6 Origin of organic matter: Interstellar medium
The interstellar medium (ISM) plays a vital role in the evolution of galaxies: The most
important aspect of Galactic ecology is probably the cycle of matter from the ISM to
stars and back to the ISM. Therefore, over many generations of stars the chemical
composition of the ISM is enriched with heavy elements. The ISM is very
heterogeneous with huge differences in chemical and physical properties, spanning
many orders of magnitudes in particle densities and temperatures from 10K in cool
molecular clouds to million degree hot bubbles. In the context of Astrobiology the
properties of the ISM are of high significance because it represents such an important
factor in the evolution of chemical elements and because it sets the stage for star and
planet formation. Of particular interest for life is the presence of large organic
molecules which can form in the ISM and which can survive the often harsh conditions
present in the ISM.
In this chapter we look at the following aspects:
 What is the general composition of the ISM?
 What are the microscopic processes responsible for cooling and heating of the
ISM?
 What is the main chemistry going on in the ISM, which creates reaction
networks and establishes atomic and molecular abundances?
 How did the first molecules (in the early Universe) form?
 How did molecules influence the formation of the first generation of stars?
 How can the ISM be traced observationally?
6.1 Introduction
The interstellar medium accounts for 10−15% of the total mass of the Galactic disk. It
tends to concentrate near the Galactic plane and along the spiral arms, while being very
inhomogeneously distributed at small scales. It consists mainly of gas (99% by mass)
plus a small fraction of dust (1% by mass).
Interstellar gas



99% of the interstellar medium is composed of interstellar gas (the rest is dust),
out of which
o 70.4% (by mass) is hydrogen (either molecular or atomic)
o 28.1% is helium
o traces of other elements, mainly C, N, O
neutral atoms and molecules, ions and electrons
average density: 1 particle cm-3 (varies from 10-2 to 106 cm-3 ). In comparison:
air on Earth ~1019 molecules cm-3
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-1
Even though the interstellar gas is very
dilute, the amount of matter adds up
over the vast distances between the
stars.
The extreme heterogeneity causes a large range of chemical and physical conditions to
exist in the ISM. In first approximation three different phases are distinguished:
1. Cold clouds of neutral atomic or molecular hydrogen
 T=10–100K
 H II regions concentrated around hot stars (ionization by UV radiation
2. Warm medium
 T=10,000K
 H II regions concentrated around hot stars (ionization by UV radiation)
 This phase has also a diffuse, low density component with a volume filling
factor of 20–50%
3. Hot gas
 T=1,000,000K
 Shock heated by supernovae and winds from early type stars.
 Very tenuous and pervasive. Fills large parts of the galactic halo.
A more detailed distinction into different phases is given in the Table:
Phase
Temperature
Densities
(cm–3)
Fractional
volume
Mass
(109 M)
Hot intercloud
1,000,000 K
10–2
30–70%
—
H II regions
10,000 K
102–104
< 1%
0.05
Warm ionized
10,000 K
0.2–0.5
20–50%
1.0
Warm neutral
10,000 K
0.2–0.5
10–20%
2.8
Cold neutral
50–100 K
20–50
1–5%
2.2
Molecular clouds
10–20 K
104
< 1%
0.05
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-2
The cold clouds of neutral or molecular
hydrogen are the birthplace of new stars if
they become gravitationally unstable and
collapse. The neutral and molecular forms
emit radiation in radio wavelengths.
The 21 cm emission line of the neutral
hydrogen is used to trace the distribution
of HI regions. It is due to hyperfine
structure:
1. changing the alignment of the electron spin relative to the nuclear spin from 
to  by collision (excitation)
2. emitting the photon at 21 cm when changing the spin from  to  (deexcitation), rate = 1 transition per106 yr!
It is found that hydrogen is concentrated to the galactic plane.
Interstellar dust
1% of the mass of ISM is dust grains. They become apparent because of
 extinction, i.e. continuum absorption and scattering of starlight
 scattering starlight while producing diffuse light in the Galaxy
 depletion of metals (Ti, Fe, Mg, Cr, Ni) by factors of 10 to 1000
 solid state spectral lines
Size:
Shape:
Composition:
Density:
~0.25-0.5 micron
irregular
Si (flakes or needles), C (graphite), H2O (ice), Fe
1 grain per cubic football field (500,000 m3)
In the Milky Way, the interstellar attenuation of visible light along the line-of-sight is
on average about AV  1.8m kpc–1. Because blue light is more strongly scattered the
presence of dust leads also to a reddening of background stellar light.
Although representing only 1% (by mass) of the ISM, dust plays a very important and
crucial role for the chemical and physical properties of the ISM as we will see later (e.g.
catalyst for molecule formation and efficient coolant).
Because the shape of dust grains is often elongated (e.g. needles) and because the
galactic magnetic field can orient these grains, passing radiation is subject to dichroism,
i.e. selective absorption of only one linear polarization direction. The perpendicular
linear polarization direction is much less absorbed, thus the transmitted radiation field
becomes linearly polarized. Measuring this linear polarization allows us to diagnose the
galactic magnetic field.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-3
Figure: galactic magnetic field inferred from linear polarization measurements.
Interstellar clouds
The distribution of the ISM is clumpy:
Diffuse clouds:
 do not completely obscure the light
from bright background stars
 electronic transitions of atoms and
molecules can be superposed on the
stellar spectra
 visible and UV wavelengths
 enriched by stars at late stages of the
evolution
Dark clouds:
 dense clouds with rich chemistry
 rotational emission of molecules
 mm, submm and radio wavelengths
 places of star births
Mass: 10-106 M
Radius: 1-1000 pc
Temperatures: 10-50 K
Density: 106- 105 molecules cm-3
Number: > 5000 in the Galaxy
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-4
Interstellar nebulae
Dark nebulae: (Horsehead, Orion):
complete blocking of starlight by dust
Emission nebulae:
hydrogen is ionized by hot stars and
emits visible (red) light when recombine
with electrons
Reflection nebulae (NGC 1999, Orion):
Is a region of dusty gas surrounding a star
where the dust reflects the starlight
V380 Ori, T=10,000 K, M=3.5M
Bok Globule:
Is a cold cloud of gas, molecules, and
cosmic dust, which is so dense that it
blocks all of the light behind it
AV~10
T~10K
M=1-1000 M
R~1 pc
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-5
Interstellar molecules
First interstellar molecules CH, CH+ and CN were identified between 1937 and 1941.
Over the last 60 years, many interstellar molecules containing up to 13 atoms have been
identified. As of 2008, there are more than 140 molecules listed as detected in the
interstellar medium or circumstellar shells.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-6
6.2 Microscopic processes
Cooling of the interstellar gas
Interstellar clouds cool by emitting radiation. The radiation mechanism is initiated by a
collisional excitation to an excited state, so that atom or molecule gains the energy from
the kinetic energy of the colliding particle. The subsequently radiated photon can escape
from the cloud. Thus, the gas loses kinetic energy, so it cools. We summarize the
process as follows:
A
+
B

