Hydrogen Bond Update by Jeffrey

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Hydrogen-Bonding: An update
George A. Jeffrey
a
a
Department of Crystallography, University of Pittsburgh,
Pittsburgh, PA 15260, USA
Published online: 12 May 2010.
To cite this article: George A. Jeffrey (2003) Hydrogen-Bonding: An update , Crystallography
Reviews, 9:2-3, 135-176, DOI: 10.1080/08893110310001621754
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Crystallography Reviews, AprilSeptember 2003,
Vol. 9, Nos. 23, pp. 135176
HYDROGEN-BONDING: AN UPDATE
GEORGE A. JEFFREY
Department of Crystallography, University of Pittsburgh, Pittsburgh, PA 15260, USA
(Originally received 17 March 1994; In final form 30 March 1994)
This article focusses on the crystallographic research aimed at a better understanding of hydrogen bonds
which has been published since January 1990. In the interest of continuity, earlier work is quoted when it
relates to that published during this period.
Keywords: Bifurcated; Two-, three- and four-centered bonds; Graph sets; and cooperativity; Resonance
assisted hydrogen bonds (RAHB); Proton sponges; CH O bonds; XH bonds; Flip-flop; Tunnelling;
Lost bonds; Clathrates; Molecular recognition
Contents
1 CONCEPTS, DEFINITIONS AND CONFIGURATIONS 136
2 PROGRESS IN METHODS 139
3 NETWORKS, MOTIFS AND COOPERATIVITY 142
3.1 Cooperativity and Resonance Assisted Hydrogen Bonding (RAHB) 144
4 METRICAL PROPERTIES OF OH O, NH O, N H N
AND O H N BONDS
146
4.1 OH O Bonds 146
4.2 NHO Bonds 148
4.3 NH N Bonds 148
4.4 OH N Bonds 149
5 STRONG HYDROGEN BONDS AND PROTON SPONGES 150
6 CH A BONDS 155
7 HYDROGEN-BOND DISORDER; TUNNELLING; FLIP-FLOP;
LOST BONDS
157
ISSN 0889-311X print/ISSN 1476-3508 online 2003 Taylor & Francis Ltd
DOI: 10.1080/08893110310001621754
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8 HYDROGEN BONDS IN INCLUSION COMPOUNDS 159
9 XH p BONDS 162
10 MOLECULAR RECOGNITION AND HYDROGEN BONDING 164
11 MISCELLANEOUS 164
References 165
Subject Index 175
1 CONCEPTS, DEFINITIONS AND CONFIGURATIONS
Concepts and definitions developed from when X-ray crystallographers could not see
hydrogen atoms still persist in some publications, especially those in the field of molecu-
lar biology and protein crystallography where hydrogen atoms are generally still unseen.
The definitions used in this article are given below.
The geometry of a hydrogen-bond XH A involves an X A distance*, which is
a function of an XH covalent bond-length, an H A hydrogen bond length, and
an XH A hydrogen bond angle. As pointed out by Kroon et al. (1975), this angle
is statistically unlikely to be 180
due to the conic correction. When X A distances

had to be used as the criteria for hydrogen bonding in crystals, it was considered
necessary that they be less than the sum of the van der Waals radii. Since the attractive
component of the van der Waals interaction attenuates as r
6
, whereas the attractive
electrostatic component of the hydrogen bond attraction attenuates as r
1
, this concept
was non-sensical. This was made very apparent by the ab-initio (HF-631G*)
calculation by Singh and Kollman (1985) of the potential for the water dimer which
was decomposed into its various components.
In practice, the H A bond lengths in crystals rarely exceed 3.0 A
and the XH A
angles are greater than 90
. The role of the repulsive forces in determining hydrogen

bond geometry in the ices and hydrates was discussed by Savage and Finney (1986)
and by Savage (1986). The same concepts of an excluded region determined by the
repulsive forces will apply to other types of hydrogen bonds. As a consequence
of these repulsive forces, the X A distances tend to remain relatively constant,
while permitting large variations in H A bond lengths and angles, as shown in
Fig. 1. For this reason, hydrogen-bonded O O distances also rarely exceed 3.0 A
.
Clearly hydrogen-bond distances and angles are a much more sensitive criterion of
hydrogen bonding than the O O or N O distances, despite their lower accuracy.
Fortunately NH hydrogen positions can be calculated with reasonable accuracy,
when they are not observed experimentally. This is not true for OH hydrogen
atoms. The precision of hydrogen bond lengths can be improved if the OH or NH
covalent bond lengths are normalized to internuclear (i.e. neutron diffraction) values
(Jeffrey and Lewis, 1978). A very precise X-ray single crystal analysis of Ice I
h
at
243 K by Goto, Hondok and Mae (1990) gave O
1
2
H distances of 0.85(2) and
*Sometimes referred to erroneously as a hydrogen bond length.
136 G.A. JEFFREY
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0.82(3) A
, corresponding to a displacement of 0.15 to 0.18 A
between the electron and

Fermi density peaks (see however, Kuhs and Lehman, 1983).
The terms bifurcated and three-centered, and sometimes bifurcated three-centered,
are used interchangeably in current literature. The term bifurcated was first used in
the X-ray crystal structure analysis of -glycine by Albrecht and Corey (1939)
to describe the configuration I. However, Pimental and McClellan (1960), in the
first text devoted solely to hydrogen bonding, applied the term to configuration II.
This configuration, which only applies to H
2
O and the NH
2
group, is in fact, rarely,
if ever, observed in crystals, except as part of three-center bonds.
FIGURE 1 Distribution of O
w
H O angles versus H O bond lengths in some hydrates of small biolo-
gical molecules. [from Jeffrey (1992b)]
HYDROGEN BONDING 137
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To avoid confusion in terminology, the term three-centered was introduced for I to
describe the hydrogen bonding in carbohydrate crystals by Ceccarelli, Jeffrey and
Taylor (1981) and in amino acid crystals by Jeffrey and Maluszynska (1982) and
Jeffrey and Mitra (1984). It is a requirement that the hydrogen atom is bonded to
three other atoms, one by a covalent bond and two by hydrogen bonds. The hydrogen
atom should therefore lie close to the plane of X, A and A
/
, so the sum of the three
angles about H should be -360
.
This type of bond occurs frequently (70%) in the crystal structures of the
zwitterionic amino acids and is attributed to a proton deficiency, since N
H
3
has
three protons and O=

CC=O prefers to accept four hydrogen bonds. Hence the
analogy with electron deficient three-center bonds in the boron hydrides.
A study of three-center NH
O=C
O=C
bonds in 1509 crystal structures by Taylor,
Kennard and Versichel (1984a, b) found about 20 percent of such bonds.
In the crystal structures of the carbohydrates, nucleosides and nucleotides, purines
and pyrimidines, the proportion of three-center bonds is about 25 percent (Jeffrey
and Saenger, 1991). Neutron diffraction studies of the hydrogen bonding
in -cyclodextrin. EtOH 8H
2
O (Steiner, Mason and Saenger, 1991) and partially deut-
erated -cyclodextrin 17.7D
2
O by Ding et al. (1991) showed that 32 percent of the
hydrogen bonds were three-centered and 4 percent were four-centered. An extension
to protein crystal structures by an analysis of three-center bonds in thirteen high-reso-
lution protein crystal structures is now reported by Preissner, Enger and Saenger
(1991). Of the 4974 hydrogen bonds examined, 24 percent were three-centered.
However of the 620 peptide NH O=C bonds involved in -helix formation, 92
percent are three-centered. The major components are (n 4)NH O=C(n) bonds
of the 3.6
13
helix and the minor components are (n 4)NH O=C(n 1) bonds in
the 3
10
helical distortions at the C-termini of the -helices. In the -sheets, 40 percent
of the bonds are three-centered. The majority of three-center bonds are asymmetrical,
with the major components having H O bond lengths from 1.6 to 2.9 A
, with angles
175 to 90
. The distribution of these bond lengths rises at 1.8 A
with a peak at 2.1 A
,
dropping slowly to 2.6 A
. The minor components have bond lengths from 2.05 to

3.0 A
with angles 175 to 90
, with a maximum in the distribution of a H A distance

of 2.8 A
. In the earlier analysis of hydrogen bonding in protein structures by Baker

and Hubbard (1984), XH A angles from 180 to 90
were considered, but the

H O cut-off was at 2.5 A
. This would result in 80 percent of the three-center bonds

