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An Atoms-in-Molecules Theory Interpretation for the Structure of Di-n-

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DOI: 10.1007/s40009-018-0756-5

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An Atoms-in-Molecules Theory
Interpretation for the Structure of Di-n-
Butyltin(IV) Derivative of Glycylvaline

Sandeep Pokharia, Swatantra Kumar

Yadav & Hirdyesh Mishra

National Academy Science Letters

ISSN 0250-541X

Natl. Acad. Sci. Lett.

DOI 10.1007/s40009-018-0756-5

1 23
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 Author's personal copy
Natl. Acad. Sci. Lett.
https://doi.org/10.1007/s40009-018-0756-5
SHORT COMMUNICATION
An Atoms-in-Molecules Theory Interpretation for the Structure
of Di-n-Butyltin(IV) Derivative of Glycylvaline
Sandeep Pokharia1 • Swatantra Kumar Yadav2 • Hirdyesh Mishra2
Received: 6 March 2016 / Revised: 9 July 2017 / Accepted: 27 December 2018
 The National Academy of Sciences, India 2019
Abstract The topological and energetic properties of the
electron density distribution q ðr
~Þ for the tin–ligand inter-
action in n-Bu2SnL, the geometric configuration of which
was optimized at B3LYP/6-31G(d,p)/LANL2DZ(Sn) level
of theory, have been theoretically calculated at the bonds
around the central Sn atom in terms of atoms-in-molecules
(AIM) theory using AIMAll (Version 16.01.09, standard).
In n-Bu2SnL, the formation of a (3, - 1) critical point in
the internuclear region between tin atom and bonded/co-
ordinated atoms provided an evidence of a bonding inter-
atomic interaction, and calculated bond path angles
indicated a distorted trigonal bipyramidal geometry. The
calculated topological and energetic parameters suggested
a weak closed-shell interaction in all the bonded/coordi-
nated bonds to Sn atom. This interaction possessed cova-
lent character in Sn–Npeptide, Sn–Ca and Sn–Ca0 , whereas
an electrostatic interaction was observed in Sn–Namino and
Sn–Ocarboxyl bonds. The calculated atomic charges sug-
gested negatively charged centers around the central Sn
atom.
Keywords AIM  DFT  Di-n-butyltin(IV)  Glycylvaline
& Sandeep Pokharia
sandeepp@bhu.ac.in
1 involving organotin(IV) complexes with hetero donor
Organometallics and Molecular Modeling Group, Chemistry
Section, M.M.V., Banaras Hindu University, Varanasi
221005, India
2
Physics Section, M.M.V., Banaras Hindu University,
Varanasi 221005, India
Introduction
The chemistry of organotin(IV) complexes has witnessed a
great interest in recent times, owing to their structural
diversity and wide range of industrial and biological
applications [1]. The ability of these complexes to exhibit
expanded coordination upon inter- or intramolecular
interaction with hetero donor atoms owing to the low-lying
empty 5d atomic orbitals and pronounced electron-acceptor
ability of the Sn atoms makes them suitable for the design
of newer materials with unique structural features [2].
Further, it is the antiproliferative activity of these com-
plexes, which is dependent on the nature of coordinated
bonds with the central Sn atom that led to a considerable
attention toward them. Consequently, several organ-
otin(IV) complexes of dipeptides have been modeled for
metal–protein interactions and also been shown to exhibit
wide range of biological activities [3–5]. These organ-
