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International Journal of
Molecular Sciences
Review
Metal Coordination Enhances Chalcogen Bonds: CSD Survey
and Theoretical Calculations
Antonio Frontera * and Antonio Bauza *
Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5,
07122 Palma de Mllorca, Baleares, Spain
* Correspondence: toni.frontera@uib.es (A.F.); antonio.bauza@uib.es (A.B.)
Abstract: In this study the ability of metal coordinated Chalcogen (Ch) atoms to undergo Chalcogen
bonding (ChB) interactions has been evaluated at the PBE0-D3/def2-TZVP level of theory. An initial
CSD (Cambridge Structural Database) inspection revealed the presence of square planar Pd/Pt
coordination complexes where divalent Ch atoms (Se/Te) were used as ligands. Interestingly, the
coordination to the metal center enhanced the σ-hole donor ability of the Ch atom, which participates
in ChBs with neighboring units present in the X-ray crystal structure, therefore dictating the solid state
architecture. The X-ray analyses were complemented with a computational study (PBE0-D3/def2-
TZVP level of theory), which shed light into the strength and directionality of the ChBs studied herein.
Owing to the new possibilities that metal coordination offers to enhance or modulate the σ-hole
donor ability of Chs, we believe that the findings presented herein are of remarkable importance for
supramolecular chemists as well as for those scientists working in the field of solid state chemistry.
Keywords: σ-hole interactions; chalcogen bonding; supramolecular chemistry; DFT study;
metal coordination
Citation: Frontera, A.; Bauza, A.
Metal Coordination Enhances 1. Introduction
Chalcogen Bonds: CSD Survey and
Since the beginning of the 21st century, the ability of elements from Groups 13–18
Theoretical Calculations. Int. J. Mol.
Sci. 2022, 23, 4188. https://doi.org/
covalently bound to electron withdrawing groups (EWG) to favorably interact with Lewis
10.3390/ijms23084188
bases (e.g., lone pair donors, π-systems and anions) has been subject of extensive investi-
gation [1–13]. It all began with the standardization of the electropositive site to describe
Academic Editor: Luísa Margarida the main features of the hydrogen bonding (HB) interaction and from there, it became
Martins
common to name the noncovalent interactions (NCIs) between nucleophile and electrophile
Received: 21 February 2022 sites (known as σ-holes) by using the name of the group to which the electrophilic atom
Accepted: 7 April 2022 belongs [14,15]. In this context, the International Union of Pure and Applied Chemistry
Published: 10 April 2022 (IUPAC) have already recommended the terms halogen bond (HaB) [16] and chalcogen
bond (ChB) [17] for naming the NCIs encompassing atoms from groups 17 and 18, respec-
Publisher’s Note: MDPI stays neutral
tively. Furthermore, a specific name is given to each group, being aerogen or noble gas
with regard to jurisdictional claims in
bonding (NgB, group 18) [12], pnictogen bonding (PnB, group 15), [18,19] tetrel bonding
published maps and institutional affil-
iations.
(TtB, group 14) [20], and triel bonding (TrB, group 13) [7]. Furthermore, elements from
groups 7, 8, 11 and 12 acting as Lewis acids have recently received the names of matere
bonding (MaB, group 7) [21], osme bonding (OmB, group 8) [22], spodium bonding (SpB,
group 12) [23] and regium or coinage bonding (CiB, group 11) [24–27].
Copyright: © 2022 by the authors. The use of σ-holes as an alternative to HB interactions has been reported in many
Licensee MDPI, Basel, Switzerland. studies belonging to a broad spectrum of fields, such as host-guest chemistry, catalysis,
This article is an open access article supramolecular chemistry, membrane transport, crystal engineering, etc. [28–45]. In addi-
distributed under the terms and tion, comparisons have been made to unveil similarities and differences between σ-hole
conditions of the Creative Commons interactions and the HB in both energetic and geometric characteristics [46–51].
Attribution (CC BY) license (https:// Nowadays a remarkable progress has been achieved regarding the supramolecular
creativecommons.org/licenses/by/ chemistry of chalcogen bonding, particularly in regulating and fine tuning novel chemical
4.0/).
Int. J. Mol. Sci. 2022, 23, 4188. https://doi.org/10.3390/ijms23084188 https://www.mdpi.com/journal/ijms
Int. J. Mol. Sci. 2022, 23, 4188 2 of 18
systems for applications in crystal engineering, supramolecular chemistry, catalysis, trans-
port of anions and functional materials [3,9,10,42]. As a common feature among the σ-hole
family of interactions, the physical nature of the ChB is mainly based on electrostatics, while
dispersion forces, polarization, charge-transfer, orbital delocalization and π-conjugation are
also potential contributors to the ChB formation and strengthening [52–55]. In this context,
two key features of the ChB interaction are both the strength and directionality. The former
is related to the difference between the sum of van der Waals radii of the interacting atoms
(ΣrvdW (Ch···A), where A = Lewis base) and the experimental Ch···A distance. The latter
is related to the location of a σ-hole (opposite to the R–Ch bond), hence, the strength of
the interaction is maximized at a ∠R–Ch···A angle of 180◦ , representing a measure of the
directionality. In a parallel way to other σ-hole based interactions, both the strength and
directionality of ChBs mainly depend on several factors:
Ch atom involved: Conversely to HB, the σ-hole donor ability varies upon modifi-
cation of the Ch atom [39,56,57]. In Table 1 are gathered the atomic polarizabilities (α)
and van der Waals radii (RvdW ) of the chalcogen elements from period 2 to 5. As noted,
the atomic α value becomes higher from 3.0 a.u. in O to 25.9 a.u. in Te. Interestingly, the
difference in the atomic polarizability between O and S is noticeable (around 4 times higher
for S), whilst the variations between S and Se or Se and Te are of lesser magnitude.
Table 1. Atomic polarizabilities (α, a.u.) calculated at the MP2/def2-TZVP level of theory of chalcogen
(Ch) elements and their van der Waals radii (RvdW , Å).
Ch α RvdW
O 3.0 1.52
S 11.8 1.80
Se 17.5 1.90
Te 25.9 2.06
R groups attached to the Ch atom: The substituents (R) effect to the Ch···A bond
features have been analysed from a theoretical perspective [58–62], evidencing that EWG
enhance the strength of the ChB through the formation of larger and deeper σ-hole(s).
Conversely, the use of electron-donating groups (EDG) resulted in a weakening of the
interaction. Both types of substituents have been used to correlate structure-property
functions, as well as a source of stabilization of the secondary coordination sphere in metal
complexes. Figure 1 shows several Molecular Electrostatic Potential (MEP) surfaces of the
–CH3 and –CF3 substituted Selenium and Tellurium derivatives. As noted, two σ-holes are
located on each Ch atom on the extension of the C–Se and C–Te bonds and their MEP values
become more positive ongoing from Se to Te, in agreement with the atomic polarizabilities
discussed above. Moreover, the use of strong EWG (e.g., –CF3 ) increases the potential of
the σ-hole, thus enhancing the σ-hole donor ability of the Ch atom and strengthening the
interaction. Finally, using EDG as substituents of the Lewis base can also enhance the ChB
interaction by increasing the nucleophilicity of the electron rich moiety [63,64].
Int. J. Mol. Sci. 2022, 23, x FOR PEER REVIEW 3 of 18
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18
Figure 1. MEP surfaces (MP2 [66]/def2-TZVP [67] level of theory) of the Ch(CH3)2 and Ch(CF3)2 (Ch
Figure
Figure 1.1. MEP
= Se and MEP surfaces (MP2
surfaces
Te) molecules. [66]/def2-TZVP
The energy values at[67]
[65]/def2-TZVP [66]level
levelof
concrete oftheory)of of
theory)
points ofthe
the Ch(CH
the Ch(CH
surface 3)23and
are Ch(CF
)2 and
given 3)2 (Ch
inCh(CF 3 )2
kcal/mol
=(0.001
(Ch Se= and Te)The
Sea.u.).
and molecules.