in the -helices being identified as two-center. As pointed out by Preissner, Enger
and Saenger (1991), this is an aspect of hydrogen-bonding that is often inadequately
considered in the computer programs that seek to investigate hydrogen-bonding in pro-
tein structures. A study of three-center bonding in a DNA model by molecular
dynamics using AMBER concluded that they occurred frequently but were a conse-
quence of the polymer geometry rather than structure determining (Fritsch and
Westhoff, 1991). The role of bifurcated, i.e. three-centered, hydrogen bonds in stabiliz-
ing non-planar amino groups in DNA bases is examined by ab-initio molecular orbital
calculations at the HF/6-31G*, MP2/6-31G* levels by Sponer and Hobza (1994).
A few configurations were observed in which the hydrogen atom has four acceptor
atoms within 3.0 A
in the forward direction of the XH bonds, i.e. XH A_90
.
There four-center bonds are relatively rare, occurring in the various recent metrical
surveys referred to later in this text at less than 4 percent.
138 G.A. JEFFREY
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Other configurations that have been observed, albeit rarely, are III and IV, and the
three and four-center bifurcated combinations V, VI and VII observed in the hydrates
of small biological molecules by Jeffrey and Maluszynska (1990) and by Steiner and
Saenger (1993a)
2 PROGRESS IN METHODS
Single crystal analysis by neutron diffraction is the experimental method par excellence
for studying the structural aspects of hydrogen bonding in crystals, since it provides
hydrogen positions with a precision comparable to that of the non-hydrogen atoms
together with their anisotropic thermal ellipsoids. In addition, any temperatures
down to 10 K are relatively easily accessible, permitting corrections for thermal
libration and anharmonic motion (Jeffrey, 1992a). There has, however, been a decline
in the number of single-crystal neutron diffraction studies in recent years due to a
regretable hiatus in the availability of suitable steady-state neutron sources. The
future availability of more powerful neutron sources should reduce the limitation
of crystal size, which has been a significant deterent to the location of hydrogen
atoms in complex biological structures. Spallation neutron sources are socially more
acceptable, but the potential of pulsed neutron powder diffraction studies of hydrogen
bonding for other than simple structures is uncertain.
The precision of data from X-ray diffractometers and area detectors has improved
and low-temperature single-crystal X-ray analysis with liquid nitrogen has become a
more common practice. In consequence, hydrogen atom coordinates with isotropic
temperature factors are reported regularly, with an accuracy about ten times less
than for the non-hydrogen atoms. The reporting of hydrogen-bond geometry in crystal
structure analyses often leaves something to be desired. The practice of reporting
hydrogen-bond lengths and angles with respect to a single molecule (symmetry 1,
xyz) is equivalent to describing the structure of a molecule by the distances and
angles relative to a single pair of atoms. The information is there, but the structural
chemistry (i.e. configuration and conformation) is not obvious. The importance of
the hydrogen-bond networks, discussed later, requires more attention to this feature
in those crystal structures where the cohesive forces between the molecule are primarily
hydrogen bonds.
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The charge-density studies on the crystal structure of formamide by Stevens (1978),
and oxalic acid dihydrate by Krijn and Feil (1988) demonstrated the expected displace-
ment of the hydrogen or deuterium electron density from the Fermi nuclear density in
the NH O=C and OH O
w
hydrogen bonds, giving rise to a dipole of the order of
1 Debye at the end of the XH bond (Craven, 1987). Disengaging the effects of thermal
motion is an undesirable complication in charge density analysis, especially since the
temperature factors from X-ray and neutron analyses at the same temperature have
a tendency to disagree. Few laboratories have yet to develop equipment for collecting
high precision X-ray data down to liquid helium temperatures to match the neutron
diffraction data at that temperature. An exception is the recent analysis of oxalic
acid dihydrate and acetamide at 15 and 23 K by Zobel et al. (1992) which provided
high quality X-ray data to complement the neutron diffraction data of Coppens and
Sabine (1969) and Jeffrey et al. (1980). For acetamide at 23 K, the number of unique
intensites measured and the intensity gain for high order reflections were about four
times greater than that from the room temperature analysis.
More recent precision electron density studies have focussed on the general
electrostatic properties of molecules (Craven and Stewart, 1990). The electrostatic
potential of a molecule, or a group of molecules, which can be derived from an accurate
charge-density distribution (Stewart, 1991), is now considered by some investigators to
be more informative and useful than the deformation density plots. A mathematical
procedure is described whereby the charge parameters of a pseudoatom model can
be used to map the electrostatic potential and show the polarizing effect of hydrogen
bonding, as demonstrated in the crystal structure of -aminobutyric acid (Stewart
and Craven, 1993).
The use of solid-state NMR, particularly C
13
cross-polarization magic-angle
spinning (CP/MAS) was reviewed in this journal by Etter, Hoye and Vojta (1988).
As pointed out in that article, the method is indeed complementary to that of crystal
structure analysis. The identification of three isomeric forms of the disaccharide lactu-
lose in the ratio 0.745 : 0.100 : 0.155 by Jeffrey et al. (1983) prompted the suggestion that
this method of analysis should be applied routinely, whenever there is the possibility of
a molecular mixture in the crystallization solution. It can also be a useful diagnostic
tool when anomalies are observed in the anisotropic thermal motion parameters
from a crystal structure analysis and for recognizing co-crystallization of different
molecules.
Although NMR
l
H chemical shifts are very sensitive to hydrogen bonding in
the solid-state (Berglund and Vaughan, 1980; Jeffrey and Yeon, 1986), there
has been relatively little recent work using this observation which relates specifically
to hydrogen bonds. In molecules with many COH groups such as carbohydrates,
differences in the
13
C isotropic chemical shifts in the crystals and in solution can be
an indication of crystal field and solvation effects (Sastry, Takegoshi and McDowell
1987). The strong OH F hydrogen bond in the complex KF (CH
2
COOH)
2
was
studied by a neutron crystal structure analysis and F solid-state NMR (Mortimer
et al. 1992). Etter, Reutzel and Vojta (1990) measured the isotropic chemical shift for
a number of hydrogen-bonded organic crystals. A study of the short hydrogen bonds
in the salts of the dicarboxylic acids by Karlsbeck, Schaumburg and Larsen (1993)
used
13
C and
2
HNMR spectroscopy.
The interesting application of solid-state NMR to single crystals to display
(by ORTEP) the anisotropic chemical shift tensors, as exemplified by the studies of
140 G.A. JEFFREY
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L-asparagine monohydrate (Naito and McDowell, 1984) and methyl -D-glucopyrano-
side (Sastry, Takegoshi and McDowell, 1987) does not seem to have been continued.
Possibly this is because it requires large crystals (cm rather than mm), the combined
skills of a crystallographer and an NMR spectroscopist, and much patience to use a
manual single-crystal NMR spectrometer.
Infrared spectroscopy preceded crystallography as a method for studying hydrogen
bonds (cf. Pimental and McClellan, 1960; Hadzi and Bratos, 1976) and solid state
FT-IR spectroscopy is a major method which often complements X-ray crystal
structure analysis, for examples in the work of Kanters et al. (1992a) on calixarenes
and of Harman, Southworth and Harman (1993) on the tetraethylammonium fluoride
hydrates.
The computer accessibility of the Cambridge Crystallographic Data Base has
made the survey of the structural features of particular types of hydrogen bonding
very convenient (Allen, Kennard and Taylor, 1983; Taylor and Kennard, 1984).
Although this method of evaluating the strength of hydrogen bonds from experimental
data has been criticized by Bu rgi and Dunitz (1988), most investigators consider
that if it is derived from homogeneous classes of molecules, it can provide reliable
qualitative information about hydrogen-bond strengths in crystals that is not readily
available from other sources.
Ab-initio quantum mechanics has now reached a level of sophistication that the
equilibrium structures of many hydrogen-bonded dimers or trimers can be calculated
(cf. Del Bene, 1988; Del Bene and Shavitt, 1991; Ha, Makenewitz and Baudes, 1993).
In fact, this is probably now a more precise method for obtaining data on the hydrogen-
bond geometries and energies for gas-phase hydrogen-bonding than that by experiment.
The water dimer is a popular guinea-pig for testing the finer details of ab-initio MO
theory, such as effects of basis-set deficiency, correlation, basis-set superposition, etc.
(cf Kroon-Batenburg and van Duijneveldt, 1985; Saeba, Tong and Pulay, 1992).
It must be frustrating for the proponents of this art that the cancellation of errors
is such that the more approximate calculations frequently seem to provide results
that agree better with experiment. The extensive use of acronyms makes this field
difficult for the non-specialist to understand, but the impression is that theory now
gives results within the experimental error bars for the distances and angles involved,
when appropriate corrections are made for the effects of anharmonicity (i.e. O O=
2.976 0.006 A
in the water dimer). Because the potential energy surface is so flat,

there seems to be less certainty about the actual location of the hydrogen-bonding
hydrogen atom.
Semi-empirical methods are generally not very satisfactory for predicting hydrogen
bond geometries and energies. However, good agreement with experiment has been
obtained using a modified MNDO method when applied to a number of structures
with short intramolecular OH O bonds (Rodr guez, 1994).
There have been many calculations of the equilibrium geometries of other hydrogen-
bonding dimers which are published in a variety of journals. The number is such
that a computerized data base for them would now be useful to the non-specialists in
this field, including the crystallographer, who might like to systematically compare
hydrogen bonding in the gas-phase with that in a crystal (i.e. to study the crystal
shrinking effect).
The theoretical treatment of hydrogen bonding is implicit in the empirical force fields
used in molecular mechanics or molecular dynamics which are becoming increasingly
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popular for predicting the structures of large molecules, such as oligonucleotides,
peptides, saccharides, proteins and nucleic acids, and for predicting molecular
interactions and solvation effects. The Allinger molecular mechanics programs
(MMn) use dipole-dipole interactions but other methods, including the popular
molecular dynamics programs CHARMM and GROMOS, rely on charges on the
donor and acceptor atoms. Calculations on carbohydrate structures are especially
sensitive to the treatment of hydrogen bonding because of the high ratio of
hydrogen-bonding groups in these molecules. They therefore provide excellent tests
for the credibility of molecular mechanics and dynamics simulations (cf. van Eijck,
Kroon-Batenburg and Kroon, 1990; Koehler, 1991; French and Miller, 1994).
When these methods are applied to the same or similar carbohydrate problems they
do not always give the same result. For example, the simulation of the structure
of -D-glucopyranose in water using CHARMM by Brady (1989) gave results which
differed from those on -D-glucopyranose in water by van Eijck, Kroon-Batenburg
and Kroon (1990), by more than would be expected from the difference between the
two anomers.
Various site models and different hydrogen-bond potentials for liquid water and
liquid methanol were tested against molar volume, heat of vaporization and the neutron
weighted radial distribution curves using the molecular dynamics program GROMOS
(Stouten and Kroon, 1988; Stouten, van Eijck and Kroon, 1991). Reasonable agreement
was obtained. All gave O O distance distributions between 2.5 and 3.5 A
with maxima
at 2.75 A
. A study of the structure and dynamics of Ice I