otin(IV) complexes of dipeptides possess unique structural
features in terms of bonding such as interaction through
hetero donor atoms (N/O) as well as existence of a dis-
torted geometrical configuration around the central Sn
atom. In order to formulate a theoretical basis of these
structural features, a thorough study of the electronic
structure of these complexes is indispensable.
In recent times, the atoms-in-molecules (AIM)
methodology is commonly used in the modeling of the
electron density distribution q ðr~Þ in intermolecular inter-
actions [6]. Though, the topological properties of q ðr ~Þ
have been well established for many molecular systems
atoms [7–10], the studies on the nature of tin–ligand bond
in organotin(IV)–peptide complexes are not reported yet.
Thus, in order to understand the nature of coordinated
bonds, we have systematically initiated the studies on
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 Author's personal copy
topological analysis of organotin(IV)–peptide system. The
present study attempts for the first time to delineate the
topological and energetic features of q ðr ~Þ using AIM
theory, in the coordinated bonds in previously synthesized
di-n-butyltin(IV) derivative (n-Bu2SnL) of glycylvaline
(H2L) [11].
Computational Details
The nature of coordinated bonds in n-Bu2SnL has been
interpreted in terms of AIM theory using AIMSum com-
ponent of AIMAll software package [12]. The wavefunc-
tion input for AIM analysis has been generated from the
previously optimized geometrical configuration of n-Bu2-
SnL at B3LYP/6-31G(d,p)/LANL2DZ(Sn) level of theory
using the Gaussian 09 program package [13]. The topo-
logical and energetic analysis of q ðr ~Þ has been carried out
in terms of (3, - 1) critical points (bond critical points)
and (3, ? 1) critical points (ring critical points) around the
central Sn atom in n-Bu2SnL derivative. The parameters
obtained at the bond critical points (BCPs) are the electron
density (q ðr~Þ), the Laplacian of the electron density (r2q
ðr
~Þ), the principal curvature of q ðr~Þ in the normal plane to
the bond path direction (k1CP and k2CP), the principal
curvature along the bond path direction (k3CP), bond
ellipticity (e), the electron kinetic (G ðr
~Þ), potential (V ðr
~Þ)
and total (H ðr ~Þ) energy densities. The atomic character-
istics such as atomic volume and atomic charge at the
selected atoms and bond path angles for a group of atoms
have also been calculated in n-Bu2SnL derivative.
Results and Discussion
The values of electron density distribution q ðr ~Þ were
calculated on the ground state optimized geometry in gas
phase of n-Bu2SnL derivative of glycylvaline (H2L) at the
B3LYP/6-31G(d,p)/LANL2DZ(Sn) level of theory, and
then q ðr
~Þ was analyzed within the framework of the AIM
theory. The structure of n-Bu2SnL along with the atom
number notation and the ground state optimized geometry
used for wavefunction calculation for AIM analysis is
depicted in Fig. 1. The insight into the intermolecular
interaction of hetero donor atoms in H2L with n-Bu2Sn(IV)
moiety was obtained from the full topological and ener-
getic analysis of the q ðr
~Þ at the selected BCPs around the
central Sn atom in n-Bu2SnL derivative. The evidence of a
bonding interatomic interaction can be obtained from the