Te) molecules.The energy
The values
energy valuesat
atconcrete
concrete points
points of
of the surface are
are given
given
calculations have been performed by means of the Turbomole 7.0 software (Karls- in
in kcal/mol
kcal/mol
(0.001
(0.001 a.u.).The
ruhe,a.u.).
Germany)Thecalculations
calculations
[68]. have
have been
been performed
performed by by means
means of the
of the Turbomole
Turbomole 7.0 software
7.0 software (Karls-
(Karlsruhe,
ruhe, Germany)
Germany) [67]. [68].
Interacting partner (A): A variety of classical nucleophile species (e.g., lone pair bear-
Interacting partner partner (A): A Avariety
variety ofof
classical
classical nucleophile
nucleophile species (e.g.,(e.g.,
lone lone
pair2 bear-
Interacting
ing chalcogen, pnictogen or halogen atoms), including metal ionsspecies
with available dz pair
(Rh+,
ing2+chalcogen, pnictogen or halogen atoms), including metal ions with available dz 2 (Rh2+,
bearing chalcogen,
Ni + , Pt 2+, Pd2+) or dx
2+ 2+ pnictogen
2 − y (Au
2 or
+ halogen
) orbitals atoms), including metal ions with
can act as electron donor moieties to form strongavailable dz
2+ 2 2 +
Ni , Pt , Pd ) or dx − y in a−similar
(Au ) orbitals can act as electron donor moieties to form strong
(Rh 2+ 2+ 2+ 2
, Pd ) or dx 2 +
ChBsNi , Pt Moreover,
[69–76]. y (Au fashion
) orbitalstocan act as electron
aromatic donor
π-systems, themoieties to form
chelate ring has
ChBs [69–76].
strong ChBs Moreover,
[68–75]. Moreover, in a similar
in a fashion
similar to aromatic
fashion to π-systems,
aromatic π-systems,the chelate
the ringring
chelate has
also been observed to participate as a ChB acceptor in intermolecular ChBs [77].
alsoalso
has beenbeenobserved
observed to participate
to participate as aasChBa ChBacceptor
acceptor in intermolecular
in intermolecular ChBsChBs[77].
[76].
In this article, we illustrate several X-ray structures to highlight that ChBs in metal
In
Inthis
thisarticle,
article, we weillustrate
illustrate severalseveral X-ray
X-raystructures
structures to tohighlight
highlight that
thatChBs
ChBsin inmetal
metal
complexes can be used as an effective tool in crystal engineering and in the generation of
complexes
complexescan canbe beused
usedas asan aneffective
effectivetool toolinincrystal
crystalengineering
engineeringand andin inthe
thegeneration
generationof of
functional materials. Particularly, we have focused our attention on a divalent Ch moiety
functional
functional materials.
materials. Particularly,
Particularly, we have
we certainly focused
have focused our attention
our attention on a divalent
onσ-hole,
a divalent Ch moiety
Ch moiety
coordinated to a metal center, which increases the R–Ch leading to new
coordinated
coordinated to toaametal
metalcenter,
center,which whichcertainly
certainlyincreases
increasesthe theR–Ch σ-hole,leading
R–Chσ-hole, leading to tonew
new
opportunities to use ChBs as a supramolecular tool in coordination chemistry [78,79]. To
opportunities
opportunities to touseuseChBs
ChBsas asaasupramolecular
supramolecular tool tool in
incoordination
coordination chemistry
chemistry [77,78].
[78,79]. ToTo
illustrate this idea, two examples have been selected (see Figure 2), where a bidentate
illustrate
illustrate this this idea,
idea, twotwo examples
examples have have been
been selected
selected (see
(see Figure
Figure 2),
2), where
where aa bidentate
bidentate
Se/Te ligand is coordinated to a Pd2+ ion 2+ in addition to two chloride ions in a square planar
Se/Te ligand isiscoordinated
Se/Te ligand coordinatedtotoa Pd a Pd2+ ionion in addition
in addition to twoto chloride
two chloride
ions in ions in a square
a square planar
geometry. Upon coordination, there is one Se/Te σ-hole still available to undergo ChB
planar
geometry. geometry.
Upon Upon coordination,
coordination, there is one Se/Te σ-hole still available to undergo
interactions, which exhibits an there enhanced is one Se/Te σ-hole
electrostatic still available
potential (up to 14tokcal/mol)
undergo com- ChB
ChB interactions,
interactions, which which
exhibitsexhibits an enhanced
an enhanced electrostatic
electrostatic potential
potential (up to (up14tokcal/mol)
14 kcal/mol)com-
pared to the uncoordinated ligand.
compared
pared to the to the uncoordinated
uncoordinated ligand.ligand.
Figure2.2. MEP surfaces
Figure surfaces of
of [PdCl
[PdCl2{1,2-C 6H
2 {1,2-C6H4(ChCH
4 (ChCH 3)23}]
)2and 1,2-C
}] and 6H46(ChCH
1,2-C 3)2 (Ch
H4 (ChCH 3 )2 =(Ch
Se and
= SeTe)andmole-
Te)
Figure 2. MEP
cules. The surfaces
energy valuesofat[PdCl 2{1,2-C6H4(ChCH3)2}] and 1,2-C6H4(ChCH3)2 (Ch = Se and Te) mole-
concrete points of the
molecules. The energy values at concrete points of surface are given
the surface in kcal/mol
are given in kcal/mol(0.001 a.u.).a.u.).
(0.001
cules. The energy values at concrete points of the surface are given in kcal/mol (0.001 a.u.).
In
Inthis
thiscontext,
context,the
theCambridge
CambridgeStructural
StructuralDatabase
Database(CSD)
(CSD)[79][80]has
hasbeen
beeninspected
inspectedand
and
In thisselected
aaseries context, the Cambridge Structural Database (CSD) [80] has been inspected and
seriesofof selectedexamples
exampleswherewhere SeSeororTeTeatoms
atomscoordinated
coordinatedto tosquare
squareplanar
planarmetal
metal
acoordinated
series of selected
coordinated behave examples
behaveas an an
as where Se
electrophilic orcenter
center
electrophilic Te atoms
(chalcogencoordinated
bondbond
(chalcogen donor) to square
have
donor) planar
been
have beenmetal
discussed.
dis-
coordinated
In a parallel behave
way to as an
X-ray electrophilic
analysis, the center
presence (chalcogen
of bond
intermolecular donor) have
chalcogen been dis-
bonding
cussed. In a parallel way to X-ray analysis, the presence of intermolecular chalcogen bond-
cussed.
in metal In a parallel
organic way to X-ray
complexes hashasanalysis,
been the
alsoalso presence
analyzed fromof intermolecular
a theoretical chalcogen bond-
perspective.
ing in metal organic complexes been analyzed from a theoretical perspective.TheThe
ing in metal
selection organic complexes has been also of
analyzed fromisatotheoretical perspective. The
selection of square planar complexes instead of octahedral is to prevent stericeffects
of square planar complexes instead octahedral prevent steric effectsthat
that
selection
may of square planar complexes instead of octahedral is to prevent steric effects that
mayhamper
hamperthe theformation
formationof ofChB
ChBinteractions,
interactions,as asrepresented
representedin inScheme
Scheme1.1. WeWebelieve
believe
may hamper the formation of ChB interactions, as represented in Scheme
this review article will attract the attention of both theoreticians and experimentalists to 1. We believe
Int. J. Mol. Sci. 2022, 23, x FOR PEER REVIEW 4 of 18
Int. J. Mol. Sci. 2022, 23, 4188 4 of 18
this review article will attract the attention of both theoreticians and experimentalists to
investigate the ChBs in coordination compounds, which can be used as a new synthon in
investigate the ChBs in coordination compounds, which can be used as a new synthon in
crystal engineering and improve the functional properties of materials.
crystal engineering and improve the functional properties of materials.