h
by means of molecular
dynamics is reported by Sciortino and Corongiu (1993).
Theoretical calculations on isolated molecules containing near neighbouring donor
and acceptor groups will predict intramolecular hydrogen bonding which is not present
in the crystal or in aqueous solution. In carbohydrates, for example, the CCOH
torsion angles had to be fixed at crystal structure angles to prevent intramolecular
hydrogen bonding in some early molecular mechanics calculations (Jeffrey and
Taylor, 1980). This problem is now overcome to some degree by using molecular
mechanics to predict carbohydrate structures and hydrogen bonding in the presence
of water molecules (e.g. Kroon-Batenburg and Kanters, 1983), or by constructing
mini-crystals (e.g. French, Miller and Aabloo, 1993), or by simulating solvent effects
by molecular dynamics (van Eijck, Kroon-Batenburg and Kroon, 1990). For carbohy-
drates where the ratio of hydrogen-bonding donors and acceptors is equal to the
number of carbon atoms (C
n
(H
2
O)
n
), satisfactory solutions are still being sought (cf.
Kounijzen et al., 1993; Bouke et al., 1993; Grootenhuis and Haasnoot, 1993; French
and Miller, 1994). For nucleic acids and proteins and their components where the
ratio of hydrogen-bonding functional groups to van der Waals interactions is less,
the problem of simulation should be less severe, since the van der Waals potential is
better understood. However, although there has been much more research, the results
seem to be similar with some successes and some failures (Teeter, 1991).
3 NETWORKS, MOTIFS AND COOPERATIVITY
In deriving a graph-set approach to rationalizing hydrogen bonding, Etter (1990)
defined a network as a subset of an array of molecules in which each molecule
is connected to another by at least one hydrogen-bonded pathway. A motif is then a
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network in which there is only one type of hydrogen bond. Hydrogen-bonding motifs
are familiar concepts in the ices and the clathrate hydrates, since the water molecules
are linked only by O
w
H O
w
bonds. The chains and loops which occur in carbohy-
drates and carbohydrate hydrates are, by this definition, networks, since the molecules
are linked by combinations of OH and O
w
H as donors, and OH, O
w
H, and O as
acceptors (Jeffrey, 1992b).
Cooperativity or non-additivity, occurs when the hydrogen-bond energy of a network
or motif is greater than the sum of the energy of the individual hydrogen bonds:
E(H A)
n
>
n
E(H A):
Two types of cooperativity have been recognized: -cooperativity, where the hydrogen
bonds are linked by covalent OH bonds, and -cooperativity or Resonance Assisted
Hydrogen Bonding* (RAHB), where the hydrogen bonds are linked by both XH
bonds and multiple C
::::
N or C
::::
O covalent bonds (Gilli et al., 1989).
The graph theory method of describing hydrogen bond networks uses captial letters
(S, C, R, D) to distinguish between inter- and intramolecular bonds and whether they
form finite or infinite chains or rings (S =intramolecular; C=infinite chains; R=rings;
D=non-cyclic dimers and finite chains). Numerical super and subscripts give the
number of different kinds of donors and acceptors. A parameter in parentheses (r)
gives the number of atoms in the ring or the repeat length of the chain including
covalent bonds. This procedure identifies hydrogen bonding as a distinct configuration.
For example, the Watson-Crick bonding VIII is R
2
2
(8)O
4
, whereas the Hoogsteen
bonding IX is R
2
2
(9)O
4
(Etter, Mac Donald and Bernstein, 1990). More complex net-
works may require several sets of symbols, i.e. first, second and third order, and for
complex networks the choice may not be unique.
Hitherto the application of graph set analysis has been relatively limited (Bernstein,
1991; Bernstein and Shimoni, 1993). Clearly a wider application would be very useful
for identifying common components of networks or motifs in crystal structures of mol-
ecules which are chemically unrelated. This would be especially so if this information
were included where appropriate, in a sub-set of the Cambridge Crystallographic
Data Base. The recognition of common hydrogen-bonding preferences is impor-
tant since it can be used to design complexes with special properties and predictable
*By analogy, -cooperativity could be called Polarization Assisted Hydrogen Bonding; in both cases
Enhanced would be a better word than Assisted.
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symmetry by co-crystallization (Etter and Frankenbach, 1989). It could play a role in
predicting the molecular recognition discussed later.
For the carbohydrates, carbohydrate hydrates, including the cyclodextrins, the
majority of the hydrogen-bond functional groups, OH, O
w
H, are both donors and
acceptors. The networks are formed by finite chains, infinite chains and rings. When
ring or glycosidic oxygens are included, they act as chain stoppers (Jeffrey and Mitra,
1983). In the hydrates, the dual acceptor/donor functionality of the water molecules
links the chains to form three-dimensional nets, or when single acceptor/double
donor, branched chains (Jeffrey, 1992b). These hydrogen-bond structures can therefore
be described by means of connectivity diagrams which link the sequences of OH and
H O hydrogen bonds. These diagrams of the hydrogen-bond structure are equivalent
to the configurational diagrams of structural chemistry.
Both the graph theory and the connectivity diagrams have the disadvantage that
they do not display the conformation of the hydrogen-bond structure that is
provided by stereoviews or computer graphics. However, the bond lengths, bond
angles and symmetry operations can be applied to make the connectivity diagrams
more informational. This information is lost in the graph-theory approach, where the
symbolism is one step further removed from the three-dimensional structure.
3.1 Cooperativity and Resonance Assisted Hydrogen Bonding (RAHB)
Neither -cooperativity nor RAHB are new concepts. The -cooperativity or non-
additivity property of the hydrogen bonding in water was known conceptually for
more than thirty years (Kavenau, 1964) and quantitatively from the early ab-initio
calculations on water trimers by Hankins, Moskowitz and Stillinger (1970) and by
Del Bene and Pople (1970) on cyclic water polymers. The energetic advantage of
sequential OH OH OH hydrogen bonding indicated by these early calcu-
lations led to the distinction between homodromic, antidromic and heterodromic descrip-
tors to describe the cyclic patterns of hydrogen bonds observed in the cyclodextrin
hydrates (Saenger, 1979; Koehler, Lesyng and Saenger, 1987; Lesyng and Saenger,
1981). An analysis of the effect of cooperativity on the H O bond lengths from neu-
tron diffraction studies of carbohydrates, mostly monosaccharides, by Ceccarelli,
Jeffrey and Taylor (1981) showed that the bonds in chains were about 0.07 A
shorter
than isolated bonds. A barely significant shortening of 0.01 A
in the covalent OH
bond lengths has been detected by Steiner and Saenger (1992a) from low-temperature
neutron diffraction data from two deuterated -cyclodextrin hydrates (-CD.11.6D
2
O
at 120 K; -CD.EtOD 8H
2
O at 12 K). They find a linear correlation from OH, H O
0.985, 1.70 A
to 0.96, 2.1 A
. They also observed a shortening of OH bond lengths as a

result of three-center bonding.
RAHB was apparent from the effect of dimer hydrogen bonding on the carboxylic
acid bond lengths of formic, acetic and propronic acids studied by gas diffraction by
Almenninger, Bastiansen and Motzfeld (1969) and Derissen (1971). Ab-initio calcula-
tions on the monomers and hydrogen-bonded dimer of formamide predicted the
effect of hydrogen bonding in shortening the length of the CN bond (by 0.023 A
)
and lengthening the C=O bond (by 0.018 A
) (Jeffrey et al., 1981). Similarly the dimer

and chain-type of hydrogen bonding observed in the crystal structures of both
carboxylic acids (X) and oximes (XI) are accompanied by significant increase in the
144 G.A. JEFFREY
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character of the adjacent CO and CN bond lengths (Bachechi and Zambonelli,
1972, 1973; Brahm and Watson, 1972 and references therein).
The descriptor RAHB has now been applied to this effect in some carboxylic acid
oximes containing the chain XII or cyclic configuration XIII (Padmanabhan, Paul
and Curtin, 1989; Maurin, Paul and Curtin, 1992a, b, 1994; Maurin et al., 1993;
Maurin, Winnicka-Maurin and Les, 1993).
An interesting study of the RAHB effect of electron supplying and withdrawing
substituents on the intramolecular hydrogen bond in malonaldehyde has been studied
by ab-initio molecular orbital theory at the 3-21G level by Rios and Rodriguez (1991).
It was the neutron diffraction studies of the monosaccharides by Jeffrey and Takagi
(1978) and of the cyclodextrins by Saenger and co-workers (KIar, Hingerty and
Saenger, 1980) that generalized -cooperativity from water to carbohydrate structures.
Similarly it was the work of Gilli et al. (1989; 1993a) on hydrogen bonding involving the
O=CC=COH moiety in -diketones which led to the introduction of the term
RAHB. More recently, this concept has been extended to the hydrogen bonding
between molecules containing O=CC=CNH and O=CC=NNH moieties
(Ferretti et al., 1993). Whereas the -cooperativity involves the polarization of
the relatively weak and essentially electrostatic hydrogen-bond interactions, the
or RAHB cooperativity occurs with strong hydrogen bonds and is considered
by Gilli et al. (1989, 1993a, 1993b) to involve a significant covalent, i.e. exchange,
component.
-cooperativity is important in the hydrogen bonding in carbohydrates and hydrates,
including the ices. RAHB or -cooperativity plays an important role in the structure of
proteins and nucleic acids, not only by strengthening the hydrogen bonds but also by
increasing the -bonding component and hence the torsional rigidity of the peptide
CN bonds.
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4 METRICAL PROPERTIES OF OH O, NH O, NH N
AND OH N BONDS
4.1 OH O Bonds
The relative abundance of both neutron and X-ray diffration studies from carbohy-
drates, oxyacids and their salts and hydrates has made the OH O bond the most
studied of all hydrogen bonds. The H O bond lengths range from the short symme-
trical almost linear bonds of 1.215 to 1.230 A
to the minor components of three-center

bonds in the range of 2.0 to 3.0 A
, with OH O angles approaching 90
(Jeffrey and
Saenger, 1991; Jeffrey, 1992b). A further study by Steiner and Saenger (1992b) of O
H O bonds in carbohydrates has extended the limits of enquiry to H O<5.0 A
and angles from 0 to 180
. The data set contained 110 hydroxyl, 53 ether oxygens

and 16 water molecules, from 17 neutron diffraction crystals structures, including
two high-resolution studies of hydrated cyclodextrin structures. Partially occupied
or orientationally disordered donor or acceptor groups were excluded and there were
no corrections for the thermal motion of the hydrogen atoms. The plot of H O vs
O
b
HH O to 5.0 A
and 90
irrespective of hydrogen-bond formation is shown in Fig.

2. There are six regions: (1) is the two-center and major components of three-center
bonds; (2) is the minor components of three-center and a few four-center bonds; (3)
is non-bonding second neighbours; (4) a random scatter of non-bonding second neigh-
bours; (5) a sparcely populated region of nearly linear stretched bonds; (6) the region
FIGURE 2 Scatterplot of OH O angles versus H O bond lengths for hydroxyl and water donors in
carbohydrate crystal structures.
(1) two-center and major component of three-center bonds.
(2) minor components of three- (and four-) center bonds.
(3) non-bonding next neighbours.
(4) non-bonding second-next neighbours.
(5) near-linear stretched bonds.
(6) excluded region due to repulsive forces. [from Steiner and Saenger (1992b), with permission.]
146 G.A. JEFFREY
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excluded by O O repulsions (Savage and Finney, 1986). Note that regions (1) and (3),
bonding and non-bonding with the same O O distances, cannot be distinguished with-
out knowledge of the positions of the hydrogen atoms, (i.e. OH O angles 90
)) whence
lies the confusion from relying on, and reporting only, O O separations to identify
hydrogen bonds. It is one of the reasons why it is so difficult to identify hydrogen-bond-
ing networks in the bound water of protein crystals.
Water molecules have less crystal packing constraints than larger molecules
where compromises have to be made to minimize the sum of the energies of both
hydrogen-bond and van der Waals interactions. The OH O vs H O plot, Fig. 3,
for hydroxyl and water donors only, although less populated, showed the same
features, except that there were no stretched bonds. It would have been interesting
to compare the plots for water donors and acceptors separately, since bond length
considerations suggest that water molecules are stronger acceptors than they are
donors (Jeffrey and Saenger, 1991). In two further studies, the correlation
between OH, H O, O O distances and OH O angles was made using only
high precision low-temperature neutron diffraction analysis. One, by Steiner
and Saenger (1992a), was based on the data from two deuterium substituted
-cyclodextrin complexes, -CD, 11.6D
2
O (Zabel, Saenger and Mason, 1986), and -
CD EtOH 8D
2
O (Steiner, Mason and Saenger, 1990). The other, by Steiner and
Saenger (1993a), was of a wide variety of molecules and included both charged and
uncharged OH O bonds.
The cyclodextrin-based paper by Steiner and Saenger (1992a) focussed on the
variation in length of the covalent OH bonds and the effect of three-center and
cooperative hydrogen bonding. The paper by Steiner and Saenger (1993a) based on
the 23 more general crystal structures examined the correlations between OH,
FIGURE 3 Scatterplot OH O angles with versus O O distances for hydroxyl and water donors in
carbohydrate crystal structures. Numbered regions as in Fig. 2. [from Steiner and Saenger (1992b), with
permission.]
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H O, O O distances and angles. In both papers, the use of low temperatures (15 K
or 120 K) reduced the uncertainties in OH bond lengths due to thermal motion. The
lower-bound and riding-motion models of Busing and Levy (1964) were used for the
cyclodextrin data. The corrections were small, with a mean shift of 0.015 A
for
the riding-motion model. No corrections were made for anharmonic motion, which
tends to compensate for the harmonic correction at low temperatures (Jeffrey,
1992a). With these corrections, the plot of OD vs D O showed a decrease of OD
from 0.99 to 0.965 A
with H O from 1.70 to 2.15 A
. There was evidence of a small

