This document is a summer project report submitted by Sayantan Mahapatra to his research supervisor Prof. E. Arunan at the Indian Institute of Science. The project examines chlorine bond distances in weakly bonded complexes between various chlorine bond donors (D=F, Cl, CN, NC, OH, SCl, CCH) and acceptors (A=CH3, NH3, C2H2, C2H4, H2) using computational methods. Key findings include defining explicit chlorine bond radii for each donor based on atoms-in-molecules analysis and observing trends in radii, stability, and charges on chlorine atoms between different donors.

1. CHLORINE BOND DISTANCES OF WEAKLY
BONDED D-Cl...A COMPLEXES
(D=F,Cl,CN,NC,OH,SCl,CCH and A=CH3,NH3,C2H2,C2H4,H2)
A Summer Project Report
By
Sayantan Mahapatra
Department of Inorganic and Physical Chemistry
INDIAN INSTITUTE OF SCIENCE
BANGALORE-560012, INDIA

2. Certificate
I hereby certify that the work presented in this project entitled by
Chlorine Bond Distances of Weakly Bonded D-Cl...A Complexes ( D=F,Cl, CN,
NC,OH, SCl, CCH and A=CH3,NH3,C2H2,C2H4,H2 ) has been carried out by
Mr. Sayantan Mahapatra at the Department of Inorganic and Physical
Chemistry, Indian Institute of Science, Bangalore, India, under my supervision.
Date: Prof. E. Arunan
(Research Supervisor)
1

3. Declaration
I hereby declare that the work presented in project report entitled
Chlorine Bond Distances of Weakly Bonded D-Cl...A Complexes ( D=F,Cl, CN,
NC,OH, SCl, CCH and A=CH3,NH3,C2H2,C2H4,H2 ) has been carried out by me
at the Department of Inorganic and Physical Chemistry, Indian Institute of
Science, Bangalore, India, under the supervision of Professor E. Arunan.
Date: Sayantan Mahapatra
2

4. Acknowledgement
I express my earnest gratitude to my guide Prof. E. Arunan for providing
me an opportunity to work in his lab and the inspiration he has given. I
specially thank him for introducing me to weak intermolecular interaction
and expanding my idea about chlorine bonding.
I would like to thank all my senior lab mates Govinda Prasad Khanal, Arijit
Das, Kabhir Kumhar, Sharon Priya, Emmanuel Etim who have helped me
during the work.
I also like to thank Prof Sai G. Ramesh for providing me the cluster facility
for computational analysis.
My special thank to Prof S. Umapathy, Chairman, Inorganic and Physical
Chemistry Department, IISc for providing facilities of the department.
I wish to thank IPC Dept. for providing the fellowship and hostel
accommodation.
Sayantan Mahapatra
3

5. Abstract
The Chlorine Bond Radii for various chlorine bond donors Cl-D(D=F, Cl, CN, NC,
OH, SCl, CCH) are defined explicitly from Atoms in Molecules(AIM) theoretical
analysis. The AIM analysis indicates that the chlorine bond radius increases
from hard to soft donor and lies between the Pauling’s covalent radii and the
Van Der Walls radii of Cl atom. The acceptor radius also increases in a regular
way. The Dipole Moment of the donors are calculated from the optimized
structure. Charges on chlorine atom(monomer)of all donors are also examined.
A detailed discussion is made on all the observation under investigation.
4

6. INDEX
INTRODUCTION...................................................................6
COMPUTATIONAL DETAILS.................................................8
RESULTS AND DISCUSSIONS.............................................10
CONCLUSION.....................................................................22
REFERENCES......................................................................22
5