Scheme1.1. Schematic
Scheme Schematic representation
representation of
ofaaChB
ChBinteraction
interactionin
inaaCh-coordinated
Ch-coordinatedoctahedral
octahedral(left)
(left) and
and
squareplanar
square planar(right)
(right) complex.
complex.
2.
2. Computational
Computational MethodsMethods
Calculations
Calculations regarding the
regarding the supramolecular
supramolecular complexes
complexes havehave been
been carried
carried outout atat the
the
PBE0 [80,81]-D3 [82]/def2-TZVP [66] level of theory using the program
PBE0 [81,82]-D3 [83]/def2-TZVP [67] level of theory using the program Turbomole Turbomole 7.2 (Karl-
7.2
sruhe, Germany)
(Karlsruhe, [67]. The
Germany) [68].binding energy
The binding values
energy (∆EBSSE
values (ΔE) BSSE
were calculated
) were as the
calculated as energy
the en-
difference between
ergy difference the optimized
between structures
the optimized of theofcomplex
structures and and
the complex isolated monomers
isolated monomers fol-
lowing the supermolecule approximation (∆E complex = E complex − E monomerA
following the supermolecule approximation (ΔEcomplex = Ecomplex − EmonomerA − EmonomerB). Us-− E monomerB ).
Using
ing the Gaussian 16 software [84], the MEP surfaces of compounds Ch(CH3)2, Ch(CF3)2,,
the Gaussian 16 software [83], the MEP surfaces of compounds Ch(CH 3 )2 , Ch(CF 3 )2
[PdCl
[PdCl22{1,2-C
{1,2-C66H Ch(CH33))22}]}]and
H44Ch(CH and 1,2-C
1,2-C66H
H44Ch(CH
Ch(CH33)2)2(Ch
(Ch==Se Seand
andTe)Te) have
have been
been computed
computed
at the MP2 [65]/def2-TZVP level of
at the MP2 [66]/def2-TZVP level of theory. theory.
To compute the contribution of the Chalcogen bond contacts (in kcal/mol) the follow-
To compute the contribution of the Chalcogen bond contacts (in kcal/mol) the follow-
ing equations were used [84]:
ing equations were used [85]:
Eint =E0.375 × V(r)
int = 0.375 − 0.5655
x V(r) (for(for
− 0.5655 those ChBs
those involving
ChBs Se) Se)
involving
Eint =E0.556 × V(r) + 0.6445 (for those ChBs involving Te)
int = 0.556 x V(r) + 0.6445 (for those ChBs involving Te)
Finally,
Finally,the
theBader’s
Bader’s“Atoms
“Atoms inin
molecules” theory
molecules” [85,86]
theory has has
[86,87] beenbeen
usedused
to analyze and
to analyze
describe the interactions discussed in this work using the AIMall calculation package
and describe the interactions discussed in this work using the AIMall calculation package [87].
The
[88].PBE0/def2-TZVP
The PBE0/def2-TZVPlevel level
of theory was used
of theory was for
usedthefor
wavefunction analysis
the wavefunction as wellasaswell
analysis for
the NBO charge analysis (also using Gaussian-16 software).
as for the NBO charge analysis (also using Gaussian-16 software).
3. Results and Discussion
3. Results and Discussion
3.1. CSD Search
3.1. CSD Search
We have inspected the CSD and found 103 structures where either divalent Se or Te is
We have
coordinated to inspected the CSD
square planar metaland foundwhich
centers, 103 structures
were in all where
caseseither divalent
Pt or Pd. Se or Te
No examples
is coordinated
with other typicalto square
square planar
planarmetals
metal centers,
like Ni andwhich werefound.
Rh were in all cases Pt or Pd.inNo
Remarkably, 73 exam-
out of
plesstructures,
103 with otherwetypical square
detected planar metals
the existence of ChBlike Ni and Rhusing
interactions, werethe found. Remarkably,
following geometric in
73 out of 103 structures, we detected the existence of ChB interactions, using
criteria: Ch···X distance shorter than the sum of van der Waals radii plus 0.2 Å (ΣRvdw + 0.2) the following
geometric
and ] R–Chcriteria: Ch···than
···X greater X distance shorter(Xthan
160 degrees = O,the sum
C, Pt, ofCl
Pd, vanandderI).Waals
Table S1radii plus 0.2
compiles Å
the
(ΣRvdw
CSD + 0.2) and
reference ∡ R–Ch·
codes, ··X greater
geometric than and
features 160 degrees (X = O, C,
donor-acceptor Pt, Pd,
atoms. Cl and
Most I). Table
of the S1
hits are
compiles for
observed theSe
CSD (40 reference
structures)codes, geometric
and chloride featuresdonor
as electron and donor-acceptor
(52 structures). atoms. Most of
Other electron
the hitsare
donors areBr,
observed
I, O andfor Se (40 belonging
C-atoms structures)toand chloride
electron richas electronrings.
aromatic donorInterestingly,
(52 structures).
we
Otheralso
have electron donors
observed somearestructures
Br, I, O and
whereC-atoms belonging
it is the to electron
metal center that actsrich
as aromatic rings.
electron donor
Interestingly,
(3 for Pd and 3we forhave also geometric
Pt). The observed some structures
features, energieswhere
and it is the metal center
characterization that
of the acts
ChBs
are provided
as electron in the(3following
donor for Pd and sections.
3 for Pt). The geometric features, energies and characteri-
zation of the ChBs are provided in the following sections.
3.2. Selenium Derivatives
3.2.1. OxygenDerivatives
3.2. Selenium as Electron Donor
3.2.1.Figure
Oxygen3aasshows a Donor
Electron self-assembled dimer that is formed in the solid state of
dichloro-(2,3:7,8-bis(methylenedioxy)-selenanthrene-Se,Se0 )-platinum(II) (refcode DUW-
MEN [88]). It can be observed that one O-atom of the methylenedioxy group is located
Int. J. Mol. Sci. 2022, 23, x FOR PEER REVIEW 5 of 18
Int. J. Mol. Sci. 2022, 23, x FOR PEER REVIEW 5 of 18
Figure 3a shows a self-assembled dimer that is formed in the solid state of dichloro-
Int. J. Mol. Sci. 2022, 23, 4188 Figure 3a shows a self-assembled dimer that is formed in the solid
(2,3:7,8-bis(methylenedioxy)-selenanthrene-Se,Se′)-platinum(II) (refcodestate ofDUWMEN
dichloro-
5 of 18
(2,3:7,8-bis(methylenedioxy)-selenanthrene-Se,Se′)-platinum(II)
[89]). It can be observed that one O-atom of the methylenedioxy group is located opposite (refcode DUWMEN
[89]).
to theItC–Se
can be observed
bond, thus that
forming one O-atom
a ChB. ofThetheMEP
methylenedioxy
surface (Figure group
3b) isoflocated opposite
this compound
to the C–Se
opposite
reveals the bond,
to the C–Se
existence thus
of forming
bond,three thus a ChB.
forming
σ-holes The MEP
a ChB.
opposite toThe surface
the MEP (Figure
threesurface
covalent 3b)
(Figureof this
bonds, compound
3b)including
of this com-the
reveals
pound the
coordination existence
revealsPt–Se of
the existencethree
bond. Itof σ-holes
three
can opposite to
σ-holes opposite
be observed the
that the to three covalent
the three
intensity bonds,
of covalent
the σ-hole including
bonds, to the
including
opposite the
coordination
the
C–Se bond is Pt–Se
coordination bond.
