Supramolecular Assembly via Hydrogen Bonds II

172 Pages·2004·8.067 MB·English

by  Dario Braga, Lucia Maini, Marco Polito (auth.), D. Michael P. Mingos (eds.)

Structure and Bonding,Vol.111 (2004):1–32
DOI 10.1007/b14139HAPTER 1
Hydrogen Bonding Interactions Between Ions:
A Powerful Tool in Molecular Crystal Engineering
Dario Braga1· Lucia Maini1· Marco Polito1· Fabrizia Grepioni2
1Dipartimento di Chimica G.Ciamician,Università degli Studi di Bologna,Via F.Selmi 2,
40126 Bologna,Italy
E-mail:[email protected]
2Dipartimento di Chimica,Università degli Studi di Sassari,Via Vienna 2,07100 Sassari,Italy
E-mail:[email protected]
Abstract Hydrogen bonding interactions are the strongest ofthe non-covalent interactions and
are highly directional (hence transportable and reproducible).With respect to hydrogen bonds
between neutral molecules the hydrogen bonding interactions between ions (inter-ionic hy-
drogen bonds) respond to additional energetic and topological constrains that depend on the
convolution ofthe proton donor- proton acceptor interactions with the Coulombic field gen-
erated by the presence ofions.Directionality and strength are exploited in the design ofmol-
ecular crystals,hence in molecular crystal engineering strategies.Molecular crystal engineer-
ing is the planning and utilisation ofcrystal-oriented syntheses for the bottom-up construction
offunctional molecular solids from molecules and ions.The success ofcrystal engineering
strategies depends on the availability ofrobust and transferable interactions togluetogether
construction materials.This chapter is devoted to an important subset ofnon-covalent inter-
actions,namely those involving hydrogen bonding and π-stacking interactions between ions.
Some relevant analogies and differences between organic-type intermolecular interactions and
those in which metal atoms are involved will be outlined.Selected examples ofthe utilization
ofinter-ionic hydrogen bonding interactions in crystal reactivity will also be described.
Keywords Hydrogen bond · Ions · Molecular crystal engineering · Crystal synthesis · Gas-solid
reactions
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2 Charge-Assistance:Internal vs External . . . . . . . . . . . . . . . . . 3
3 Data-Mining . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
4 How to Make Weak Hydrogen Bonds Less Weak  . . . . . . . . . . . . 7
5 O-H…O Interactions Between Polycarboxylic Acid Anions
and Zwitterions  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
6 External Charge-Assistance to C-H…O Interactions and to π-Stacking 15
7 How to Use Non-Covalent Interactions Between Ions . . . . . . . . . . 19
8 Hydrogen Bonded Networks Can React or Transform  . . . . . . . . . 22
9 Conclusions  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
10 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
© Springer-Verlag Berlin Heidelberg 2004
2 Dario Braga et al.
1
Introduction
The investigation ofthebonds between moleculesis one ofthe topical issues of
our time [1].It involves all areas ofchemistry,in particular the thriving areas of
supramolecular [2] and materials chemistry [3]. The motivation behind this
broad interest is both scientific and utilitarian.Studies ofintermolecular (or in-
ter-ionic) bonds have great relevance for the fundamental sciences,but are also
promising in terms ofpractical applications.It is recognized that an intelligent
control ofthe recognition and assembly processes that lead from components to
superstructures via tailoring ofintermolecular interactions will allow us to ob-
tain desired collective chemical and physical properties [4].All these ideas also
apply to crystal engineering [5],the area ofsupramolecular chemistry is devoted
to the controlled design ofmolecular crystalline materials.Theparadigmofmol-
ecular crystal engineering can be thus phrased:as non-covalent interactions are
responsible for the existence and functioning ofsupermolecules,it is the convo-
lution of crystal periodicity with intermolecular and/or interionic interactions
that determines topology,energetics and properties ofsolid supermolecules.
On this premise,those interactions thatcombinestrength and directionality
allow a better control ofthe aggregation process.Strength is synonym ofcohe-
sion and stability,while directionality implies topological control and selectivity.