A
B*

B
+
h
+
B*
Emission
Collision
Cooling processes are efficient if
 Collisions are frequent  fair density and abundance (hydrogen)
 Excitation energy is comparable or less than the thermal kinetic energy
 A high probability of de-excitation after the collision  allowed transition
 Photon is emitted before the second collision occurs  density is not too high
 The emitted photon is not reabsorbed in the cloud  gas is optically thin
Important atomic cooling transions in interstellar clouds for T ~ 100K:
Atom/ion
Transition
Colliding partners
C+
Si+
O
2
P1/2 – 2P3/2
P1/2 – 2P3/2
3
P2 – 3P1,0
2
H, e–, H2
e–
H, e–
E/k
92 K
413 K
228 K, 326 K
Important molecular cooling transitions in interstellar clouds for T ~ 100K:
E/k
Molecule
Transition
Colliding partners
(lowest transition)
H2
HD
CO
X1: J  J–2
X1: J  J–1
X1: J  J–1
H, H2
H, H2
H, H2
510 K
130 K
5.5 K
CO is the next most abundant interstellar molecule after H2. In dark dense clouds
typically
n(H2)  104 cm3
n(CO)  105 n(H2).
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-7
CO is the most important coolant in dense clouds because it possesses a dipole moment
so its rotational transitions are permitted. The CO molecule relaxes therefore to its
ground state very quickly, cooling the gas and being ready for another collisional
excitation. However, it can also become an efficient absorber of its own photons, so the
cloud can become optically thick for CO photons. When such radiation trapping occurs,
the efficiency of CO cooling is reduced and other less abundant molecules, for example
OH and H2O, may contribute significantly to the cooling.
The cooling rate for molecular transitions depends on number of excited molecules
n(J’), the energy difference between levels EJ’J’’ and the transition probability
(Einstein coefficient) AJ’J’’:
rcool   n( J ')EJ ' J '' AJ ' J ''
[erg s1 cm3]
J'
where
nJ '  n
g J '  EJ ' / kT
e
.
Q
Heating of the interstellar gas
There are several sources of energy for the interstellar gas
 Starlight
 Cosmic rays
 X-rays
 Stellar winds
 Novae
 Supernovae
Photoionization by starlight
A
+
h