effect of cooperativity on the covalent OD bond lengths resulting in a lengthening
of about 0.01 A
.
In the more general paper by Steiner and Saenger (1993a), the small corrections for
thermal motion were not included. Plots of OH vs H O extended from 1.19 to 0.95 A
and 1.20 to 2.21 A
respectively. They were smoother than previously reported (Jeffrey

and Saenger, 1991), especially for the shorter bond lengths. No dependency of covalent
OH bond length on OH O bond angle was detected. No significant differences due
to deuteration were observed.
4.2 NHO Bonds
The NH O bonds include the important NH O=C polypeptide bond.
Unfortunately, there has been no update of the very general survey of 1509
NH O=C bonds in 889 crystal structures made by Taylor, Kennard and Versichel
(1984b). This survey used a limit of H O<2.4 A
, which is more restrictive than that

currently used. It was possible to distinguish between donors ranging from R
3
NH
3
to NH and acceptors from O=
CC=O to O=C
C
C
, with mean hydrogen bond lengths
for each of the 24 different combinations from 1.72 to 1.99 A
. The donor and acceptor

properties of NH and O=C groups in 15 protein structures were reported by Baker
and Hubbard (1984). Since NH hydrogen positions can be calculated from
the adjacent bonded atoms, a new metrical study taking into account
the three-center bonding described by Preissner, Enger and Saenger (1991) should be
possible.
Surveys of NH O bonds generally were made from the crystal structures
of nucleosides and nucleotides by Jeffrey, Maluszynska and Mitra (1985) and in
barbiturates, purines and pyrimidines by Jeffrey and Maluszynska (1986). The majority
of these structures were room-temperature X-ray analyses and few were high precision.
The analyses covered N
H
3
or N
H
4
, N
H, NH, N(H)H as donors of decreasing

strength, and O=
PP, HO
w
H, O=
CC, O
C
H
and O
C
C
as acceptors with decreasing
strength. The range of H O bond lengths was 1.58 to 2.59 A
. There are still insuffi-

cient neutron diffraction or high precision low-temperature X-ray analyses to refine
these results as was done for the OH O bonds.
4.3 NH N Bonds
Surveys of the geometry of NH N with NH and NH
2
and donors, N as
acceptors and OH N bonds have been reported by Llamas-Saiz and Foces-
Foces (1990) and by Llamas-Saiz et al. (1992). The former used the Cambridge Data
148 G.A. JEFFREY
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Base to obtain 307 bonds, with a cut-off at N N<3.2 A
and NH N>140
.
The angle constraint will exclude the minor components of three-center bonds, corre-
sponding to the equivalent of region (2) in Fig. 2. For the NH O bonds, there
were 304 NH OH and 120 NH O
w
. The constraints were N O<3.1 A
and
NH O>140
, again excluding the minor components of three-center bonds.

The ranges of H N and H O distances are given in Table I and compared with the
values reported by Jeffrey (1989) from the crystal structures of purines and pyrimidines
(P & P) which provided 773 bonds and from the nucleosides and nucleotides
(N & N) which provided 710 bonds. The agreement was as good as might be expected
in view of the different types of molecules involved.
4.4 OH N Bonds
A survey of the geometry of OH N and O
w
H N has been reported by Llamas-
Saiz et al. (1992), based on the Cambridge Structural Data Base of January 1990. All
classes of compounds were included except for those containing metals. The data
were restricted to O N distances less than 3.1 A
and OH N angles greater than

140
. Therefore the minor components of three-center bonds with H N>201 A
and
OH N angles less then 140
were excluded from the survey. 304 OH N bonds

and 120 O
w
-H bonds were included. Using normalized OH bond lengths (0.97 A
for
OH, 0.96 A
for O
w
H), the mean, minimum and maximum values for the H N
bond lengths and OH N angles are given in Table I. These are compared with
values from the crystal structures of nucleosides and nucleotides by Jeffrey (1989).
Although the mean values are in reasonable agreement, the ranges differ significantly,
illustrating the danger of extending statistical analyses outside particular classes of clo-
sely related molecules.
TABLE I Comparison of NH N and NH O hydrogen bond lengths from two independent surveys
a
From Llamas-Diaz
and Foces-Foces
(1990)
P&P
2-center and
components of 3-center
Jeffrey (1989)
N and N
2-center and
components of 3-center
Jeffrey (1989)
RNH
2
N
H N (A
) mean 2.06 2.02

b
2.13
min 1.83 1.85 1.89
max 2.30 2.28 2.76
NH N
H N (A
) mean 1.96 1.93

c
1.88
min 1.75 1.73 1.78
max 2.32 2.23 1.99
COH N
H N (A
) mean 1.87 1.83 1.89

min 1.59 1.71 1.77
max 2.18 2.01 2.62
O
w
H N
H N (A
) mean 1.96 1.99

d
1.94
min 1.76 1.78 1.85
max 2.19 2.84 2.16
a
All NH bonds normalized.
b
Excluding three 3-center bonds with NH N<140
.
c
Excluding one 3-center bonds with NH N<140
.
d
Excluding one 3-center bonds with O
w
H N<140
. Including one major component of 3-center bond =2.84 A
.
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Attention has also been directed to the orientational properties of hydrogen bond
acceptor groups. Earlier studies examined the acceptor properties of C=O and O
C
C
oxygen atoms and found a broad spread of acceptor angles (Taylor, Kennard and
Versichel, 1983; Murray-Rust and Glusker, 1984). The study of the stereochemistry
of water molecules in the hydrates of small biological molecules by Jeffrey and
Maluszynska (1990) showed that single acceptor water oxygen atoms had coordinations
ranging from pyramidal to planar with no sharp demarcation. These analyses did not
consider CH O
w
bonds, which greatly reduce the number of three-coordinated
waters. Even when a CH hydrogen bond does complete the tetrahedral coordination,
it can be very distorted (Steiner and Saenger, 1993c).
A study of the nitrogen acceptor angles in OH N(sp
2
) hydrogen bonds
with O N<31 A
and OH N>140
(Llamas-Saiz et al., 1992) showed a broad

distribution of acceptor angles with the majority within 30
of the sp
2
lone-pair
axis. The distance and angle cut-off eliminated the consideration of the minor compon-
ents of three-center bonds. A comparison was made with the results from ab-initio HF/
3.21 G calculations for 72 pyridine-water hydrogen-bond interactions.
5 STRONG HYDROGEN BONDS AND PROTON SPONGES
Strong hydrogen bonds have characteristic physical properties which distinguish
them from normal or weak hydrogen bonds (Emsley, 1980). They have been studied
by crystal structure analysis since the beginnings of single crystal neutron diffraction.
Ellison and Levy (1965) reported a strong symmetrical O H

OO bond in potassium
hydrogen chloromaleate with O H bond lengths of 1.1999(5) and 1.206(5) A
. The
short O H

OO bond in the anion of imidazolium maleate (James and Matsushima,
1976) was studied by neutron diffraction leading to an XN deformation density analy-
sis by Hsu and Schlemper (1980). Their results supported the suggestion of a single
minimum hydrogen-bond potential made earlier from the IR spectra by Cardwell,
Dunitz and Orgel (1953).
However the other strong O H

OO hydrogen bonds in organic anions have been
shown by neutron diffraction analysis to be unsymmetrical or have double minima
across a center or two-fold axis of symmetry. These were distinguished as
symmetry-free by Olovsson, Olovsson and Lehman (1984), and type A, symmetry-
restricted by Currie and Speakman (1970), Catti and Ferraris (1976); see Tables 7.2
and 7.3 in Jeffrey and Saenger (1991).
More recent examples of short intramolecular O H

OO bonds are found in a neu-
tron diffraction study of hydrogen-bonded dimers in K
5
[H{ON(SO
3
)
2
}
2
]H
2
O by
Robertson et al. (1988) and in the anions of caronic acid (3,3-dimethylcyclopropane
1,2-dicarboxylic acid). The acid crystallizes in cis and trans forms with the usual
carboxylic acid dimer hydrogen bonding with H O bond lengths 1.7 A
(Jessen,
1992). In the ammonium and potassium hydrogen salts, the anions, XIV, have strong
asymmetrical intramolecular O H

OO bonds with H O and OH bond lengths of
1.47(6), 1.01(6) and 1.35(4), 1.08(4) A
respectively (Ku ppers and Jessen, 1993).

