of solid phase molecules - Radboud Universiteit · 2012-06-13 · Thickness measurement Laser interference fringe method laser beam substrate sample vacuum 0 100 200 300 400 500 600

Infrared spectroscopy

M.E. Palumbo and G.A. BarattaINAF – Ossevatorio Astrofisico di Catania, ITALY

of solid phase molecules

Why IR spectroscopyTielens and Allamandola, 1987

Why IR spectroscopy Tielens and Allamandola, 1987

Characteristic vibrationalfrequency range of variousmolecular groups made upout of the abundantelements H, C, N, and O

Optical depth

The optical depth expresses the quantity of electromagnetic radiation removedfrom a beam by scattering or absorption during its path through a medium. If I0 isthe intensity of radiation at the source and I is the observed intensity after a givenpath, then optical depth is defined by the following equation

I0 I

I/I0=e-τ

Beer-Lambert law

The law states that there is a logarithmic dependence between the transmission, T,of electromagnetic radiation through a substance and the product of theabsorption coefficient of the substance, α, and the distance the radiation travelsthrough the material (i.e., the path length), x.

T=I/I0=e-αx

α(λ)=4πk/λ where k is the imaginary part of the complex refractive index

where τ=αx

Absorbance

where I is the intensity of electromagnetic radiation at a specified wavelength λ

that has passed through a sample (transmitted intensity) and I0 is the intensity ofthe radiation entering the sample.

In spectroscopy, the absorbance A is defined as

Aλ= -log10(I/I0)

Optical depth vs Absorbance

Given the definitions above the optical depth and the absorbance are related by

τ= ln(10) A = 2.303 A

Vacuum chamber

High vacuum P 10-7 mbar residual gas H2O Ultra high vacuum P 10-9 mbar residual gas H2

Cryostat Liquid nitrogen, T=77 KClosed cycle helium cryostat, T=10 KLiquid helium, T=3 K

Substrate in thermal contact with the cryostat

Reflection Absorption Infrared Spectroscopy (RAIRS)and Transmittance Spectroscopy

School of Chemistry, University of Nottingham

NASA/Ames Research Center

Substrates

Transmittance

transparent to IR radiation

KBr

CsI

ZnSe

Si

Reflection Absorption IR spectra

reflect IR radiation

Au

Al

KBr and CsIHigh IR transmittanceNo IR bandsHygroscopic Fragile

Potassium Bromide (KBr)

Caesium Iodide (CsI)

SiliconLower transmittanceIR bands Not hygroscopicChemically very resistantResist thermal and mechanical shocks

Deposition angle

Directed deposition

clean chamber

very low deposit on the back of the

substrate

non-uniform film (unless an array of

capillaries is used)

Substrate T=15 K

Substrate T=15 K

Background deposition

uniform film

molecules everywhere

deposit on the back of the substrate

How to protect the back of the substrate

see Sicilia et al. 2012

Laboratorio di Astrofisica Sperimentale, Catania

Laboratorio di Astrofisica Sperimentale, Catania

Experimental procedure

Substrate (Si, KBr, CsI) T=10-300 K

IR beam

Background (mid-infrared) at 16 K (KBr substrate)


Sample T=10-150 K

IR beam

Mid-IR spectrum of the sample as deposited (CH3OH at 16 K)


Continuum normalization

τ = - ln (I/I0)

Band’s profile

Profile = shape, width and peak position

Band’s profile may strongly depend on the optical set-up geometry

IR spectra of solid CO

RAIRS

Transmittance at normal incidence

Transmittance at oblique incidence

e.g. Sandford et al. 1988Tielens et al. 1991Gerakines et al. 1996Collings et al. 2003Palumbo et al. 2006Fuchs et al. 2009

TO-mode

TO-mode

LO-mode

LO-mode

LO-TO splitting

Almeida 1992, Phys. Rev. B 45, 161

LO-TO splitting

A band due to the LO mode CANNOT be present in the spectra taken in

transmittance at normal incidence.

