Observations of chemical differentiation
in clumpy molecular clouds
Jane V. Buckle1, Steven D. Rodgers2, Eva S. Wirström3, Steven B. Charnley2,
Andrew J. Markwick-Kemper2,4, Harold M. Butner5 and Shigehisa Takakuwa6,7
1 Astrophysics Group, Cavendish Laboratory, J J Thomson Avenue, Cambridge, CB3 0HE, UK.
email: j.buckle@mrao.cam.ac.uk
2 Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
3 Onsala Space Observatory, Chalmers University of Technology, SE - 43992 Onsala, Sweden
4 Astronomy Department, University of Virginia, USA
5 Joint Astronomy Centre, 660 North A’ohoku Place, Hilo, HI 96720, USA
6Harvard-Smithsonian Center for Astrophysics, Submillimeter Array Project,
645 North A’ohoku, Hilo, HI 96720 USA.
7 ALMA Office, National Astronomical Observatory of Japan, Tokyo, 181-8588, Japan
We have extensively mapped a sample of dense molecular clouds (L1512, TMC-1C, L1262, Per 7, L1389,
L1251E) in lines of HC3N, CH3OH, SO and C18O. We demonstrate that a high degree of chemical
differentiation is present in all of the observed clouds. We analyse the molecular maps for each cloud,
demonstrating a systematic chemical differentiation across the sample, which we relate to the evolutionary
state of the cloud. We relate our observations to the cloud physical, kinematical and evolutionary
properties, and also compare them to the predictions of simple chemical models. The implications of
this work for understanding the origin of the clumpy structures and chemical differentiation observed in
dense clouds are discussed.
1 Introduction
Low-mass stars form in dense cloud cores. Understanding how stars form thus requires detailed knowledge
of the physical and chemical evolution of molecular clouds. The classic picture, in which star formation is
magnetically-dominated and mediated by ambipolar diffusion [e.g. 1], posits long molecular cloud lifetimes
(∼ 107 years). However, there is an increasing realisation that dissipation of turbulence, driven externally
at large scales, plays a vital role [e.g. 2]. In this case, star formation is dynamic and rapid, and molecular
cloud lifetimes are short (∼ 105−106 years). Dense cloud chemistry will follow different evolutionary paths
depending upon the lifetime of molecular clouds, and hence on the time-scale of low-mass star formation
[e.g. 3]. One may also expect that the spatial distribution of molecules should also reflect the underlying
cloud dynamics. Observations of dense interstellar clouds in a variety of molecular tracers show that they
contain a distribution of dense gaseous structures [4]. These structures exhibit a size distribution ranging
from that of dense cores [∼ 0.05 − 0.1 pc, 5], to clumps [∼ 0.01 − 0.05 pc, 6, 7] down to so-called small
clumpinos [∼ 0.005 pc, 8]. The spatial distributions of molecules in cold, apparently quiescent, clouds do
appear to show chemical abundance gradients, i.e. chemical differentiation. Previously, the best studied
sources have been the clouds TMC-1 and L134N [9, 10, 11]. These clouds show striking differences in the
location of the emission peaks in several molecules. In TMC-1, for example, emission from the carbon
chain molecules (e.g. the cyanopolyynes) is observed to be anticorrelated with that of ammonia and
N2H+ and several deuterated species [e.g. 12, 13, 14]. These clouds also show distinct emission peaks
from other specific molecules, such as methanol and SO. High resolution observations show that chemical
differentiation is present at all spatial scales [8, 15, 16]. Although, in dense cores, depletion of CO, CS
and other heavy molecules on to dust grains is undoubtedly important [17, 18], the reason for the spatial
differentiation seen amongst other molecules is unclear, as is its prevalence in other molecular clouds.
It is possible that there is a link between the observed chemical differentiation and the clumpy struc-
ture, and hence to the physical origin of clumps through the cloud turbulence. There are currently two
possibilities [see 19, 20]. First, numerical simulations show that dissipation of externally driven turbu-
lence can produce structures, similar to the clumps and cores that are observed, through the process of
‘turbulent fragmentation’ [2]. Second, winds and outflows have a significant effect on the structure and
Table 1: Core Properties
Core RA(1950) DEC(1950) Class Vlsr D
(km s−1) (pc)
Per7 03:29:39.5 +30:49:50 I 6.81 350
L1389 04:00:38.0 +56:47:59 prestellar/0 -4.65 600
TMC-1C 04:38:34.5 +25:55:00 prestellar 5.27 140
L1512 05:00:54.4 +32:39:00 prestellar 7.11 140
L1251E 22:38:36.4 +74:55:50 mixed -3.93 350
L1262 23:23:32.2 +74:01:45 0 4.11 200
evolution of the surrounding protostellar envelope, containing energies sufficient to physically disrupt the
envelope material and to alter the chemistry. These outflows begin very early in the star formation pro-
cess, and cloud turbulence could be excited by them [21]. In this case, the cloud structure is regulated by
the action of stars [e.g. 22]. The presence of parsec-scale flows [e.g. 23] and wind blown bubbles [24] are
clear observational evidence that protostars affect their environment in this way, and that the influence of
existing star formation can have a very long reach. In this picture, the turbulence should be a function of
the local star-formation activity, however it is unclear if enough kinetic energy can be injected in all clouds
to sustain the observed level of turbulence. As the nature of the turbulence should affect the formation
and evolution of clumpy structure, we might therefore expect that there should be chemical differences
between starless cores and those containing protostars at the Class 0 and/or Class I stages [25], with the
former being the product solely of turbulent fragmentation. Models have previously been developed of
the spatial and temporal chemical evolution in clumpy molecular clouds [e.g. 17, 26, 27, 28, 29, 30, 31],
but with limited success.
To quantify the chemical effects that embedded protostars may have on cloud structure and chemistry,
we have previously mapped the Barnard 5 cloud (B5) in many molecular lines. B5 is an active region of
star formation in Perseus and contains molecular outflows, wind-blown bubbles, and regions where the
outflows appear to be interacting with dense clumps [32, 33, 34]. Most previous observations have focused
on the region containing the Class I source, B5 IRS1, and the molecular distributions over the rest of the
cloud were previously poorly known. These observations revealed a high degree of spatial differentiation,
with similarities to the molecular distributions in TMC-1 [35], but also to some other starless cores in
Taurus [36]. Comparison with dynamical-chemical models of B5 [26], based on the Norman & Silk [22]
picture, appear to indicate that molecular ices are continually being formed and destroyed [7, 36], but
that processes not included in these models must be responsible. However, B5 is only one such source;
to constrain any chemical models multi-molecule maps of more sources are needed, for example, to see
if similar molecular differentiation occurs in dense clouds with varying degrees of star formation activity
and protostellar evolution. We have therefore increased our sample to observe dense core chemistry in
different natal environments: starless cores, and those containing young stellar objects (YSOs) at the
Class 0 and Class I phases. The sources were selected from the sample mapped by Caselli et al. [37]
in N2H+ at 0.063 km s−1, 54′′ resolution; lower resolution ammonia maps also exist [5]. Caselli et al.
[37] found that the position of the N2H+ peak emission tended to be close to the position of peak NH3
emission but generally not coincident with that of the star. From our B5 observations, we found that
several molecules are strongly anticorrelated with N2H+ and NH3 emission at small scales, as well as
with each other (e.g. methanol and the carbon chains). Hence, the N2H+ maps of Caselli et al. [37] can
be useful to predict where other molecules could be expected to peak in a cloud, assuming the chemical
differentiation has the same underlying cause.
The six cores we observed have a range of star-forming activity (see Table 1). TMC-1C is a starless
core, with a region of diffuse sub-mm emission to the south, which extends in a ridge beyond our map to
the north [38]. This cloud has previously been mapped in carbon chain molecules [39] and in methanol
and HC13O+ [8]. L1389 is associated with an IRAS source, IRAS 04005+5647, although it has been
classified as pre-stellar, or an extremely young protostellar source [40]. L1262 contains both a stellar
core, IRAS 23238+7401, which drives a protostellar outflow, and a starless core [41]. L1251E contains
a YSO, IRAS 22385+7457, which drives an outflow, as well as two infrared sources likely to be T Tauri
stars [42]. There are also several infrared sources in the immediate vicinity of our map. L1512 is a starless
core, containing a north-south ridge of diffuse sub-mm emission [41]. Per7 contains a sub-mm peak in
addition to the Class I source, IRAS 03295+3050 [23].
Table 2: Molecular Line Properties
Molecule Transition Frequency Eupper Einstein A ncrit
(GHz) (K) (s−1) (cm−3)
C18O 1→0 109.782 5.27 6.30 ×10−08 2× 103
SO 23 →12 99.300 9.22 1.10 ×10−05 3× 105
HC3N 10→9 90.979 24.01 5.81 ×10−05 7× 105
CH3OH 21 →11(E) 96.739 12.55 2.56 ×10−06 1× 105
20 →10(A+) 96.741 6.97 3.38 ×10−06 5× 104
20 →10(E) 96.744 20.11 3.41 ×10−06 4× 104
21 →11(E) 96.755 28.04 2.62 ×10−06 5× 104
We chose to observe four molecular species (see Table 2). The isotope C18O serves to trace much
of the low density (∼ 103 cm−3) material in the cloud. Methanol is formed solely on grains in dense
clouds [e.g. 43]. Once desorbed into the gas, methanol molecules only have a finite lifetime until they are
destroyed. Hence, the CH3OH distribution provides an excellent observational measure of the degree of
gas-grain cycling in clumpy clouds. Cores showing weak methanol emission will tend to be older since
any CH3OH liberated previously will gradually re-accrete back onto the dust. As we discovered a new
’cyanopolyyne-peak’ position in B5, similar to that in TMC-1 [35], we also mapped the cyanoacetylene
emission in these clouds. The formation and destruction of cyanopolyynes can provide information on
those molecules returned to the gas, and also define chemical time-scales in dynamically-evolving clouds
[29]. Markwick et al. [29] concluded that such chemically interesting positions should appear to be offset
from the position of any YSO present; as well as from the peak ammonia emission. The detection of these
organic molecule ‘hotspots’ is thus only possible by making large-scale HC3N maps, to include positions
distinct from the nominal (0,0) positions of previous searches [cf. 27]. The HC3N transition chosen
traces gas at densities above ∼ 105 cm−3. Finally, to explain the large number of S-bearing molecules
detected in dense clouds, chemical models infer that elemental sulphur is only modestly depleted in dense
clouds, relative to more refractory elements [45]. Interstellar sulphur chemistry involves primarily neutral
reactions, and so it defines yet another, albeit slow, chemical time-scale. Shock chemistry or grain-surface
catalysis have been proposed to be important for S chemistry [30, 46]; the latter mechanism is supported
by the detection of OCS in interstellar ices [47]. We therefore mapped the JK = 32 − 21 line of SO.
The plan of the paper is as follows. In Section 2 we describe the observations and how the data
analysis was performed. In Section 3, we detail the chemical morphology of each source and note the
general trends we see in chemical differentiation. Simple chemical models of the chemical evolution in
clumpy media are presented and compared to the observational data in Section 4. Conclusions from this
study are given in Section 5.
2 Observations, Data Reduction and Analysis
Single dish maps of HC3N, SO, CH3OH and C18O transitions at 3mm were made using the Onsala 20m
telescope, Sweden, in April 2005. With the exception of CH3OH, the spectra were observed in frequency-
switched mode, using 12.5 kHz channels to provide a velocity resolution of ∼0.04 km s−1. CH3OH was
observed with the same resolution, but in position-switched mode due to the number of transitions in
the band. The 20m beam size at these frequencies is approximately 40′′, and the main beam efficiency,
ηmb, is 0.46. Table 2 lists molecular line details for the transitions that we observed.