A+
+
e
The electron possesses the energy of (h  Eion). It interacts with the gas and shares its
energy through elastic collisions with atoms and molecules, thus providing a heat
source.
Some of the energy is lost due to inelastic collisions when electrons excite transitions in
atoms or molecules which is subsequently radiated.
In cool clouds the heating by photoionization of C, Si and Fe occurs.
Ionization by cosmic rays and X-rays
Cosmic ray particles consist primarily of high-energy protons and electrons with
energies of a few MeV.
Soft X-rays occur with a range of photon energies but their peak intensity is at 0.1 keV.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-8
Cosmic ray protons and X-rays can both ionize H atoms:
(p, X)
+
H

(p’, X’)
+
H+ +
e.
For a 2 MeV proton, the electrons arising due to ionization have a wide distribution in
energy, with a mean energy of 30 eV. In a mainly neutral medium, these electrons may
cause excitations or further ionizations. Collisions with other electrons will slowly share
the energy with the gas. When the electron energy is reduced below 13.6 eV, hydrogen
ionization can no longer occur. When it is below 10.2 eV, excitation of H atoms is not
possible. Calculations show that about 3.4 eV of kinetic energy is injected per electron
produced by the ionization.
X-ray ionization is more important for He atoms than for H (because of the cross
section to absorb X-rays). A 50 eV X-ray photon colliding with a he atom produces and
electron of 25 eV, but only 6 eV is deposited as heat.
Ionization of H2 by cosmic rays or X-rays (ionization potential 15.4 eV) produces H2+:
(p, X)
+
H2

(p’, X’)
+
H 2+
+
H
+
e
H2+ undergoes a series of reaction:
H 2+ +
H2

H3 +
+
H
H 3+ +
e

H2
+
H
H 3+ +
e

H
+
H
The last two reactions are exothermic (actually also the first one) and the total excess of
energy in the products is about 11 eV. Two-thirds of it is used for heating.
The secondary electron produced in ionization can take part in reactions with H2:
e
+
H2

e
+ H2
ellastic collision
e
+
H2

e
+ H 2*
inellastic collision
(H2 is excited to upper states
including the electronic B1+ state)
e
+
H2

e
+ H 2+
+ e
ionization
e
+
H2

e
+ H
+ H
dissociation
Relaxation of electronically excited H2* molecules produces an UV radiation which can
be important deep inside dark clouds where starlight cannot penetrate but cosmic ray
protons can.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-9
6.3 Astrochemistry: introduction
Synthesis
A
+
B

AB
+ h
radiative association
A
+
B:g

AB
+ g
grain surface formation
B

AB
+ e
associative detachment
(less important in clouds)
+ h

A
+
B
Photodissociation
AB+ + e

A
+
B
Dissociative recombination (low T)
AB

A
+
B + M
Collisional dissociation (high T)
A +
Destruction
AB
+ M
Rearrangement
A+ +
BC

AB+ + C
A+ +
BC

A
+ BC+
Charge transfer
A
BC

AB
+ C
Neutral-neutral exchange (radicalradical reactions are rapid)
+
Ion-molecule exchange
(very rapid)
Reaction networks
Exploring the reaction networks we hope to describe the chemistry of the interstellar
medium and calculate abundances of molecules formed in the chemistry.
Let us consider the formation of molecule M in the following chemical reaction:
A
+ B

M
+
N,
which has a reaction rate coefficient kf [s1 cm3 per molecule].
The molecule M can be destroyed by photodissociation with rate kph [s1]
and by the reaction
M
+ X

Y
+
Z,
with the rate kd [s1 cm3 per molecule].
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-10
Then, we can write an equation for number density of M changing with time:
d
n( M )  k f n( A)n( B )  k ph ( M )n( M )  kd n( M )n( X )
dt
Since the chemistry proceeds rapidly, we can calculate equilibrium abundances
assuming
d
n( M )  0 .
dt
To find n(M), we need to know abundances of all other species, A, B, X, etc, so that we
have to write down a set of equations as above for each atom, molecule and ion
involved in the chemistry. Such sets of equations are usually solved numerically.
Sometimes useful estimates can be done from simple calculations (exercises).
6.4 Primordial chemistry and the first molecules
Molecular astrophysics began in the recombination era. As soon as electrons and nuclei
combined to form atoms, these atoms began to form molecular ions and molecules. The
appearance of the first molecules marked the dawn of chemistry and set the stage for the
subsequent evolution of the Universe.
First molecules
A study of the early Universe is severely limited by the lack of observational data. To
predict the behaviour of the primordial gas, we must rely upon our knowledge of nonequilibrium chemistry, physical cosmology, hydrodynamics, and nucleosynthesis with
constraints provided by the nature of the present Universe and few objects from the
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-11
observable distant past, such as quasars and Lyman  absorption systems. Future
satellite missions offer the hope of observing the first generation of cosmological
objects.
Recombination
  3 to 4 105 years, T  4500 to 3000 K, E  1/4 eV, z  2500
The recombination era began at a redshift of about z  2500 when the temperature of the
Universe became cool enough for nuclei and electrons to combine to form atoms.
Before this time, the primordial gas was hot, dense, and completely ionized due to the
cosmic background radiation (CBR). The matter and radiation were strongly coupled.
As the Universe expanded, the total particle density fell as
n  (1  z )3 ,
and the temperature of the CBR decreased as
Tr  2.725(1  z ) K .
The chemistry of this era was relatively simple. The only nuclei that were present were
Element
H
D
4
He
3
He
7
Li
Be
B
First ionization energy, eV
13.6
24.6
Second ionization energy, V
54.4
5.4
9.3
8.3
75.6
18.2
25.2
Recombination took place only at temperatures corresponding to 1/4 eV, which is much
smaller than the ionization energies given above. The reason is the very small ratio of
the baryon to photon number densities, which leads to a sufficient amount of high
energy photons in the tail of the black body distribution that can ionize atoms even
when the temperature has dropped clearly below the ionization energy (cf. Chapter 1:
the same reason also caused the deuterium bottleneck).
At lower temperature, electrons and nuclei combined for the first time and formed first
atomic ions and neutral atoms through radiative recombination:
He++ + e-