7. INTRODUCTION:
The nature of chemical bonding, specifically the interaction between the atoms
within a molecule, is very well realised.1
However, our understanding in the
area of intermolecular interactions is still enlarging.2
The importance of weak
interactions between molecules to life and all part of science is undeniable
and there have been enormous interests in this topic. Among all the weak
interactions, hydrogen bonding is the most popular and has enjoyed the most
attention in the scientific area of research. There are many new kind of weak
intermolecular interactions that have been identified in last two decades. A set
of such interaction was proposed by Benesi and Hildebrand, 3
named as charge
transfer bond first and latter Mulliken, 4
termed this kind of complexes as
electron donor-acceptor complexes. He also classified such complexes as outer
and inner type complexes according to their strength of their interaction. The
interesting position of hydrogen in the periodic table drive us to have some
knowledge about halogen bonding. 5
The term “Halogen Bond” was introduced
by Hassel 6
. Recently, It has been shown that halogen bonds can be as useful
as hydrogen bond in biomolecules(DNA), both plying crucial roles. 7
Intermolecular distances in weakly bonded
complexes have been usually interpreted in terms of van der Walls radii of the
atom/molecules. It has been shown that for hydrogen bonded complexes, one
6

8. could empirically define the hydrogen bond radius 8
. Recently it was shown
that the B...H distances in the B...HX complexes(X=F,Cl,Br,CN,OH and CCH) one
could interpret differently as the sum of the contribution from B and H in HX
where B could be the binding centre 8,9
. Gadre and Bhadane 10
calculated the
electrostatic potential of several hydrogen bond acceptors and defined the
distance from B to the minimum in the electrostatic potential. They explained
the B...H distance as the sum of the van der Walls radii of B and H. Later, it was
defined the contribution from H in HX as hydrogen bond radius 8
. It includes
the molecular electrostatic potential (MESP) of the isolated molecule B
(acceptor part). The distance from bonding atom of B to the electrostatic
minima in B is denoted as RE. The RBH-RE vs RE was plotted and set the slope to
zero. From the intercept of the plots, one could find the hydrogen bond radius.
Research on intermolecular interaction
other than hydrogen bonding is very effective now a days. The main topic of
this work is about halogen bonding specially chlorine bonding. We have
defined the “Chlorine Bond distance” for various chlorine bond donors, D...Cl
where D=F, Cl, CN,NC,OH, SCl , CCH from theoretical analysis. From our lab,
work has been done on chlorine bond distance for ClF and Cl2 complexes11
.The
bond distances in both of the complexes have been analyzed in a similar way
which was reported previously for hydrogen bonding 9
. This present work
7

9. reports the determination of chlorine bond radii for these molecules
from Atom in Molecules (AIM) theoretical analysis 12
. Five different and diverse
acceptors, NH3 having a lone pair, CH3 with an unpaired electron , C2H2 and
C2H4 with π pair , and H2 with σ pair of electrons have been selected . 13
All
these complexes have linear D-Cl.....A (A is the atom /centre for all acceptors)
geometry. Bond Critical Point (BCP, denoted as X) of the right topology (3,-1) is
readily observed for all complexes between the Cl and the A. The distance
from BCP to Cl (RCl...X)is taken and the distance from BCP to A (RX....A) is taken
into account. The average of RCl...X for a given donor can be related to the
chlorine bond radius (RCl) of that donor and the average of RX...A is defined as
acceptor radius (RA).
COMPUTATIONAL DETAILS:
The computational studies involve the use various software including Gaussian
09 14
, Chemcraft and Gaussview. The initial structures of all intermolecular
complexes were built on Chemcarft/ Gussview and submitted to Gaussian
Software for geometry optimization and frequency calculations. All the
8

10. structures were optimized at MP2(full) 15
(second order Mᴓller-Plesset
perturbation theory) level of theory which does not assume a frozen core. The
Dunning 16
basis set is used for this level of theory is aug-cc-PVTZ (augmented
correlation-consistent polarised valance triple-zeta basis set).
The Atoms In Molecules (AIM) analysis 12
was
performed using AIMALL 17
software. The Bond Critical Points (BCP) are
calculated for each complexes. The MP2(full)/aug-cc-PVTZ level of calculation
offer both reliability and speed for the complexes under investigation.
9