Pt–Se
large, which Itiscan
bond. Itbe
can
quite observed that
be observed
unexpected the
thatintensity
considering theofelectronegativity
the intensity theofσ-hole opposite
the σ-hole to the
opposite
of carbon
C–Se
to thebond
(C–Se bondisbond
C–Se islarge, which
notismuch is quiteisunexpected
large,polarized).
which quite considering
Thisunexpected
is explained thecoordination
considering
by the electronegativity of Seoftocarbon
the electronegativity the ofPt
(C–Se
carbon bond
(C–Se is not
bond much
is not polarized).
much This is
polarized). explained
This is by the
explained coordination
by
that increases the Lewis acidity of the Se-atom. It can be also observed that the approxi- the of Se
coordination to the
of Pt
Se
that
to increases
the
mation Ptofthat the Lewis
the increases
O-atom totheacidity
the Lewis ofacidity
Se could the Se-atom.
not It can
ofpossible
be forbe
the Se-atom. also
It canobserved that the approxi-
be alsooctahedral
a hypothetical observed that the
complex
mation of
approximationthe O-atom
due to the presence to the
of theofO-atom
an apicalSe could
to the not be possible for a hypothetical octahedral
Se could not be possible for a hypothetical octahedral
ligand. complex
due to thedue
complex presence of an apical
to the presence ligand.
of an apical ligand.
Figure 3. (a) Partial view of refcode DUWMEN structure. Distance in Å . H-atoms omitted for clarity.
Figure 3. (a)
(b) MEP (a) Partial
Partial
surface view
view of
ofrefcode
(isodensityrefcode DUWMEN
DUWMEN
0.001 a.u.) structure.
structure.
of DUWMEN. TheDistance
Distance in
energiesinÅat
Å.. H-atoms
H-atoms
the omitted
omitted
σ-holes for
forclarity.
clarity.
are indicated in
(b) MEP
kcal/mol.surface (isodensity
(isodensity 0.001
0.001 a.u.)
a.u.)ofofDUWMEN.
DUWMEN. The energies
The energiesat the
at σ-holes
the are
σ-holes indicated
are indicatedin
kcal/mol.
in kcal/mol.
Two additional examples showing Ch···O contacts with a clear structure directing
role Two additional
are shown examples
examples
in Figure showing
showing
4. Both Ch····
Ch·
complexes ·OOcontacts
contactswith
present thewitha clear
a clear
same structure
ligand structure directing
direct-
[2-(phenyl((2-
role
ing are
role shown
are shown in Figure
in Figure4. 4.Both
Both complexes
complexes present
present the
the same
same
(phenylselanyl)ethyl)imino)methyl)phenolato], coligand (chloride) and the difference re- ligand
ligand [2-(phenyl((2-
[2-(phenyl((2-
(phenylselanyl)ethyl)imino)methyl)phenolato],
(phenylselanyl)ethyl)imino)methyl)phenolato], coligand (chloride)
coligand (chloride) and
and thethe difference
difference re-re-
sides in the transition metal (Pd for XUFHEM [90] and Pt for XUFHIQ [90]). Both struc-
sides in the transition metal (Pd for XUFHEM XUFHEM [90] [89] and Pt for XUFHIQ [90]). [89]). Both
Both struc-
struc-
tures form very similar self-assembled dimers in the solid state where two symmetrically
tures form very similar self-assembled dimers in the solid state where two symmetrically
equivalent Se···O contacts are established. Both dimers also present metal···metal (M···M)
equivalent Se ··· established. Both dimers also present
present metal ·····metal (M ···
interactionsSe· ··O contacts
with distancesare shorter than 3.45 Å . The Se· also
··O distances metal·
are shorter (M·
in ··M)
XUF-
interactions
interactions with
with distances
distances shorter
shorter than
than 3.45 Å. ÅThe
3.45 . Se···
The Se·O··distances
O are are
distances shorter
shorterin XUFHEM
in XUF-
HEM (Figure 4a) structure, likely influenced by the shorter Pd···Pd distance. The direc-
(Figure
HEM 4a) structure,
(Figure likely influenced by the shorter Pd···PdPd· distance. The directionality
tionality of the4a) structure,
ChBs is worse likely
(withinfluenced
respect toby the shorter
linearity) than the··Pd distance.
observed The direc-
in DUWMEN
of the ChBs
tionality is worse (with respect to linearity) than the observed in DUWMEN structure
structureof the ChBs
(Figure 4b), is worse
which is (with respect
also due to thetorestriction
linearity)imposed
than the by observed
the M···in M DUWMEN
interaction.
(Figure 4b), which is also due to the restriction imposed by the M ···
structure (Figure 4b), which is also due to the restriction imposed by the M···M interaction. M interaction.
Figure 4. Partial views of the refcodes XUFHEM (a) and XUFHIQ (b) structures. Distances in Å.
H-atoms omitted for clarity.
Int.
Int.J.J.Mol.
Mol.Sci.
Sci.2022,
2022,23,
23,xxFOR
FORPEER
PEERREVIEW
REVIEW 66 of
of 18
18
Int. J. Mol. Sci. 2022, 23, 4188 Figure
Figure4.4.Partial
Partialviews
viewsofofthe
therefcodes
refcodesXUFHEM
XUFHEM(a)
(a)and
andXUFHIQ
XUFHIQ(b)
(b)structures.
structures.Distances
Distancesin
inÅÅ
6.of
.H-
H-18
atoms
atomsomitted
omittedfor forclarity.
clarity.
3.2.2.
3.2.2.Halogen as Electron Donor
3.2.2. Halogen
Halogen as as Electron
Electron Donor
Donor
As
As commented above, most hits from the CSD search present an halogen atom as
As commented above, most
commented above, most hitshits from
from thethe CSD
CSD search
search present
present an an halogen
halogen atom atom asas
electron
electron donor, basically because chloride is widely used in the synthesis of Pd and Pt
electron donor,
donor, basically
basically because
because chloride
chloride is is widely
widely usedused in in the
the synthesis
synthesis of of Pd
Pd and and Pt
Pt
complexes.
complexes. Figure 5a highlights aaself-assembled dimer that is formed in the solid state of
complexes. Figure
Figure 5a
5a highlights
highlights a self-assembled
self-assembled dimer dimer thatthat isis formed
formed in in the
the solid
solid state
state of
of
(1,2-bis(phenylseleno)benzene)-dichlorido-palladium(II)
(1,2-bis(phenylseleno)benzene)-dichlorido-palladium(II) (refcode
(refcodeXILFEEXILFEE [91]),
XILFEE[90]),[91]), selected
selected
(1,2-bis(phenylseleno)benzene)-dichlorido-palladium(II) (refcode selected as
as
asrepresentative
representative X-ray
X-ray structure
structure with
with Se····Cl contacts.
contacts.It can
canbe beobserved
observedthat thatthe chloride
representative X-ray structure with SeSe· ·Clcontacts.