He+ + h
Ei=54.4eV z > 2500
 < 105 years
He+ + e-

He + h
Ei=24.6eV z ~ 2500
 ~ 105 years
H+

H
+ h
Ei=13.6eV z ~ 1300
 ~ 3105 years
+ e-
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-12
Since the hydrogen nuclei account for ~76% of the mass of the baryonic-gas, its
formation at z ~ 1300 resulted in a phase transition to a mostly neutral Universe and
decoupling of matter from radiation.
(Primordial) molecule formation processes
In the early Universe, formation of molecules occurred in a very different environment
compared to the present interstellar medium. The important catalyst of chemical
reactions – interstellar dust – was yet to form in later stages of the Universe evolution.
Molecule formation in a dust-poor environment often takes place through two-body
association reactions, as densities are usually too low to allow for the more common
three-body association reactions.
In order to conserve momentum in the formation of a molecule from two colliding
species, either a photon or an electron must also be given off. The following two-body
reactions are important in a dust-poor environment.
Radiative association
A
+
B

AB*

AB
+
h
The collision complex AB* is stabilized after the photon is emitted. The photon can be
emitted spontaneously or its emission may be stimulated by the ambient radiation field.
In the simplest case A and B are atoms, but they can also be neutral molecules. Usually,
A and B are considered to be in their respective ground electronic states. However, if
one collision partner is in an excited state due to some sort of optical or collisional
pumping mechanism, the rate for radiative association may be considerably enhanced.
The reaction rate is also generally larger for more complex reactants. Therefore,
radiative associations are thought to play a significant role in the formation of large
molecules in dense molecular clouds. The opposite process is called photodissociation.
Figure: Illustration of the direct
radiative association process. The
two atoms A and B approach in
the vibrational continuum of an
excited electronic state and then
emit a photon, thereby forming
the molecule AB in a vibrationrotational state.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-13
For a collision energy E and when creating a molecule AB in the lower v”J” vibrationalrotational state, the emitted photon has an energy
h = E + Ev”J”
For the gas temperature T characterized by a Maxwellian distribution, the spectral
signature is an emission continuum.
The total cross section (T) for radiative association is obtained by summing cross
sections over all initial electronic states. The cross sections scale as the third power of
the emitted photon energy:
(T)  (E + Ev”J”)3
In the Table below radiative cross sections for some molecules are listed.
Molecule
H2 +
T (K)
10
100
1000
4000
He2+
100
1000
10000
(T) (cm3 s1)
1.51020
7.91020
5.31018
6.21017
7.21021
5.81020
2.61017
HD
100
1000
10000
0.81026
1.01026
0.41026
LiH
100
1000
5000
3.21020
2.11020
4.01021
Some typical features:






radiative association can also occur within a single electronic state, but such a
mechanism is very slow
energetic transitions are highly favored
in collisions of ground state atoms, cross sections are larger for formation of
molecules with larger binding energies
radiative associations of electronically excited atoms may be particularly
favored but a significant excitation mechanism should exist
spontaneous emission of a photon in the association process can be enhanced by
the stimulated emission if a strong background radiation field present
there are competing processes which can occur for more energetic radiative
association reactions:
o for molecular ions, the radiative association mechanism competes with
radiative and non-radiative charge transfer
o for excited atoms, associative ionization can overwhelm radiative association
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-14
Associative detachment
A +
B

AB
+
e
This process is important when formation of stable negative ions is possible. Light
elements such as H, Li, B, C, F and O have positive electron affinities and can form
stable negative ions. This process is very important for formation of H2 in dustless
environment.
Associative ionization
A* +
B