Directionality combined with strength are essential requisites to assemble build-
ing blocks in a desired and stable way.Directionality also implies reproducibil-
ity:only if the topological properties of a given interaction persist in different
structural environments,i.e.on passing from one solid supermolecule to another,
is the interaction useful in the construction of new solids [6].The topological
control can be reinforced by the use ofmultiple directional interactions within
the same molecule [7].
The intermolecular interaction that best combines strength and directional-
ity is the hydrogen bond (HB).The number ofpapers,reviews and books deal-
ing with hydrogen bonds is countless.A recent ISI [8] search of the keywords
“hydrogen bond”in abstracts and titles yielded a count of 15356 and 2794 oc-
currences in abstracts and titles,respectively,in the years 2000–2002.Some recent
review articles or relevant books are listed in [9] but the reader is warned that
new papers and new interesting findings are likely to appear in the literature by
the time this contribution inStructure and Bondingis published.
Because ofthe vastness ofthe subject matter,we shall focus our attention on
hydrogen bonding interactions between ionsand on the possibilities and limita-
tions of their use in the design and construction of molecular materials of de-
sired architectures and/or destined to predetermined functions.Obviously,the
crystal engineer (or supramolecular chemist) needs to know the nature of the
forces s/he is planning to master, since molecular and ionic crystals, even if
constructed with similar building blocks,differ substantially in chemical and
physical properties (solubility,melting points,conductivity,mechanical robust-
ness,etc.).
Since the identification ofbona-fide hydrogen bonds in solid state studies is
often a controversial issue,in particular in the cases involving weak donors [10]
Hydrogen Bonding Interactions Between Ions:A Powerful Tool in Molecular Crystal Engineering 3
or ions [11], we will remain in the following with Linus Pauling’s definition:
“There is a chemical bond between two atoms or groups ofatoms in case that the
forces acting between them are such as to lead to the formation ofan aggregate
with sufficient stability to make it convenient for the chemist to consider it as an
independent molecular species”[12].In Pauling’s approach the existence of a
bond is linked to the energetic stability ofthe aggregate formed as consequence
ofthe bond.This definition was adapted to intermolecular bonding by M.Etter
[13]:“A hydrogen bond is an interaction that directs the association ofa covalently
bound hydrogen atom with one or more other atoms,groups ofatoms,or molecules
into an aggregate structure that is sufficiently stable to make it convenient for the
chemist to consider it as an independent chemical species”.The focus is on the
concept of“directed”association and ofstability,and the existence ofan inter-
molecular bond is conceptually associated to the energetic stability of the ag-
gregate.In terms ofenergy,hydrogen bonding interactions span a large interval,
ranging from tiny energies (few kJ/mol in the case of C-H…O or comparably
weak interactions,see below) [10] to large values when the acceptor is an anion
(more than a hundred kJ/mol in the case ofO-H…O(–) or F-H…F(–) and similar
interactions) [14].Generally speaking,however,the HB interaction is generally
stronger (when not much stronger) than the strongest van der Waals interaction.
For this reason,within X-H…Y HB systems,H…Y and X…Y separations shorter
than van der Waals contact distances and X-H…Y angles that tend to linearity are
considered diagnostic ofthe presence ofstrong HB [9].The X…Y distance cri-
terion is,however,not sufficient when dealing with weak and very weak HB in-
teractions [10].It has been pointed out by Jeffrey and Saenger [9a] that”The use
of a van der Waals distance cut-off criterion carries the wrong implication that
hydrogen bonds become van der Waals interactions at longer distances”and over-
looks the essentially electrostatic nature ofthe interaction.While van der Waals
interactions fall offvery rapidly (r–6),electrostatic interactions follow anr–1de-
pendence (assuming primarily monopole-monopole and monopole-dipole in-
teractions);thus HB can be stabilising at distances much greater than the sum
of van der Waals radii.Furthermore,the distinction between strong and weak
hydrogen bonds is,often,only conventional,and there is a difference between hy-
drogen bonding interactions involving ions and those involving neutral mole-
cules in crystals because ofthe fundamentally different nature ofthe dominant
forces,the differences in physical properties (solubility,melting point,behaviour
under mechanical stress,etc.) arising from the presence ofions or neutral mol-
ecules.