topological analysis of q ðr ~Þ through the formation of a
(3, - 1) critical point in the internuclear region between
the central Sn atom and bonded/coordinated atoms in the
trigonal bipyramidal arrangement around it. The bond path
123
S. Pokharia et al.
corresponding to these critical points links the BCP with
two (3, - 3) critical points located at the coordinated/
bonded atoms and the central Sn atom, thus providing an
evidence that, in terms of AIM theory, the group of atoms
are bonded to one another [14]. The values of selected AIM
topological parameters at these selected BCPs are pre-
sented in Table 1.
The magnitude of q ðr ~Þ in the internuclear region,
specifically at the critical point, is a measure of the inter-
action strength, and hence, greater the value of q ðr ~Þ,
stronger will be the interaction [15]. Further, the topolog-
ical properties of q ðr
~Þ at the critical point also characterize
the interaction between the involved atoms, and according
to the AIM methodology, the classification of this inter-
action is defined by the sign of the Laplacian r2q ðr ~Þ.
Thus, the strong shared-shell (SS-) interatomic interaction
is evidenced by a local concentration of the electron den-
sity distribution at the critical point when r2q ðr ~Þ \ 0,
whereas the weak closed-shell (CS-) interaction exhibits its
local depletion when r2q ðr ~Þ [ 0. As evident from the
results (Table 1), the value of q ðr ~Þ is small and the
Laplacian r2q ðr ~Þ is positive, which suggests a contraction
of an electron charge away from the interatomic region
between the bonded atom and the Sn atom. According to
the q ðr~Þ values (Table 1), the bond strength around the
central Sn atom increases in the order: Sn–N1(amino) \ Sn–
O17(carboxyl) \ Sn–N9(peptide) \ Sn–C26(a) = Sn–C39(a0 ).
The positive values of r2q ðr ~Þ were often found at the BCP
between atoms involved in the dative bonds, including the
intramolecular N ? Sn [7], and O ? Sn [9] bonds. The
magnitude of the curvature or eigenvalue of the Hessian of
q ðr~Þ in an atomic surface k1CP and k2CP is negative,
whereas along a bond path k3CP is positive, a behavior at
the BCP around the central Sn atom in n-Bu2SnL which is
in accordance to the fact put forwarded earlier [6]. Further,
the results (Table 1) suggest that all the bonds in the
coordination sphere around the central Sn atom involve
weak CS interaction as the magnitude of the ratio of the
perpendicular contractions of q ðr ~Þ to its parallel expan-
sion, i.e., |- k1CP/k3CP| \ 1 (where, k1CP and k3CP are the
lowest and highest eigenvalues of the Hessian matrix of q
ðr
~Þ) [6, 15]. Furthermore, the order of ellipticity,
e = [(k1CP/k2CP) - 1] (Table 1), for the selected BCPs
around the central Sn atom is: Sn–Namino [ Sn–Npeptide-
[ Sn–Ocarboxyl [ Sn–Ca [ Sn–Ca0 , which indicates that
the interaction of hetero donor atoms in the ligand (H2L)
results in a weaker bond in comparison with the covalently
bonded carbon atoms of the two n-butyl groups in the n-
Bu2SnL derivative.
The AIM energetic parameters at the selected BCPs are
also presented in Table 1. The G ðr ~Þ outweighs the V ðr ~Þ
for Sn–Namino and Sn–Ocarboxyl, resulting in the positive
sign of the H ðr~Þ (= G ðr~Þ ? V ðr ~Þ), whereas G ðr~Þ is less
 Author's personal copy
An Atoms-in-Molecules Theory Interpretation for the Structure of Di-n-Butyltin(IV) Derivative…
