Biosignature detection in Mars analogue aqueous alteration minerals using Raman spectroscopy

136 Pages·2016·14.51 MB·English

Biosignature detection in Mars analogue
aqueous alteration minerals using Raman
spectroscopy
David Hamilton
A Thesis submitted to the Faculty of Graduate Studies in Partial Ful(cid:28)llment
of the Requirements for the Degree of Master of Science
Graduate Program in Earth and Space Science, York University, Toronto,
Ontario
August 2016
' David Hamilton 2016
Abstract
The Mars Exploration Program Analysis Group states in their documentation
regarding science goals, objectives, investigations and priorities, that the num-
ber one goal of Mars exploration is to determine if Mars ever supported life[1].
A Raman spectrometer is suggested to be a prime candidate instrument for
the detection of organic compounds[2], the building blocks of terrestrial life.
Though Raman spectroscopy has no space heritage, both NASA and ESA have
Raman instruments planned for their next Mars rovers. The ideal place to
search for organic matter which could provide evidence for past or present life
wouldbeinthepresenceofmineralsthatwereformedinwater. Thisstudywas
carried out to determine if a molecular biosignature can be detected in a mix-
ture with either a phyllosilicate or a hydrated sulphate. We present this data
at UV excitation wavelength using a prototype in-situ stand o(cid:27) Raman system
intendedtorepresentaninstrumentforaroverplatform. Dataisalsopresented
for the same samples using green excitation wavelength and a commercial Ra-
man microscope. The spectral resolution of the short focal length prototype
in-situ UV Raman system leads to less numerous bands than the green Raman
microscope system. Ultraviolet electronic absorption transitions in the samples
containingtransitionmetals,eitheraspartofamineral’scrystalstructureoras
impurities, result in no Raman spectra from the minerals and poor or limited
detection of the organic. Only the synthetic calcium sulphate dihydrate, which
contains no transition metals, allowed for both acquisition of the mineral spec-
trum and detection of the embedded biosignature at all concentrations tested
usingeitherexcitationwavelength. Certainsamplesallowedforthedetectionof
an organic through the observation of a C-H stretching vibration, but did not
provide enough clear peaks to de(cid:28)ne which organic was present.
ii
Acknowledgments
I o(cid:27)er my gratitude to my supervisor Professor Mike Daly for his advice and
support. I would like to thank Kim Tait, Ed Cloutis, Matt Izawa, Veronica Di
Cecco,BrendtHyde,andEvanEshelmanforbeingextremelyhelpfulthroughout
this project. I would also like to thank NSERC for funding a portion of this
research.
iii
Table of Contents
Contents
Abstract ii
Acknowledgments iii
Table of Contents iv
1 Introduction 1
1.1 The ingredients for life on Mars . . . . . . . . . . . . . . . . . . 1
1.2 Motivation to utilize UV and green excitation wavelengths . . . . 3
1.3 Scope and limitations of study . . . . . . . . . . . . . . . . . . . 4
2 Raman scattering: The classical description 6
3 Life and organic carbon 12
3.1 Astrobiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.2 Biosignatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.3 Habitability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.4 Preservation of molecular biosignatures . . . . . . . . . . . . . . 14
3.5 What we currently know about organics on Mars . . . . . . . . . 16
3.6 Properties of organic carbon bonding . . . . . . . . . . . . . . . . 16
4 Methodology I: Experimental techniques, sample suite, equip-
ment, and data analysis used 18
4.1 Samples used . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.1.1 Organic biosignature . . . . . . . . . . . . . . . . . . . . . 19