2
Charge-Assistance:Internal vs External
In this chapter,we shall focus on cases where the combination ofionic charges
and non-covalent interactions,especially ofthe hydrogen bonding type,provides
not only a simple means to devise stable architectures but also affords properties
that are a convolution ofthose ofmolecular crystals and ofmolecular salts.In the
case ofhydrogen bonding it is,however,useful to recall in a schematic way how
charges and location ofdonor-acceptor hydrogen bonding systems can be “com-
4 Dario Braga et al.
Table1 The possible combinations ofneutral and ionic proton
donor/proton acceptor systems and the relationship between
internal and external charge assistance
Neutral HB Internal charge Requires external
assistance charge assistance
X-H…Y X-H…Y(–) (–)X-H…Y(–)
(+)X-H…Y (+)X-H…Y(+)
(+)X-H…Y(–)
(–)X-H…Y(+)
X-H…Y(+)
bined”.This is summarised in Table1 [15].The ionic charge in brackets indicates
the charge carried by the whole fragment carrying the HB donor or acceptor
group.
Leaving aside the “null option”,i.e.when both fragments are neutral,we dis-
tinguish between “internal”and “external”charge assistance to the hydrogen
bonding interactions.This discrimination depends on whether the proton ac-
ceptor/proton donor systems carry charges of opposite sign,e.g.(+)X-H…Y(–),
or one of them is neutral (middle column),or charges of the same sign,e.g.
(–)XH…Y(–)and (+)X-H…Y(+) (right column).In the case of“external”charge as-
sistance the stability ofthe hydrogen bonding aggregate towards dissociation will
depend upon the presence ofcounterions.This is the case,for instance,ofchains
ofcations or ofchains ofanions,which would be unstable towards dissociation
in the absence ofcounterions [16] that are need to (over)compensate for the elec-
trostatic repulsions. The implications are quite relevant: (i) even though the
stabilisingcontribution ofthe HB interaction is small,the directionality is fully
a
b
c
d
Fig.1a–d Schematic representation of the relationship between neutral,internally charge-
assisted and externally charge-assisted hydrogen bonds
Hydrogen Bonding Interactions Between Ions:A Powerful Tool in Molecular Crystal Engineering 5
operative and (ii) the common assumption that the intermolecular separation be-
tween atoms or groups ofatoms reflect the strength ofthelocalinteraction is not
directly transferable from neutral to ionic environments [16].The comparison
between neutral HB and inter-ionic HB interactions is schematically represented
in Fig.1.
“Internal”or “external”charge assistance can be successfully used to build pe-
riodical supermolecules based on HB.The utilization ofionic building blocks is,
however,more common in inorganic crystal engineering,where metal atoms give
easy access to charged species.Moreover,the variability ofoxidation states makes
possible the utilization ofthe same building block in both neutral and ionic en-
vironments.
3
Data-Mining
The Cambridge structural database (CSD) [17] is a primary source ofstructural
information validated statistically via the observation ofrecurring behaviours in
large numerical sets ofdata.For this reasondata-miningis yet another power-
ful tool available to the crystal engineer,mainly in the initial steps of project
analysis and architecture design.The identification in a large number ofdiffer-
ent structural environments ofthe sameinteraction,or ofthe same packing mo-
tifassociated with several interactions,guarantees that,when this motifis pur-
posely encoded into a molecular or ionic building block,the chances that it will
lead to the desired supramolecular arrangement are proportional to its frequency
ofoccurrence in different crystal packings.This approach has led to the exten-
sion to the area ofmolecular crystal engineering ofthe concepts ofretrosynthe-
sisand supramolecularsynthons[18] originally developed in the field oforganic
chemistry.Hydrogen bonding functional molecules are thesynthonsofchoice in
many crystal construction strategies [19].By comparing organic and inorganic
supramolecular synthons it has been shown that strong hydrogen bonding
donor/acceptor groups,such as -COOH and -OH systems,as well as primary
-CONH and secondary -CONHR amido groups,form essentially the same type
2
of hydrogen bonding interactions whether as part of organic molecules or as
metal co-ordinated ligands.This is not surprising,since hydrogen bonds formed
by these groups are at least one order ofmagnitude stronger than most non-co-
valent interactions,and are most often already present in solution.In addition to
these strong bonds and to the plethora ofweaker (e.g.C-H…O,C-H…N,C-H…π
etc.) ‘organic’-type hydrogen bonding interactions,the presence ofmetal atoms
in molecular building blocks generatesnewtypes ofinteractions,which are char-
acteristic ofinorganic and organometallic systems.Several research groups are
exploiting hydrogen bonded synthons tocombineco-ordination chemistry and
hydrogen bonding functionalities.Some examples ofthe utilization ofthe CSD
in the evaluation of some cases of neutral vs ionic HB interactions will be dis-
cussed in the following section.