The cores observed were taken from Caselli et al. [37], and include cores at a range of evolutionary
stages, from prestellar to Class I (Table 1). The areas mapped cover the N2H+ emission regions within
each core [37], ranging in size from 3–20 sq. arcmin. The typical RMS noise level in the maps is 0.1–0.3 K.
Contour plots and channel maps are shown in Figs 3.1–3.1.
Data reduction was carried out using the radio data reduction packages XS (bespoke software for the
Onsala 20m telescope), CLASS and SPECX. Single Gaussian fits provide a good fit to the line profiles.
For CH3OH, the transitions detected in each spectra were fit with dependent Gaussians. The velocity
and linewidth of each transition was fixed with respect to the 20 →10(A+) transition at 96.741 GHz, since
the separation of the K transitions is fixed by the structure of the molecule. The results of the fitting
procedures are given in Table 3, and for CH3OH, values are given for the 20 →10(A+) transition. For
lines that were not detected, the 3σ error estimate is given as the upper limit to the integrated intensity.
Since we have observed single transitions in C18O, SO and HC3N, and detect only one or two CH3OH
transitions in a large fraction of the spectra, we determine a lower limit to the column density [48]. In
this procedure, the rotation temperature can be approximated as Trot =
for non-linear molecules
(CH3OH), and as Trot =
for linear molecules (C18O, SO and HC3N). A lower limit to the column
density can then be calculated as:
Nmin = 8πkν
hc3Aulgu
Tmbdv Q(
)e3/2 non− linear (1)
Nmin = 8πkν
hc3Aulgu
Tmbdv Q(
)e linear (2)
where Tmb has been calculated from T∗A using ηmb, partition functions (Q[T]) and statistical weights (gu)
have been taken from the JPL molecular line database [49], energy levels and Einstein A values (Aul)
have been taken from the Leiden Atomic and Molecular Database [50] and Cragg et al. [51], listed in
Table 2. For CH3OH, the partition function Q(Trot)=1.28T1.5rot was adopted from Menten et al. [52], and
takes into account equal populations of A and E species [53].
For sources where we have detected 3 or 4 CH3OH transitions, we have also carried out a rotation
diagram analysis. The resulting column densities generally agree to within a factor of a few. However,
as we have detected only one strong transitions in each A and E species towards most positions, we have
based our CH3OH analysis in this paper upon the 20 → 10(A+) transition, in the same manner as for the
other molecules. This provides a coherent analysis of this data that we can compare with simple chemical
models.
From our C18O observations, we can then derive abundances relative to H2 following Frerking et al.
[54] for N(C18O) ≥ 3 ×1014 cm−2:
N(H2) =
N(C18O)
1.7× 1014
+ 1.3
× 1021 cm−2 (3)
We derive H2 column densities ∼ 2 × 1022 cm−2 within the clumpy regions of our data, leading to
abundances on the order of x(CH3OH) ∼ 2 × 10−8, x(HC3N) ∼ 8 × 10−11 and x(SO) ∼ 4 × 10−10 in
the molecular clumps, or ‘hotspots’.
3 Molecular Morphology
We now describe the observed chemical morphology. We first discuss the trends between the four
molecules in each individual source, focusing on the emission present in the position-velocity channel
maps (Fig. 3.1–3.1). We then summarise the apparent general trends.
3.1 Individual Sources
L1512
L1512 shows several extended clumps and ridges of emission in C18O. The southern part of the map
shows two clumps ((-60′′,-30′′) and (0′′,-30′′)) which surround the compact HC3N clump (-30′′,-30′′).
Emission from SO is also seen in extended ridges and clumps. The strongest clump is associated with
the single HC3N clump (-30′′,-30′′), while the second strong clump is associated with the CH3OH peak
to the north (-60′′,120′′).
We see SO emission at 6.62 km s−1 with none apparent in either CH3OH or HC3N. The strongest
SO emission clump appear in gas in which CH3OH is present, at 6.88 km s−1, the SO and CH3OH
emission peaks are offset by approximately 30′′. The methanol peak is at 7.12 km s−1, where most of
the weaker clumpy emission is found; at this velocity, there is no corresponding spatial SO emission in
this region. There are a couple of weak CH3OH emission clumps present to the south, and these are
embedded in the same gas as two SO clumps. An HC3N clump shows up at -6.88 km s−1 that is spatially
distinct from the SO and CH3OH clumps but partially overlaps the weaker extended SO emission. The
main HC3N clump is at 7.12 km s−1, overlaps the extended SO and CH3OH there, but is distinct from
the weak SO and CH3OH clumps, and is located about 100′′ from the major SO-CH3OH clumps. In
fact, we find that both these HC3N clumps coincide with minima in the C18O distributions, as well as
with the N2H+ peak (VLSR = 5.27 km s−1), perhaps indicating that molecular depletion is important
at these positions. However, the fact that a methanol clump is present at 7.12 km s−1 in a region with
Figure 1: L1512. Top: Contour maps of integrated intensity, from left: C18O, SO, HC3N and CH3OH.
Contours are 50%–100% in 10% intervals of the peak integrated intensity in K km s−1, and 1σ rms is
∼ 0.04 K km s−1. A cross marks the N2H+ peak [37]. Bottom: Channel maps of integrated intensity.
Contours levels are marked on each plot. Clockwise from top left: C18O, SO, CH3OH and HC3N.
little/no C18O emission somewhat confuses this interpretation. C18O emission peaks are anti-correlated
with emission peaks in all other molecules.
In summary, we see gas with only SO, gas with strong SO and CH3OH emission intermingled but with
distinct emission peaks (i.e. clumps), as well as gas with strong CH3OH emission and no/weak SO. The
HC3N clumps are markedly anticorrelated with SO and CH3OH clumps in position and are correlated
with C18O troughs. These could be cyanopolyyne late-time depletion peaks [55].
TMC-1C
TMC-1C shows several clumps of emission in C18O extending in a north-south ridge. The peak of emission
is near the centre of the diffuse sub-mm emission (-30′′,-60′′), with several smaller clumps leading north
to a more extended emission region at the edge of our map (-90′′,120′′). HC3N emission is confined to
the southern half of our map, where it appears in a ring, part of which overlaps the C18O clump. SO
emission appears in a relatively narrow ridge of emission extending to the north-west. Emission from
CH3OH has a similar morphology to emission from SO, but is more extended, and peaks further to the
Figure 2: TMC-1C. As Fig. 3.1. A triangle marks the approximate centre of the diffuse sub-mm emission
to the south, which extends slightly to the east, and to the north beyond our map [38]. A cross marks
the N2H+ peak [37].
north.
In this source SO displays very clumpy emission at 5.12 and 5.38 km s−1; there is only weak/no
CH3OH emission at 5.12 km s−1, where most of the SO molecular clumps are. At 5.38 km s−1, CH3OH
has 3 clumps and there is evidence for coincident weak SO emission. There is an SO clump coincident
with a minimum in C18O emission; this is approximately the location of N2H+ emission maximum [37],
and suggests a depletion zone here. This is curious: in L1512 we have HC3N correlated with a possible
depletion zone, whereas here it is SO and there is only weak/no HC3N present - or at least tending to
avoid it. The N2H+ peak is at VLSR of 5.27 km s−1, at a similar velocity to emission from C18O, CH3OH
and HC3N. The velocity of SO emission at this position is blue-shifted by 0.1 km s−1, which presumably
means that the depleted material does not contain the SO peak. The structure of the C18O, HC3N and
SO emission could be interpreted as that of a clumpy, fragmented torus in 3D. In this scenario, the SO
emission is actually coming from a chemically differentiated fragment of the torus/ring. The HC3N peaks
are spatially distinct from the CH3OH clumps at 5.38 km s−1 but there is weak SO emission in them; an
exception is the SO clump near (0,+60′′) which appears to have no HC3N. Again, C18O emission peaks
are anti-correlated with emission peaks in all other molecules.
Thus, in the SO clumps, methanol is either deficient or absent. To some degree, SO and HC3N
appear to be intermingled, although the clumps/peaks are physically distinct, and one SO clump has
no HC3N. The CH3OH clumps probably have some SO in them but are spatially distinct from the
Figure 3: L1262. As Fig. 3.1. The IRAS source is marked with a star, and sub-mm peaks with triangles
[41]. A cross marks the N2H+ peak [37].
HC3N distribution. C18O emission minima correspond to SO maximum (0,-60′′) and to HC3N maximum
(-60,-90).
L1262
Emission from C18O towards L1262 is seen in two strong clumps, one just to the east of of the IRAS
source (0′′,0′′), and one just to the east of the sub-mm source (60′′,-30′′). Emission from HC3N is seen in
a clumped ridge, with one clump, like that of C18O, to the east of the sub-mm peak, and one associated
with the IRAS source, west of the C18O clump (30′′,-30′′). SO emission peaks in a clump to the north
of the sub-mm peak (0′′,30′′), and extends in a clumpy ridge to the north and south. A further clump is
seen to the west, at the edge of our map, where the C18O emission also extends. Emission from CH3OH
is seen in an extended clump associated with the sub-mm source (0′′,30′′), and also in a compact clump
to the east of the IRAS source (60′′,-30′′). The main SO and CH3OH clumps are co-incident with the
HC3N clump that is near the sub-mm peak.
There is an SO clump at 3.62 km s−1 that appears to grow and merge into the major SO clump at
3.88 km s−1, where CH3OH emission becomes more evident. At 4.12 km s−1, the SO emission clearly
shows up as ∼ 4 clumps. There are 2 CH3OH clumps and these are evident at 4.12 and 4.38 km s−1. In
both cases, the CH3OH appears to be mixed with the enhanced SO emission, although at 4.38 km s−1
the SO emission is absent. The strongest SO and CH3OH emission are to the north - the clumps/peaks
are spatially distinct and should have different SO/CH3OH ratios. The methanol clump at 4.38 km s−1
is almost ‘pure’ CH3OH - emission from other molecules is weak/absent. There are 2 HC3N clumps with
the strongest to the north at 3.88 km s−1. This clump is associated with the strongest SO peak. Only
the weaker HC3N clump to the south is also evident at 4.12 km s−1 which is located across a region of
Figure 4: Per7. As Fig. 3.1. A star marks the IRAS source, a triangle marks the sub-mm peak [23], and
a cross marks the N2H+ peak [37].
weak/absent SO and CH3OH emission. There are two C18O clumps, which are distinct both spatially
and kinematically. Through both of these, we see a kinematic sequence of C18O and SO, then C18O and
SO plus CH3OH, then just CH3OH as we move from the blue to the red in velocity channels, although
the spatial peak in emission from these molecules are offset from each other.
In L1262, we detected 4 SO clumps. The strongest one also contains quite strong HC3N and weak
CH3OH emission at 3.88 km s−1; however, at 4.12 km s−1 the CH3OH clump grows stronger and more
distinct while the HC3N emission disappears. This is similar to that seen previously, where the strongest
SO and CH3OH clumps tend to be in gas where the molecules coexist. We note that the methanol
clumps are spatially anticorrelated with the positions of the HC3N ones, and that the weaker CH3OH
and HC3N clumps have little SO. However, the positional offset of the emission peaks of each molecule
is only marginal (∼0.5 beamwidth).
The SO, CH3OH and HC3N peaks are all anticorrelated with C18O peaks. These molecules also tend
to avoid the region around the N2H+ emission peak (at VLSR = 4.11 km s−1), suggesting that molecular
depletion on grains could be influencing the observed morphology. There may be a kinematical sequence
through the clumpy structures around (-60, 0).