4.1.2 Hydrated sulphates. . . . . . . . . . . . . . . . . . . . . . 19
4.1.3 Phyllosilicates. . . . . . . . . . . . . . . . . . . . . . . . . 20
4.2 Pre-treatment of mineral samples . . . . . . . . . . . . . . . . . . 20
4.3 Raman equipment . . . . . . . . . . . . . . . . . . . . . . . . . . 21
4.3.1 Green excitation (532nm) commercial Raman microscope 21
4.3.2 Ultraviolet excitation (266nm) prototype in-situ Raman
system . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
4.4 Raman windows . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.5 Data analysis methods . . . . . . . . . . . . . . . . . . . . . . . . 26
5 The biosignature stearic acid 28
5.1 Raman peaks in stearic acid . . . . . . . . . . . . . . . . . . . . 30
5.1.1 Methyl and methylene groups . . . . . . . . . . . . . . . . 30
5.1.2 Carbonyl section of carboxyl group . . . . . . . . . . . . . 33
5.1.3 Hydroxyl section of carboxyl group . . . . . . . . . . . . . 34
5.1.4 Fermi-resonance in stearic acid . . . . . . . . . . . . . . . 34
5.1.5 Additional band made possible due to hydrogen bonding. 35
5.2 Band broadening in stearic acid . . . . . . . . . . . . . . . . . . . 35
iv
5.3 Stearic acid results . . . . . . . . . . . . . . . . . . . . . . . . . . 36
5.3.1 Uncertain region from 2100-2700 cm−1 . . . . . . . . . . . 40
5.3.2 Lowest frequency observable band as chain length identi(cid:28)er 40
6 Aqueous alteration minerals 41
6.1 Minerals and abiogenesis . . . . . . . . . . . . . . . . . . . . . . . 42
6.2 Hydrated sulphates . . . . . . . . . . . . . . . . . . . . . . . . . . 43
6.2.1 Gypsum . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
6.2.2 Natrojarosite . . . . . . . . . . . . . . . . . . . . . . . . . 48
6.3 Phyllosilicates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
6.3.1 Kaolinite . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
6.3.2 Smectites . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
6.3.3 Imperfections in the crystal lattice of clays . . . . . . . . 70
6.3.4 Clays and the current organics budget . . . . . . . . . . . 70
6.3.5 Problems with clay optical spectroscopy other than UV
absorption. . . . . . . . . . . . . . . . . . . . . . . . . . . 70
7 Transition metal bearing coordination complexes and UV ab-
sorption 72
7.1 What is the problem that we are concerned with?. . . . . . . . . 72
7.2 Transition metals . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
7.3 Quantum numbers for electron orbital theories . . . . . . . . . . 75
7.4 Orbital (cid:28)lling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
7.5 Coordination complexes . . . . . . . . . . . . . . . . . . . . . . . 76
7.6 Crystal (cid:28)eld theory . . . . . . . . . . . . . . . . . . . . . . . . . . 77
7.7 Ligand (cid:28)eld theory . . . . . . . . . . . . . . . . . . . . . . . . . . 83
7.8 Selection rules for electronic transitions . . . . . . . . . . . . . . 85
7.9 Possible electronic transitions in coordination complexes . . . . . 86
7.9.1 Crystal (cid:28)eld transitions (d-d) . . . . . . . . . . . . . . . . 86
7.9.2 Intervalence charge transfers . . . . . . . . . . . . . . . . 88
7.9.3 Ligand-metal charge transfers . . . . . . . . . . . . . . . . 88
7.9.4 Charge transfers and delocalized electrons . . . . . . . . . 89
7.10 Experimentally observed and theoretically predicted UV elec-
tronic transitions in previous studies . . . . . . . . . . . . . . . . 90
7.10.1 Wells et al . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
7.10.2 Lo(cid:31)er et al . . . . . . . . . . . . . . . . . . . . . . . . . . 90
7.10.3 Cloutis et al. . . . . . . . . . . . . . . . . . . . . . . . . . 90