The power of the CSD [17] and,of course,of the ICSD (although this latter
database has yet to develop auser friendlyinterface for data mining) [20] – in the
context ofcrystal engineering – lies in the statistical approach it permits in the
6 Dario Braga et al.
analysis ofcrystal structures,which,in turns,allows the identification ofrecur-
ring synthons.As the number of crystal structures in the databases have in-
creased enormously in the recent past,intermolecular interactions have begun
to be reliably examined.Quite apart from the fact that it is impossible today to
exhaustively peruse the crystallographic literature manually,the sort ofchemi-
calconclusions that a CSD/ICSD analysis permits cannot be obtained fromread-
ingof the journals.Indeed,it is (conservatively) estimated that the number of
entries in the CSD will increase to not less than 500,000 within the first decade
ofthis century.Moreover,both CSD and ICSD can nowadays be utilized on con-
ventional personal computers or on the web,with no need for expensive main-
frame computers.
Thanks to these factorsnewinteractions are being discovered,or re-discov-
ered,almost daily anddata-mining is still one of the preliminary steps of any
crystal engineering project [21].For this reason some cautionary words may be
in order.Very weak interactions,falling in the fluctuations ofthe crystal structure
energetics – those due,for instance,to motions ofatoms or atomic groups – may
be useless in design strategies,because they are too feeble to control crystal con-
struction.It is dangerous to focus exclusively on pairwise interactions,as one may
forget that it is the overall balance ofinteractions,some acting at short range only,
some acting at very long range,that accounts for cohesion in molecular crystals
[22].Only strong pairwise interactions (e.g.O-H…O,but also Cl…Cl,or Au…Au)
may stand out above the noise level and act as true packing directors [23].Preser-
vation or preformation ofrobust intermolecular bonds often leads to molecular
packings that do not correspond to the best van der Waals energy.This is,for in-
stance,the case ofwater and accounts for the absorption ofca.6kJ mol–1upon
melting [24a].This energy is required to break about 10% ofthe O-H…O bonds
from the HB scaffolding ofice,hence determining the lower density ofice with
respect to liquid water.
One further point of concern arises from the customary ‘frozen’picture of
molecules in crystals,and from the consequent ‘frozen’perception ofthe network
ofintermolecular interactions.When a non-rigid molecule or ion is taken from
solution or gas phase into the solid state its geometry is distorted along soft de-
formational paths,and its rotations and vibrations,though restricted,often per-
sist to a very large extent.Large amplitude oscillations and full-scale reorienta-
tional motions are often observed in crystals.The deformation on passing from
vacuum to solid state is particularly dramatic in the case ofsupermolecules held
together by intermolecular interactions;simple examples are the NH :BH Lewis
3 3
acid/base system or the acetic acid dimer CH COOH…CH COOH [24b],where
3 3
the distinction between inter- and intramolecular structures is not so straight-
forward.In these cases the solid state structure ofthe molecular aggregate does
not correspond to the vacuum or solution structure,because the supramolecu-
lar bonding energies are low enough to be significantly perturbed by intermol-
ecular interactions.Distortions and dynamics are obviously significant in the
case of flexible compounds: structural non-rigidity of the building blocks
needs to be taken into account in evaluating the factors responsible for crystal
stability,since molecular and crystal structure may affect each other in an often
unpredictable manner.
Hydrogen Bonding Interactions Between Ions:A Powerful Tool in Molecular Crystal Engineering 7
4
How to Make Weak Hydrogen Bonds Less Weak
For the reasons given in the previous section,one can anticipate that database
searches ofintermolecular interactions that do no discriminate between ionic and
neutral fragments may end up with unreliable (or only partially reliable) results.