Per 7
Per7 shows several regions of clumpy, asymmetric emission from all four molecules, most of it contained
in ridge extending to the north-east and south-west from the sub-mm peak. Emission from C18O is
relatively bright towards this source, while emission from HC3N, CH3OH and SO is fairly weak. C18O
peaks in an extended region to the NE of the sub-mm peak (around (30′′,30′′)). HC3N peaks in the
same place, but emission is much more compact, with a second emission peak to the SW (-90′′,-60′′). SO
appears in a series of clumps along the NE-SW ridge, with the brighter clumps those to the SW (-90′′,-
60′′). CH3OH also appears in a series of clumps along the NE-SW ridge, but the brightest clump is to
the far NE (90′′,90′′), where no SO emission is seen. Another peak occurs in between the two strongest
SO emission clumps (-60′′,0′′).
Very clumpy structure is evident in emission from SO. At 6.38 km s−1 there are 2 SO clumps to the
north with no/little CH3OH or HC3N emission. However, the peak emission clumps of SO and CH3OH
are in the same gas, but physically distinct (there is also a possible/weak HC3N clump at this velocity).
At 6.62 km s−1, SO and CH3OH show several clumps in gas where they are comingled but with the peaks
positionally offset from each other. There are 3 major CH3OH clumps and it seems that the northern
one contains little or no SO and definitely no HC3N. At 6.62 km s−1, there is one clear HC3N clump that
actually sits in the CH3OH minimum. In fact, once again, the HC3N and CH3OH emission is generally
anticorrelated. The C18O does not show compact peaks in the contour map, but is also anticorrelated
with HC3N and SO. All the molecules avoid the associated N2H+ peak.
In this source we again see clumps with essentially only SO present, as well as that the peak emis-
sion from SO and CH3OH emanates from gas in which they are comingled, but where their emission
peaks/clumps are spatially distinct. There appear to be methanol clumps with no HC3N and little or no
SO. Again, there appears to be a chemical gradient through the clumpy structures at around (+100, 0):
6.38 km s−1 : SO only - 6.62 km s−1 : strong CH3OH and unchanged SO : 5.88 km s−1 strong CH3OH
no SO.
L1389
L1389 shows relatively compact and weak emission from all four molecules. C18O peaks in a clump to
the east of the IRAS source (-30′′,0′′). HC3N peaks in a clump south of the C18O emission. Emission
from SO also peaks to the east of the IRAS source (-30′′,-30′′), but is more extended. CH3OH emission
appears in a strong clump to the south of the IRAS source, extending to the west (-60′′,-30′′).
Chemically, this is a morphologically simple cloud. The SO shows a single clump at -4.88 km s−1
with weak, diffuse emission at -4.62 km s−1; this clump appears to have very weak HC3N emission but
no CH3OH. The CH3OH clump is at -4.62 km s−1 and this corresponds to a region of relatively weaker
SO emission. The HC3N clump appears at -4.62 km s−1 and and is spatially distinct from the SO peak
in velocity and the CH3OH peak in position.
So, there is a clump in which SO is prevalent, although it does contain some HC3N. A distinct
HC3N-CH3OH anticorrelation is also evident. All the molecular clumps (positions of peak emission) are
located away from N2H+ peak, supporting the idea that molecular depletion is important here.
L1251E
Towards L1251E, emission from C18O is seen in several small clumps, the strongest of which is associated
with the IRAS source (-210′′,0′′). Two clumps are also seen to the north and south of an infrared source,
either side of a clump of HC3N emission (-150′′,0′′). HC3N emission is seen in a second clump associated
with the IRAS source (-210′′,0′′). SO emission is seen in a ridge of emission extending to the north
(-120′′,120′′), not clearly associated with emission from any of the other molecules, nor any of the infra-
red/IRAS sources. The clumps near the second infra-red source are associated with the weaker CH3OH
clumps. CH3OH emission is seen strongly peaked in a clump associated with both the IRAS source and
the first infrared source (-180′′,0′′), with a second peak to the north, just south of the main SO clump
(-90′′,60′′).
The strong SO emission clump to the north, evident from -4.88 to 4.12 km s−1, contains little or no
CH3OH, no HC3N, and is unconnected to the level of C18O emission present. The CH3OH emission is
extended and fragmented and three main clumps are evident. There are 2 HC3N clumps present. The
HC3N peak/clump at (-120, 0) appears quite extended, shows weak CH3OH emission but none from SO.
In summary, there is an SO clump that contains a small amount of HC3N emission and only a small
amount of CH3OH emission. The HC3N - CH3OH peaks are anti-correlated to the east, where the
HC3N peak appears in a region with no CH3OH emission. To the west, HC3N and CH3OH emission are
comingled, but the peaks are offset.
Figure 5: L1389. As Fig. 3.1. A star marks the IRAS source, a triangle marks the sub-mm peak [40],
and a cross marks the N2H+ peak [37].
3.2 General Trends - Summary
Several trends in the chemical differentiation are evident in our maps. The morphology throughout
our sample ranges from one or two isolated clumps detected in each molecules, to extended emission
containing a strongly-emitting clump and a several weaker ones.
SO and CH3OH Clumps
We find clumps of gas that contain significant emission only from SO (e.g. L1389, L1251E, PER 7,
TMC-1C), with only one of these showing significant emission from HC3N (L1262). There is evidence
that some SO emission maxima could correspond to depleted regions (TMC-1C). Strong extended SO
emission is also evident where CH3OH emission becomes stronger; in this case we find that the dominant
CH3OH and SO clumps can exist in the same gas but that they are always offset from each other. On
the other hand, there are some methanol clumps from which SO emission appears to be absent. Based
on comparing maps in velocity space, there is some kinematical evidence (e.g. in L1262, PER 7, L1512)
for well-defined emission sequence in which there are : regions with only SO, then a region with SO
and CH3OH intermingled - then a region with only CH3OH, suggesting we could be looking down a
cylinder/filament.
Figure 6: L1251E. As Fig. 3.1. The IRAS source is marked with a filled star, and unidentified IR sources
with empty stars [42]. A cross marks the N2H+ peak [37].
The HC3N Clumps
We find that the HC3N clumps are always spatially anticorrelated with the CH3OH clumps. Some of
these clumps can contain some very weak CH3OH emission, and moderately strong SO emission (L1262),
but there are others where the HC3N is the sole molecule present (L1251E).
Depletion: C18O Distribution & N2H+ Cores
C18O emission is tracing the less dense gas towards these sources, since the critical density of the transition
we have observed is 1 or 2 orders of magnitude less than the transitions we observed in SO, HC3N and
CH3OH. The emission generally has several clumps embedded within an extended, diffuse region, and
emission from spatially distinct regions is generally seen to be kinematically distinct as well. For example,
towards L1512, emission to the north-west is seen at 6.88 km s−1, while emission to the south-east is seen
at 7.12 km s−1. There is a clear anti-correlation between emission from C18O and all other molecules
towards the youngest sources, those classified as prestellar cores. Towards the older sources, where
protostars have formed, emission becomes more intermingled, and C18O emission can be seen associated
with SO and CH3OH peaks, although the spatial positions are offset (e.g. L1262).
Another population of objects implicitly present in our maps are the N2H+ cores mapped by Caselli
et al. [37]. These are probably the most stable, longest lived cores in the clouds, apart from the ones
that apparently harbour protostars, and are almost certainly sites of extensive molecular depletion onto
grains. All molecules in our sample tend to avoid these positions. An exception is in L1512 where the
HC3N clump is coincident with the N2H+ peak in both position and velocity.
4 Chemical Differentiation in a Clumpy Medium: Theory
We conclude that we are observing chemical morphologies which are produced by a time-dependent
gas-grain chemistry which is evolving in a turbulent dense medium. Clumps form and dissipate, perhaps
coalescing, and long-lived stable structures (i.e. dense cores) are produced in which star formation occurs.
In this section we show how simple chemical models can help explain these observations.
Clumps are formed out of the interclump medium (nH ∼ 103cm−3), perhaps by compression in
shock waves [56], or in MHD waves [31]. Our observations indicate that molecular desorption/depletion
from/onto dust grains plays an important role in determining the chemical differentiation. For a molecule,
X say, of molecular weight µX, the depletion (accretion) time-scale at 10K is
tX = 2.2× 109
yr (4)
where a total grain surface area per H nucleon of 3 × 10−22 cm2 and unit sticking efficiency have been
assumed [cf. 57]. In these dense regions (nH ∼ 104 − 105 cm−3) accretion and chemical reactions are
driven more rapidly and dynamical fate of the clump becomes an issue. It is therefore useful to know the
relevant physical time-scales that are important for clump evolution.
4.1 Clump Physics
The fate of clumps can be related simply to parameters that can be derived from observations. From our
observational data we can obtain estimates for the clump mass, M , its virial mass, Mvir, and radius R.
With R known, the virial mass for a sphere of constant density can be estimated from [58]
Mvir ∼ 210(∆v)2avR M� (5)
where (∆v)av is the average line-width of the clump gas (H2 and He) in km s−1 and R is in parsec
For clumps in molecular clouds, there are three possible evolutionary tracks [cf. 6]. A clump will be
stable against gravitational collapse if (0.5Mvir < M < Mvir), whereas if it is gravitationally unstable
(M > Mvir) it will collapse on the free-fall time-scale
tff =
4.35× 107
yr (6)
If (M < 0.5Mvir) then the clump is gravitationally unbound and so it will dissipate on a time-scale
tdiss ∼
where Ceff is the effective sound speed in the gas. The fate of some clumps can also depend upon the
local environment. A cloud volume containing a number of clumps of filling factor γ, and line-of-sight
relative velocity vrel can collide and coalesce (i.e. merge) with a time-scale
tmerge ∼
Clumps with any dynamical fate can grow when the merger time-scale is sufficiently short; unbound
clumps can do so when this is comparable or less than the dissipation time-scale, i.e. when tmerge<∼ tdiss
[6, 8, 15]. If we take the derived clump properties of the Taurus clouds (TMC-1C and L1512) as an
example, we then, following Peng et al. [6], we estimate that typically R ∼ 0.02− 0.03 pc and the clump
masses are in the range M ∼ 0.3− 1 M�. A detailed analysis of clump properties is beyond the scope of
this paper, however, we note that throughout our sample we can identify clumps that are unbound, as
well as some that are gravitationally stable and others that are unstable. Some clumps, such as CH3OH
and SO clumps in TMC-1C and L1512, may actually show substructure at higher spatial resolution. In
this case, such smaller clumps would be more likely to be unbound and, given their proximity, perhaps
more prone to interaction.
4.2 Chemical Model
We now show how a simple static model of clump chemical evolution, with accretion on to dust and
selective injection of simple mantle molecules, can explain the observations.
As discussed in section 1, methanol cannot be produced efficiently in the gas phase, and is thought to
be formed on the surfaces of dust grains. Hence, the CH3OH-rich clumps in our sources must necessarily
trace clumps in which grain ice mantles have recently been liberated into the gas phase. The exact
mechanism that causes the desorption of the ices is unknown but we expect that it will be connected to
clump evolution. Markwick et al. [29] proposed that the desorption is driven by grain-grain collisions,
induced by MHD waves generated by clump motions. Alternatively, Dickens et al. [65] speculated that
grain-grain streaming resulting from clump collisions may be responsible. In this paper, we make no
assumptions about the dynamical mechanism, other than that it is related to clump formation, and so
ice mantle liberation, if it occurs, happens at the same time that the clump is formed. This is obviously
a simplification since there must be a period of CO accretion to provide the precursor ices for CH3OH
production. We assume that a clump forms instantaneously from the interclump medium, and simply
follow the chemistry until all the molecules are condensed on grains. In reality, the chemical evolution
will be sensitive to the dynamical evolution of the clump (e.g. whether it is collapsing, coalescing or
dissipating). We do not consider the clump physical evolution explicitly in this static model; this is
discussed in detail elsewhere [59].