···Cl ItItcan be observed that the
the chloride
chloride
ligands
ligands are located
are located opposite
locatedopposite to
oppositetotothe the C–Se
theC–Se bonds,
C–Sebonds,bonds, thus
thus forming
forming four
four concurrent
concurrent ChBs
ChBs and
ligands are thus forming four concurrent ChBs andand
one
one
one Pd· ·
· Pd contact. The MEP surface of this compound (see Figure 5b) reveals the exist-
Pd···Pd·
Pd··contact.
Pd contact.
TheTheMEP MEP surface
surface of this
of this compound
compound (see(see Figure
Figure 5b) 5b) reveals
reveals the the exist-
existence
ence
ence of
oftwo
twoσ-holes
σ-holes opposite
opposite to (i)(i)one C–Se covalent bond and (ii) to
toone Pt–Se coordina-
of two σ-holes opposite to (i)toone one
C–SeC–Se covalent
covalent bond bondandand (ii)one
(ii) to one
Pt–SePt–Se coordina-
coordination
tion
tion bond.
bond. The
The second
second C–Se
C–Se σ-hole
σ-hole is
is buried
buried by
by the
the large
large negative
negative belt
belt of
of Cl.
Cl. ItIt can
can be
be
bond. The second C–Se σ-hole is buried by the large negative belt of Cl. It can be observed
observed
observed that
that the
the MEP
MEP value
value at
at the
the σ-hole
σ-hole opposite
opposite to
tothe
the Pd–Se
Pd–Se
that the MEP value at the σ-hole opposite to the Pd–Se bond is larger likely due to the bond
bond is
is larger
larger likely
likely due
due
to
tothe
thecontributionof theof
contribution
contribution ofthe
thenearby
nearby nearby
C–H bond.C–H
C–Hbond.bond.
Figure
Figure5.5.
Figure 5.(a)
(a)Partial
(a) Partialview
Partial viewof
view refcode
ofofrefcode
refcodeXILFEE
XILFEE
XILFEE structure.
structure.Distances
Distances
structure. in
inÅin
Distances Å. .H-atoms
H-atoms
Å. omitted
H-atomsomitted for
omittedforclarity.
clarity.
for clar-
(b)
(b) MEP
MEP surface
surface (isodensity
(isodensity 0.001
0.001 a.u.)
a.u.) of
of XILFEE.
XILFEE. The
The energies
energies at
at the
the σ-holes
σ-holes are
are indicated
indicated in
in
ity. (b) MEP surface (isodensity 0.001 a.u.) of XILFEE. The energies at the σ-holes are indicated
kcal/mol.
kcal/mol.
in kcal/mol.
Three
Threeadditional
Three additionalexamples
additional examplesshowing
examples showingCh·
showing Ch····
Ch· ··Cl
Clcontacts
·Cl contactsare
contacts arerepresented
are representedin
represented inFigure
in Figure6,6,
Figure 6,inin
in
all
all cases
all cases the adducts are self-assembled
cases the adducts are self-assembled dimers. In dimers. In the
In the dimer
the dimer
dimer ofof dichloro-(diphenyl(2-
of dichloro-(diphenyl(2-
dichloro-(diphenyl(2-
(phenylselanyl)phenyl)phosphine)-platinum
(phenylselanyl)phenyl)phosphine)-platinum(PUYWUC
(phenylselanyl)phenyl)phosphine)-platinum (PUYWUC[92],
(PUYWUC [91],Figure
[92], Figure6a),
Figure 6a),the
6a), thePt·
the Pt····
Pt· ··PtPtinter-
·Pt inter-
inter-
action
action is not
action isisnot established
notestablished and
establishedand andthe formation
thetheformation of
formation the
of the dimer
dimer
of the is dominated
is dominated
dimer is dominated by ChBs.
by ChBs.
by ChBs.In the
In theIn other
otherthe
two
two
otherstructures
structures (refcodes
(refcodes
two structures TAFWIJ
TAFWIJ
(refcodes [93],
TAFWIJ[93],Figure
Figure
[92], 6b 6band
Figure 6bEPULIM
and EPULIM
and EPULIM [94], Figure
[94],[93],
Figure 6c),
Figure6c),Pd· Pd·
6c), ··
·Pd
·Pd
Pd ···in-
in-
Pd
teractions
teractions
interactions coexist
coexist with
with
coexist the
with Se·
thethe
Se··Se
··Cl···contacts.
·Cl contacts. Among
Cl contacts. Among Amongthem,
them, TAFWIJ
TAFWIJ
them, structure
TAFWIJ structure isisthe
structure isone
the the ex-
one ex-
one
hibiting
hibiting
exhibiting the highest
thethe
highest directionality
highestdirectionality
directionality (∡C–Se·
(C–Se······
(∡C–Se· Cl
·Cl ==176.1°)
Cl 176.1◦and
=176.1°) and
) andthe
the
theshortest
shortest
shortest M·
M····M
M ····
MM distance.
distance.
distance.
Figure 6. Partial views of the X-ray structures of PUYWUC (a), TAFWIJ (b) and EPULIM (c). Distances
in Å. H-atoms omitted for clarity.
Int. J. Mol. Sci. 2022, 23, x FOR PEER REVIEW 7 of 18
Int. J. Mol. Sci. 2022, 23, x FOR PEER REVIEW 7 of 18
Int. J. Mol. Sci. 2022, 23, 4188 Figure 6. Partial views of the X-ray structures of PUYWUC (a), TAFWIJ (b) and EPULIM (c). Dis-
Figure 6. Partial views of the X-ray structures of PUYWUC (a), TAFWIJ (b) and EPULIM (c).7 of 18
Dis-
tances in Å . H-atoms omitted for clarity.
tances in Å . H-atoms omitted for clarity.
3.2.3. Carbon as
3.2.3. as Electron Donor
Donor
3.2.3. Carbon
Carbon as Electron
Electron Donor
Figure 7a
Figure 7a shows
shows aa dimer
dimer extracted
extracted from
from an
an 1D
1D supramolecular
supramolecular assembly
assembly thatthat propa-
propa-
Figure
gates in
in the 7a shows
the crystal a dimer
crystal packing
packing of extracted from an 1D supramolecular assembly
of chloro-[8-({[2-(phenylselanyl)ethyl]imino}methyl)naphtha-
chloro-[8-({[2-(phenylselanyl)ethyl]imino}methyl)naphtha- that propa-
gates
gates in the crystal packing of chloro-[8-({[2-(phenylselanyl)ethyl]imino}methyl)naphthalen-
len-1-yl]-palladium(II) complex
len-1-yl]-palladium(II) complex (refcode
(refcode BEJWIZ
BEJWIZ [95]).
[95]). The
The C-atom
C-atom bonded
bonded to to the
the PdPd is
is
1-yl]-palladium(II)
located opposite tocomplex
the C–Se(refcode
bond, BEJWIZ
thus [94]).
playing theThe C-atom
electron bonded
donor roletointhe PdChB
this is located
inter-
located
oppositeopposite to thebond,
to the C–Se C–Sethus
bond, thus playing
playing the electron
the electron donor donor
role inrole
thisinChBthisinteraction,
ChB inter-
action, which
action, which isis facilitated
facilitated by
by the
the anionic
anionic nature
nature of
of this
this C-atom.
C-atom. The
The MEP
MEP surface
surface (Figure
(Figure
which is facilitated by the anionic nature of this C-atom. The MEP surface (Figure 7b)
7b)
7b) shows
shows a small
a small σ-hole
σ-hole opposite
opposite to the C–Se bond that merges with the large blue region
shows a small σ-hole opposite to to
thethe C–Se
C–Se bondthat
bond thatmerges
mergeswith
withthethelarge
large blue
blue region
region
under the influence
under influence ofof the
the methylene
methylene group.
group.
under the
the influence of the methylene group.