AB+
+
e
This process involves an electronically excited collision partner A*. It can in some cases
compete with radiative association. The opposite process, dissociative recombination, is
a major destruction process for molecular ions in a variety of astronomical
environments.
Very few rate coefficients (cross sections) for the two-body association reactions have
been measured reliably in the laboratory. At normal laboratory densities, measurements
of these processes are usually swamped by three-body association reactions. Most of the
information on rates of molecule formation comes from detailed theoretical
calculations.
First molecules: Helium chemistry
The first element to become neutral was He, with an ionization potential of 24.6 eV.
Thus, the first molecules to be formed were He2+, HeH+, HeD+ and LiHe+ from the
radiative associations of ions with neutral and ionized He
He+ + He

He2+ +
h
H+ +
He

HeH+ +
h
Li+ +
He

LiHe+ +
h
He+ +
D

HeD+ +
h
z ~ 2500
 ~ 105 years
These molecular ions would have been rapidly destroyed by dissociative recombination
(collisions with electrons). They never reached significant amounts.
Primordial Hydrogen chemistry
By T ~ 3000 K, the recombination of protons and electrons was accomplished and the
Universe had become almost completely neutral. Radiative associations of ions with
neutral hydrogen formed other important molecules
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-15
H+ +
H

H2 +
+
h
H+ +
D

HD+
+
h
H
D

HD
+
h
+
However, the H2 molecule could NOT be formed through the process of radiative
association
H
+
H

H2
+
h
The association of two hydrogen atoms in the ground electronic state, H(1s) and H(1s),
can only lead to one of two electronic states of the H2 molecule:
b3u+ (spin S=1)
or
X1g+ (spin S=0)
Formation along the triplet state potential energy curve does not occur, since this state is
repulsive and would thus require a highly forbidden triplet-singlet radiative transition
(selection rule S=0) to form the stable singlet state..
Formation along the singlet state potential energy curve is not possible because the
dipole moment of H2 is zero.
Formation along the excited singlet states is possible but requires higher energies and
densities.
H  H+ (ionization)
H2 dissociation
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-16
Two main mechanisms for H2 formation in the early Universe have been generally
accepted. They were important at different epochs:
100 < z < 500
H 2+ +
H

H2
+
H+
This is a charge transfer reaction.
z < 100
+
e

H
+
h
H +
H

H2
+
e
H
This is the so-called H sequence. The first reaction is the radiative recombination and
the second one is the associative detachment. This process becomes important at lower
redshifts because the negative hydrogen ion can not be instantly destroyed by the cooled
CBR (ionization energy of H is ~1.6eV).
The HD molecule can be formed by radiative association, because its dipole moment is
not zero. It is however very small and, in fact, the reactions analogous to the H2
formation are more efficient.
Other important reactions producing and involving molecular hydrogen in the early
Universe include
 radiative association of H(n=1) and H(n=2) (beginning of the recombination era)
 formation of H2+ through proton exchange of HeH+ with H (z>500)
 formation of H3+ through association of H2+ and H2
The molecular abundances settled to a constant value by z ~ 100, since their timescales
for formation became larger than the age of the Universe due to the decrease in density.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-17
Figure: The fractional abundances of the first molecules in the recombination era as a function of the
redshift. Neutral species (solid lines), positive ions (dotted lines), negative ions (dashed lines), and
triatomics (dot-dashed lines).
The most abundant molecule was H2. Although its abundance was only 106 of the
atomic hydrogen, it played an important role in the formation of the first astrophysical
objects.
6.5 Structure formation: The role of the H2 molecule
Molecules were not formed homogeneously in the space. Numerical simulations show
that the molecular abundance fluctuations for H2, HD and LiH are up to several times
larger than the baryonic fluctuations.
z = 1425
z = 1200
z = 600
z = 10
Figure: H2 number density in slices cut through the simulation box (size 8.85 Mpc) at four redshifts. The
scale of the pixel values are indicated at right (from −100010−6 to 100010−6).
These results indicate that pronounced inhomogeneous chemical abundances were
present already during the dark age. This has direct implications for the spectrum of the
first bound objects since gas cooling depends mainly on the molecules H2 and HD. The
imprint of the chemical fluctuations could be in principle searched in CBR fluctuations.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-18
Thus, the recombination era provided initial conditions for the next stage in the
evolution of the Universe – the epoch of structure formation.
Collapse of the First Objects
The gas would have remained in the same state unless some type of perturbation was
introduced. Perturbations may have resulted from the gravitational collapse. Collapse is
expected to have begun near z ~ 100 to 20, and the first stars (Population III) could have
formed by z ~ 20 to 10.
Due to the homogeneity of globular clusters observed in the Milky Way and other
galaxies, it was suggested that globular clusters were the first objects to form. From the
mass of globular clusters M ~ 105 M we estimate that the minimum mass of a
primordial gas cloud being unstable to collapse should be of the same order of
magnitude.
Gravitational collapse can only be initiated and it can only continue if the gravitational
energy can be removed (cf. Chapter 2). In primordial gas energy removal is primarily
provided by radiative cooling from the H2 molecule via rotational and vibrational line
emission.
Line emission of H2
Since the dipole moment of the H2 molecule is zero, electric dipole
transitions do not occur in the ground electronic state X1g+.
Only magnetic quadrupole transitions
probability. The selection rule for them:
will
have
J
12 
4
non-zero
17 
J  2
These transitions are form the so called S-branch (analogous to R-,
P- and Q-branches). Do not confuse this with the spin!
3
28 
Notation: S(0), S(1), S(2), … for J”=0, 1, 2, …
1
0
Because of relatively small energy differences between rotational levels (as compared to
the levels of atomic hydrogen), the molecular hydrogen is an efficient cooling agent for
T ~ 100 to 10 000 K.
With H2 cooling, a proto-globular cluster can continue to collapse and even fragment
into objects which later will become stars. The masses of fragments are predicted to be
as large as 100 to 1000 M. Density of the fragments also increases allowing for more
efficient three-body reactions for the H2 formation
H
+
H
+
H