11. RESULTS AND DISCUSSIONS:
We can describe all complexes as D-Cl...A, where D-Cl is the donor part and A
is the acceptor part of the complexes. Three dots denote weak intermolecular
interactions. The donors are ClF, Cl2, ClCN, ClNC, ClOH, SCl2, ClCCH with five
diverse type of acceptors such as NH3 ( lone pair), CH3 ( unpaired electron),
C2H4, C2H2(π pair) and H2(σ pair). It should be mentioned here that the main
aspect of this work is finding the intermolecular distances of these complexes
to define explicitly the value of chlorine bond radii. Hence, no effort have been
given on the energetic part as it was previously reported 13
from our lab.
The AIM calculation were done using
MP2(full)/aug-cc-PVTZ level. BCP could be found between the Cl and A atom
/centre for all the complexes mentioned above. The optimized geometry for
all the Cl2 and SCl2 complexes are presented in Figure 1 and Figure 2
respectively. Investigated and interested distances( in Å) are shown in the
respective place in the figures. The distance from the BCP to Cl atom (RCl...X)
and A(RX...A) are both listed in Table 1 for all the complexes. The Chlorine Bond
Radii determined in this method is 1.30±0.13 Å, 1.45±0.12Å, 1.45±0.10Å
1.46±0.10Å, 1.59±0.08Å, 1.60±0.08Å, 1.62±0.07Å for ClF, Cl2, ClNC, ClOH
ClCN, ClSCl(SCl2), ClCCH respectively. The Dipole moments of every donor and
the Mulliken charges on chlorine atom of the donor (monomer) are calculated
from their optimized structure. Also the AIM charges on chlorine atom of the
10

12. donors are visualised after AIM analysis. All these data are listed in Table 2.
The Mulliken and AIM charges are plotted against the chlorine bond radii of
the donors and it is presented in Figure 3. Also dipole moment of the donors
are plotted against the chlorine bond radii and it is presented in Figure 4. As it
is said previously, the acceptor radii also increases with the chlorine bond radii
of donors in a systematic way, so the acceptor radii are also plotted against the
chlorine bond radii and it is presented in Figure 5.
11

13. (a) (b)
(c) (d)
(e)
Figure 1: (a) NH3...Cl2 complex, (b) CH3...Cl2complex, (c)C2H2...Cl2 complex
(d)C2H4...Cl2 complex, (e) H2...Cl2 complex.
•all the BCPs are represented by the red dots and the green dots are the Non-nuclear
Attractors(NNA).
12

14. (a) (b)
(c) (d)
(e)
Figure 2: (a) NH3...ClSCl complex, (b) CH3...ClSCl complex, (c) C2H2...ClSCl
complex, (d) C2H4...ClSCl complex (e) H2...ClSCl complex.
•BCPs and NNAs are represented as red dots and green dots respectively.
13