Figure 7. (a) Partial
(a) Partial view
Partialview of
viewof refcode
ofrefcode BEJWIZ
refcodeBEJWIZ structure.
BEJWIZstructure. Distance
structure.Distance
Distancein Å .Å.H-atoms omitted for clarity.
Figure 7. (a) in in H-atoms
Å . H-atoms omitted
omitted forfor clar-
clarity.
(b) MEP surface (isodensity 0.001 a.u.) of BEJWIZ. The energies at the σ-holes are indicated in
(b)
ity. MEP surface
(b) MEP (isodensity
surface 0.001
(isodensity a.u.)a.u.)
0.001 of BEJWIZ. TheThe
of BEJWIZ. energies at the
energies σ-holes
at the areare
σ-holes indicated
indicatedin
kcal/mol.
kcal/mol.
in kcal/mol.
Other two
Other two examples
examples of of X-ray
X-ray structures
structures exhibiting
exhibiting Se Se·
Se· ····C
··· C contacts,
C contacts, where
contacts, where
where thethe electron
electron
donor C-atom
donor C-atombelongs
C-atom belongstoto
belongs toanan
anaromatic
aromatic
aromatic system,
system,
system, are
areare given
given
given in Figure
in
in Figure Figure 8.
8. It 8. It is
is It is interesting
interesting
interesting to
to
to high-
highlight that
light that for
highlight for chloro-(2,4-di-t-butyl-6-(((2-(phenylselanyl)ethyl)imino)methyl)phe-
chloro-(2,4-di-t-butyl-6-(((2-(phenylselanyl)ethyl)imino)methyl)phenolato)-
that for chloro-(2,4-di-t-butyl-6-(((2-(phenylselanyl)ethyl)imino)methyl)phe-
nolato)-palladium(II)
palladium(II)
nolato)-palladium(II) structure
structurestructure
(Figure 8a, (Figure
refcode
(Figure 8a,
8a, refcode[95]),
COKFIT
refcode COKFIT
COKFIT [96]), the
the self-assembled
[96]), the self-assembled
self-assembled
dimer does not di-
di-
mer does
present
mer does not
M···
not present
Mpresent
interactionsM· ·
M···M·M interactions
and the C-atomand
interactions and the
is locatedC-atom
opposite
the C-atom is located opposite
to the Pd–Se
is located oppositebond.to the Pd–Se
Therefore,
to the Pd–Se
bond.
in this Therefore,
compound, in this
the compound,
third σ-hole the
at third
the σ-hole
Se-atom at
that the Se-atom
emerges
bond. Therefore, in this compound, the third σ-hole at the Se-atom that emerges upon Pd- uponthat emerges upon
Pd-complexation Pd-is
complexation
responsible foris responsible
the formation for
of the
the formation
dimers. Inof the
this dimers.
example,
complexation is responsible for the formation of the dimers. In this example, the ChBs areInthethis example,
ChBs are thethe ChBs
only are
forces
the only
the only forces
governing forces governingFor
the assembly.
governing thethe
the assembly. For the
other example
assembly. For the other
other
(TOQPEVexample
example (TOQPEV
[96],(TOQPEV
Figure 8b), [97], Figure 8b),
in addition
[97], Figure 8b),
to
in addition
theaddition
in to
ChBs opposite the ChBs opposite
to the opposite
to the ChBs C–Se bonds, to the
to the C–Se bonds,
M···Mbonds,
an C–Se an
interaction
an M· M· · ·
is··MM interaction
established
interaction is established
further support-
is established
further
ing supportingofthe
the formation
further supporting the formation
theformation of the
self-assembled
of the dimer.
self-assembled
Curiously,
self-assembled dimer.
the Pd–Se
dimer. Curiously,
···C ChBs
Curiously, the (dimer
the Pd–Se·····
Pd–Se· C
of
C
ChBs
COKFIT)
ChBs (dimer of
are of
(dimer moreCOKFIT) are
directional
COKFIT) more directional
the C–Se···C
than directional
are more than the
(dimer
than C–Se·
of TOPQEV).
the C–Se· ··C (dimer
··C (dimer of TOPQEV).
Toofour knowledge,
TOPQEV). To
To
our knowledge, there are not previous examples in the literature of M–CH·····X
our
thereknowledge,
are not there
previous are
examplesnot previous
in the examples
literature of in
M–CH the··· X literature
ChBs, of
where M–CH·
the X ChBs,
electronChBs,
rich
whereisthe
atom
where the electron
opposite
electron rich
torich
a M–Ch atombond.
atom is opposite
is opposite to aa M–Ch
This interesting
to M–Ch and bond.
bond. This interesting
unexplored
This interesting and unexplored
topic deserves
and unexplored
further
topic deserves
investigation byfurther
the investigation
scientific community.by the scientific
topic deserves further investigation by the scientific community. community.
Figure 8. Partial views of the X-ray structures of refcodes COKFIT (a) and TOQPEV (b). Distances in
Å. H-atoms omitted for clarity.
Int. J. Mol. Sci. 2022, 23, x FOR PEER REVIEW 8 of 18
Int. J. Mol. Sci. 2022, 23, x FOR PEER REVIEW 8 of 18
Figure 8. Partial views of the X-ray structures of refcodes COKFIT (a) and TOQPEV (b). Distances
Int. J. Mol. Sci. 2022, 23, 4188 Figure 8. Partial views of the X-ray structures of refcodes COKFIT (a) and TOQPEV (b). Distances
8 of 18
in Å . H-atoms omitted for clarity.
in Å . H-atoms omitted for clarity.
3.2.4. Metal as Electron Donor
3.2.4. Metal as Electron Donor
3.2.4.The
Metal
roleasofElectron Donorin d8 or d10 configuration as electron donors has been recently
metal centers
The role of metal centers in d88 or d10 configuration as electron donors has been recently
The role
analyzed for of metal centers
halogen bonding d or d10 configuration
ininteractions as electron
[98]. However, similardonors has been for
investigations recently
chal-
analyzed for halogen bonding interactions [98]. However, similar investigations for chal-
analyzed for halogen
cogen bonding bonding interactions
are unprecedented. In this [97]. However,
section, we show similar investigations
several for chalco-
examples where Pt or
cogen bonding are unprecedented. In this section, we show several examples where Pt or
gen bonding
Pd act are unprecedented.
as electron donors in ChBs. In this section,
Figure we show
9a shows several examples
a self-assembled where
dimer Pt or Pd
observed in
Pd as
act actelectron
as electron donors
donors in ChBs.
inVUGWOK
ChBs. Figure
Figure 9a shows a self-assembled dimer observed in
the solid state of refcode [99].9aThe
shows
Pd isalocated
self-assembled
oppositedimer observed
to the C–Se bond,inthus
the
the solid
solid state of refcode VUGWOK [99]. The
PdPd is locatedopposite
oppositetotothe
theC–Se
C–Sebond,
bond, thus
thus
actingstate of refcode
as electron donorVUGWOK
in the ChB [98]. The
interaction. isThe
located
MEP surface (Figure 9b) shows a small
acting
acting as electron donor in the ChB interaction. The MEP surface (Figure 9b) shows a small
σ-holeas electronto
opposite donor in the bond
the Pd–Se ChB interaction. The MEP
(+8.1 kcal/mol) and asurface (Figure 9b)
more intense oneshows a small
opposite to a
σ-hole opposite
σ-hole opposite to to the
the Pd–Se
Pd–Se bond
bond (+8.1
(+8.1 kcal/mol)
kcal/mol) andand aa more
more intense
intense one
one opposite
opposite to
to aa
C–Se bond (+16.9 kcal/mol).