H2
+
2
H
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-19
The role of the third particle is to carry away the excess of the energy.
Other primordial molecules such as HD and LiH can also effectively cool the collapsing
gas. Since their electric dipole moment is not zero, they are expected to be important for
cooling at temperatures below which H2 is an efficient coolant.
The abundance of LiH, being quite low in the recombination era, can be increased in
protostellar clouds by three-body reactions
Li
+
H
+
H

LiH
+
H
Observations of the first molecules
The earliest gas is observed in quasars at z < 7, which corresponds to a galaxy where the
first generation stars have already significantly evolved.
It is expected that recombination era primordial gas cannot be directly observed. The
flux calculated for vibration-rotational transitions of H2, HD and LiH integrated over
redshifts z=1000 to z=0 is found to be 108 times smaller than the measured microwave
background radiation.
It is suggested though that high redshift primordial material can be observed during
protostellar formation. For example, at z = 50 about 1047 erg/M of gravitational energy
must be radiated away for a protocloud to collapse to a protostar. This energy can only
leave the cloud in form of line emission due to molecular cooling! One of the candidates
for searching the primordial molecular emission is LiH as it contributes at later stages of
the collapse, meaning smaller redshifts.
Molecules in the first supernova ejecta
Most Population III stars are expected to be massive and finish their lives with a
supernova explosion.
Core of a massive star at the end of Silicon Burning:
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-20
Because of the layered structure of the core, the ejecta are also layered, with successive
shells consisting of Fe, Si, O, C, He and H. Molecules in the expanding envelope will be
preferentially made from the constituents within a shell or in an adjacent shell.
In addition to the He and H chemistry, C, O and Si are candidates to produce new
molecules, in particular CO and SiO.
CO
C+ +
O

CO+
+
h
radiative association
CO+ +
O

CO
+
O+
charge transfer
Si+ +
O

SiO+
+
h
SiO+ +
O

SiO
+
O+
SiO
The supernova ejecta created the interstellar medium!
6.6 “Modern” astrochemistry
Modern Hydrogen chemistry
Reactions taking place in the early Universe to produce H2 are not sufficient to explain
the observed abundances of H2 in interstellar clouds because of low concentrations of
H+ and H. The only plausible formation route of H2 is therefore on the surfaces of
grains.
The grain surface plays a role of the third body
 prolongs the contact of atoms to combine into a molecule
 stabilizes the molecule by taking the excess of the energy
The atom sticks to the grain’s surface and can move across the surface in searching of
the second atom. Clearly, it should be bound to the surface long enough for a second
atom to arrive. This seems to be satisfied.
Other molecules can also be formed on the grain surface as binding energies for other
atoms are larger than for hydrogen.
For instance, before H2 is detached from the surface, O can arrive and form H2O, which
in cool clouds will be deposited as ice on the grain surface.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-21
Carbon chemistry
Hydrocarbons are important constituents of molecular clouds.
In diffuse clouds, atomic carbon is mostly in the form of C+, because its ionization
potential is less than 13.6 eV. Here the carbon chemistry is most probably initiated by
the radiative association reaction
+
H2

CH2+ +
h,
CH2+ +
H2

CH3+ +
H
CH3+ +
e

CH2
H
C+
+
followed by
The build-up of polyatomic hydrocarbons is limited by rapid photodissociation by UV
radiation. In denser parts of clouds, neutral hydrocarbons CH, CH2 and CH3 react with
O and form CO and H2CO. Once the carbon is locked up in the very stable CO
molecule, formation of more complex hydrocarbons ceases.
In dense clouds, shielded from the UV radiation, the amount of C+ is low. The carbon
chemistry is initiated by
C
+
H 3+