Strong intramolecular OH O bonds are also formed in the absence of deprotoni-
zation when the oxygen atoms are constrained to short distances due to the molecular
configuration, as in the -diketo-enols (XV). The crystal structures of two of these
150 G.A. JEFFREY
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compounds were studied by X-ray and neutron diffraction analyses by Jones (1976a, b),
and Bertolasi et al. (1991) have added eight more X-ray crystal structure analyses. As
shown in Table II, the H O bond lengths range from normal, 1.70 A
, to short, 1.32 A
,
with a corresponding almost linear correlation with the covalent OH bond lengths.
The O O separations are less systematic, indicating variations in the OH O
angles. This suggests a quite flat asymmetrical potential well for the hydrogen atom,
which is sensitive both to the RAHB effect and the crystal environment.
Pentachlorophenol forms strong hydrogen bonds when complexed with N- and
O-bases which have been studied by Wozniak et al. (1991). There is a corresponding
shortening of the CO(H) bond lengths between 1.267 and 1.341 A
, and a closing of
the aromatic ipso angles from 118 to 113
. The adjacent C
::::
C bond lengths range
between 1.335 and 1.416 A
. There are roughly linear relationships between pairs of

these dimensions.
TABLE II Intramolecular hydrogen-bond geometries in 1,3-diaryl-1-hydroxy-3-keto-
propanes (1,3-propane dione enols)
Compound H O (A
) OH (A
) O O (A
)
1 1.70 0.91 2.554
2A 1.53 0.98 2.432
3 1.49 1.07 2.502
4 1.42 1.10 2.499
5 1.39 1.10 2.434
6 1.38 1.12 2.405
7 1.37 1.15 2.470
8 1.36 1.16 2.463
9 1.35 1.20 2.492
10 1.33 1.20 2.401
11 1.32 1.24 2.489
(O-H) and (H O) -0.01 A
, (O O) -0.004 A
1 1-mesityl-3-(O-nitrophenyl)
2 & 5 1-(p-methoxyphenyl)-3-(m-nitrophenyl)-
3 1-(p-nitrophenyl)-3-mesityl-
4 1-mesityl-3-(p-methoxyphenyl)-
6 1-phenyl-3-(p-nitrophenyl)-
7 1-phenyl-3-(p-methoxyphenyl)-
8 1-phenyl-3-phenyl- (by neutron diffraction)
9 1-mesityl-3-(m-nitrophenyl)-
10 1-phenyl-3-mesityl
11 1-phenyl-
Compounds 8 and 11 (Jones, 1976a, b). All other compounds, Bertolasi et al. (1991).
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Crystallographic interest in strong hydrogen bonds was further stimulated by the
discovery of the so-called proton sponges*. These are fused-ring aromatic diamines
with exceptionally high basicity due to the close proximity of the basic centers
(Alder et al., 1968); Staub, Saupe and Kru ger, 1983; Saupe, Kru ger and Staub, 1986;
Staub and Saupe, 1988). Examples are 4,5-bis (dimethylamine) fluorine, XVI, 4,5-bis
(dimethylamine)phenanthrine, XVII, 1,8-bis-(dimethylamine)naphthalene, XVIII.
These molecules with short constrained N N separations can gain a proton to
become a cation with the formation of a strong N
H N hydrogen bond. This is the

reverse of the strong anionic OH

OO bonds discussed above. IR spectroscopy suggests
that these strong bonds are formed in solution as well as in crystals (Pawelka and
Zeegers-Nuyskens, 1989; Brzezinski et al., 1990).
In the crystal structure of DMAN, the naphthalene ring is distorted from planar
such that the two nitrogen atoms are 0.4 A
either side of the mean plane resulting in a

non-bonding N N separation of 2.792(8) A
(Einspar et al., 1973). In the many

[DMANH]
salts for which there are crystal structures, see Table III, the naphthalene
ring distortion is much less and the N
(H) N separations range from 2.55 to 2.65 A
.
As with the OH O and OH

OO hydrogen bonds, the N
N separations are rela-

tively constant, but the hydrogen bond lengths vary by 0.5 A
, accompanied by a change
in the covalent NH bond lengths by 0.4 A
, see Table III. Some of the bonds are disor-

dered N
1
2
H
1
2
HN with or without a crystallographic symmetry element. In the
absence of a symmetry element, the two sites are not equally populated. In the later crys-
tal structure analyses carried out at 100 K, the hydrogen electron densities were resolved
by difference Fouriers, indicating a rather flat asymmetric double minimum potential.
Generally the anions and hydrated anions from a separated hydrogen-bonded
network, but in two structures, [DMANH]
[Hsquarate]
and the tetrahydrate, there

are weak hydrogen bond linkages through minor three-center components from the
NH N bond, see Fig. 4. In the Hsquarate, it is NH O=C with H O=2.85 A
,
NH O=108
. In the tetrahydrate, where the N

1
2
H
1
2
HN bond is crystallo-
graphically disordered, they are N
H O=C and NH O
w
, 2.15, 2.55 A
, 103,
113
, respectively. In [DMANH]
3,4-furan-dicarboxylate, the transfer of the proton

results in both a strong NH N bond and also a strong OH

OO bond with
OH=1.04(3), H O=1.44(3) A
and OH O=167(3)
.
A strong unsymmetrical N
H N bond between a cation and a molecule,

XIX, is observed in phthalazine semi-tetrafluoroborate with N
H = 1:07(2) and
H N=1.63(2) A
.
*A name introduced by Aldrich Chemical Company for [DMANH]
.
152 G.A. JEFFREY
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In phthalazine 1-methyl-5-tetraazothionate, the N
1
2
H
1
2
HN bond is symmetrical
with disordered hydrogens (Wozniak, Krygowski and Grech, 1992). A strong symme-
trical [N H N]
bond with N H=1.317 (1) A
and N N=2.635 A
was observed
by low-temperature neutron diffraction in hydrogen diquinuclidinone, XX, by Rozie` re,
Bilen and Lehman (1982).
TABLE III Hydrogen-bond lengths in the [DMANH]
cations
Anion N N H N
NH NH N
Ref
BF
4
2.562(x) (1.31 m 1.31) 159 a

Br
2.554(5) (1.31 m 1.31) 153(3) b

[tetrazole]
H
2
O 2.573(2) (1.312) 1.312(5) 157(2) c
OTeF
5
(triclinic) 2.574() 1.46() 1.17() 159() d

(orthorhombic) (1.37 m 1.37) 140(3) d
/
[tris(hexafluoracetato]
3
Cu
2
2.65(2) 1.48(17) 1.27(21) 148(12) e
[2,4-dinitroimidazolate]
1
2.606(3) 1.48(3) 1.18(3) 160(3) f
[pentachlorophenolate]
2.555(3) 1.49(2) 1.11(2) 162(2) g

[pentachlorophenol] at 100 K
[1-oxo-2-phenyl 1,2-dicarbo-
dodecaborate]
2.577(3) 1.50(3) 1.22(3) 140(3) h

[chloranilate]
2H
2
O at 295 K 2.589(3) 1.51(3) 1.14(3) 155(2) i
at 150 K 2.588(2) 1.59(3) 1.07(3) 152(2)
[pentaflurophenolate]
2.565(3) 1.56(6)
*
154(6) j
[pentaflurophenol] at 100 K 1.84(7) 141(6)
[hydrogen squarate]
2.583(2) 1.59(2) 1.08(2) 157(2) k

[3,4-furan dicarboxylate]
2.621(3) 1.62(3) 1.06(2) 155(2) l

[tris(hexafluoracetato]
3
Mg
2
2.60(1) 1.63(11) 1.25(11) 134(8) e
1,8-bis(4-toluenesulphonamido)-
2,4,5,7-tetranitronaphthalene
2.610(5) 1.63(5) 1.05(5) 152(5) m
[hydrogen squarate]
2
4H
2
O 2.594(3) 1.66(6)
*
0.97(6) 162(5) n
at 100 K 2.574(3) 1.69(6)
*
0.94(6) 156(5)
[dihydrogen hemimellitate]
0.5H
2
O 2.604(2) 1.72(2)
**
0.94(3) 155(2) o
at 100 K 1.72
**
0.94(6) 164(5)
[D-hydrogentartrate]
3H
2
O 2.610 1.75(5)
f
0.91(5)
f
157(5) p
at 100 K 1.8
f
0.8(1) 160(10)
8-dimethylaminomethyl-1- 2.629(2) 1.61(3)
1.04(3) 165(3) q
dimethylammoniomethyl-
naphthalene nitrate at 100 K 183(5)
0.83(6) 161(5)
*
m=mirror symmetry
*
H disordered over two sites in 0.54:0.46 ratio.
**
H disordered over two sites in 0.7:0.3 ratio
f
H disordered over two sites in 0.71:0.29 ratio.
H disordered over two sites in 0.66:0.34 ratio

Ref.
(a) Woznial et al. (1990).
(b) Pyzalska, Pyzalska and Borowiak (1983).
(c) Glowiak et al. (1992).
(d) Miller et al. (1988).
(d) Kellett, Anderson and Strauss (1989).
(e) Truter and Vickery (1972).
(f) Glowiak et al. (1987).
(g) Kanters et al. (1992b).
(h) Brown et al. (1987).
(i) Kanters et al. (1991b).
(j) Odiaga et al. (1992).
(k) Kanters et al. (1991c).
(l) Glowiak et al. (1993).
(m) Malarski et al. (1990).
(n) Kanters et al. (1990c).
(o) Raves, Kanters and Grech (1992).
(p) Israe l, Kanters and Grech (1992).
(q) Salas, Kanters and Grech (1992).
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FIGURE 4 Top: Unsymmetrical N
H N bond in [DMANH]
[squarate]
complex. Bottom: Symmetrical

N(H)(H)N bond in [DMANH]
[squarate]
2
4H
2
O. [from Kanters et al. (1991c, 1992c) with permission.]
154 G.A. JEFFREY
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In the complex of 1,8-bis(dimethylamino)naphthalene with 1,8-bis(4-toluenesulphon-
amido)-2,4,5,7-tetranitronaphthalene, the H N
hydrogen bond in the anion is

significantly longer than that in the cation (Table IV). The [NHN]
geometry is
N
N=2.600(5) A
, H N
=1.85(5) A
, NH=0.82(5) A
, N
H N153(5)
, while
the N N separations are much the same. The relationship between the crystal field
environment and the location of the hydrogen atom in the NH N and NH N
potential functions presents an interesting challenge for both crystallographers and

theoreticians.
6 CH A BONDS
The discussion of CH groups as hydrogen bond donors has recurred. Biological
macromolecules, where the hydrogen bond acceptor functionality often exceeds that
of the donors, contain many methylene and methyl groups. It is therefore of interest
to ascertain whether CH O hydrogen bonds could influence molecular conforma-
tions and inter-molecular interactions. Should they be included in the computational
methods that attempt to predict intermolecular interactions? The CH O hydrogen
bond was first suggested as a chemical bond by Glasstone (1937) as an explanation
for the deviations from ideal properties of mixtures of chloroform and acetone or
diethyl ether. This hydrogen bond was enthusiastically sponsored by Sutor (1962,
1963) and denounced by Donohue (1968). The strongest evidence for CH A hydro-
gen bonding has come consistently from infrared vibrational spectroscopy (Dippy,
1939; Allerhand and Schleyer, 1963; Krumm, Kurowa and Rebare, 1967; Green,
1974; Jeng and Ault, 1991; Steinwender et al., 1993). Crystallographers, who for
many years had a fixation on comparison with van der Waals radii, have been more
skeptical.
A survey of 113 neutron diffraction crystal structures by Taylor and Kennard (1982)
favored the existence of CH O, CH N and CH Cl bonds with mean H O
distances of 2.04 to 2.40 A
, H N 2.52 to 2.72 A
, H Cl 2.57 to 2.91 A
. More recently
Desiraju (1989, 1990, 1991) examined the CH O distances in crystal structures
containing (Cl
3n
C
n
) CH O, where 0 _n _3, and in some alkyl and alkene struc-
tures. The distances ranged from 3.0 to 4.0 A
and decreased smoothly with increasing

donor group acidity. The more acidic the CH, the shorter the C O distance in the
sequence alkyne >quinone >alkene >aromatic >aliphatic. Since C O distances
alone are not reliable criteria for hydrogen-bonding, it is unfortunate that H O
bond lengths and CH O bond angles were not analyzed from those data where
the hydrogen atoms were observed, or their positions could be calculated with reason-
able certainty from those of the adjacent non-hydrogen atoms. Some examples of
(CCl
3
) CH O hydrogen bond lengths 2.5 A
in crystal structures are reported by