The situation ofthe prototype ofstrong hydrogen bonds,namely that between
an O-H donor and an O acceptor in solid protonated or partially deprotonated
polycarboxylic acids,provides an educative example.Figure2 shows the result of
an “acritical”CSD search ofthe O(H)…O distance distribution for all intermol-
ecular interactions satisfying the criterion of O…O separations shorter than
2.80Å.In order to avoid low quality X-ray structures,the R-factor was required
to be <10%.One can see that the mean value for such an interaction (Fig.2,top
histogram) is at 2.632 Å and that the lowest 10% percentile distances being
1
shorter that 2.551Å.When the presence ofan ionic charge is taken into account
and the distribution is split in COOH…COOH (Fig.2,middle histogram),and-
COOH…COO(–)(Fig.2,bottom histogram) one can see that inter-neutral and in-
ter-ionic distances follow different distributions,with shorter separations usually
associated with the latter cases (mean O…O values 2.650 ,2.533 Å and lowest
1 3
10% percentile 2.614, 2.462 Å, respectively). Clearly, neglect of the effect of
charges can lead to untrustworthy conclusions.However,even this analysis is not
entirely correct,as it does not take into account the possibility that the ionic
charge could be localized on a given fragment and not on the entire ion.This is
the case,for instance,ofamino acid molecules in zwitterionic form and will be
discussed later on within this chapter.
The distinction between inter-neutral and inter-ionic interactions is not only
important when dealing with strong interactions,those with a high directional-
ity feature,but also when the interactions are weak or very weak.As an example,
the role ofionic charges on C-H…O interactions between anions and cations has
been investigated [25] by searching the CSD for inter-molecular and inter-ionic
(C)H…O distances (H…O in the range 2.0–3.0 Å,C-H…O angles larger than
110°) for metal bound C-H systems,i.e.neutral systems containing (M)C-H…O
interactions, and charged systems containing [(M)C-H]+…[O]–, respectively,
where M=first row transition metal.
The analysis is statistically sound because C-H…O hydrogen bonds,though
weak,are very numerous in organometallic crystals as a consequence ofthe pop-
ularity of ligands such as arenes and cylopentadienyl ligands which carry a
plethora ofC-H units [26].The analysis shows that interionic C-H…O hydrogen
bond distances follow the order [(M)C-H]+…[O]–<(M)C-H…O (M=first row
transition metal),which is the order ofdecreasingcharge assistanceto the weak
hydrogen bonds (mean H…O values 2.629 ,2.741 Å,and lowest deciles 2.347,
15 12
2.491Å,respectively,see Fig.3).
Further insight on the effect ofcharges on weak bonds has been obtained by
analysing C-H…O interactions involving the cations [PPh ]+and [PPN]+and the
4
anion[BPh ]– and O-acceptors in anionic and cationic transition metal complexes
4
[O ] (see Fig.4).[PPh ]+,[PPN]+and [BPh ]– are amongst the most commonly
M 4 4
used counterions for the crystallization of charged species and are very com-
8 Dario Braga et al.
Fig.2 O…O intermolecular/interionic interactions between COOH and COOH/COO(–)
groups in protonated or partially deprotonated polycarboxylic acids.Top histogram:the dis-
tribution ofO…O interactions obtained without neutral/charge discrimination (mean value
2.632 Å).When the presence ofan ionic charge is taken into account the distributions ofO…O
1
distances are those in the middle [(n)O(H)…O (n) and(n)O(H)…O (–), mean value
COOH COOH
2.650 Å] and in thebottom[(–)O(H) …O (–),mean value 2.533 Å] histograms
1 COO 3
monly used when X-ray suitable crystals of large coordination compounds are
sought.The results are shown in Fig.4.As in the previous case the analysis affords
a rather consistent picture:the H…O distances,in both average and percentile
values,follow the order [(PPh )C-H]+…[O ]–<[(PPN)C-H]+…[O ]–<[(BPh )C-
4 M M 4
H]–…[O ]+ (mean H…O distance 2.700 , 2.723 and 2.756 Å, lowest deciles
M 4 3 9
2.428,2.475 and 2.551Å,respectively) which is the order ofdecreasing electro-
Hydrogen Bonding Interactions Between Ions:A Powerful Tool in Molecular Crystal Engineering 9
Fig.3 CSD intermolecular searches on H…O interactions in (M)C-H…O; and [(M)C-
H]+…[O]–systems [metal bound C-atoms with M=first row transition metal)
Fig.4 CSD intermolecular searches on H…O interactions in [(PPh)C-H]+…[OM]–,[(PPN)C-
4
H]+…[OM]-,[(BPh)C-H]–…[OM]+systems (OM indicates that the oxygen atom belongs to an
4
organometallic or coordination complex)