CH+

CH2 + +
H

CH3 + +
h
+
H2
Complex hydrocarbons are formed mainly by carbon insertion reactions, e.g.
C
+
C2H2 
C3H
+
H
This gas chemistry produces strongly unsaturated hydrocarbons, in agreement with
observations.
Oxygen chemistry
Oxygen is mostly neutral even in diffuse clouds. The gas-phase oxygen chemistry is
initiated by charge exchange reaction and forming OH+:
O
+
H+

O+
+
H
O+
+
H2

OH+
+
H
OH+ is highly reactive and lead to formation of neutral oxygen-bearing molecules like
OH and H2O.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-22
In cold dense clouds, the reaction
OH
+
O

O2
+
H
rapidly transform a significant part of the oxygen into O2.
Nitrogen chemistry
In contrast to the carbon and oxygen chemistries, the reactions that initiate the nitrogen
chemistry are still not well understood. Most probably it stars with
N+
+
H2

NH+
+
H
which leads further to NH2+ and NH4+ and then, via dissociative recombination, to
neutral NH, NH2 and NH3.
The N+ ions are mainly produces by cosmic ray ionization.
Neutral-neutral reactions play an important role in formation of other species. Reactions
of atomic N with CH, OH and NO lead to CN, NO and N2, respectively.
Reactions of CN with C2H2 are probably a major source of complex molecules as
cyanopolyynes HC2nCN.
Other element chemistries
These involve sulfur, chlorine, metals, large molecules such as PAH (polycyclic
aromatic hydrocarbons), carbon chain molecules and grain surface chemistry.
6.7 Observations
Studying molecules in the ISM is important, not only because it allows us to improve
our understanding of the chemical and physical properties of the ISM itself, but also
because of the close relation with stars and the galactic evolution and because of
possible implications for the development of life on Earth and maybe on other planets.
Understanding physical and chemical processes in ISM:
 Detection and identification of complex molecules in different environment
(e.g., cold clouds, PDRs, diffuse clouds, etc.) provides critical information for
understanding the possible formation (and destruction) pathways of these
molecules.
 Constraining chemical models.
 Can be used to study evolution of clouds and the star formation process.
 Long carbon chain molecules (e.g., PAH’s) play a major role in ISM physics
and chemistry.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-23
Implications for life on Earth:
 Some of the complex molecules found in the ISM are large organic molecules,
thought to be important to life.
 It is possible that chemical processes in the interstellar medium provided
essential material that allowed the emergence of life.
Discovery of interstellar spectral lines
1904
1920s
1937
1940
1941
1969
1970
…
Ca II line at 3900 Å
Na I 5890 Å
CH
CN
CH+
H2O (maser)
CO
H3+
Mc Call et al. (2003)
The H3+ molecular ion plays a fundamental role in interstellar chemistry, as it initiates a
network of chemical reactions that produce many molecules. For example, the reaction
of H3+ with atomic O leads, eventually, to the production of water, while the reaction
with HD leads to the production of a wide variety of deuterated isotopomers.
Molecules in the ISM and molecular lines are identified by comparing observed spectra
with laboratory data and/or simulated spectra. Once identified, we can start to employ
the lines for diagnostics. For example, with the above observations combined with
theoretical considerations of the chemical network of H3+ (remember e.g. that H3+ is
produced via cosmic-ray ionization of H2) it was possible to determine the cosmic-ray
flux in a diffuse cloud (observed towards  Persei), which was found to be 40 times
larger than previously believed.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-24
H2O
González-Alfonso et al. (1998)
H2O lines between 5.3 and 7.2 m observed with the Short Wavelength Spectrometer
(SWS) on board the Infrared Space Observatory toward the Orion BN/KL complex, a
deeply imbedded star forming region in the Orion nebula. Surprisingly, the H2O
rovibrational lines with  < 6.3 m  the R-branch  are observed in absorption, while
those  > 6.3 m  the P-branch  are observed in emission. This behavior is a
consequence of H2O absorption and reemission of continuum photons (look at the paper
for details, though it involves some molecular physics). The main point however is that
such measurements can be used to determine the abundances of water vapour in the
observed molecular cloud.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-25
H2O
Cernicharo et al. (1997)
Sgr B2 is a molecular cloud complex near the galaxy center. The infrared spectrum is
dominated by a Planck distribution caused by dust at a temperature of 30 K. On top of
the continuum a series of molecular lines are apparent, in particular water vapor lines in
absorption. The fact that H2O is seen here in absorption, rather than emission, suggests
that in Sgr B2, where the continuum emission by dust in the far infrared is optically
thick, the H2O lines arise in a region where the excitation temperatures are smaller than
the dust temperature (30 K). It is concluded that the H2O absorption lines probably
arise in the tenuous and extended envelope of Sgr B2 where collisional excitation is
negligible and the excitation is mainly due to absorption of photons emitted by the dust.