7.10.4 Sherman and Vergo . . . . . . . . . . . . . . . . . . . . . 90
7.10.5 Burns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
7.11 Summary of UV absorption in transition metal bearing minerals
and the implications for Raman usage on Mars . . . . . . . . . . 91
8 Methodology II: Organic + mineral mixtures 92
8.1 Published parallel research. . . . . . . . . . . . . . . . . . . . . . 92
8.2 Rotary Evaporation . . . . . . . . . . . . . . . . . . . . . . . . . 92
v
9 Results of mixtures 96
9.1 Raman spectra of mixtures . . . . . . . . . . . . . . . . . . . . . 96
9.2 Organic detection . . . . . . . . . . . . . . . . . . . . . . . . . . 96
10 Conclusion 105
11 Future work 108
12 Appendices 109
12.1 Raman systems bound for Mars . . . . . . . . . . . . . . . . . . . 109
12.1.1 Scanning Habitable Environments with Raman and Lu-
minescence for Organics and Chemicals (SHERLOC) . . . 109
12.1.2 SuperCam . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
12.1.3 Laser Raman Instrument (RLS) . . . . . . . . . . . . . . 109
12.2 Detailed descriptions of phyllosilicate samples . . . . . . . . . . 109
12.3 Additional information concerning the induced dipole moment
and molecular polarizability tensor . . . . . . . . . . . . . . . . . 111
12.4 York University 266 nm Raman system . . . . . . . . . . . . . . 113
12.5 No deconvolution of C-H stretching region . . . . . . . . . . . . . 114
References 115
vi
List of Tables
1 Typical spectral regions for vibrations in general saturated fatty
acids [3, 4]. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2 StearicacidRamanbandsreportedbyLarkin[4]. Intensitieswere
not reported. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3 Stearic acid Raman bands reported by Eshelman[5]. . . . . . . . 32
4 Stearic acid green Raman bands from this study. (*uncertain,
but probable) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
5 Stearic acid UV Raman bands from this study (*uncertain, but
probable). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
6 Typical spectral regions for vibrations in hydrated sulphates [4, 6]. 43
7 Typical spectral regions for vibrations in phyllosilicates. . . . . . 53
8 Detection and identi(cid:28)cation of organics in mineral substrate. . . 104
vii
List of Figures
1 Energy levels of photon-matter interactions: a) Rayleigh scatter-
ing, b) Stokes Raman scattering, c) anti-Stokes Raman scatter-
ing, d) IR absorption, e) electronic absorption, and f) (cid:29)uores-
cence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2 Organic molecules attached to interlayer surfaces of a clay. . . . . 15
3 Collection of mineral samples used in this study. The white cir-
cular paper is 42.5 mm in diameter. a) natrojarosite b) STx1b
montmorillonite c) SAz2 montmorillonite d) KGa2 kaolinite e)
synthetic gypsum f) Swy2 montmorillonite g) SCa3 montmoril-
lonite h) KGa1b kaolinite i) NG1 nontronite j) NAu2 nontronite
k) NAu1 nontronite . . . . . . . . . . . . . . . . . . . . . . . . . 21
4 Hematite content in clay samples. Note that oxygen-bonded
structural iron and iron bearing impurities are grouped together
as hematite. The x-axis lists the di(cid:27)erent clay samples. . . . . . 22
5 Horiba LabRam ARAMIS commercial Raman microscope at the
Royal Ontario Museum . . . . . . . . . . . . . . . . . . . . . . . 23
6 Prototype in-situ stand-o(cid:27) Raman system at the Planetary Ex-
ploration Instrumentation Laboratory (York University). Top:
colour image labels components. Bottom: Schematic of system
used with permission from Eshelman et al [2]. L1 is a quartz
beam sampler used to trigger a photodetector which opens the
gate on the camera. L2 is a beam expander. M1, M2 (mirrors)
andL3(lens)areusedtodirectlighttowardsthesample. L4and