10 Dario Braga et al.
static reinforcement ofthe C-H…O interaction.The comparison between BPh–
4
and PPh+is particularly educative,since the [(BPh )C-H]–…[O ]+ represents a
4 4 M
situation ofcharge oppositionto the C-H…O bonds and,in fact,this group ofdata
is characterized by average distance values longer also with respect to the neu-
tral sample.In terms ofangularity,all these interactions follow the trend expected
for hydrogen bonds,namely the C-H…O angle opens up as the distance between
donor and acceptor increases.
Another case which has given rise to controversial interpretations is that ofthe
C-H…F interactions.The analysis ofstatistical data has led authors to conclude
that,at least in the case ofC-H…F contacts between neutral organic molecules,
when fluorine is covalently bound to carbon it does not form hydrogen bonds
with conventional hydrogen bond donors,including O-H,N-H and C-H groups
[27].The situation is different in crystals of coordination and organometallic
cationic complexes crystallized with the “very popular”[PF ]– and [BF ]–anions.
6 4
The CSD has been searched for intermolecular H-bonds ofthe (+)C-H…F(–) type
involving the [PF ]– and the [BF ]–anions [28] (data have been updated for this
6 4
work on the basis ofthe April 2002 version ofthe CSD).Since the number ofcom-
pounds containing C-H groups is very large,two separate searches were carried
out.In the first only C-H fragments for which the C atom is directly bound to the
metal atom were considered (561 and 452 hits,for a total of 3972 and 2925 ob-
servations,for [PF ]–and [BF ]–compounds,respectively).In the second one no
6 4
restrictions were applied to the C atom (1354 and 930 hits,for a total of31,639
and 17,057 observations,for [PF ]– and [BF ]– compounds,respectively).Scat-
6 4
tergrams of(Tr)C-H…F angles vs (Tr-C)H…F distances and of(Tr)C-
[PF6]– [PF6]–
H…F angles vs (Tr-C)H…F distances,respectively,are shown in Fig.5.
[BF4]– [BF4]–
Although the number ofhits is different in the two cases,the two types ofinter-
actions follow the normal trend observed for hydrogen bonds,i.e.as the distance
between hydrogen and acceptor atoms decreases,the C-H…F vectors becomes
straighter and the bond approaches linearity. Beside this general behaviour,
there are a large number of bonds that fall below the van der Waals cut-off
distances and are clearly indicative of specific and directional interactions in-
volving donors and acceptors.Comparison ofthe two types ofsearch also show
that there is no appreciable effect ofthe direct bonding to transition metal atoms
on the geometry ofthe interaction,as the two populations have the same distri-
butions.Interestingly,while 10% ofthe contacts fall in the range 2.000–2.391Å
in the case of(Tr-C)H…F interactions,the same percentage ofcontacts falls
[PF6]–
in the narrower range 2.000–2.322 on passing to (Tr-C)H…F interactions.
[BF4]–
This difference may be equally well explained with two hypotheses:(i) the pres-
ence of a large number of short contacts in the case of phosphorus bound to
boron than in the case of phosphorus may reflect the higher polarity of the F-
atom in the formed anion than in the latter (the anion charge is shared by four
vs six fluorine atoms),and (ii) the smaller [BF ]–anion can approach the C-H
4
donors more effectively than the bulkier [PF ]–.
6
All examples discussed above,whether concerning very strong O-H…O hy-
drogen bonds or weak C-H…O and C-H…F interactions,clearly show that a
donor-acceptor distance criterion is an unsafe instrument to check the relevance
ofhydrogen bonding interactions ifthe effect ofionic charges is neglected.