This illustrates a nice example of how we can infer information about the physical and
chemical properties of the ISM, in particular also its structure.
Carbohydrides, etc.
Cernicharo et al.
Many organic molecules have been identified in the ISM, such as acetylene (C2H2) or
benzene (C6H6).
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-26
Acetone = (CH3)2CO
n ~ 510–11 n(H2)
T ~ 20 K
Combes et al. (1987)
The figure shows the first detection of acetone in interstellar space (in Sgr B2). Acetone
is one of the complex molecules, clearly identified with three transitions.
PAH (?)
C5H12 ?
C 6 H6 ?
Leger & Puget (1984)
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-27
Polycyclic Aromatic Hydrocarbons (PAHs) are an important and ubiquitous component
of the organic materials. The infrared bands are observed at 3.29, 6.2, 7.7, 8.7, 11.3, and
12.7 μm and are often accompanied by minor, weaker, bands and underlying broad
structures in the 3.1 - 3.7, 6.0 - 6.9, and 11 - 15 μm ranges. In the model dealing with
the interstellar spectral features, PAHs are present as a mixture of radicals, ions, and
neutral species. The proposed excitation (pumping) mechanism of the IR bands is a onephoton mechanism that leads to the transient heating of the PAH molecules and ions by
stellar ultraviolet (UV), visible, and/or NIR photons. The IR bands are associated with
the molecular vibrations of PAH structures present either as free molecules and ions. It
should be mentioned though that the presence of PAH is in principle only suspected but
not really robustly proven. However, the PAH model has considerably evolved over the
years thanks in large part to the extensive laboratory and theoretical efforts that have
been devoted to this issue over the years. There is a wide consensus now that PAHs are
the best candidates to account for the IR emission bands.
PAHs actually represent a big current challenge to ISM chemists. The infrared emission
bands associated with PAHs arise from vibrational transitions (such as C-C or C-H
stretching or bending modes), which are relatively similar for most PAH molecules.
However, the electronic spectra are unique; therefore, if the electronic spectra of PAHs
or their cations were known, astronomers could search for specific molecules.
Laboratory studies of reaction rates with appropriate modeling can identify PAHs for
spectroscopic study, which in turn can enable identification of PAHs in the ISM.
Solid state spectral lines
Solid state spectral lines: we see vibrational bands without rotational structure (broad
absorption). This means that molecules vibrate and absorb while being in dust
conglomerates (solid-state vibrations).
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-28
Sgr A
Figure: (a–c) Spectra of the stretching mode of CO. (d–f ) The bending mode of water vapor in the
direction of Sgr A*. Panels (a) and (d) show the observations and the continuum (including ices); (b) and
(e) show the contribution of the ices and of the war CO; (c) and ( f ) show the normalized spectrum and
model spectrum (shifted for clarity); and (g) shows the details of the ortho- and para-H2O transitions.
Moneti et al. (2001).
Here we see solid state CO and H2O lines (broad absorptions) plus a superimposed
rotational spectrum due to gas phase molecules. Comparison to the model gives an idea
about physical properties such as temperature (requires strong cold, but also some weak
warm gas component).
The CO data indicate that the absorbing gas is extremely cold, T  10 K, suggesting that
it is located in the dark clouds of the different spiral arms that K intersect the lines of
sight. It is found that nearly all the CO is in the gas phase, while the H2O is almost
entirely frozen onto dust grains.
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-29
6.8 Molecular clouds in other galaxies
1970s
CO detection in other galaxies soon after the detection in ISM
CO traces molecular clouds and star formation regions (CO specially used as tracer for
H2, which we cannot see), here shown for the examples of Andromeda and NGC 1068.
M31, Andromeda, in the optical (on the left) and CO (on the left)
NGC1068
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-30
NGC253
SiO
H13CO+
3mm-cont
Observations in molecular lines can reveal much more information than just continuum
observations. We see structure of the inner buldge of NGC 253 revealed by different
molecules (different conditions for chemistry).
QSO J1148 +5251
One of the
distant quasars
z ~ 6.42
d ~ 13109 lyr
t ~ 870106 yr
CO ~ 107 M
CO (3-2)
dust at 1.2 mm
At z~6, we see already the molecule CO, which means that the first SNe already
exploded and formed ISM, which is remarkable taken the age of the universe of ~800
Myr only at this redshift!
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-31
most
IC 342 (nearby galaxy)
A nearby galaxy: another example, showing various sites of chemistry "factories".
Meier & Turner (2005).
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-32
Advantage of molecular lines
140 K
40 K
20 K
Advantage of molecular lines: measuring different transitions (i.e. different excitation
energies) one can get the energy distribution and find the temperature of the medium
very precisely (much more precisely than with atoms).
Astrobiology: 6 Origin of organic matter: Interstellar medium
S.V. Berdyugina, University of Freiburg
6-33