15. A↓ DONOR→
ClF Cl2 ClNC ClOH ClCN ClSCl(SCl2) ClCCH
RA RCl RA RCl RA RCl RA RCl RA RCl RA RCl RA RCl
CH3 1.28 1.33 1.34 1.45 1.46 1.48 1.49 1.49 1.62 1.61 1.55 1.61 1.64 1.66
NH3 1.12 1.09 1.29 1.27 1.34 1.27 1.31 1.29 1.47 1.46 1.47 1.48 1.52 1.51
C2H2 1.36 1.34 1.49 1.48 1.50 1.46 1.49 1.47 1.62 1.59 1.59 1.59 1.65 1.62
C2H4 1.21 1.25 1.41 1.43 1.46 1.44 1.43 1.43 1.61 1.58 1.56 1.57 1.66 1.59
H2 1.18 1.48 1.31 1.64 1.28 1.59 1.28 1.60 1.38 1.70 1.39 1.74 1.39 1.73
<RCl> 1.30±0.13 1.45±0.12 1.45±0.10 1.46±0.10 1.59±0.08 1.60±0.08 1.62±0.07
˂RA˃ 1.23±0.08 1.37±0.07 1.41±0.08 1.40±0.08 1.54±0.09 1.51±0.07 1.57±0.10
Table 1: All the acceptor radii(RA) and chlorine bond radii(RCl) are listed(A means acceptor).
Here the last two row is the average chlorine bond radii for all the donor and acceptor radii.
All the lengths are in Å.
Donor Dipole Moment(D) Charge(Mulliken) on Cl Charge(AIM) on Cl
ClF 1.10 +0.367 +0.424
Cl2 0 0.0 0.0
ClNC 2.34 +0.245 +0.345
ClOH 1.61 +0.175 +0.215
ClCN 3.37 +0.204 +0.013
SCl2 0.65 +0.080 -0.230
ClCCH 0.84 -0.196 -0.057
Table 2: Dipole Moment ,Charges on chlorine atom(Mulliken,AIM) of the donors are listed.
Exact Dipole Moments are measured from their optimized geometry. Charges are in a.u.
14

16. (a)
(b)
Figure 3:
(a) plot of RCl vs AIM charges on Cl atom with correlation coefficient= -0.84
(b) plot of RCl vs Mulliken charges of Cl atom with correlation coefficient=-0.68
15

17. Figure 4:
plot of RCl vs dipole moment of donor with correlation coefficient=0.17
Figure 5: plot of RA vs RCl with correlation coefficient=0.99
16

18. •Main discussion from the investigated result are presented in this section:
1.The Cl bond donor radius increases in the order ClF˂ Cl2≈ ClNC˂ ClOH˂ ClCN
˂SCl2˂ ClCCH but lies in between Pauling’s covalent radii (0.99Å) and Van Der
Walls radii (1.80Å) of Chlorine atom. It is quite clear that, the chlorine bond
radii can’t exceed 1.80Å for even the weakest of donors. It is also noticed that
the chlorine bond radii shows many similarities with hydrogen bond radius
and the given trend of radii matches well with the H bond radii which was
previously reported18
.
2. The stability of these complexes of all the donors with the acceptors shows
the trend as ClF˃Cl2˃ClNC˃ClOH˃ClCN˃SCl2˃ClCCH. It is quite expected that,
more hard the donor is, more strong is the interaction and more stable is the
donor-acceptor complex. This is clear from Table 1.
3. It was previously reported 11
that, the Cl bond distances in the ClF and Cl2
complexes is 1.28±0.11Å and 1.55±0.07Å respectively from empirical analysis
which was based on microwave spectroscopy, x ray and neutron diffraction
result. It includes the molecular electrostatic potential (MESP) of the isolated
molecule B (acceptor part). The distance from bonding atom B to the electro-
static minima in B is denoted as RE which is close to van der Walls radii of the B.
But from AIM calculation, it is figured out that the Cl bond radius of these
complexes is 1.30±0.13Å and 1.45±0.12Å respectively. It is seen that. For the
strongest donor ClF, the AIM radius is larger than the empirical estimate and
for the weak donor Cl2, the AIM radii is smaller than empirical calculation. The
17