L5 (lenses) are the collection optics which direct light towards
the detector. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
7 3600 lines/mm di(cid:27)raction grating for UV spectroscopy. . . . . . . 26
8 Sample area of prototype in-situ system from various viewing
angles. 1) dichroic beamsplitter 2) sample stage 3) harmonic
mirror 4) collection optics including edge (cid:28)lter . . . . . . . . . . 27
9 Stearic acid 3D Matlab images made using data (cid:28)le from the
ChemEd Java applet[7]. The magenta atoms are hydrogen, the
redatomsarecarbon,andthegreenatomsareoxygen. Allbonds
are single except that between C and O in the carbonyl. . . . . . 29
10 Deformation vibrations for CH groups. . . . . . . . . . . . . . . 31
2
11 Bandsduetonormalstretchandbendingovertonea)beforeand
b) after Fermi-resonance phenomenon. . . . . . . . . . . . . . . . 35
12 Dotted lines represent hydrogen bonding between two carboxylic
acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
13 Ramanspectrumofstearicacidat532nmexcitationwithacom-
mercial Raman microscope. . . . . . . . . . . . . . . . . . . . . . 36
14 Ramanspectrumofstearicacidat532nmexcitationwithacom-
mercial Raman microscope, zoomed in to show a smaller (cid:28)nger-
print window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
viii
15 Ramanspectrumofstearicacidat266nmexcitationwithapro-
totype in-situ stand o(cid:27) Raman system. . . . . . . . . . . . . . . . 38
16 Raman spectrum of stearic acid at 532 nm excitation with a
prototype in-situ stand o(cid:27) Raman system, corrected for minor
amounts of (cid:29)uorescence. . . . . . . . . . . . . . . . . . . . . . . . 38
17 Ramanspectrumofstearicacidat266nmexcitationwithapro-
totypein-situstando(cid:27)Ramansystem,correctedfor(cid:29)uorescence
and zoomed in to show a smaller (cid:28)ngerprint window. . . . . . . . 39
18 Decreaseinenergyoflowestenergydeformationvibrationinsat-
urated fatty acids from C=10 to C=18. . . . . . . . . . . . . . . 41
19 Gypsum 3D Matlab images made using data (cid:28)le from the Amer-
ican Mineralogist Crystal Structure Database[8]. The magenta
atoms are hydrogen, the red atoms are sulphur, the green atoms
are oxygen, and the blue atoms are calcium. . . . . . . . . . . . 45
20 Raman spectrum of gypsum at 532 nm excitation with a com-
mercial Raman microscope. . . . . . . . . . . . . . . . . . . . . . 46
21 Vibrational modes of the sulphate ion. . . . . . . . . . . . . . . . 46
22 Low energy lattice vibrations of gypsum at 532 nm excitation
with a commercial Raman microscope. . . . . . . . . . . . . . . . 47
23 Raman spectrum of gypsum at 266 nm excitation with a proto-
type in-situ stand o(cid:27) Raman system. . . . . . . . . . . . . . . . . 48
24 Natrojarosite 3D Matlab images made using data (cid:28)le from the
American Mineralogist Crystal Structure Database[8]. The cyan
atoms are iron, the magenta atoms are hydrogen, the red atoms
are sulphur, the green atoms are oxygen, and the blue atoms are
sodium. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
25 Raman spectrum of natrojarosite at 532 nm excitation with a
commercial Raman microscope. . . . . . . . . . . . . . . . . . . . 51
26 Raman spectrum of natrojarosite at 266 nm excitation with a
prototype in-situ stand o(cid:27) Raman system. . . . . . . . . . . . . . 51
27 Hexagonal network of linked SiO tetrahedra comprising the T
4
sheet in phyllosilicates. . . . . . . . . . . . . . . . . . . . . . . . 52
28 T-O layered structure of kaolinite . . . . . . . . . . . . . . . . . . 54
29 Raman spectrum of kaolinte KGa1b at 532 nm excitation with a
commercial Raman microscope. . . . . . . . . . . . . . . . . . . . 55
30 Raman spectrum of kaolinte KGa1b at 532 nm excitation with a