The bands due to the LO-TO modes are observed in transmittance at

oblique incidence.

In RAIR spectra of thin films on a metal surface (e.g. Au) only the LO

mode band is observed. The band due to the TO mode is not observed

because in a metal the electric field close to the surface is normal to

the surface.

IR spectra of solid CO2

Baratta et al. 2000, A&A 357, 1045

TO-mode

TO-mode

TO-mode

LO-mode

LO-mode

RAIR spectra of solid CO

The profile of the CO banddepends on the thicknessof the underlying ice layer

Palumbo et al. 2006

Transmittance spectra of solid CO


Palumbo et al. 2006

Transmittance spectra of solid CO


Palumbo et al. 2006

4000 3500 3000 2500 2000 1500

0.8

0.9

1.0

1.1

1.2

1.3

TRANSMITTANCE SPECTRA

CO on N2

S polarization

Si substrate

T=16 K

N2 thickness

0 m

1.1 m

2.2 m

transm

itta

nce

wavenumber (cm-1)

Use of a polarizer

Laboratorio di Astrofisica SperimentaleCatania

Baratta et al. 2002

LO mode

At oblique incidence a band due to the LO modeCANNOT be present in the spectra taken whenyou select the S component with the polarizer. Itcan be observed when you select with thepolarizer the P component.

The LO-TO splitting is usuallyobserved in strong bands (i.e.fundamental modes).

Solid CH4

Use of a polarizer

Laboratorio di Astrofisica SperimentaleCatania LO mode

LO mode

Fulvio et al. 2009

Fulvio et al. 2009

Use of a polarizer


Palumbo 2006

Use of a polarizer


13C16O

13C18O

Loeffler et al. 2005

Use of a polarizer


Sicilia et al. 2012

Use of a polarizer


Sicilia et al. 2012

Use of a polarizer


Abdulgalil et al., submitted

CH3CN When band’s profiles in transmittance spectra at oblique incidence in P and S polarization are similar, band’s profile in transmittance and RAIR spectra are similar as well.

CH3CNAbdulgalil et al., submitted

Use of a polarizer


CO2 formed after ion bombardment of solid COIoppolo et al. 2009

Amorphous vs crystalline samples

It was formerly believed that the LO-TO slitting is onlyobserved in crystalline samples.

Several experimental results indicate that amorphoussamples (glasses) show the LO-TO splitting (e.g. Almeida1992; Wackelgard 1996; Trasferetti et al. 2001)

Quantitative analysis

Given an IR spectrum (both experimental and astronomical) we want to know how many molecules are present in the sample.

Column density (molecules cm-2) = band area (cm-1) / band strength (cm molecule-1)

Available band strength values

Yamada and Person, 1964, J. Chem. Phys., 41, 2478 CO2,

Jiang et al., 1975, J. Chem. Phys., 64, 1201 CO

D’Hendecourt and Allamandola ,1986, A&AS 64, 453 H2O, CH4, NH3, CH3OH, CH3CN, hydrocarbons

Hudgins et al., 1993, ApJSS, 86, 713 H2O, CH3OH, CH4, CO2, OCS, mixtures

Gerakines et al. 1995, A&A, 296, 810 H2O, CO, CO2

Kerkhof et al., 1999, A&A, 346, 990 CH3OH, NH3, CH4

Gerakines et al., 2005, ApJ, 620, 1140 CO, CO2, C3O2, CH4, H2O, CH3OH, NH3

Brunetto et al., 2008 ApJ, 686, 1480 CH4, mixtures

Oberg et al. 2007, A&A, 462, 1187 H2O, CO2, mixtures

Fulvio et al., 2009, Spectroch. Acta A, 72, 1007 N2O, NO2

Modica and Palumbo, 2010, A&A, 519, A22 HCOOCH3

etc., etc.

Band strength values

Uncertainties as large as 30% (e.g., Hudgins et al. 1993);

Depend on the substrate (e.g., Fulvio et al. 2009; Modica and Palumbo 2010);

Depend on the structure (crystalline or amorphous) of the sample (e.g. Gerakines et al. 1995).