Based on the critical densities of the observed molecular tracers, we adopt a value of nH = 2×105 cm−3
as representative of the clump densities, which we consider to be approximately spatially constant. This
choice yields tff ∼ 1 × 105 years, and tdiss ∼ 2 × 105 years, and clump masses similar to those derived
from the observations, viz
M = 0.35M�
0.02 pc
2× 105 cm−3
We assume a cosmic ray ionization rate of 3× 10−17 s−1, a temperature of 10 K, and a visual extinction
of 10 magnitudes, which is sufficiently large to render photo-processes effectively irrelevant. Freeze-out
of molecules onto grains occurs at a rate given by eqn. (4), except for N2 which is assumed to remain in
the gas phase [e.g. 17]. The chemical model is based on the model of Rodgers & Charnley [60], and has
been updated to incorporate recent laboratory measurements of the dissociative recombination channels
for several ions, including CH3OH
2 [44, 61, 62, 63, 64].
The initial molecular abundances in the newly-formed clump are determined by those in the interclump
medium, which are themselves controlled by both (i) the chemistry in these regions, and (ii) whether
the material previously passed through a dense phase. This latter effect may be important, since if
most clumps eventually dissipate, recycling dense cloud material back into the surrounding gas, the
abundances in the interclump medium retain a memory of the higher density phase [cf. 26]. We assume
that the material in the interclump medium is predominantly molecular, and that ≈ 99% of the carbon
and nitrogen incorporated into a clump is initially present as CO and N2, with ≈ 1% in neutral atomic
form. The oxygen not bound up in CO is assumed to be atomic, as is all the initial sulphur. To account
for depletion, the gas-phase sulphur abundance is assumed to be 10−8 [45], and we assume complete
depletion of all metals. The initial fractional ionization is 1.5× 10−7.
4.3 Results
Based on the relative binding energies of species thought to be present on interstellar grains [67], we
consider three types of clumps:
• Type I. No sublimation of any ice species. The initial gas-phase composition is equal to that of the
interclump medium.
• Type II. Sublimation of the most volatile ice species. We assume injection of CO2 and H2S with
abundances of 10−5 and 10−7 respectively.
• Type III. Sublimation of tightly-bound species. We inject CO2, CH3OH, and H2O with abundances
of 10−5, 2× 10−8, and 3× 10−5 respectively.
tff tdiss
102 103 104 105 106
10-11
10-10
Time (yr)                                     
CO x 10-4 
HC3N  
SO2  
tff tdiss
102 103 104 105 106
10-11
10-10
Time (yr)                                     
CO x 10-4 
HC3N  
SO  N2H
SO2  
tff tdiss
102 103 104 105 106
10-11
10-10
Time (yr)                                     
CO x 10-4 
HC3N  
CH3OH  
SO2  
Figure 7: Abundances versus time for selected species. The vertical dotted lines mark the time-scales for
gravitational collapse (tff) and clump dissipation (tdiss). Top: type I cores (no ice sublimation). Middle:
type II cores (CO2 and H2S sublimation). Bottom: type III cores (CO2, H2O, and CH3OH sublimation).
The abundances of sublimated CO2 and H2O are based on observations of interstellar ices in dark clouds
[66], and the CH3OH abundance is chosen to match our derived column densities (see section 2). H2S has
not been detected in interstellar ices, but based on the fact that many of the most abundant ice species
are simple hydrides, it is likely to be present; our assumed abundance is consistent with the observed
upper limits [68]. Hydrogen sulphide has a low sublimation enthalpy [67], and so it will be released along
with CO2 in type II cores. We neglect H2S injection in type III cores in order to distinguish between the
amount of SO that can be formed from H2S, and the amount that can be formed by simply boosting the
OH abundance (as will occur when water is injected).
Figure 4.3 shows the time evolution of each of the four observed species – CO, SO, HC3N, and CH3OH
– in each clump. Also shown are N2H+ and SO2. The free-fall time, tff , and the clump dissipation time,
tdiss are marked on each panel. In all cases, molecules are depleted from the gas on a freeze-out timescale
of a few ×105 yr. For type I clumps, SO and HC3N are produced by chemical reactions in the dense
gas, peaking between 5 × 104 and 105 yr. SO is formed via the reaction of atomic S with OH, and
HC3N from CN + C2H2. Type I clumps younger than ∼ 105 yr can account for regions with both SO
and HC3N emission but no methanol. At longer times, SO is destroyed faster than HC3N, so long-lived
clumps of this type are able to explain those regions which are HC3N-rich but SO-poor. In type II
clumps, the injection of H2S significantly enhances the amount of SO produced in the gas. Compared
to type I clumps, the HC3N peak is slightly reduced, and shifted to later times. This is due to the
reduced hydrocarbon abundances which result from the fact that the injected CO2 drives down the C+
abundance. Type II cores can explain regions with large SO abundances, together with small HC3N
abundances and no CH3OH. Type III clumps are obviously the only ones which can explain CH3OH-rich
clumps, but we find that the methanol only survives for ∼ 104 yr before it is destroyed by protonation
followed by dissociative recombination. The HC3N in these clumps only peaks after all the CH3OH has
been lost, which naturally explains the anti-correlation between methanol and cyanoacetylene. The SO
abundances in type III clumps are intermediate between those of types I and II, and peaks occur at
around 2 × 104 yr. At this time, much of the initial CH3OH has been destroyed, and no significant
amounts of HC3N have been formed. Therefore, type III cores younger than ∼ 104 yr will contain both
CH3OH and SO, whereas slightly older cores will only contain SO. Because the injected water leads to
an increased OH abundance in the gas, type III cores eventually evolve to a state with SO2/SO > 1, so
the SO/SO2 ratio may potentially be used to place more firm constraints on the ages of these clumps
[c.f. 68, 69].
4.4 Application to Observations
We can compare our model results with the observational dataset, to try to place constraints on the
ages and the dynamical states of specific objects. Considering the general trends described in section
3.2, we find that our model naturally accounts for the CH3OH–HC3N anti-correlation. Clumps with
CH3OH emission must have ages of t<∼ 10
4 yr, and those with no SO emission must be even younger
(t<∼ 5 × 10
3 yr). Because these ages are much less than those associated with the dynamical evolution
of the clumps, the dynamical state of methanol clumps cannot be constrained from the observations. As
these type III clumps evolve, they eventually lose all the initial methanol; for 3×104<∼ t<∼ 10
5 yr, they will
appear only in SO, after which time the HC3N abundance rises. The evolution of type III clumps provides
a simple explanation for the observed transition from pure-CH3OH to mixed-CH3OH-SO to pure-SO gas
in different velocity channels. Clumps with both SO and HC3N emission could be old type II or III
(t > 105 yr), or possibly younger type I clumps. Regions containing only HC3N emission are likely to be
old type I clumps, with ages t ∼ 2× 105 yr ∼ tdiss. As these latter clumps have ages comparable to tdiss,
it is probable that pure HC3N clumps represent long-lived, stable clumps: gravitationally bound against
dissipation, but not collapsing. If so, then some of these regions should also be associated with enhanced
N2H+ abundances, as we in fact see in L1512.
We now briefly consider each source in turn:
L1512
The strong CH3OH and SO clump in the northwest must have an age of ∼ 104 yr. In contrast, the
SO cores toward the southeast have only weak methanol emission and must be older. This SO emission
surrounds the HC3N peak which must be even older, as no SO is seen at this position, suggesting an
age of ∼ 2× 105 yr. This is consistent with the CO depletion and N2H+ emission also seen toward this
position [37]
TMC-1C
The methanol clumps in this source have only weak SO emission, and so must be t<∼ 5000 yr. The clumpy
ring of material to the southeast has little or no methanol, but SO and HC3N are somewhat co-mingled.
This is best explained by type I clumps, implying that the mechanism which formed the clumpy ring was
not energetic enough to cause significant desorption of grain mantles.
L1262
In this source, the channel velocity maps at 4.12 km s−1 show a clumpy ring of SO emission surrounding
the HC3N peak. As is the case in L1512 these may represent evolved type III clumps which have lost the
original methanol. The central HC3N clump will be older (t>∼ 10
5 yr) than the surrounding SO clumps
(3× 104 < t < 105 yr). Both CO clumps in this source display the kinematical sequence of SO followed
by SO plus CH3OH, followed by only CH3OH, that is typical of the time evolution of type II clumps.
Per 7
Again, we see a transition in velocity space from pure SO to pure CH3OH via mixed gas. As in L1262,
this indicates the evolution of clumps where CH3OH ice is liberated along the line of sight. The HC3N
peak toward the northeast is associated with weak SO, and may represent evolved gas. However, the
peak does not appear to be correlated with the N2H+ peak or with significant CO depletion.
L1389
Again, we see SO-rich gas surrounding a HC3N-rich region. As in L1512, this suggests an older, stable
clump in the center surrounded by regions in which clump formation and/or ice mantle sublimation
occurred more recently. This source also shows a clear HC3N-CH3OH anti-correlation.
L1251E
SO is only visible in this map toward the north and east, and appears to be associated with some CH3OH,
implying an age for this gas of ∼ 104 yr. Towards the south and west, CH3OH and HC3N clumps are
prevalent yet SO is absent, which requires the presence of both young and old cores. This is the only
area in which we see co-mingling of HC3N and CH3OH emission – although the peak positions are offset
– and is the only region whose chemistry is not readily explained by our simple model.
5 Conclusions
We have mapped several prestellar and protostellar cores in CH3OH, HC3N, SO and C18O. We find that
the emission from these molecules traces clumpy structure across all of the cores. The molecular clumps
show striking differences in the location and velocity of emission peaks between molecules.
We see a similar degree of chemical differentiation in all of the cores that we have observed, despite
the differences in known star forming activity. The HC3N clumps are generally anti-correlated with
N2H+ peaks, and with CH3OH clumps. In L1512, a HC3N clump does appear along with a N2H+
peak, perhaps indicative of ongoing molecular depletion. CH3OH clumps and SO clumps also show
distinct emission peaks. C18O clump peaks are not generally correlated with emission peaks in any of the
other molecules that we observed. These morphological differences in molecular peaks towards sources
of different evolutionary stage suggest that depletion is important, but that other processes must also be
driving the chemical differentiation that we see.
Our observations suggest there is a kinematic sequence through the clumps of different molecular
species within the core. There is a well defined emission sequence in velocity space where we see only
clumps of SO, then clumps where SO and CH3OH are intermingled, and then a region with CH3OH only.
This may indicate that we are looking down a cylinder, or filament.
We have investigated the origin of the chemical differentiation using a simple chemical model, in
which clumps form rapidly and in which sublimation of ice mantles can occur as the clump is formed.
Despite its simplicity, this model is able to account for a wide variety of the chemical differentiation
observed in our sources. For clumps in which CH3OH is injected, the methanol survives for ∼ 104 yr,
so the observed CH3OH-rich clumps are young compared to the time-scale for dynamical evolution.
In these clumps, HC3N is not produced until all the CH3OH has been destroyed, which explains the
observed anti-correlation of methanol and cyanoacetylene. The model also predicts some some regions
will have HC3N/SO > 1 whereas others will have HC3N/SO < 1, depending on the age of the source
and/or the degree of mantle sublimation. HC3N peaks at late times, and the observed regions with only
HC3N emission are most likely tracing older clumps which are dynamically stable against both collapse
and dissipation. Such regions should also be associated with marked CO depletion and elevated N2H+
abundances.
In conclusion, it appears that molecular clouds containing protostars at different epochs of star for-
mation exhibit similar trends in their chemical spatial differentiation. The origin of this differentiation
can be understood through simple models of the molecular gas-grain interaction, and suggests that peri-
odic removal of ice mantles is occurring in dark clouds. Mantle disruption and dark cloud chemistry are
probably closely connected to the physics of clump evolution, dynamical-chemical models incorporating
of these processes are currently being developed [59].