Irving and Irving (1992). The CH O distances in 551 crystal structures was shown
to correlate with pK
(Me
2
SO) values, suggesting a new scale of carbon acidic
(Pedireddi and Desiraju, 1992).
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A survey of CH O bonds in carbohydrate crystal structures only by Steiner and
Saenger (1992c) was based on 30 neutron diffraction analyses providing 395 potential
donors and 328 potential acceptors. All donors were Csp
3
H; the acceptors were
COH (61%), COC (27%), O
w
H
2
(11%), O=C or O=C (1.5%). With a cut-off of
the CH O angle greater than 90
, 5 percent have CH O contacts between 2.27

and 2.4 A
, 21 percent <2.5 A
, 65 percent with contacts <2.7 A
; if the cut-off is
extended to 3.0 A
, there are 93 percent contacts. More than half the contacts less
than 2.7 A
are intramolecular. Many have the configuration XXI or XXII, which is a

characteristic of syndiaxial interactions in carbohydrate molecules.
About 14 percent of the bonds >2.7 A
are three-centered. This is smaller than the 25

percent for OH O bonds in carbohydrates (Ceccarelli, Jeffrey and Taylor, 1981).
A subsequent survey of CH OH
2
bonds based on 101 water molecules in 46 neu-
tron diffraction crystal structure analyses by Steiner and Saenger (1993a) showed that 8
percent of the water molecules had CH O
w
, distances <2.5 A
. For longer distances,

the proportion increased to 39 percent <2.8 A
and 57 percent<3.0 A
.
Comparison with the analysis of the stereochemistry of water molecules in 311
hydrates, amino acids, carbohydrates, purines and pyrimidines and nucleosides and
nucleotides is given in Table IV. These data were mainly from X-ray analyses and
CH O
w
bonds were excluded (Jeffrey and Maluszynska, 1990). The difference in
the water donor percentages is likely to be a consequence of the difference in the
data sets used. The CH O
w
analysis contained a number of salts and data from
TABLE IV Comparison (in percentages) of hydrogen-bond donor and acceptor properties of water
molecules, including C-H O
w
bonds from Steiner and Saenger (1993a) (S & S), and excluding C-H O
w
bonds from from Jeffrey and Maluszynska (1990) (J & M)
*
Water donors Water acceptors
S & S J & M S & S J & M
zero 0 6
single 0 >1 single 17 43
double 43 68 double 57 48
triple 32 19 triple 21 3
quadruple 22 12 quadruple 3 0
quintuple
f
3 0 quintuple
1 0
*H A<3.0 A
, CH A>90
, those involving metal cations were excluded.

156 G.A. JEFFREY
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the neutron diffraction analyses of the cyclodextrin hydrates. The water acceptor
percentages show the expected trend towards higher levels of coordination when
CH O
w
bonds are included. CH O single and bifurcated hydrogen bonds are
observed in the crystal structures of nucleosides and nucleotides with H O distances
ranging from 2.17 to 2.56 A
. The CH O angles range from 170 to 90
(see Tables
10.1 and 10.2 in Jeffrey and Saenger, 1991).
An examination of the high-resolution neutron diffraction of vitamin B
l2
co-enzyme
(Bouquiere et al., 1993) for CH O interactions by Steiner and Saenger (1993b)
found several examples of water molecules where the tetrahedral hydrogen-bond coor-
dination is completed by CH O
w
interactions. Crystal structures containing dimers
linked by CH O hydrogen bonds have been reported by Hariharan and Srinivasan
(1990) and Jaulmes et al. (1993). In the crystal structure of 8-dimethylaminomethyl-l-
dimethylammonio-methyl-naphthalene nitrate, the molecular packing is determined
chiefly by CH O
interactions to the nitrate oxygens with nine H O
distances
from 2.31(1) to 2.57(2) A
and CH O
angles of 144 to 171
(Salas, Kanters and

Grech, 1992). A novel crystallographic way for testing for CH X hydrogen bonding
is proposed by Steiner (1994). He examined the U
eq
vibrational thermal motion par-
ameters for the carbon atoms in 51 terminal C(1) C(2)H groups in 42 crystal struc-
tures. Plotting U
eq
C(2)/U
eq
C(1) he found that with H X>3.0 A
, the ratio was 1.4 or

above. With H X<3.0 A
, the ratio was below 1.4, with a rough correlation between

the U
eq
ratio and the H X distances. The implication is that hydrogen bonding reduces
the normal increase in thermal motion along these relatively rigid terminal groups.
Now that CH hydrogen bonds have become fashionable again, crystallographers
will watch for them and no doubt many more will be reported.
7 HYDROGEN-BOND DISORDER; TUNNELLING; FLIP-FLOP; LOST BONDS
In strong symmetrical double minimum disordered hydrogen bonds such as
N(H) (H)N
, O(H) (H)

OO, the proton crosses the potential energy barrier
by tunnelling. This configurational change, i.e. bond breaking and making, has long
been associated with characteristic intense infrared continua (Zundel, 1976, 1992;
Eckert and Zundel, 1988). The proton polarizability of chains of such strong bonds
has been described recently by Zundel and Brzezinski (1992), with application to
proton jumping in bacteriorhodopsin (Olejnik, Brzezinski and Zundel, 1992). For the
weaker uncharged O(H) (H)O hydrogen bonds observed in the cyclodextrin
hydrates, an alternative conformational mechanism has been proposed, known as
flip-flop (Saenger et al., 1982; Betzel et al., 1984). This mechanism, XXIII, can also
be applied to hydrogen bond disorder in the ices, where it involves a 120
rotation about the oxygen atom, and where there is frequently an intermediate
energy minimum due to the formation of a three-center bond.
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The dynamics of the hydrogen-bonding disorder in -cyclodextrin undecahydrate
(-CD-11H
2
O) was studied at room temperature by quasi-elastic incoherent neutron
scattering by Steiner et al. (1989). The mean residence time of various different protons
is estimated to be _0.6 10
11
s. A later study by Steiner, Saenger and Lechner (1991)
gives a more detailed description of the hydrogen-bond disorder in -CD-11H
2
O and of
the water molecules, some of which are guests in the cyclodextrin cavity. The quasi-elas-
tic spectra were satisfactorily interpreted using a simple two-site jump model with reor-
ientational jumps over H H distances of 1.5 A
and diffusive motions of water

molecules in the cavity over H H distances of 3 A
. The jump rates extend from

2 10
10
to 2 10
11
s
1
.
An example of multiple proton transfers in hydrogen-bonded dimers and trimers of
pyrazole derivatives in the solid state is observed with
15
N NMR by Aquilas-Parrilla
et al. (1992). The ices are a fertile field for studying hydrogen-bond disorder (Kamb,
1968; Kuhs and Lehman, 1983). Powder neutron diffraction studies of the ices III
and X by Londono, Kuhs and Finney (1993) show that the hydrogen atoms are not
fully ordered in III and not quite symmetrically disordered in X.
In many of the carboxylic acid hydrogen-bonded dimers, the hydrogen atoms are dis-
ordered (Dunitz and Strickler, 1968). Two mechanisms have been proposed; a double
proton tunnelling (XXIV) or a dynamic double 180
flip (XXV) (Furic , 1984). While

the flip model might be energetically feasible in the gas phase, it seems very
unlikely in the solid state (Nagawa, 1984; Kanters et al., 1991a).
The interesting concept of lost hydrogen bonds in proteins is developed by Savage
et al. (1993). The maximum hydrogen bond functionality for each amino acid residue
is obtained by adding lone-pairs and hydrogen-bonding hydrogen atoms. The
number of observed hydrogen bonds based on O O<3.4 A
, N N or
N O<3.5 A
and N S or O S<3.8 A
and angles >90
criteria is calculated for

236 crystallographically independent protein molecules. For donors the number of
lost bonds ranges from 5.7 percent for main chains to 0.3 for threonine. For acceptors,
it is much larger, 34 percent for threonine (CO) to 3 percent for glutamic acid (CO).
The excess of acceptor functionality over number of donor hydrogen atoms available is
consistent with the large number of three-center bonds reported by Preissner, Enger and
Saenger (1991). There is an excellent linear correlation between the number of lost
hydrogen bonds (LHB) and the sum of the calculated stability factors for the proteins,
as shown in Fig. 5.
158 G.A. JEFFREY
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8 HYDROGEN BONDS IN INCLUSION COMPOUNDS
Since the crystal structure determination of the hydroquinone-SO
2
complex by Palin
and Powell (1947), and the urea n-hydrocarbon complex by Smith (1952), the
number of inclusion compounds based on hydrogen-bond formation has steadily
increased (Weber, 1987).*Water continues to be a source of new inclusion compounds.
The air-hydrate has been found in deep-core ice. It is the 17A type II structure
with air occupying both the 12- and 16-hedra (Hondok et al., 1990). The 164 year
old mystery of the bromine clathrate hydrate (Lo wing, 1829; Allen and Jeffrey, 1963)
has been resolved by a single-crystal neutron diffraction analysis at 100 K. The tetrago-
nal crystal structure is a new type with a (H
2
O)
n
framework of 12-hedra, 14-hedra and
15-hedra, with the Br
2
molecules occupying the 14- and 15-hedra (Brammer and
McMullan, 1993).
FIGURE 5 Plot of number of lost hydrogen bonds, LHB, versus the sum of the stabilizing energy com-
ponents. HP: hydrophobic energy; IP: ion pairs; SS: disulphide bonds.; Top for proteins better that 1.9 A
resolution. Bottom for proteins better than 1.7 A
resolution. [from Savage et al. (1993), with permission.]