Fig. 1 a Structure of n-Bu2SnL along with the atom number notation,
and b ground state optimized geometry of n-Bu2SnL at B3LYP/6-
31G(d,p)/LANL2DZ(Sn) level of theory used for the generation of
than V ðr~Þ for Sn–Npeptide, Sn–Ca and Sn–Ca0 , resulting in
the negative sign of H ðr ~Þ. Since, H ðr ~Þ \ 0 has been
suggested as one of the sufficient condition for a covalent
bond even though a CS interaction is involved [15]; thus,
Sn–Npeptide, Sn–Ca and Sn–Ca0 bonds possess a covalent
character, whereas an electrostatic interaction is present in
Sn–Namino and Sn–Ocarboxyl. Further, V ðr ~Þ and G ðr ~Þ are
interpreted as the pressures exerted on and by the electrons
at the critical point, and hence, the ratio |V ðr~Þ|/G ðr~Þ [ 1
for Sn–Npeptide indicates that the interaction is stabilized by
a local concentration of the charge, and the ratio |V ðr ~Þ|/G
ðr
~Þ \ 1 for Sn–Namino and Sn–Ocarboxyl indicates a weak
CS character of the N ? Sn and O ? Sn interaction
[6, 15]. Further, the magnitude of the bond degree (BD = H
ðr
~Þ/q ðr~Þ) (Table 1) indicates a weaker non-covalent
interaction quantifying a softening degree (d [ dcov) per
electron density unit at the BCP for Sn–Namino and Sn–
Ocarboxyl, and a strong interaction quantifying a covalence
degree (d \ dcov) for Sn–Npeptide, Sn–Ca and Sn–Ca0 [15].
The structure of n-Bu2SnL is further analyzed in terms
of the formed five (3, ? 1) critical points (RCPs), thus
satisfying Poincare–Hopf relationship [12]. The topologi-
cal and energetic parameters for two RCPs, viz. N1-C2-C5-
N9-Sn25 and N9-C10-C13-O17-Sn25, are presented in
Table 1, which demonstrates a trigonal bipyramidal
wavefunction for calculation of topological and energetic parameters
in AIM analysis
arrangement around the central Sn atom in n-Bu2SnL and
weaker CS interaction between the involved atoms.
The significant aspect of AIM analysis is to understand
and analyze hydrogen bonds, which for n-Bu2SnL indicates
presence of one intramolecular hydrogen bond between
O18(carboxyl)H24. The small value of q ðr ~Þ and the posi-
tive Laplacian r2q ðr ~Þ for the bond indicate a weak CS
interaction, which is further confirmed by the magnitude of
|- k1CP/k3CP| \ 1 (Table 1). Further, the magnitude of
ellipticity, (e) (Table 1), of the bond suggests it to be an
unstable bond [6]. Furthermore, it has been put forwarded
that the magnitude of both k1CP and k3CP increases upon
strengthening of an interaction [15]; therefore, the calcu-
lated values of these parameters for the bond suggest it to
be a weaker interaction. Moreover, the charge density
along a bond path usually attains its minimum value at the
BCP; and thus, the associated curvature (k3CP) is positive
[6]; however, for the hydrogen bond, k3CP is negative
(Table 1). Since all the three eigenvalues of the Hessian of
q ðr~Þ are negative (Table 1), therefore q ðr ~Þ is a local
maximum at the BCP, which reflects the dominance of the
nuclear-electron attractive force in the bond [6]. The
magnitude of H ðr ~Þ [ 0, the ratio |V ðr~Þ|/G ðr
~Þ \ 1 and
softening degree (SD) H ðr ~Þ/q ðr
~Þ [ 1 (Table 1) indicates a
weaker non-covalent interaction in the hydrogen bond [15].
Hence, on the basis of topological and energetic
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 Author's personal copy
S. Pokharia et al.