Acknowledgements
SBC and SDR acknowledge support by the NASA Goddard Center for Astrobiology and the NASA
Long Term Space Astrophysics Program, with partial support from the NASA Origins of Solar Systems
Program.
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∫ T∗ A
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	Introduction
	Observations, Data Reduction and Analysis
	Molecular Morphology 
	Individual Sources
	General Trends - Summary 
	Chemical Differentiation in a Clumpy Medium: Theory
	Clump Physics
	Chemical Model
	Results
	Application to Observations
	Conclusions

  We have extensively mapped a sample of dense molecular clouds (L1512, TMC-1C,
L1262, Per 7, L1389, L1251E) in lines of HC3N, CH3OH, SO and C^{18}O. We
demonstrate that a high degree of chemical differentiation is present in all of
the observed clouds. We analyse the molecular maps for each cloud,
demonstrating a systematic chemical differentiation across the sample, which we
relate to the evolutionary state of the cloud. We relate our observations to
the cloud physical, kinematical and evolutionary properties, and also compare
them to the predictions of simple chemical models. The implications of this
work for understanding the origin of the clumpy structures and chemical
differentiation observed in dense clouds are discussed.

Introduction
Low-mass stars form in dense cloud cores. Understanding how stars form thus requires detailed knowledge
of the physical and chemical evolution of molecular clouds. The classic picture, in which star formation is
magnetically-dominated and mediated by ambipolar diffusion [e.g. 1], posits long molecular cloud lifetimes
(∼ 107 years). However, there is an increasing realisation that dissipation of turbulence, driven externally
at large scales, plays a vital role [e.g. 2]. In this case, star formation is dynamic and rapid, and molecular
cloud lifetimes are short (∼ 105−106 years). Dense cloud chemistry will follow different evolutionary paths
depending upon the lifetime of molecular clouds, and hence on the time-scale of low-mass star formation
[e.g. 3]. One may also expect that the spatial distribution of molecules should also reflect the underlying
cloud dynamics. Observations of dense interstellar clouds in a variety of molecular tracers show that they
contain a distribution of dense gaseous structures [4]. These structures exhibit a size distribution ranging
from that of dense cores [∼ 0.05 − 0.1 pc, 5], to clumps [∼ 0.01 − 0.05 pc, 6, 7] down to so-called small
clumpinos [∼ 0.005 pc, 8]. The spatial distributions of molecules in cold, apparently quiescent, clouds do
appear to show chemical abundance gradients, i.e. chemical differentiation. Previously, the best studied
sources have been the clouds TMC-1 and L134N [9, 10, 11]. These clouds show striking differences in the
location of the emission peaks in several molecules. In TMC-1, for example, emission from the carbon
chain molecules (e.g. the cyanopolyynes) is observed to be anticorrelated with that of ammonia and
N2H+ and several deuterated species [e.g. 12, 13, 14]. These clouds also show distinct emission peaks
from other specific molecules, such as methanol and SO. High resolution observations show that chemical
differentiation is present at all spatial scales [8, 15, 16]. Although, in dense cores, depletion of CO, CS
and other heavy molecules on to dust grains is undoubtedly important [17, 18], the reason for the spatial
differentiation seen amongst other molecules is unclear, as is its prevalence in other molecular clouds.
It is possible that there is a link between the observed chemical differentiation and the clumpy struc-
ture, and hence to the physical origin of clumps through the cloud turbulence. There are currently two
possibilities [see 19, 20]. First, numerical simulations show that dissipation of externally driven turbu-
lence can produce structures, similar to the clumps and cores that are observed, through the process of
‘turbulent fragmentation’ [2]. Second, winds and outflows have a significant effect on the structure and
Table 1: Core Properties
Core RA(1950) DEC(1950) Class Vlsr D
(km s−1) (pc)
Per7 03:29:39.5 +30:49:50 I 6.81 350
L1389 04:00:38.0 +56:47:59 prestellar/0 -4.65 600
TMC-1C 04:38:34.5 +25:55:00 prestellar 5.27 140
L1512 05:00:54.4 +32:39:00 prestellar 7.11 140
L1251E 22:38:36.4 +74:55:50 mixed -3.93 350
L1262 23:23:32.2 +74:01:45 0 4.11 200
evolution of the surrounding protostellar envelope, containing energies sufficient to physically disrupt the
envelope material and to alter the chemistry. These outflows begin very early in the star formation pro-
cess, and cloud turbulence could be excited by them [21]. In this case, the cloud structure is regulated by
the action of stars [e.g. 22]. The presence of parsec-scale flows [e.g. 23] and wind blown bubbles [24] are
clear observational evidence that protostars affect their environment in this way, and that the influence of
existing star formation can have a very long reach. In this picture, the turbulence should be a function of
the local star-formation activity, however it is unclear if enough kinetic energy can be injected in all clouds
to sustain the observed level of turbulence. As the nature of the turbulence should affect the formation
and evolution of clumpy structure, we might therefore expect that there should be chemical differences
between starless cores and those containing protostars at the Class 0 and/or Class I stages [25], with the
former being the product solely of turbulent fragmentation. Models have previously been developed of
the spatial and temporal chemical evolution in clumpy molecular clouds [e.g. 17, 26, 27, 28, 29, 30, 31],
but with limited success.
To quantify the chemical effects that embedded protostars may have on cloud structure and chemistry,
we have previously mapped the Barnard 5 cloud (B5) in many molecular lines. B5 is an active region of
star formation in Perseus and contains molecular outflows, wind-blown bubbles, and regions where the
outflows appear to be interacting with dense clumps [32, 33, 34]. Most previous observations have focused
on the region containing the Class I source, B5 IRS1, and the molecular distributions over the rest of the
cloud were previously poorly known. These observations revealed a high degree of spatial differentiation,
with similarities to the molecular distributions in TMC-1 [35], but also to some other starless cores in
Taurus [36]. Comparison with dynamical-chemical models of B5 [26], based on the Norman & Silk [22]
picture, appear to indicate that molecular ices are continually being formed and destroyed [7, 36], but
that processes not included in these models must be responsible. However, B5 is only one such source;
to constrain any chemical models multi-molecule maps of more sources are needed, for example, to see
if similar molecular differentiation occurs in dense clouds with varying degrees of star formation activity
and protostellar evolution. We have therefore increased our sample to observe dense core chemistry in
different natal environments: starless cores, and those containing young stellar objects (YSOs) at the
Class 0 and Class I phases. The sources were selected from the sample mapped by Caselli et al. [37]
in N2H+ at 0.063 km s−1, 54′′ resolution; lower resolution ammonia maps also exist [5]. Caselli et al.
[37] found that the position of the N2H+ peak emission tended to be close to the position of peak NH3
emission but generally not coincident with that of the star. From our B5 observations, we found that
several molecules are strongly anticorrelated with N2H+ and NH3 emission at small scales, as well as
with each other (e.g. methanol and the carbon chains). Hence, the N2H+ maps of Caselli et al. [37] can
be useful to predict where other molecules could be expected to peak in a cloud, assuming the chemical
differentiation has the same underlying cause.
The six cores we observed have a range of star-forming activity (see Table 1). TMC-1C is a starless
core, with a region of diffuse sub-mm emission to the south, which extends in a ridge beyond our map to
the north [38]. This cloud has previously been mapped in carbon chain molecules [39] and in methanol
and HC13O+ [8]. L1389 is associated with an IRAS source, IRAS 04005+5647, although it has been
classified as pre-stellar, or an extremely young protostellar source [40]. L1262 contains both a stellar
core, IRAS 23238+7401, which drives a protostellar outflow, and a starless core [41]. L1251E contains
a YSO, IRAS 22385+7457, which drives an outflow, as well as two infrared sources likely to be T Tauri
stars [42]. There are also several infrared sources in the immediate vicinity of our map. L1512 is a starless
core, containing a north-south ridge of diffuse sub-mm emission [41]. Per7 contains a sub-mm peak in
addition to the Class I source, IRAS 03295+3050 [23].
Table 2: Molecular Line Properties
Molecule Transition Frequency Eupper Einstein A ncrit
(GHz) (K) (s−1) (cm−3)
C18O 1→0 109.782 5.27 6.30 ×10−08 2× 103
SO 23 →12 99.300 9.22 1.10 ×10−05 3× 105
HC3N 10→9 90.979 24.01 5.81 ×10−05 7× 105
CH3OH 21 →11(E) 96.739 12.55 2.56 ×10−06 1× 105
20 →10(A+) 96.741 6.97 3.38 ×10−06 5× 104
20 →10(E) 96.744 20.11 3.41 ×10−06 4× 104
21 →11(E) 96.755 28.04 2.62 ×10−06 5× 104
We chose to observe four molecular species (see Table 2). The isotope C18O serves to trace much
of the low density (∼ 103 cm−3) material in the cloud. Methanol is formed solely on grains in dense
clouds [e.g. 43]. Once desorbed into the gas, methanol molecules only have a finite lifetime until they are
destroyed. Hence, the CH3OH distribution provides an excellent observational measure of the degree of
gas-grain cycling in clumpy clouds. Cores showing weak methanol emission will tend to be older since
any CH3OH liberated previously will gradually re-accrete back onto the dust. As we discovered a new
’cyanopolyyne-peak’ position in B5, similar to that in TMC-1 [35], we also mapped the cyanoacetylene
emission in these clouds. The formation and destruction of cyanopolyynes can provide information on
those molecules returned to the gas, and also define chemical time-scales in dynamically-evolving clouds
[29]. Markwick et al. [29] concluded that such chemically interesting positions should appear to be offset
from the position of any YSO present; as well as from the peak ammonia emission. The detection of these
organic molecule ‘hotspots’ is thus only possible by making large-scale HC3N maps, to include positions
distinct from the nominal (0,0) positions of previous searches [cf. 27]. The HC3N transition chosen
traces gas at densities above ∼ 105 cm−3. Finally, to explain the large number of S-bearing molecules
detected in dense clouds, chemical models infer that elemental sulphur is only modestly depleted in dense
clouds, relative to more refractory elements [45]. Interstellar sulphur chemistry involves primarily neutral
reactions, and so it defines yet another, albeit slow, chemical time-scale. Shock chemistry or grain-surface
catalysis have been proposed to be important for S chemistry [30, 46]; the latter mechanism is supported
by the detection of OCS in interstellar ices [47]. We therefore mapped the JK = 32 − 21 line of SO.
The plan of the paper is as follows. In Section 2 we describe the observations and how the data
analysis was performed. In Section 3, we detail the chemical morphology of each source and note the
general trends we see in chemical differentiation. Simple chemical models of the chemical evolution in
clumpy media are presented and compared to the observational data in Section 4. Conclusions from this
study are given in Section 5.
2 Observations, Data Reduction and Analysis
Single dish maps of HC3N, SO, CH3OH and C18O transitions at 3mm were made using the Onsala 20m
telescope, Sweden, in April 2005. With the exception of CH3OH, the spectra were observed in frequency-
switched mode, using 12.5 kHz channels to provide a velocity resolution of ∼0.04 km s−1. CH3OH was
observed with the same resolution, but in position-switched mode due to the number of transitions in
the band. The 20m beam size at these frequencies is approximately 40′′, and the main beam efficiency,
ηmb, is 0.46. Table 2 lists molecular line details for the transitions that we observed.
The cores observed were taken from Caselli et al. [37], and include cores at a range of evolutionary
stages, from prestellar to Class I (Table 1). The areas mapped cover the N2H+ emission regions within
each core [37], ranging in size from 3–20 sq. arcmin. The typical RMS noise level in the maps is 0.1–0.3 K.
Contour plots and channel maps are shown in Figs 3.1–3.1.
Data reduction was carried out using the radio data reduction packages XS (bespoke software for the
Onsala 20m telescope), CLASS and SPECX. Single Gaussian fits provide a good fit to the line profiles.