Measurements of band strength values

Usually measured form IR spectra when an independent measurement of the column density is available.The column density can be obtained form the knowledge of the thickness of the sample if the density is known.

Thickness measurement

Laser interference fringe method

laser beam

substrate

sample

vacuum

Experimental interference curve

For thick ice layers the damping in the interference curve is due to: absorption by the sample, diffusion by the bulk or surface, loss of coherence of the reflected light (non-uniform growth of the sample) Palumbo et al. 2008

Solid CO



laser beam

substrate

sample

vacuum

0 100 200 300 400 500 600

0.0

1.0x10-6

2.0x10-6

3.0x10-6

4.0x10-6

5.0x10-6

6.0x10-6

7.0x10-6

8.0x10-6

inte

nsity (

a.u

.)

time (s)


Baratta & Palumbo 1998, JOSA 15, 3076Westley et al. 1998, J. Chem. Phys. 108, 3321Fulvio et al. 2009, Spectr. Acta A 72, 1007Modica & Palumbo 2010, A&A 519, A22

Solid HCOOCH3Modica and Palumbo 2010



0 100 200 300 400 500 600

0.0

1.0x10-6

2.0x10-6

3.0x10-6

4.0x10-6

5.0x10-6

6.0x10-6

7.0x10-6

8.0x10-6

inte

nsity (

a.u

.)

time (s)


The distance between two maxima or two minima is given by

0 = laser wavelengthnf = refractive index of the filmi = incidence angle





0 = laser wavelength (known)nf = refractive index of the filmi = incidence angle (geometrically measured)

i = arctg a/2b




0 = laser wavelength (known)nf = refractive index of the filmi = incidence angle (geometrically measured)

0 100 200 300 400 500 600

0.0

1.0x10-6

2.0x10-6

3.0x10-6

4.0x10-6

5.0x10-6

6.0x10-6

7.0x10-6

8.0x10-6

inte

nsity (

a.u

.)

time (s)


If the substrate is opaque (e.g. Si, Au) the refractiveindex can be obtained by a numerical method fromthe ratio between the first maximum and the firstminimum because the amplitude depends on nf .




From the knowledge of0 = laser wavelength (known)nf = refractive index of the film (numerical method)i = incidence angle (geometrically measured)ns = refractive index of the substrate (database)it is possible to draw the theoretical interference curve

0 100 200 300 400 500 600

0.0

1.0x10-6

2.0x10-6

3.0x10-6

4.0x10-6

5.0x10-6

6.0x10-6

7.0x10-6

8.0x10-6

inte

nsity (

a.u

.)

time (s)


0.0 0.2 0.4 0.6 0.8

0.0

0.2

0.4

0.6

0.8

1.0

no

rma

lize

d r

efle

cta

nce

thickness (m)

Normalized theoretical interference curve





The absolute accuracy of the thickness measured in this way is about 5%and it is mainly limited by the uncertainties in the knowledge of therefractive index of the substrate at low temperature and by the error inmeasuring the incidence angle of the laser.

0 100 200 300 400 500 600

0.0

1.0x10-6

2.0x10-6

3.0x10-6

4.0x10-6

5.0x10-6

6.0x10-6

7.0x10-6

8.0x10-6

inte

nsity (

a.u

.)

time (s)


0.0 0.2 0.4 0.6 0.8

0.0

0.2

0.4

0.6

0.8

1.0

no

rma

lize

d r

efle

cta

nce

thickness (m)

Normalized theoretical interference curve





The choice of the substrate and laser wavelength

Lorentz-Lorenz relation

For a given species the Lorentz-Lorenz coefficient, L, is nearly constant for afixed wavelength regardless of the material phase and temperature.If the density and the refractive index of a molecular species are known at roomtemperature, the density at low temperature can be derived when therefractive index at low temperature is also known.The Lorentz-Lorenz relation is valid as far as the sample is opticallyhomogeneous.