Table 1 Topological and energetic properties of q ðr

~Þ calculated at the (3, - 1) and (3, ? 1) critical point of the selected bonded interactions in
n-Bu2SnL derivative of glycylvaline (H2L) at B3LYP/6-31G(d,p)/LANL2DZ(Sn) level of theory
Typea q r2q k1dCP k2CP k3CP ee ~Þf V ðr
G ðr ~Þg ~Þh
H ðr |V ðr
~Þ|/G H ðr~Þ/q - k1CP/
~Þb
ðr ~Þc
ðr ðr
~Þ ~Þi
ðr k3CP

(3, - 1) critical point or bond critical point (BCP)

Sn–N1 0.028 0.242 - 0.038 - 0.032 0.312 0.189 0.022 - 0.021 0.0004 0.982 0.014 0.122
Sn–N9 0.086 0.682 - 0.164 - 0.140 0.984 0.169 0.064 - 0.071 - 0.0065 1.102 - 0.076 0.167
Sn–O17 0.083 0.768 - 0.163 - 0.146 1.077 0.112 0.076 - 0.074 0.0024 0.968 0.029 0.151
Sn–C26 0.109 0.187 - 0.135 - 0.133 0.455 0.015 0.018 - 0.063 - 0.0453 3.517 - 0.416 0.297
Sn–C39 0.110 0.186 - 0.136 - 0.133 0.455 0.018 0.018 - 0.063 - 0.0450 3.528 - 0.409 0.299
O18H24 0.011 0.044 - 0.011 - 0.009 - 0.064 0.235 0.010 - 0.009 0.0011 0.900 0.100 - 0.172
(3, ? 1) critical point or ring critical point (RCP)
N1–C2–C5–N9–Sn25 0.013 0.104 - 0.011 0.039 0.076 – 0.0152 - 0.014 0.0012 0.921 0.092 0.145
N9–C10–C13–O17– 0.016 0.127 - 0.015 0.034 0.107 – 0.0213 - 0.019 0.0022 0.8967 0.138 0.140
Sn25
All the values are in atomic units
a
Atom number as represented in Fig. 1a
b
Electron density distribution at the critical point (CP)
c
Laplacian of the electron density at CP
d
kiCP (i = 1,2,3) are the eigenvalues of the Hessian of q ðr
~Þ in ascending order, where k1CP and k2CP are the principal curvature of q ðr
~Þ in the
normal plane to the bond path direction, and k3CP is the principal curvature along the bond path direction
e
Bond ellipticity = [(k1CP/k2CP) - 1]
f
Lagrangian form of kinetic energy density
g
Potential energy density
h
Total energy density = G ðr
~Þ ? V ðr
~Þ
i
Bond degree parameter

Table 2 Atomic charge (a.u.) and atomic volume (bohr3) at the parameters, this hydrogen bond can be classified as a weak
selected atoms, and bond path angles () at the selected group of
atoms in n-Bu2SnL at B3LYP/6-31G(d,p)/LANL2DZ(Sn) level of
hydrogen bond [15, 16].
theory The atomic charges and atomic volumes at all the atoms
of n-Bu2SnL have been also calculated using AIM theory,
Atom characteristics Bond path angle
and the results for the selected atoms as presented in
a b
Atom (k) Net charge Volume A–B–C Angle Table 2 suggest that relative to the positively charged Sn
Sn 2.651 96.8 N9–Sn25–N1 74.67 atom, all the atoms bonded to it bear negative charge,
C26 - 0.377 85.5 O17–Sn25–N1 154.63 which further confirms a partial transfer of charge density
C39 - 0.373 85.3 O17–Sn25–N9 80.0
toward these atoms. The evidence for a distorted trigonal
N1 - 1.252 100.9 C26–Sn25–N1 89.12
bipyramidal arrangement is further obtained from the cal-
culated bond path angles around the central Sn atom
N9 - 1.893 93.2 C26–Sn25–N9 119.42
(Table 2).
O17 - 1.663 123.7 C26–Sn25–O17 102.16
In conclusion, the present study demonstrates that, in the
C2 0.352 61.5 C39–Sn25–N1 90.84
coordination sphere around the central Sn atom in n-Bu2-
C5 1.853 35.3 C39–Sn25–N9 116.11
SnL, the bonds Sn–Npeptide, Sn–Ca and Sn–Ca0 are suffi-
C10 0.391 45.3 C39–Sn25–O17 101.77
ciently covalent, whereas an electrostatic interaction
C13 1.931 33.1 C39–Sn25–C26 122.21
(coordination bonding character) is present in Sn–Namino
O8 - 1.307 149.0 C16–H24O18 27.95
and Sn–Ocarboxyl bonds, with a distorted trigonal bipyra-
O18 - 1.312 146.1
midal arrangement around the central Sn atom, thus sig-
a
Atom number as represented in Fig. 1a nifying the importance of AIM theory in understanding the
b
Volume bounded by interatomic surfaces of atom k and by an iso- bonding nature in diorganotin(IV)–dipeptide system.
surface of the electron density distribution (isodensity
surface = 0.0004)

123
 Author's personal copy
An Atoms-in-Molecules Theory Interpretation for the Structure of Di-n-Butyltin(IV) Derivative…
Acknowledgements The authors are thankful to Banaras Hindu
University, Varanasi, for providing necessary infrastructural and
computational facilities.
Compliance with Ethical Standards
Conflict of interest The authors declare that they have no conflict of
interest.
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