19. fact for that larger radii of ClF complex in AIM analysis is due to significant
penetration of Cl in ClF into the electron cloud of the acceptor. This also leads
to shorter acceptor radii from empirical method. For little weak donor (Cl2) the
penetration is not so much. That’s why in the case of Cl2, the AIM analysis
suggests shorter radii than empirical measurement.
4. It is visualised from Table 2 that, the Cl bond radii of the donor has an
inverse relationship with the charge on chlorine atom. Here both the AIM
and Mulliken charges on the Cl atom are taken into account. From Figure 3,
it is clear that AIM charge seems to be more reliable as it has better correlation
coefficient (-0.84) than for Mulliken charge (-0.68).
5. AIM analysis indicates that both the chlorine bond radii for the donor and
acceptor radii vary in a regular way from strong to weak chlorine bonds. This
observation matches very well with the case of hydrogen bonding 18
. From
Figure 5, we have the correlation coefficient 0.99 which supports the result.
6. All the Dipole Moments of the donors are listed in Table 2. And from
Figure 4, it is clear that there is no such relationship between the chlorine
bond radii of the donor and the dipole moment of the donor( correlation
coefficient 0.17). This observation reflects dissimilarity with the hydrogen
bonding 18
. In the case of hydrogen bonding, the H bond radii increases with
decreasing the dipole moment of the donor. But, in case of Cl bonding, no such
relationship is found.
7. Some special attention is given on three chlorine bond donor Cl2, ClCCH and
18

20. SCl2. The charges (AIM) on chlorine atom are 0.0, -0.057, -0.230 respectively.
It was well understood 20
that σ-hole interaction plays an important role in
halogen bonded complexes. For Cl2 and ClCCH, there exist σ-hole behind the
chlorine by which they can form weakly bonded complex with electron rich
centre. Figure 6 shows the σ-hole for ClCCH.
Figure 6: Molecular Surface Electrostatic Potential of HCCCl, computed on the 0.004 a.u
contour of the electron density. Blue side is more positive than green and green side is more
positive than red. Blue side is the σ-hole.
Figure 7: Molecular Surface Electrostatic Potential of SCl2, computed on the 0.004 a.u
contour of the electron density. Blue side is more positive than green and green side is more
positive than red. Blue side is the σ-hole.
19

21. There are two kind of σ-hole present in SCl2 . Figure 7 shows it. One is behind
the sulphur and another one is behind the chlorine. Through the σ-hole, it can
make weak interaction where sulphur is involved. Again, weak interaction is
possible through chlorine atom also. BCP’s are found for both the approach of
the nucleophile. Figure 8 shows that.
(a) (b)
Figure 8: (a) SCl2 interacts with NH3 through chlorine end forming halogen(chlorine) bond.
(b) SCl2 interacts with NH3 through sulphur end forming chalcogen (sulphur) bond.
It is observed that, these two approach is possible for SCl2. The first one shows
the existence of chlorine bonding and for the second structure interaction
occurs through sulphur atom. The binding energy of these two complexes
is -3.02kcal/mole and -6.25 kcal/mole respectively. So it is clear that the
approach (b) leads to the more stable complex. But , the structure (a) is also
possible so more effort is given in that as this work is on chlorine bonding.
20

22. For structure (a), the AIM charges are analyzed for both the monomer and
weakly bonded SCl2. It is found that the charge of the weakly bonded Cl
atom is getting reduced and the charge is shifted towards the sulphur and
free chlorine atom and as a whole the SCl2 accepts some electron density
from the electron rich part. It forms the complex through σ-hole interaction,
and chlorine bonding is there. Figure 9 shows it.
Figure 9: charges for SCl2 and NH3...ClSCl. All charges are in atomic units.
21

23. CONCLUTION:
AIM theoretical calculations at MP2(full)/aug-cc-PVTZ level have been used to
determine the Chlorine Bond Radius for ClF, Cl2, ClNC, ClOH, ClCN, ClSCl and
ClCCH. The chlorine bond order increases in the order as ClF˂ Cl2≈ ClNC˂ ClOH
˂ ClCN˂ SCl2˂ ClCCH. Again the AIM calculation shows the acceptor radii also
vary in a systematic way. The RCl and RA varies linearly with correlation
coefficient 0.99 . There exists an inverse relationship between charge on Cl
atom and the RCl. But the RCl is independent of the dipole moment of the
donor. We can also separate the donors as hard or soft donor according to
their interaction with the acceptors. Thus, F is strongest donor and CCH(ClCCH)
is the weakest donor among them.
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