*
A monograph by Sister Martinette Hagen (1962) gives an excellent review of the early days of clathrate
inclusion compounds.
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A neutron diffraction analysis of the type II hydrate, 3.5Xe 8CCl
4
136D
2
O, at 13
and 100 K is reported by McMullan and Kvick (1990). The D O hydrogen bond
lengths range from 1.738 (3) to 1.802(1) A
with OD O angles from 174.8(1) to

180
. These are similar to the values from the neutron diffraction analysis of the type
I, 6C
2
H
4
O.46D
2
O, at 80 K (Hollander and Jeffrey, 1977) where the D O lengths
ranged from 1.726 (2) to 1.815 (5) A
with angles from 171.6(4) to 180
. Although the
CCl
4
molecules have the same point symmetry as the center of the 5
12
6
2
polyhedra
that they occupy, they exhibit large amplitude 1ibration, with seven preferred
orientations with CCl bonds directed towards the vertices of the polyhedron in
which they are enclosed.
A neutron powder diffraction study of helium hydrate at 0.25 GPa by Londono,
Finney and Kuhs (1992) showed a gas hydrate with composition He (6 x)H
2
O that
has a host structure resembling that of ice II, space group R
33. A new clathrate hydrate

of tetraisoamyl ammonium fluoride has been briefly reported. The alkyl chains of
the cations are enclosed in 6
3
5
7
4
2
polyhedra in a tetragonal I4
1
/a structure
(Lipkowski et al., 1990).
The polyhedral hydrates of the strong acids HPF
6
, HBF
4
and HClO
4
(Mootz, Oellers
and Wiebcke, 1987) and of the strong base (CH
3
)
4
N OH (Mootz and Seidel, 1990)
provide a most interesting series of hydrogen-bonded water-ionic inclusion compounds.
In the strong acid series, the host lattices are H
(H
2
O)
n
. They are isostructural with the
type I, cubic 12 A
gas hydrates despite an extra proton.

The structure of the low-temperature, tetramethyl ammonium hydroxide 5H
2
O
was determined by McMullan, Mak and Jeffrey (1966) in which the cage is a broken
truncated octahedron.
Mootz and Seidel (1990), Mootz and Sta ben (1992) have now characterized the whole
phase diagram and analyzed the crystal structures of twelve hydrates: and 2H
2
O;
and 4H
2
O; and 4.6H
2
O; 5H
2
O; 6.67H
2
O; and 7.5H
2
O; 8. 75H
2
O; 10H
2
O.
The and forms of the dihydrate have one-dimensional (H

OO(HOH)
4
chains with
one OH
proton not participating. The tetrahydrates have deprotonated water

channels with OH O
w
bonds. The 4.6, 5, 6.67, 7.5 hydrates form incomplete
polyhedral cages with some oxygens three-coordinated. The high temperature 7.5,
and the 8.75 and 10 hydrates are true clathrates with complete four-connected
(

OOH:nH
2
O) cages. The 7.5 hydrate has the 15-hedron [5
12
6
3
] and a vacant [4
2
5
8
]
decahedra. The 10-hydrate has two new cages, a 17-hedra [4
1
5
10
6
6
] and a vacant
nonahedron [4
3
6
6
].
A most interesting structure of Cs{(CH
3
)
4
N}
2
(OH)
3
14H
2
O has recently been
reported by Mootz and Sta ben (1994). It is isostructural with the (CH
4
)
4
N OH.7.5
hydrate with the Cs
ions occupying the small monohedra. In contrast to the hydrates

of the strong acids, which have an extra proton, these host lattices are proton deficient.
In both cases, proton excess and proton deficiency result in disorder, but the details of
how the proton distribution in the bonds adjusts to the excess or deficiency are not
clear. The capability of forming hydrogen-bond water lattices with an excess or
deficiency of protons is an interesting feature of clathrate hydration which merits
further study by careful neutron diffraction analyses.
The channel type of hydrate inclusion compounds, of which (CH
3
)
4
NOH 4H
2
O is an
example, is a common form of inclusion hydrate in which the water-anion layers are
composed of fused polyhedra including quadrilaterals, pentagons, hexagons and
heptagons, as shown in Table V. The recent additions are [12CH
3
N]
[12F 28H
2
O]
160 G.A. JEFFREY

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with quadrilaterals and hexagons, [CH
3
N]
[F 5H
2
O]
with pentagons only (Sta ben

and Mootz, 1993), CH
3
COH 2H
2
O with pentagons only, and CH
3
COH 7H
2
O with
quadrilaterals, pentagons and hexagons (Mootz and Sta ben, 1993).
There is a brief report of a hydrate of tetrapropyl ammonium fluoride with water-
fluoride layers containing fused quadrilaterals, pentagons and hexagons with the
layer interspersed by the propyl groups (Lipkowski et al., 1992). Hydrogen-bonded
channel clathrate structures of 1,2-naphthalene dicarboxylic acid which include a
variety of organic solvents or water are described by Fitzgerald, Gallucci and Gerkin
(1992). The diacetylenic diols form crystalline inclusion complexes which are used for
commercial extraction processes (Toda, 1987). The crystal structure of one of these
clathrates with dichloromethane as the guest species is reported by Leigh, Moody
and Pritchard (1994). The host lattice is an unusual tubular structure with double-
walled channels formed by infinite columns of OH O hydrogen bonds.
Fused polyhedra were observed in a drug-deoxydinucleotide phosphate complex by
Neidle et al. (1980). A recent high-resolution neutron diffraction refinement of vitamin
B
12
coenzyme showed fused quadrilaterals and pentagons in the hydrogen-bonded
water network with O O distances between 2.61 and 3.03 A
at 15 K (Bouquie` re
et al., 1993).
The crystal structure at 80
C of a dodecahydrate of the oligopeptide cyclic D-valyl-

(N
2
-methyl-L-arginyl)-glycyl-L-aspartyl-3-(aminomethyl)-benzoic acid 12 H
2
O (27.3
percent water by weight) has recently been reported (Harlow, 1993). The water mol-
ecules form a semi-clathrate-like structure with a 4- and several 5-, 6- and 7-membered
rings. This water structure is hydrogen-bonded at several points to the peptide
molecule.
Since proteins in the crystalline state are completely surrounded by bound water,
these crystal structures could be regarded as semi-clathrate hydrates. Only in the case
of the small plant protein, crambin, have polyhedral arrangements of hydrogen
bonds been identified (Teeter and Whitlow, 1987). The problem of identifying
hydrogen-bond motifs in the hydration of proteins lies in the inability to distinguish
hydrogen-bonded and non-bonded O O separations from O O distances alone
(see Fig. 2), particularly when disorder is likely to be present. Fascinating
super-diamond host lattices are formed by pair-wise hydrogen bonding between the
COOH groups in 2,6-dimethylidine adamantane 1,3,5,7-tetracarboxylic acids (Ermer,
TABLE V Channel- and layer-type inclusion hydrates with hydrogen-bonded layers of fused quadrilaterals
(Q), pentagons (P), hexagons (H
6
) and heptagons (H
7
).
Compound Layer topology Reference
[(CH
3
)
4
N]
[F 4H
2
O]
H
6
McLean and Jeffrey (1967)
[(CH
3
)4N]
2
[SO
4
4H
2
O]
2
H
6
McLean and Jeffrey (1968)
[(C
2
H
5
)
4
N]
[Cl 4H
2
O]
Q, H
6
Mak, Bruinslot and Beurskens (1986)
[4(H
2
H
5
)
4
N]
[F 11H
2
O]
Q Mak (1985)
[(C
2
H
5
)
4
n]
[CH
3
COO 4H
2
O]
P, H
7
Mak (2985)
Pyridine 3H
2
O Q, P, H
6
Mootz and Wussow (1981)
Pinacol 6H
2
O P Kim and Jeffrey (1970)
Piperazine 6H
2
O P Schwarzenbach (1968)
2,5-dimethyl 2,5-hexanediol 4H
2
O P Jeffrey and Shen (1972)
2,5-dimethyl 2,5-octanediol 4H
2
O P Jeffrey and Mastropaolo (1978)
[C
12
H
28
N]
[F 11H
2
O]
Q, P, H Lipkowski et al. (1992)

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1988). Five more crystal structures of this type are reported by Ermer and Lindenberg
(1991).
In the phenol-formaldehyde oligomer inclusion compounds, the calixarenes, the
phenolic components are linked by covalent bonds (Andretti and Ugozzoli, 1991).
The phenolic OH bond can be unsubstituted or substituted. A four-membered
homodromic ring of strong OH O bonds influences the conformation of the
calixarene, forcing a cone-conformation which is not present when the hydroxyl
groups are partially or wholly substituted. Bavoux and Perrin (1992) report a
OH N (C
2
H
6
)
3
hydrogen bond with O N distance of 2.632 (8) A
in the crystal
structure of p-t-butyl-dihomooxa-calix [4] arene: triethylamine (1 : 2) clathrate.
Some of the oldest known inclusion compounds are those of the cholic acids. The
crystal structures of the 1 : 1 inclusion compounds of cholic acid with methanol, ethanol
and 1-propanol have been studied by Jones and Nassimbeni (1990). The molecules
which form the cage are linked by hydrogen bonds with O O separations from 2.55
to 2.85 A
; the hydrogen bond lengths and angles were not reported.

Hydrogen-bonded cyclamers of 1,3-cyclohexanedione have been reported by Etter
el al. (1990). These form hexameric rings which enclose benzene. A clathrate-type
host lattice is formed by hydrogen-bonded molecules of 9-benzamido-6, 7, 8, 9, 10, 11-
hexahydro-5, 9, 7, 11-dimethano-5H-benzocyclonen-7-o1 (XXVI) through the forma-
tion of OH O=C and NH OH bonds. The guest species are carbon tetrachloride
or ethyl acetate (Bishop et al., 1991).
9 XH p BONDS
The concept of NH hydrogen bonding is a tempting concept which has been sug-
gested in protein structures (Burley and Petsko, 1985; Levitt and Perutz, 1988). A
search for the most favorable scenario, OH [[[
C
C
, yielded only one example, the crystal
structure of 2-ethyladamantin-2-ol, which revealed a cyclic dimer motif with CH
bond lengths of 2.22 A
(Steinwendet et al., 1993). O-H hydrogen bonding to

aromatic rings has been reported in crystal structures by Hardy and MacNicol
(1976), Atwood et al. (1991, 1992) and Ferguson et al. (1994), with H C
arom
distances
from 2.1 to 2.7 A
. The role of CH hydrogen bonds in stabilizing cyclophane host-

guest complexes in organic solutions is discussed by Cochran et al. (1992).
Crystalline complexes of 2-butyne-HCl and 2-butyne-2HCl, decomposing at 100
C
and melting at 113
C respectively, were identified and the crystal structures were

determined by Mootz and Deeg (1992), showing ClH [[[
C
C
with H [[[ bonds of
162 G.A. JEFFREY
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2.30 A
and ClH [[[ angles of 180
and 165
. Deeg and Mootz (1993) have also deter-