commercial Raman microscope, corrected for (cid:29)uorescence. . . . . 56
31 Raman spectrum of kaolinite KGa1b at 266 nm excitation with
a prototype in-situ stand o(cid:27) Raman system. . . . . . . . . . . . . 56
32 RamanspectrumofkaoliniteKGa1bat266nmexcitationwitha
prototype in-situ stand o(cid:27) Raman system, corrected for (cid:29)uores-
cence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
33 Raman spectrum of kaolinte KGa2 at 532 nm excitation with a
commercial Raman microscope. . . . . . . . . . . . . . . . . . . . 57
34 Raman spectrum of kaolinte KGa2 at 532 nm excitation with a
commercial Raman microscope, corrected for (cid:29)uorescence. . . . . 57
ix
35 Raman spectrum of kaolinite KGa2 at 266 nm excitation with a
prototype in-situ stand o(cid:27) Raman system. . . . . . . . . . . . . . 57
36 Raman spectrum of kaolinite KGa2 at 266 nm excitation with a
prototype in-situ stand o(cid:27) Raman system, corrected for (cid:29)uores-
cence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
37 T-O-T layered structure of montmorillonite. Nontronite has the
same structure, but with aluminum and magnesium partially re-
placed by iron. Smaller amounts of silicon may also be replaced
with iron. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
38 Raman spectrum of calcium rich montmorillonite STx1b at 532
nm excitation with a commercial Raman microscope. . . . . . . . 60
39 Raman spectrum of calcium rich montmorillonite STx1b at 532
nm excitation with a commercial Raman microscope, corrected
for (cid:29)uorescence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
40 Raman spectrum of calcium rich montmorillonite STx1b at 266
nm excitation with a prototype in-situ stand o(cid:27) Raman system. . 61
41 Raman spectrum of sodium rich montmorillonite SWy2 at 532
nm excitation with a commercial Raman microscope. . . . . . . . 61
42 Raman spectrum of sodium rich montmorillonite SWy2 at 532
nm excitation with a commercial Raman microscope, corrected
for (cid:29)uorescence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
43 Raman spectrum of sodium rich montmorillonite SWy2 at 266
nm excitation with a prototype in-situ stand o(cid:27) Raman system. . 62
44 Raman spectrum of calcium and sodium rich montmorillonite
SAz2 at 532 nm excitation with a commercial Raman microscope. 62
45 Raman spectrum of calcium and sodium rich montmorillonite
SAz2at532nmexcitationwithacommercialRamanmicroscope,
corrected for (cid:29)uorescence. . . . . . . . . . . . . . . . . . . . . . . 62
46 Raman spectrum of calcium and sodium rich montmorillonite
SAz2 at 266 nm excitation with a prototype in-situ stand o(cid:27)
Raman system. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
47 Raman spectrum of calcium and sodium rich montmorillonite
SAz2 at 266 nm excitation with a prototype in-situ stand o(cid:27)
Raman system, corrected for (cid:29)uorescence. . . . . . . . . . . . . . 63
48 Raman spectrum of calcium, sodium and magnesium rich mont-
morilloniteSCa3at532nmexcitationwithacommercialRaman
microscope. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
49 Raman spectrum of calcium, sodium and magnesium rich mont-
morilloniteSCa3at532nmexcitationwithacommercialRaman
microscope, corrected for (cid:29)uorescence. . . . . . . . . . . . . . . . 64
50 Raman spectrum of calcium, sodium and magnesium rich mont-
morillonite SCa3 at 266 nm excitation with a prototype in-situ
stand o(cid:27) Raman system. . . . . . . . . . . . . . . . . . . . . . . . 64
51 Ramanspectrumofsodiumandmagnesiumrichmontmorillonite
SCa3 at 266 nm excitation with a prototype in-situ stand o(cid:27)
Raman system, corrected for (cid:29)uorescence. . . . . . . . . . . . . . 65
x