For CH3OH, the transitions detected in each spectra were fit with dependent Gaussians. The velocity
and linewidth of each transition was fixed with respect to the 20 →10(A+) transition at 96.741 GHz, since
the separation of the K transitions is fixed by the structure of the molecule. The results of the fitting
procedures are given in Table 3, and for CH3OH, values are given for the 20 →10(A+) transition. For
lines that were not detected, the 3σ error estimate is given as the upper limit to the integrated intensity.
Since we have observed single transitions in C18O, SO and HC3N, and detect only one or two CH3OH
transitions in a large fraction of the spectra, we determine a lower limit to the column density [48]. In
this procedure, the rotation temperature can be approximated as Trot =
for non-linear molecules
(CH3OH), and as Trot =
for linear molecules (C18O, SO and HC3N). A lower limit to the column
density can then be calculated as:
Nmin = 8πkν
hc3Aulgu
Tmbdv Q(
)e3/2 non− linear (1)
Nmin = 8πkν
hc3Aulgu
Tmbdv Q(
)e linear (2)
where Tmb has been calculated from T∗A using ηmb, partition functions (Q[T]) and statistical weights (gu)
have been taken from the JPL molecular line database [49], energy levels and Einstein A values (Aul)
have been taken from the Leiden Atomic and Molecular Database [50] and Cragg et al. [51], listed in
Table 2. For CH3OH, the partition function Q(Trot)=1.28T1.5rot was adopted from Menten et al. [52], and
takes into account equal populations of A and E species [53].
For sources where we have detected 3 or 4 CH3OH transitions, we have also carried out a rotation
diagram analysis. The resulting column densities generally agree to within a factor of a few. However,
as we have detected only one strong transitions in each A and E species towards most positions, we have
based our CH3OH analysis in this paper upon the 20 → 10(A+) transition, in the same manner as for the
other molecules. This provides a coherent analysis of this data that we can compare with simple chemical
models.
From our C18O observations, we can then derive abundances relative to H2 following Frerking et al.
[54] for N(C18O) ≥ 3 ×1014 cm−2:
N(H2) =
N(C18O)
1.7× 1014
+ 1.3
× 1021 cm−2 (3)
We derive H2 column densities ∼ 2 × 1022 cm−2 within the clumpy regions of our data, leading to
abundances on the order of x(CH3OH) ∼ 2 × 10−8, x(HC3N) ∼ 8 × 10−11 and x(SO) ∼ 4 × 10−10 in
the molecular clumps, or ‘hotspots’.
3 Molecular Morphology
We now describe the observed chemical morphology. We first discuss the trends between the four
molecules in each individual source, focusing on the emission present in the position-velocity channel
maps (Fig. 3.1–3.1). We then summarise the apparent general trends.
3.1 Individual Sources
L1512
L1512 shows several extended clumps and ridges of emission in C18O. The southern part of the map
shows two clumps ((-60′′,-30′′) and (0′′,-30′′)) which surround the compact HC3N clump (-30′′,-30′′).
Emission from SO is also seen in extended ridges and clumps. The strongest clump is associated with
the single HC3N clump (-30′′,-30′′), while the second strong clump is associated with the CH3OH peak
to the north (-60′′,120′′).
We see SO emission at 6.62 km s−1 with none apparent in either CH3OH or HC3N. The strongest
SO emission clump appear in gas in which CH3OH is present, at 6.88 km s−1, the SO and CH3OH
emission peaks are offset by approximately 30′′. The methanol peak is at 7.12 km s−1, where most of
the weaker clumpy emission is found; at this velocity, there is no corresponding spatial SO emission in
this region. There are a couple of weak CH3OH emission clumps present to the south, and these are
embedded in the same gas as two SO clumps. An HC3N clump shows up at -6.88 km s−1 that is spatially
distinct from the SO and CH3OH clumps but partially overlaps the weaker extended SO emission. The
main HC3N clump is at 7.12 km s−1, overlaps the extended SO and CH3OH there, but is distinct from
the weak SO and CH3OH clumps, and is located about 100′′ from the major SO-CH3OH clumps. In
fact, we find that both these HC3N clumps coincide with minima in the C18O distributions, as well as
with the N2H+ peak (VLSR = 5.27 km s−1), perhaps indicating that molecular depletion is important
at these positions. However, the fact that a methanol clump is present at 7.12 km s−1 in a region with
Figure 1: L1512. Top: Contour maps of integrated intensity, from left: C18O, SO, HC3N and CH3OH.
Contours are 50%–100% in 10% intervals of the peak integrated intensity in K km s−1, and 1σ rms is
∼ 0.04 K km s−1. A cross marks the N2H+ peak [37]. Bottom: Channel maps of integrated intensity.
Contours levels are marked on each plot. Clockwise from top left: C18O, SO, CH3OH and HC3N.
little/no C18O emission somewhat confuses this interpretation. C18O emission peaks are anti-correlated
with emission peaks in all other molecules.
In summary, we see gas with only SO, gas with strong SO and CH3OH emission intermingled but with
distinct emission peaks (i.e. clumps), as well as gas with strong CH3OH emission and no/weak SO. The
HC3N clumps are markedly anticorrelated with SO and CH3OH clumps in position and are correlated
with C18O troughs. These could be cyanopolyyne late-time depletion peaks [55].
TMC-1C
TMC-1C shows several clumps of emission in C18O extending in a north-south ridge. The peak of emission
is near the centre of the diffuse sub-mm emission (-30′′,-60′′), with several smaller clumps leading north
to a more extended emission region at the edge of our map (-90′′,120′′). HC3N emission is confined to
the southern half of our map, where it appears in a ring, part of which overlaps the C18O clump. SO
emission appears in a relatively narrow ridge of emission extending to the north-west. Emission from
CH3OH has a similar morphology to emission from SO, but is more extended, and peaks further to the
Figure 2: TMC-1C. As Fig. 3.1. A triangle marks the approximate centre of the diffuse sub-mm emission
to the south, which extends slightly to the east, and to the north beyond our map [38]. A cross marks
the N2H+ peak [37].
north.
In this source SO displays very clumpy emission at 5.12 and 5.38 km s−1; there is only weak/no
CH3OH emission at 5.12 km s−1, where most of the SO molecular clumps are. At 5.38 km s−1, CH3OH
has 3 clumps and there is evidence for coincident weak SO emission. There is an SO clump coincident
with a minimum in C18O emission; this is approximately the location of N2H+ emission maximum [37],
and suggests a depletion zone here. This is curious: in L1512 we have HC3N correlated with a possible
depletion zone, whereas here it is SO and there is only weak/no HC3N present - or at least tending to
avoid it. The N2H+ peak is at VLSR of 5.27 km s−1, at a similar velocity to emission from C18O, CH3OH
and HC3N. The velocity of SO emission at this position is blue-shifted by 0.1 km s−1, which presumably
means that the depleted material does not contain the SO peak. The structure of the C18O, HC3N and
SO emission could be interpreted as that of a clumpy, fragmented torus in 3D. In this scenario, the SO
emission is actually coming from a chemically differentiated fragment of the torus/ring. The HC3N peaks
are spatially distinct from the CH3OH clumps at 5.38 km s−1 but there is weak SO emission in them; an
exception is the SO clump near (0,+60′′) which appears to have no HC3N. Again, C18O emission peaks
are anti-correlated with emission peaks in all other molecules.
Thus, in the SO clumps, methanol is either deficient or absent. To some degree, SO and HC3N
appear to be intermingled, although the clumps/peaks are physically distinct, and one SO clump has
no HC3N. The CH3OH clumps probably have some SO in them but are spatially distinct from the
Figure 3: L1262. As Fig. 3.1. The IRAS source is marked with a star, and sub-mm peaks with triangles
[41]. A cross marks the N2H+ peak [37].
HC3N distribution. C18O emission minima correspond to SO maximum (0,-60′′) and to HC3N maximum
(-60,-90).
L1262
Emission from C18O towards L1262 is seen in two strong clumps, one just to the east of of the IRAS
source (0′′,0′′), and one just to the east of the sub-mm source (60′′,-30′′). Emission from HC3N is seen in
a clumped ridge, with one clump, like that of C18O, to the east of the sub-mm peak, and one associated
with the IRAS source, west of the C18O clump (30′′,-30′′). SO emission peaks in a clump to the north
of the sub-mm peak (0′′,30′′), and extends in a clumpy ridge to the north and south. A further clump is
seen to the west, at the edge of our map, where the C18O emission also extends. Emission from CH3OH
is seen in an extended clump associated with the sub-mm source (0′′,30′′), and also in a compact clump
to the east of the IRAS source (60′′,-30′′). The main SO and CH3OH clumps are co-incident with the
HC3N clump that is near the sub-mm peak.
There is an SO clump at 3.62 km s−1 that appears to grow and merge into the major SO clump at
3.88 km s−1, where CH3OH emission becomes more evident. At 4.12 km s−1, the SO emission clearly
shows up as ∼ 4 clumps. There are 2 CH3OH clumps and these are evident at 4.12 and 4.38 km s−1. In
both cases, the CH3OH appears to be mixed with the enhanced SO emission, although at 4.38 km s−1
the SO emission is absent. The strongest SO and CH3OH emission are to the north - the clumps/peaks
are spatially distinct and should have different SO/CH3OH ratios. The methanol clump at 4.38 km s−1
is almost ‘pure’ CH3OH - emission from other molecules is weak/absent. There are 2 HC3N clumps with
the strongest to the north at 3.88 km s−1. This clump is associated with the strongest SO peak. Only
the weaker HC3N clump to the south is also evident at 4.12 km s−1 which is located across a region of
Figure 4: Per7. As Fig. 3.1. A star marks the IRAS source, a triangle marks the sub-mm peak [23], and
a cross marks the N2H+ peak [37].
weak/absent SO and CH3OH emission. There are two C18O clumps, which are distinct both spatially
and kinematically. Through both of these, we see a kinematic sequence of C18O and SO, then C18O and
SO plus CH3OH, then just CH3OH as we move from the blue to the red in velocity channels, although
the spatial peak in emission from these molecules are offset from each other.
In L1262, we detected 4 SO clumps. The strongest one also contains quite strong HC3N and weak
CH3OH emission at 3.88 km s−1; however, at 4.12 km s−1 the CH3OH clump grows stronger and more
distinct while the HC3N emission disappears. This is similar to that seen previously, where the strongest
SO and CH3OH clumps tend to be in gas where the molecules coexist. We note that the methanol
clumps are spatially anticorrelated with the positions of the HC3N ones, and that the weaker CH3OH
and HC3N clumps have little SO. However, the positional offset of the emission peaks of each molecule
is only marginal (∼0.5 beamwidth).
The SO, CH3OH and HC3N peaks are all anticorrelated with C18O peaks. These molecules also tend
to avoid the region around the N2H+ emission peak (at VLSR = 4.11 km s−1), suggesting that molecular
depletion on grains could be influencing the observed morphology. There may be a kinematical sequence
through the clumpy structures around (-60, 0).
Per 7
Per7 shows several regions of clumpy, asymmetric emission from all four molecules, most of it contained
in ridge extending to the north-east and south-west from the sub-mm peak. Emission from C18O is
relatively bright towards this source, while emission from HC3N, CH3OH and SO is fairly weak. C18O
peaks in an extended region to the NE of the sub-mm peak (around (30′′,30′′)). HC3N peaks in the
same place, but emission is much more compact, with a second emission peak to the SW (-90′′,-60′′). SO
appears in a series of clumps along the NE-SW ridge, with the brighter clumps those to the SW (-90′′,-
60′′). CH3OH also appears in a series of clumps along the NE-SW ridge, but the brightest clump is to
the far NE (90′′,90′′), where no SO emission is seen. Another peak occurs in between the two strongest
SO emission clumps (-60′′,0′′).
