................................30

4.02
Relative energy level diagram of the singlet and triplet states of
methanediol. ...........................................................................................................31

4.03
Example triplet dissociation structure of methoxymethanol. ....................32

About this Master's Thesis

Rights statement
  • Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.
School
Department
Degree
Submission
Language
  • English
Research field
Keyword
Committee Chair / Thesis Advisor
Committee Members
Last modified

Primary PDF

Supplemental Files