C–Se bond
C–Se bond (+16.9
(+16.9 kcal/mol).
kcal/mol).
Figure 9. (a) Partial view of refcode VUGWOK structure. Distance in Å . H-atoms omitted for clarity.
Figure 9. (a) Partial view of refcode
refcode VUGWOK
VUGWOK structure.
structure. Distance
Distance in
in ÅÅ.. H-atoms
H-atoms omitted
omitted for
forclarity.
clarity.
(b) MEP surface (isodensity 0.001 a.u.) of VUGWOK. The energies at the σ-holes are indicated in
(b) MEP surface (isodensity
(b) (isodensity 0.001
0.001 a.u.)
a.u.) ofofVUGWOK.
VUGWOK. The
Theenergies
energies at atthethe
σ-holes areare
σ-holes indicated
indicatedin
kcal/mol.
kcal/mol.
in kcal/mol.
Other three interesting examples of X-ray structures exhibiting Se···M (M = Pt, Pd)
Other three interesting
interesting examples of X-rayX-ray structures
structures exhibiting
exhibiting Se ···
Se···M (M = = Pt, Pd)
are depicted in Figure 10. It is worthy to comment that the C–Se···M angle is in all cases
depicted in Figure
are depicted Figure 10.
10. It is
is worthy
worthy toto comment
comment thatthat the
the C–Se
C–Se· ·····M angle is in all cases
higher than 170°, thus confirming the strong directionality of the interaction and that the
◦ , thus
170°,
higher than 170 confirming the strong directionality of the interaction and that the
nucleophilic metal center (filled dz2 orbital) is pointing to the σ-hole opposite to the C–Se
nucleophilic metal center (filled ddzz22 orbital)
orbital) is pointing to the σ-hole opposite to the C–Se
bond. For the three selected examples (QETFED [100] (Figure 10a), QETFAZ [100] (Figure
bond.
bond. For the
the three
threeselected
selectedexamples
examples(QETFED
(QETFED[99] (Figure
[100] 10a),
(Figure QETFAZ
10a), QETFAZ[99][100]
(Figure 10b)
(Figure
10b) and MELJUJ [101] (Figure 10c)) the distances are similar (around 3.7 Å ). Finally, in
and
10b)MELJUJ [100] (Figure
and MELJUJ 10c)) the
[101] (Figure distances
10c)) are similar
the distances (around
are similar 3.7 Å). Finally,
(around in Table in
3.7 Å ). Finally, 2,
Table 2, the list of CSD codes including compound names and formulas of the Se involving
the list of CSD codes including compound names and formulas of the Se involving
Table 2, the list of CSD codes including compound names and formulas of the Se involving dimers
dimers is given.
is given.is given.
dimers
Figure 10.
Figure 10. Partial
Partialviews
viewsofofthe
theX-ray
X-raystructures
structuresofof refcodes
refcodes QETFED
QETFED (a),(a), QETFAZ
QETFAZ (b) (b)
andand MELJUJ
MELJUJ (c).
Figure 10. Partial views of the X-ray structures of refcodes QETFED (a), QETFAZ (b) and MELJUJ
(c). Distances
Distances in Å.inH-atoms
Å . H-atoms omitted
omitted for clarity.
for clarity.
(c). Distances in Å . H-atoms omitted for clarity.
Int. J. Mol. Sci. 2022, 23, 4188 9 of 18
Table 2. List of CSD codes, compound names and formulas of the Se involving dimers.
CSD Code Name Formula
dichloro-(2,3:7,8-bis(methylenedioxy)-
DUWMEN selenanthrene-Se,Se0 )-platinum(II) C14 H8 Cl2 O4 PtSe2 , C3 H6 O
acetone solvate
chloro-(2-(phenyl((2-(phenylselanyl-
XUFHEM kSe)ethyl)imino-kN)methyl)phenolato-kO)- C21 H18 ClNOPdSe
palladium(II)
chloro-(2-(phenyl((2-(phenylselanyl-
XUFHIQ kSe)ethyl)imino-kN)methyl)phenolato-kO)- C21 H18 ClNOPtSe
platinum(II)
(1,2-bis(phenylseleno)benzene)-dichlorido-
XILFEE C18 H14 Cl2 PdSe2
palladium(II)
cichloro-(diphenyl(2-
PUYWUC C24 H19 Cl2 PPtSe
(phenylselanyl)phenyl)phosphine)-platinum
dichloro-(2-(phenylselanyl)aniline)-palladium(II)
TAFWIJ C12 H11 Cl2 NPdSe, C2 H3 N
acetonitrile solvate
dichloro-(1-(2,6-di-isopropylphenyl)-4-
EPULIM ((phenylselanyl)methyl)-1H-1,2,3-triazole)- C21 H25 Cl2 N3 PdSe
palladium(II)
chloro-[8-({[2-
BEJWIZ (phenylselanyl)ethyl]imino}methyl)naphthalen-1- C19 H16 ClNPdSe
yl]-palladium(II)
chloro-(2,4-di-t-butyl-6-(((2-
COKFIT (phenylselanyl)ethyl)imino)methyl)phenolato)- C23 H30 ClNOPdSe
palladium(II)
chloro-(2-(1-(2-(phenylselanyl)ethylimino)ethyl)-
TOQPEV C20 H18 ClNOPdSe
1-naphtholato-N,O,Se)-palladium(II)
chloro-(1,7-bis(phenylselenomethyl)-1,7-dicarba-
VUGWOK C16 H23 B10 ClPdSe2
closo-dodecaborate-B,S,S0 )-palladium(II)
dichloro-(1-methyl-3-[(phenylselanyl)methyl]-
C11 H12 Cl2 N2 PtSe,
QETFED imidazol-2-ylidene)-platinum(II)
0.5(C2 H3 N)
acetonitrile solvate
dichloro-(1-methyl-3-[(phenylselanyl)methyl]-
C11 H12 Cl2 N2 PdSe,
QETFAZ imidazol-2-ylidene)-palladium(II)
0.5(C2 H3 N)
acetonitrile solvate
chloro-((2-((2-methylselanyl)ethyl)iminomethyl)-
MELJUJ C15 H22 ClNOPdSe
6-(1-ethylpropyl)phenolato)-palladium(II)
3.3. Tellurium Derivatives
In case of tellurium complexes, the CSD search shows that there are no examples
involving oxygen as electron donor. In most of the hits, the electron donor is a halogen atom
(Cl, Br or I), a π-system or a metal center (Pd and Pt) as discussed in the following sections.
3.3.1. Halogen as Electron Donor
Figure 11a highlights a self-assembled dimer that is formed in the X-ray packing of
bis(benzenetellurenyl iodide)-di-iodo-palladium(II) (refcode CUHMOJ [101]), selected as
representative structure showing Te···I contacts. It can be observed that the iodide ligands
are located approximately opposite to the C–Te bonds (] C–Te···I = 161.1◦ ), thus forming
four concurrent ChBs and one Pd···Pd contact (3.402 Å). The MEP surface of this compound
(see Figure 11b) reveals the existence of two σ-holes opposite to (i) one C–Te covalent bond
and (ii) to a Pd–Te coordination bond. The third σ-hole (expected opposite to the I–Te
bond) is completely covered by the large and negative belt of I. It can be observed that the
Int. J. Mol. Sci. 2022, 23, 4188 10 of 18
Int.
Int. J.J. Mol.
Mol. Sci.
Sci. 2022,
2022, 23,
23, xx FOR
FOR PEER
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REVIEW 10
10 of
of 18
18
MEP value at the σ-hole opposite to the Pd–Te bond is smaller (+15.7 kcal/mol) than that
opposite to the C–I bond (+18.8 kcal/mol).