= densitynf = refractive index

Column density

The column density can be obtained using the following relation

d = thickness (cm) = density (g cm-3) = molecular weight (g)

Methyl formate

Modica and Palumbo, 2010

Methyl formate

Plot of the band area fromspectra taken in P and Spolarization vs. the columndensity for the most intensebands of HCOOCH3. Theslope of the fit (solid line)gives the value of the bandstrength A.

(Modica and Palumbo, 2010)

Methyl formate

Plot of the band area fromspectra taken in P and Spolarization vs. the columndensity for the most intensebands of HCOOCH3. Theslope of the fit (solid line)gives the value of the bandstrength A.


Methyl formate


We note differences due to the substrate in the obtained A values between 6−25%.

These differences can be explained by the limits of applicability of the Beer-Lambert law.

Saturated bandsoptical depth > 1

Fulvio et al. 2009

The profile of a non-saturated band does not depend on the thickness of the sample.

Saturated bandsBand area could not be proportional to column density

Fulvio et al. 2009

Quantitative analysis from RAIR spectra

A-values obtained from transmittancespectra cannot be used for quantitativeanalysis from RAIR spectra.

Quantitative analysis from RAIR spectra

Oberg et al. 2009

Optical constants

There are two sets of quantities, both known as optical constants, that can be used todescribe the intrinsic optical properties of matter:

the real and imaginary parts of the complex refractive indexN = n + ik

the real and imaginary parts of the complex dielectric function = ’+ i’’

These sets of quantities are not independent: if the material is non-magnetic therelationship between the two is:

= N2

’ = n2 - k2 and ’’ = 2n k

Available mid-IR optical constants of molecules in the solid phase

Wood and Roux, 1982, J. Opt. Soc. Am. ,72, 720 H2O, NH3, CO2

Tielens et al. 1991, ApJ, 381, 181 CO

Hudgins et al., 1993, ApJSS, 86, 713 H2O, CH3OH, CH4, CO, CO2, OCS, mixtures

Trotta, 1996, PhD Thesis, Univ. J. Fourier, Grenoble, F CO, H2O, CO2, NH3, CH4, C2H4, C2H6, H2S, SO2, CH3OH

Ehrenfreund et al., 1997, A&A, 328, 649 CO, CO2, mixtures

Elsila et al., 1997, ApJ, 479, 818 CO, mixtures

Baratta and Palumbo, 1998, J. Opt. Soc. Am. 15, 3076 CO, CO2

Dartois, 2006, A&A 445, 959 CO

Palumbo et al., 2006, PCCP, 8, 279 CO

Moore et al., 2010, ApJSS, 191, 96 HCN, C2N2, CH3CN, C2H5CN, HC3N

etc. etc.

A few examples solid CO2

Strong bandsk > 0.5

Weak bandsk 0.5

α(λ)=4πk(λ)/λ

where α is the absorption

coefficient and k is the

imaginary part of the complex

refractive index

Baratta and Palumbo 1998

Baratta and Palumbo 1998

A few examples solid CO

Strong band k > 0.5

Solid COPalumbo et al. 2006


Real and imaginary part of the dielectric function in the CO stretching region for solid CO

Tielens et al. 1991

Dartois 2006


Real and imaginary part of the dielectric function in the CO stretching region for solid CO

Palumbo et al. 2006

The wave numbers of the LO and TO modescan be approximated either by theminimum and maximum of || respectively(solid lines in Fig. 3), or by the maximum ofthe energy-loss function given by Im(1/)and maximum of ’’ respectively (dashedlines in Fig. 3).

When the real part of the complex dielectricfunction has negative values, the reflectivityis very high. This spectral region is confinedby the LO and TO mode frequency.