Very clumpy structure is evident in emission from SO. At 6.38 km s−1 there are 2 SO clumps to the
north with no/little CH3OH or HC3N emission. However, the peak emission clumps of SO and CH3OH
are in the same gas, but physically distinct (there is also a possible/weak HC3N clump at this velocity).
At 6.62 km s−1, SO and CH3OH show several clumps in gas where they are comingled but with the peaks
positionally offset from each other. There are 3 major CH3OH clumps and it seems that the northern
one contains little or no SO and definitely no HC3N. At 6.62 km s−1, there is one clear HC3N clump that
actually sits in the CH3OH minimum. In fact, once again, the HC3N and CH3OH emission is generally
anticorrelated. The C18O does not show compact peaks in the contour map, but is also anticorrelated
with HC3N and SO. All the molecules avoid the associated N2H+ peak.
In this source we again see clumps with essentially only SO present, as well as that the peak emis-
sion from SO and CH3OH emanates from gas in which they are comingled, but where their emission
peaks/clumps are spatially distinct. There appear to be methanol clumps with no HC3N and little or no
SO. Again, there appears to be a chemical gradient through the clumpy structures at around (+100, 0):
6.38 km s−1 : SO only - 6.62 km s−1 : strong CH3OH and unchanged SO : 5.88 km s−1 strong CH3OH
no SO.
L1389
L1389 shows relatively compact and weak emission from all four molecules. C18O peaks in a clump to
the east of the IRAS source (-30′′,0′′). HC3N peaks in a clump south of the C18O emission. Emission
from SO also peaks to the east of the IRAS source (-30′′,-30′′), but is more extended. CH3OH emission
appears in a strong clump to the south of the IRAS source, extending to the west (-60′′,-30′′).
Chemically, this is a morphologically simple cloud. The SO shows a single clump at -4.88 km s−1
with weak, diffuse emission at -4.62 km s−1; this clump appears to have very weak HC3N emission but
no CH3OH. The CH3OH clump is at -4.62 km s−1 and this corresponds to a region of relatively weaker
SO emission. The HC3N clump appears at -4.62 km s−1 and and is spatially distinct from the SO peak
in velocity and the CH3OH peak in position.
So, there is a clump in which SO is prevalent, although it does contain some HC3N. A distinct
HC3N-CH3OH anticorrelation is also evident. All the molecular clumps (positions of peak emission) are
located away from N2H+ peak, supporting the idea that molecular depletion is important here.
L1251E
Towards L1251E, emission from C18O is seen in several small clumps, the strongest of which is associated
with the IRAS source (-210′′,0′′). Two clumps are also seen to the north and south of an infrared source,
either side of a clump of HC3N emission (-150′′,0′′). HC3N emission is seen in a second clump associated
with the IRAS source (-210′′,0′′). SO emission is seen in a ridge of emission extending to the north
(-120′′,120′′), not clearly associated with emission from any of the other molecules, nor any of the infra-
red/IRAS sources. The clumps near the second infra-red source are associated with the weaker CH3OH
clumps. CH3OH emission is seen strongly peaked in a clump associated with both the IRAS source and
the first infrared source (-180′′,0′′), with a second peak to the north, just south of the main SO clump
(-90′′,60′′).
The strong SO emission clump to the north, evident from -4.88 to 4.12 km s−1, contains little or no
CH3OH, no HC3N, and is unconnected to the level of C18O emission present. The CH3OH emission is
extended and fragmented and three main clumps are evident. There are 2 HC3N clumps present. The
HC3N peak/clump at (-120, 0) appears quite extended, shows weak CH3OH emission but none from SO.
In summary, there is an SO clump that contains a small amount of HC3N emission and only a small
amount of CH3OH emission. The HC3N - CH3OH peaks are anti-correlated to the east, where the
HC3N peak appears in a region with no CH3OH emission. To the west, HC3N and CH3OH emission are
comingled, but the peaks are offset.
Figure 5: L1389. As Fig. 3.1. A star marks the IRAS source, a triangle marks the sub-mm peak [40],
and a cross marks the N2H+ peak [37].
3.2 General Trends - Summary
Several trends in the chemical differentiation are evident in our maps. The morphology throughout
our sample ranges from one or two isolated clumps detected in each molecules, to extended emission
containing a strongly-emitting clump and a several weaker ones.
SO and CH3OH Clumps
We find clumps of gas that contain significant emission only from SO (e.g. L1389, L1251E, PER 7,
TMC-1C), with only one of these showing significant emission from HC3N (L1262). There is evidence
that some SO emission maxima could correspond to depleted regions (TMC-1C). Strong extended SO
emission is also evident where CH3OH emission becomes stronger; in this case we find that the dominant
CH3OH and SO clumps can exist in the same gas but that they are always offset from each other. On
the other hand, there are some methanol clumps from which SO emission appears to be absent. Based
on comparing maps in velocity space, there is some kinematical evidence (e.g. in L1262, PER 7, L1512)
for well-defined emission sequence in which there are : regions with only SO, then a region with SO
and CH3OH intermingled - then a region with only CH3OH, suggesting we could be looking down a
cylinder/filament.
Figure 6: L1251E. As Fig. 3.1. The IRAS source is marked with a filled star, and unidentified IR sources
with empty stars [42]. A cross marks the N2H+ peak [37].
The HC3N Clumps
We find that the HC3N clumps are always spatially anticorrelated with the CH3OH clumps. Some of
these clumps can contain some very weak CH3OH emission, and moderately strong SO emission (L1262),
but there are others where the HC3N is the sole molecule present (L1251E).
Depletion: C18O Distribution & N2H+ Cores
C18O emission is tracing the less dense gas towards these sources, since the critical density of the transition
we have observed is 1 or 2 orders of magnitude less than the transitions we observed in SO, HC3N and
CH3OH. The emission generally has several clumps embedded within an extended, diffuse region, and
emission from spatially distinct regions is generally seen to be kinematically distinct as well. For example,
towards L1512, emission to the north-west is seen at 6.88 km s−1, while emission to the south-east is seen
at 7.12 km s−1. There is a clear anti-correlation between emission from C18O and all other molecules
towards the youngest sources, those classified as prestellar cores. Towards the older sources, where
protostars have formed, emission becomes more intermingled, and C18O emission can be seen associated
with SO and CH3OH peaks, although the spatial positions are offset (e.g. L1262).
Another population of objects implicitly present in our maps are the N2H+ cores mapped by Caselli
et al. [37]. These are probably the most stable, longest lived cores in the clouds, apart from the ones
that apparently harbour protostars, and are almost certainly sites of extensive molecular depletion onto
grains. All molecules in our sample tend to avoid these positions. An exception is in L1512 where the
HC3N clump is coincident with the N2H+ peak in both position and velocity.
4 Chemical Differentiation in a Clumpy Medium: Theory
We conclude that we are observing chemical morphologies which are produced by a time-dependent
gas-grain chemistry which is evolving in a turbulent dense medium. Clumps form and dissipate, perhaps
coalescing, and long-lived stable structures (i.e. dense cores) are produced in which star formation occurs.
In this section we show how simple chemical models can help explain these observations.
Clumps are formed out of the interclump medium (nH ∼ 103cm−3), perhaps by compression in
shock waves [56], or in MHD waves [31]. Our observations indicate that molecular desorption/depletion
from/onto dust grains plays an important role in determining the chemical differentiation. For a molecule,
X say, of molecular weight µX, the depletion (accretion) time-scale at 10K is
tX = 2.2× 109
yr (4)
where a total grain surface area per H nucleon of 3 × 10−22 cm2 and unit sticking efficiency have been
assumed [cf. 57]. In these dense regions (nH ∼ 104 − 105 cm−3) accretion and chemical reactions are
driven more rapidly and dynamical fate of the clump becomes an issue. It is therefore useful to know the
relevant physical time-scales that are important for clump evolution.
4.1 Clump Physics
The fate of clumps can be related simply to parameters that can be derived from observations. From our
observational data we can obtain estimates for the clump mass, M , its virial mass, Mvir, and radius R.
With R known, the virial mass for a sphere of constant density can be estimated from [58]
Mvir ∼ 210(∆v)2avR M� (5)
where (∆v)av is the average line-width of the clump gas (H2 and He) in km s−1 and R is in parsec
For clumps in molecular clouds, there are three possible evolutionary tracks [cf. 6]. A clump will be
stable against gravitational collapse if (0.5Mvir < M < Mvir), whereas if it is gravitationally unstable
(M > Mvir) it will collapse on the free-fall time-scale
tff =
4.35× 107
yr (6)
If (M < 0.5Mvir) then the clump is gravitationally unbound and so it will dissipate on a time-scale
tdiss ∼
where Ceff is the effective sound speed in the gas. The fate of some clumps can also depend upon the
local environment. A cloud volume containing a number of clumps of filling factor γ, and line-of-sight
relative velocity vrel can collide and coalesce (i.e. merge) with a time-scale
tmerge ∼
Clumps with any dynamical fate can grow when the merger time-scale is sufficiently short; unbound
clumps can do so when this is comparable or less than the dissipation time-scale, i.e. when tmerge<∼ tdiss
[6, 8, 15]. If we take the derived clump properties of the Taurus clouds (TMC-1C and L1512) as an
example, we then, following Peng et al. [6], we estimate that typically R ∼ 0.02− 0.03 pc and the clump
masses are in the range M ∼ 0.3− 1 M�. A detailed analysis of clump properties is beyond the scope of
this paper, however, we note that throughout our sample we can identify clumps that are unbound, as
well as some that are gravitationally stable and others that are unstable. Some clumps, such as CH3OH
and SO clumps in TMC-1C and L1512, may actually show substructure at higher spatial resolution. In
this case, such smaller clumps would be more likely to be unbound and, given their proximity, perhaps
more prone to interaction.
4.2 Chemical Model
We now show how a simple static model of clump chemical evolution, with accretion on to dust and
selective injection of simple mantle molecules, can explain the observations.
As discussed in section 1, methanol cannot be produced efficiently in the gas phase, and is thought to
be formed on the surfaces of dust grains. Hence, the CH3OH-rich clumps in our sources must necessarily
trace clumps in which grain ice mantles have recently been liberated into the gas phase. The exact
mechanism that causes the desorption of the ices is unknown but we expect that it will be connected to
clump evolution. Markwick et al. [29] proposed that the desorption is driven by grain-grain collisions,
induced by MHD waves generated by clump motions. Alternatively, Dickens et al. [65] speculated that
grain-grain streaming resulting from clump collisions may be responsible. In this paper, we make no
assumptions about the dynamical mechanism, other than that it is related to clump formation, and so
ice mantle liberation, if it occurs, happens at the same time that the clump is formed. This is obviously
a simplification since there must be a period of CO accretion to provide the precursor ices for CH3OH
production. We assume that a clump forms instantaneously from the interclump medium, and simply
follow the chemistry until all the molecules are condensed on grains. In reality, the chemical evolution
will be sensitive to the dynamical evolution of the clump (e.g. whether it is collapsing, coalescing or
dissipating). We do not consider the clump physical evolution explicitly in this static model; this is
discussed in detail elsewhere [59].
Based on the critical densities of the observed molecular tracers, we adopt a value of nH = 2×105 cm−3
as representative of the clump densities, which we consider to be approximately spatially constant. This
choice yields tff ∼ 1 × 105 years, and tdiss ∼ 2 × 105 years, and clump masses similar to those derived
from the observations, viz
M = 0.35M�
0.02 pc
2× 105 cm−3
We assume a cosmic ray ionization rate of 3× 10−17 s−1, a temperature of 10 K, and a visual extinction
of 10 magnitudes, which is sufficiently large to render photo-processes effectively irrelevant. Freeze-out
of molecules onto grains occurs at a rate given by eqn. (4), except for N2 which is assumed to remain in
the gas phase [e.g. 17]. The chemical model is based on the model of Rodgers & Charnley [60], and has
been updated to incorporate recent laboratory measurements of the dissociative recombination channels
for several ions, including CH3OH
2 [44, 61, 62, 63, 64].