Figure
Figure 11.
11. (a)
(a)Partial
(a) Partialview
Partial view
viewof refcode
ofof
refcode
refcodeCUHMOJ
CUHMOJ
CUHMOJ structure.
structure. Distances
Distances
structure. in
in ÅÅin
Distances .. H-atoms
H-atoms omitted
omitted
Å. H-atoms for
for clar-
omitted clar-
for
ity.
ity. (b)
(b) MEP
clarity. MEP
(b) surface
MEPsurface (isodensity
(isodensity
surface 0.001
0.001
(isodensity a.u.)
a.u.)
0.001 of
of CUHMOJ.
a.u.) CUHMOJ.
of CUHMOJ. The energies
TheThe
energies at
at the
energies the σ-holes
σ-holes
at the are indicated
areare
σ-holes indicated
indicatedin
in
kcal/mol.
kcal/mol.
in kcal/mol.
Three
Three additional
additional examples
examples showing
showing Te· Te· ····Cl,
Te··· Cl,Br
Cl, Brcontacts
Br contactsare
contacts arerepresented
are representedin
represented inFigure
in Figure12,
Figure 12,
12,
where
where all allthree
all threeform
three form
form self-assembled
self-assembled
self-assembled dimers
dimers
dimers in
in thein solid
the solidsolid
the state that
that are
statestate are
thatrelevant
relevant in
in the
are relevant the crystal
crystal
in the
packing.
packing.
crystal In
In the
packing. the dimer
In theof
dimer dichloro-[1-(2-{[2,6-di-isopropylphenyl]tellanyl}phenyl)-N,N-di-
ofdimer
dichloro-[1-(2-{[2,6-di-isopropylphenyl]tellanyl}phenyl)-N,N-di-
of dichloro-[1-(2-{[2,6-di-isopropylphenyl]tellanyl}phenyl)-
methylmethanamine]-palladium(II)
methylmethanamine]-palladium(II) (CODTEX
N,N-dimethylmethanamine]-palladium(II) (CODTEX [103]),
(CODTEX[103]), the M·
[102]),
the M···the
··M M ···M interaction
M interaction
interaction is
is not
not estab-
is not
estab-
lished
lished and
establishedand the and
the dimer formation
the dimer
dimer is
is basically
formation
formation dominated
is basically
basically dominated dominated by
by Te·
Te·· ···Cl
by ClTe ···Clthat
ChBs
ChBs ChBs
that are
are less
that direc-
lessare less
direc-
tional ◦ ) compared
tional (157°)
directional(157°)(157 compared
compared to
to those previously
to those
those previously
previously described
described for
for Se
described (Figure
Sefor 12a).
Se (Figure
(Figure It
12a).12a).It is
is known
It is known
known that
that
that
the the directionality
the directionality
directionality of
of ChBs
ChBsof ChBs decreases
decreases
decreases on
on going
goingon goingfrom SSfrom
from to
to Te TeSbecause
to Te because
because the sizethe
the size of size
of the of the
the σ-hole
σ-hole
σ-hole
is
is larger
larger isinlarger
in the
the morein thepolarizable
more more polarizable
polarizable Ch Ch In
Ch atoms.
atoms. atoms.
In the In thetwo
the other
other other
two two structures
structures
structures represented
represented represented
in
in Fig-
Fig-
in
ure Figure
12 12
(refcodes (refcodes
JAGZIA JAGZIA
[104] [103]
(Figure(Figure
12b) 12b)
and and
TAPYEO TAPYEO
ure 12 (refcodes JAGZIA [104] (Figure 12b) and TAPYEO [105] (Figure 12c)), Pd···Pd and [105] [104]
(Figure(Figure
12c)), 12c)),
Pd· ·Pd
· ···
andPd
and
Pt· Pt
Pt·····Pt ··· Pt interactions
Pt interactions
interactions coexist coexist
coexist with with
with the the
the Te· Te ···
Te·····Br Br
Br and and
and Te· Te ···
Te·····Cl Cl contacts,
Cl contacts, respectively.
contacts, respectively.
respectively. JAGZIA JAGZIA
structure isthetheoneonewithwithhigher
higherdirectionality
directionality(∡C–Te· (] C–Te ···Br = 171.7 ◦ ) and shorter M···M
structure
structure is is the one with higher directionality (∡C–Te· ····Br
Br == 171.7°)
171.7°) and
and shorter
shorter M· M·····MM dis-
dis-
distance
tance
tance (3.568
(3.568(3.568 Å) whilst
ÅÅ )) whilst
whilst TAPYEO
TAPYEOTAPYEO exhibits
exhibits
exhibits longer
longer longer
M·
M·····M
M ···M distance
Mdistance
distance (3.730(3.730
(3.730 ÅÅ )) and
and Å)smaller
and smaller
smaller angle
angle
angle
(∡C–Te·
(∡C–Te· (]····Cl
C–Te ···Cl = 154.7◦ ).
Cl == 154.7°).
154.7°).
Figure
Figure 12.
12. Partial
Partialviews
Partial views of the
ofof
views X-ray
thethe
X-ray structures
X-raystructures of
of CODTEX
structures CODTEX (a),
(a), JAGZIA
of CODTEX JAGZIA
(a), (b)
(b) and
JAGZIA (b) TAPYEO
and TAPYEO (c).
(c). Dis-
and TAPYEO Dis-
(c).
tances
tances in
in ÅÅin
Distances .. H-atoms
H-atoms
Å. H-atomsomitted
omitted
omitted for
for clarity.
clarity.
for clarity.
3.3.2.
3.3.2. Carbon as
3.3.2. Carbon
Carbon as Electron
as Electron Donor
Electron Donor
Donor
We
We have
We have found
have found only
found only two
only two structures
two structures
structuresin the
in database
in the
the databaseshowing
database Te···CTe·
showing
showing interactions,
Te·····C which
C interactions,
interactions,
are
which
whichrepresented
are in Figure
are represented
represented in 13, refcodes
in Figure
Figure 13, SIDDAL
13, refcodes
refcodes SIDDAL
SIDDAL [105][106]
and WIXSEB
[106] and
and WIXSEB
WIXSEB [106]. In the
[107].
[107]. In former
In the
the for-
for-
the
merchloro-(2-(1-((2-((4-methoxyphenyl)tellanyl)ethyl)amino)ethyl)phenolato)-palladium(II)
mer the
the chloro-(2-(1-((2-((4-methoxyphenyl)tellanyl)ethyl)amino)ethyl)phenolato)-palla-
chloro-(2-(1-((2-((4-methoxyphenyl)tellanyl)ethyl)amino)ethyl)phenolato)-palla-
forms
dium(II)
dium(II) discrete
forms dimers
forms discretewith
discrete dimers
dimers short
with
with ···
PdshortPd Pd·
short distance
Pd·····Pd (3.203 Å)
Pd distance
distance reinforced
(3.203
(3.203 by shortby
ÅÅ )) reinforced
reinforced byand di-
short
short
and
and directional
directional Te···Cl
Te···Cl contacts
contacts (see(see Figure
Figure 13a)
13a) using
using the
the σ-hole
σ-hole opposite
opposite to to the
the C Aromatic–
CAromatic –
Te
Te bond.
bond. In In addition,
addition, these
these dimers
dimers self-assemble
self-assemble via via the
the formation
formation of of ChBs
ChBs using
using the
the σ-
σ-
hole
hole opposite
opposite the
the C aliphatic–Te
Caliphatic –Te bond
bond where
where the the electron
electron donor
donor C-atom
C-atom belongs belongs to to the
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