A few examples solid CH3CN

weak bands k < 0.5

A few examples solid CH3CN

In this case the real partof the dielectric functionis always positive then noLO-TO splitting can beobserved.CH3CN

Moore et al. 2010

Comparison between different sets of optical constants

Ehrenfreund et al. 1997

Solid CO

Solid CO2

stretching mode and bending mode

With correct optical constants it is possible to reproduce experimental spectra

IMD is a free IDL application (http://www.rxollc.com/idl/imd/index.html)












All these sets of optical constants, except one, have been obtained from spectra taken at normal incidence. In these experimental conditions the LO mode is not observed and an important constraint is missing.

Baratta and Palumbo, 1998



Baratta and Palumbo, 1998

stretching mode bending mode

Not all optical constants canproperly reproduce experimentalspectra (in transmittance at obliqueincidence and RAIR spectra).

Warning!

Why should astronomers worry about optical constants?

Particle size and shape effects

In the laboratory we take spectra of thin films

In space we observe ice grain mantles

Is it possible to compare the profile of absorption bands ofthin films (bulk) to the band’s profiles in astronomical spectra?

SOMETIMES!


Shift of peak position with respect to laboratory (bulk) spectraSub-peaks appearDepend on optical constants (n and k)

Particle size and shape can have very important effects on the profile ofabsorption features. For strong transitions in small particles, this class ofelectromagnetic modes is referred to as “surface modes” (van de Hulst1957; Bohren and Huffman 1983).


These effects can be understood in the Rayleigh limit (2πa << λ, a being the radius ofthe particle and λ the wavelength of the incident photon) since the particle may beconsidered placed in a homogeneous electric field and electrostatic applies. Because ofits electric polarization, the applied homogeneous electric field induces a dipole in theparticle the strength of which depends on the complex dielectric constant = ’+ i’’of the particle as well as its shape. The field outside the particle is then a superpositionof the uniform field and the particle’s dipole field, while inside the particle the field ishomogeneous. In the spectral range of an absorption feature where variesconsiderably and its real part may even be negative, the internal field of the particlecan be very large. In these instances an oscillator inside the particle is strongly affectedby this field and the spectral feature can be shifted with respect to the bulk materialfrom about the maximum of ’’ to frequencies where ’ is small or negative. Inaddition spheroidal particles give rise to subpeaks not present in the laboratoryspectra.


Sphere (a/b = 1 ; c = b)

Prolate (b/a < 1; c = b)

Oblate (a/b < 1; c = b)

Rods (b/a = 0; c = b)

Disks (a/b = 0; c = b)

Mie scattering calculations

Tielens et al. 1991

Calculated solid CO absorption cross sections (solid lines) for various solid mixturescontaining CO are compared to bulk absorption spectra (dashed lines). Homogeneousspheres have been assumed in the calculations.

Solid CO


Tielens et al. 1991

Absorption cross sections calculated in theRayleigh limit for various homogeneousspheroids consisting of pure CO. The prolateand oblate spheroids have axial ratio of 1/5.

Solid CO


Tielens et al. 1991Calculated absorption cross sections for acontinuous distribution of ellipsoid shapes(CDE). Upper panel: homogeneous particlesconsisting of a mixture CO/H2O=10/1. Lowerpanel: silicate core-mantle (CO/H2O=10/1)spheroids.

Solid CO


Palumbo et al. 1995

Solid OCS


Solid CO

Different band’s profilesresult from different setsof optical constants.


Solid CO2

Different band’s profilesresult from different setsof optical constants.


Baratta et al. 2000CH3OH:CO2 deposited at 12.5 K and warmed-up to 105 K

Baratta et al. 2000

Quoting Bohren & Huffman (1983): “All of thisillustrates a general rule, which we can state butnot prove: if there is an interesting effect in athin film, there will be a corresponding effect insmall particles”.

In summary

Transmittance spectra

Relatively easy quantitative analysis

First choice to obtain optical constants (better at oblique incidence)

Low sensitivity

RAIR spectra

Difficult quantitative analysis (not impossible)

Second choice to obtain optical constants

High sensitivity (sub-monolayer)

Documents

of solid phase molecules - Radboud Universiteit · 2012-06-13 · Thickness measurement Laser interference fringe method laser beam substrate sample vacuum 0 100 200 300 400 500 600