The initial molecular abundances in the newly-formed clump are determined by those in the interclump
medium, which are themselves controlled by both (i) the chemistry in these regions, and (ii) whether
the material previously passed through a dense phase. This latter effect may be important, since if
most clumps eventually dissipate, recycling dense cloud material back into the surrounding gas, the
abundances in the interclump medium retain a memory of the higher density phase [cf. 26]. We assume
that the material in the interclump medium is predominantly molecular, and that ≈ 99% of the carbon
and nitrogen incorporated into a clump is initially present as CO and N2, with ≈ 1% in neutral atomic
form. The oxygen not bound up in CO is assumed to be atomic, as is all the initial sulphur. To account
for depletion, the gas-phase sulphur abundance is assumed to be 10−8 [45], and we assume complete
depletion of all metals. The initial fractional ionization is 1.5× 10−7.
4.3 Results
Based on the relative binding energies of species thought to be present on interstellar grains [67], we
consider three types of clumps:
• Type I. No sublimation of any ice species. The initial gas-phase composition is equal to that of the
interclump medium.
• Type II. Sublimation of the most volatile ice species. We assume injection of CO2 and H2S with
abundances of 10−5 and 10−7 respectively.
• Type III. Sublimation of tightly-bound species. We inject CO2, CH3OH, and H2O with abundances
of 10−5, 2× 10−8, and 3× 10−5 respectively.
tff tdiss
102 103 104 105 106
10-11
10-10
Time (yr)                                     
CO x 10-4 
HC3N  
SO2  
tff tdiss
102 103 104 105 106
10-11
10-10
Time (yr)                                     
CO x 10-4 
HC3N  
SO  N2H
SO2  
tff tdiss
102 103 104 105 106
10-11
10-10
Time (yr)                                     
CO x 10-4 
HC3N  
CH3OH  
SO2  
Figure 7: Abundances versus time for selected species. The vertical dotted lines mark the time-scales for
gravitational collapse (tff) and clump dissipation (tdiss). Top: type I cores (no ice sublimation). Middle:
type II cores (CO2 and H2S sublimation). Bottom: type III cores (CO2, H2O, and CH3OH sublimation).
The abundances of sublimated CO2 and H2O are based on observations of interstellar ices in dark clouds
[66], and the CH3OH abundance is chosen to match our derived column densities (see section 2). H2S has
not been detected in interstellar ices, but based on the fact that many of the most abundant ice species
are simple hydrides, it is likely to be present; our assumed abundance is consistent with the observed
upper limits [68]. Hydrogen sulphide has a low sublimation enthalpy [67], and so it will be released along
with CO2 in type II cores. We neglect H2S injection in type III cores in order to distinguish between the
amount of SO that can be formed from H2S, and the amount that can be formed by simply boosting the
OH abundance (as will occur when water is injected).
Figure 4.3 shows the time evolution of each of the four observed species – CO, SO, HC3N, and CH3OH
– in each clump. Also shown are N2H+ and SO2. The free-fall time, tff , and the clump dissipation time,
tdiss are marked on each panel. In all cases, molecules are depleted from the gas on a freeze-out timescale
of a few ×105 yr. For type I clumps, SO and HC3N are produced by chemical reactions in the dense
gas, peaking between 5 × 104 and 105 yr. SO is formed via the reaction of atomic S with OH, and
HC3N from CN + C2H2. Type I clumps younger than ∼ 105 yr can account for regions with both SO
and HC3N emission but no methanol. At longer times, SO is destroyed faster than HC3N, so long-lived
clumps of this type are able to explain those regions which are HC3N-rich but SO-poor. In type II
clumps, the injection of H2S significantly enhances the amount of SO produced in the gas. Compared
to type I clumps, the HC3N peak is slightly reduced, and shifted to later times. This is due to the
reduced hydrocarbon abundances which result from the fact that the injected CO2 drives down the C+
abundance. Type II cores can explain regions with large SO abundances, together with small HC3N
abundances and no CH3OH. Type III clumps are obviously the only ones which can explain CH3OH-rich
clumps, but we find that the methanol only survives for ∼ 104 yr before it is destroyed by protonation
followed by dissociative recombination. The HC3N in these clumps only peaks after all the CH3OH has
been lost, which naturally explains the anti-correlation between methanol and cyanoacetylene. The SO
abundances in type III clumps are intermediate between those of types I and II, and peaks occur at
around 2 × 104 yr. At this time, much of the initial CH3OH has been destroyed, and no significant
amounts of HC3N have been formed. Therefore, type III cores younger than ∼ 104 yr will contain both
CH3OH and SO, whereas slightly older cores will only contain SO. Because the injected water leads to
an increased OH abundance in the gas, type III cores eventually evolve to a state with SO2/SO > 1, so
the SO/SO2 ratio may potentially be used to place more firm constraints on the ages of these clumps
[c.f. 68, 69].
4.4 Application to Observations
We can compare our model results with the observational dataset, to try to place constraints on the
ages and the dynamical states of specific objects. Considering the general trends described in section
3.2, we find that our model naturally accounts for the CH3OH–HC3N anti-correlation. Clumps with
CH3OH emission must have ages of t<∼ 10
4 yr, and those with no SO emission must be even younger
(t<∼ 5 × 10
3 yr). Because these ages are much less than those associated with the dynamical evolution
of the clumps, the dynamical state of methanol clumps cannot be constrained from the observations. As
these type III clumps evolve, they eventually lose all the initial methanol; for 3×104<∼ t<∼ 10
5 yr, they will
appear only in SO, after which time the HC3N abundance rises. The evolution of type III clumps provides
a simple explanation for the observed transition from pure-CH3OH to mixed-CH3OH-SO to pure-SO gas
in different velocity channels. Clumps with both SO and HC3N emission could be old type II or III
(t > 105 yr), or possibly younger type I clumps. Regions containing only HC3N emission are likely to be
old type I clumps, with ages t ∼ 2× 105 yr ∼ tdiss. As these latter clumps have ages comparable to tdiss,
it is probable that pure HC3N clumps represent long-lived, stable clumps: gravitationally bound against
dissipation, but not collapsing. If so, then some of these regions should also be associated with enhanced
N2H+ abundances, as we in fact see in L1512.
We now briefly consider each source in turn:
L1512
The strong CH3OH and SO clump in the northwest must have an age of ∼ 104 yr. In contrast, the
SO cores toward the southeast have only weak methanol emission and must be older. This SO emission
surrounds the HC3N peak which must be even older, as no SO is seen at this position, suggesting an
age of ∼ 2× 105 yr. This is consistent with the CO depletion and N2H+ emission also seen toward this
position [37]
TMC-1C
The methanol clumps in this source have only weak SO emission, and so must be t<∼ 5000 yr. The clumpy
ring of material to the southeast has little or no methanol, but SO and HC3N are somewhat co-mingled.
This is best explained by type I clumps, implying that the mechanism which formed the clumpy ring was
not energetic enough to cause significant desorption of grain mantles.
L1262
In this source, the channel velocity maps at 4.12 km s−1 show a clumpy ring of SO emission surrounding
the HC3N peak. As is the case in L1512 these may represent evolved type III clumps which have lost the
original methanol. The central HC3N clump will be older (t>∼ 10
5 yr) than the surrounding SO clumps
(3× 104 < t < 105 yr). Both CO clumps in this source display the kinematical sequence of SO followed
by SO plus CH3OH, followed by only CH3OH, that is typical of the time evolution of type II clumps.
Per 7
Again, we see a transition in velocity space from pure SO to pure CH3OH via mixed gas. As in L1262,
this indicates the evolution of clumps where CH3OH ice is liberated along the line of sight. The HC3N
peak toward the northeast is associated with weak SO, and may represent evolved gas. However, the
peak does not appear to be correlated with the N2H+ peak or with significant CO depletion.
L1389
Again, we see SO-rich gas surrounding a HC3N-rich region. As in L1512, this suggests an older, stable
clump in the center surrounded by regions in which clump formation and/or ice mantle sublimation
occurred more recently. This source also shows a clear HC3N-CH3OH anti-correlation.
L1251E
SO is only visible in this map toward the north and east, and appears to be associated with some CH3OH,
implying an age for this gas of ∼ 104 yr. Towards the south and west, CH3OH and HC3N clumps are
prevalent yet SO is absent, which requires the presence of both young and old cores. This is the only
area in which we see co-mingling of HC3N and CH3OH emission – although the peak positions are offset
– and is the only region whose chemistry is not readily explained by our simple model.
5 Conclusions
We have mapped several prestellar and protostellar cores in CH3OH, HC3N, SO and C18O. We find that
the emission from these molecules traces clumpy structure across all of the cores. The molecular clumps
show striking differences in the location and velocity of emission peaks between molecules.
We see a similar degree of chemical differentiation in all of the cores that we have observed, despite
the differences in known star forming activity. The HC3N clumps are generally anti-correlated with
N2H+ peaks, and with CH3OH clumps. In L1512, a HC3N clump does appear along with a N2H+
peak, perhaps indicative of ongoing molecular depletion. CH3OH clumps and SO clumps also show
distinct emission peaks. C18O clump peaks are not generally correlated with emission peaks in any of the
other molecules that we observed. These morphological differences in molecular peaks towards sources
of different evolutionary stage suggest that depletion is important, but that other processes must also be
driving the chemical differentiation that we see.
Our observations suggest there is a kinematic sequence through the clumps of different molecular
species within the core. There is a well defined emission sequence in velocity space where we see only
clumps of SO, then clumps where SO and CH3OH are intermingled, and then a region with CH3OH only.
This may indicate that we are looking down a cylinder, or filament.
We have investigated the origin of the chemical differentiation using a simple chemical model, in
which clumps form rapidly and in which sublimation of ice mantles can occur as the clump is formed.
Despite its simplicity, this model is able to account for a wide variety of the chemical differentiation
observed in our sources. For clumps in which CH3OH is injected, the methanol survives for ∼ 104 yr,
so the observed CH3OH-rich clumps are young compared to the time-scale for dynamical evolution.
In these clumps, HC3N is not produced until all the CH3OH has been destroyed, which explains the
observed anti-correlation of methanol and cyanoacetylene. The model also predicts some some regions
will have HC3N/SO > 1 whereas others will have HC3N/SO < 1, depending on the age of the source
and/or the degree of mantle sublimation. HC3N peaks at late times, and the observed regions with only
HC3N emission are most likely tracing older clumps which are dynamically stable against both collapse
and dissipation. Such regions should also be associated with marked CO depletion and elevated N2H+
abundances.
In conclusion, it appears that molecular clouds containing protostars at different epochs of star for-
mation exhibit similar trends in their chemical spatial differentiation. The origin of this differentiation
can be understood through simple models of the molecular gas-grain interaction, and suggests that peri-
odic removal of ice mantles is occurring in dark clouds. Mantle disruption and dark cloud chemistry are
probably closely connected to the physics of clump evolution, dynamical-chemical models incorporating
of these processes are currently being developed [59].
Acknowledgements
SBC and SDR acknowledge support by the NASA Goddard Center for Astrobiology and the NASA
Long Term Space Astrophysics Program, with partial support from the NASA Origins of Solar Systems
Program.
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∫ T∗ A
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	Introduction
	Observations, Data Reduction and Analysis
	Molecular Morphology 
	Individual Sources
	General Trends - Summary 
	Chemical Differentiation in a Clumpy Medium: Theory
	Clump Physics
	Chemical Model
	Results
	Application to Observations
	Conclusions