mined the crystal structures of toluene-2HCl and mesitylene-HCl. The HCI
molecules are located on both sides and one side respectively of the benzene rings,
with the ClH bonds pointing to the center and nearly perpendicular to the benzene
rings, as shown in Fig. 6. The H (center) distances are 2.51 (8) and 2.32(5) A
.
Recent vibrational spectroscopic evidence for OH has been provided by
Steinwender et al. (1993). There is little doubt that this is a weak hydrogen-
bond-interaction (as defined by Pimental and McClellan, 1960, p. 6) which is observed
when the other stronger intermolecular forces allow a CH bond to be directed normal
and towards the center of a CC bond or an aromatic ring.
FIGURE 6 The toluene 2HCl hydrogen-bonded complex, ORTEP at 25% probability. [from Deeg and
Mootz (1992), with permission.]
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10 MOLECULAR RECOGNITION AND HYDROGEN BONDING
Molecular recognition is one of the buzz-words* of the 1990s. Presumably it is a process
whereby molecules self-assemble to form crystals with the reduction of thermal motion
or the evaporation of solvent. However, this mundane process is not what attracts
attention; rather it is heterogeneous molecular recognition. This is a process that results
in complex formation, co-crystallization and the adherence of substrates to enzymes,
so-called supra-molecular chemistry. The concept is defined by a definitive article by
Rebek (1988) who described molecular recognition as a process at the foundation of the
current revolution in molecular biology and technology. A glance at the illustrative
examples in this article shows that hydrogen bonding frequently plays a key role. The
recognition of hydrogen-bonding motifs or nets by graph theory may permit the iden-
tification of possible substrates to the known structure of proteins and nucleic acids.
It can lead to the synthesis of crystals with special properties (Etter, 1990) and the
design of host systems for small biological molecules, including drugs (Rebek, 1990)
and the formation of supramolecular assemblies (e.g. Seto and Whitesides, 1991;
Chang et al., 1991; Kikuchi et al., 1991). Crystallography can play a key role in
molecular recognition, not only in providing the known structure of the macromole-
cules, but also as a means of identifying potential complexing molecules by searches
using the Cambridge Crystallographic Data Base.
The related concept of using hydrogen-bond interactions to form aggregate
structures with predictable connectivities and symmetry developed from, or was
responsible for, the graph theory approach of Etter discussed earlier.
In the biological field, molecular recognition generally takes place through an
aqueous medium, and hydrogen-bonding will certainly play a role (cf. Kurihara et al.,
1991). It has been suggested that electron or proton polarizability through the transient
cooperative hydrogen-bonded chains in the water motifs provides a mechanism
for molecular recognition prior to actual intermolecular contact, i.e. Natures radar
guidance system (Zundel, 1992; Zundel and Brzezinski, 1992; Jeffrey, 1993, 1994).
11 MISCELLANEOUS
A configuration change on deuteration. Mootz and Schilling (1992) observed a
unique structural change in the crystal structure of trifluoroacetic acid tetrahydrate (mp
12
C) on deuteration. The hydrogenated phase is ionic [H

5
O
2
]
[(CHCOO)
2
H]
6H
2
O, while the deuterated phase (mp 15
C) is molecular CF
3
COOD 4H
2
O. The
topologies of the two structures are very similar, with buckled layers of water molecules
consisting of condensed four- and six-membered rings of OH(D) O hydrogen bonds.
The difference lies in the distribution of the hydrogen and deuterium atoms. In the
H
2
O structure, the four-membered rings are homodromic, one six-membered ring is
homodromic and the other heterodromic. In the D
2
O structure, the four-membered
rings are heterodromic and both six-membered rings are homodromic. The shortest
hydrogen bonds are COD OD
2
, 1.60(2) A
, and CO(H) (H)O

CC, 1.65(4) A
,
which is symmetrically disordered.
*A buzz-word is a word that is added to the title or abstract of a paper or a grant proposal in order to
enhance the chances of (a) an oral presentation, (b) an accepted publication, or (c) a funded research grant.
164 G.A. JEFFREY
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Liquid-crystal mesogens. The crystal structures of the 36 glyco-lipids carried out
from the 1965 to 1992 have recently been summarized by Pascher et al. (1992). In
these crystals the glycosidic head groups are linked by networks of hydrogen bonds
which interface with water molecules in the lyotropic liquid crystal phases.
The more recent interest in non-biological carbohydrate-based liquid crystals formed
by alkyl substitution (C
n
H
2n 1
with n >6) of cyclic and acyclic monosaccharides
(Jeffrey, 1986) has resulted in crystal structure analyses of seven n-alkyl pyranosides
and eight acyclic aldonamides and amido-alditols (Jeffrey and Wingert, 1992). In
these crystal structures, the carbohydrate head-groups are hydrogen-bonded to form
bilayers with interdigitizing alkyl chains. An exception is a group of structures with
monolayer head-to-tail packing. These structures which have three different space
groups have a similar hydrogen-bonding motif. This motif includes a homodromic
quadrilateral of OH O bonds. On heating, the crystal structures transform to a
bilayer head-to-head packing prior to forming a bilayer (smectic) liquid crystal.
It is proposed that the homodromic cyclic pattern of bonds stabilizes the unusual
head-to-tail packing (Jeffrey, 1990). The same type of homodromic quadrilateral
of hydrogen bonds is observed in the crystal structures of alditol derivatives and is pos-
tulated to play a significant role in the molecular packing (Andre et al., 1993). The more
soluble of these compounds, such as n-octyl, -glucopyranoside, form lyotropic liquid
crystals in which the hydrogen-bonded carbohydrate moieties interface with the water
molecules (Chung and Jeffrey, 1989).
Apologies
As with all reviews, this article reflects the interests of the author. The present-day ever-
increasing multiplicity of publications, authors and journals makes it almost impossible
to cover all aspects of a complex field. Apologies are offered to those whose favorite
publication has been omitted.
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SUBJECT INDEX
acetic acid 144
alditol derivatives 165
aldonamides 165
amido-alditols 165
amino acids 138, 156, 158
aminobutyric acid 140
asparagine monohydrate 141
bacteriorhodopsin 157
barbiturates 148
bifurcated 137
bond angle 136, 144, 148
bond-length 136
bromine clathrate hydrate 159
butyne-HCl 162
calixarenes 141, 162
carbohydrates 138, 140, 142, 143, 144, 145,
146
carbohydrate hydrates 143
carboxylic acids 140, 150
caronic acids 150
CHARMM 142
cholic acids 162
clathrate hydrates 143
conic correction 136
cooperativity 142, 144
crambin 161
cyclic water polymers 144
cyclodextrin 138, 144, 147
cyclodextrin deuterate 138
cyclodextrin-ethanol-octahydrate 138
cyclodextrin hydrates 144, 157
cyclodextrin undecahydrate 158
cyclohexanedione 162
cyclophane 162
deoxydinucleotide phosphate complex
161
deuteration 148, 164
diacetylenic diols 161
diamines 152
diketones 145
diketo-enols 150
dimethylamine fluorine 152
dimethylamine naphthalene 152
dimethylamine phenanthrine 152
dimethylaminomethyl-dimethylammonio-
methyl-naphthalene nitrate 157
dimethylidine adamantane
tetracarboxylic acids 161
DNA 138
drugs 164
ethyladamentinol 162
excluded region 136
flip-flop 157
formamide 140, 144
formic acid 144
glucopyranose 142
glutamic acid 158
glycine 137
glyco-lipids 165
graph theory 143
GROMOS 142
helium hydrate 160
Hsquarate 152
hydrogen-bond structure 142
hydrogen diquinuclidinone 153
hydroquinone-SO
2
complex 159
ice, ices 136, 142, 143, 145, 157, 158, 159
imidazolium maleate 150
inclusion compounds 159
KF (CH
2
COOH)
2
141
lactulose 140
liquid-crystal mesogens 165
lost hydrogen bonds 157
lower-bound model 148
malonaldehyde 145
mesitylene-HCl 163
methyl-glucopyranoside 141
molecular mechanics program 141
molecular recognition 164
monosaccharides 144, 145
motif 142
neutron diffraction 138
nucleic acids 142, 145, 164
nucleosides 138, 148
nucleotides 138, 142, 148
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oligopeptide 161
oxalic acid acetamide 140
oxalic acid dihydrate 140
oximes 144
oxyacids 146
pentachlorophenol 151
phthalazine methyl tetraazothionate 153
phthalazine semi-tetrafluoroborate 152
polypeptide bond 148
potassium hydrogen chloromaleate 150
propronic acid 144
protein crystal structures 138, 147
proteins 142, 145, 158
proton polarizability 157
proton sponges 150
purines 138, 148, 156
pyrimidines 138, 148, 156
pyranosides 165
pyrazole derivatives 158
resonance assisted hydrogen bonding
(RAHB) 143, 144, 145, 151
riding-motion model 148
strong acids 160
strong base 160
tetraethylammonium fluoride
hydrates 141
tetraisoamyl ammonium fluoride 160
tetramethyl ammonium hydroxide 160
tetrapropyl ammonium fluoride 161
three-centered 137
threonine 158
toluene-2HCl 163
trifluoroacetic acid tetrahydrate 164
urea hydrocarbon complex 159
vitamin B
12
co-enzyme 157, 161
water 136, 141, 142, 143, 144, 156
zwitterionic amino acids 138
176 G.A. JEFFREY
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Hydrogen Bond Update by Jeffrey

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due to the conic correction. When X A distances

. The role of the repulsive forces in determining hydrogen

, corresponding to a displacement of 0.15 to 0.18 A

between the electron and

. The distribution of these bond lengths rises at 1.8 A

with a peak at 2.1 A

. The minor components have bond lengths from 2.05 to

with angles 175 to 90

, with a maximum in the distribution of a H A distance

. In the earlier analysis of hydrogen bonding in protein structures by Baker

were considered, but the

. This would result in 80 percent of the three-center bonds

in the forward direction of the XH bonds, i.e. XH A_90

in the water dimer). Because the potential energy surface is so flat,

. A study of the structure and dynamics of Ice I

. They also observed a shortening of OH bond lengths as a

) (Jeffrey et al., 1981). Similarly the dimer

to the minor components of three-center

, with OH O angles approaching 90

and angles from 0 to 180

. The data set contained 110 hydroxyl, 53 ether oxygens

irrespective of hydrogen-bond formation is shown in Fig.

with H O from 1.70 to 2.15 A

. There was evidence of a small

and 1.20 to 2.21 A

respectively. They were smoother than previously reported (Jeffrey

, which is more restrictive than that

. The donor and acceptor

H, NH, N(H)H as donors of decreasing

. There are still insuffi-

, again excluding the minor components of three-center bonds.

and OH N angles greater than

. Therefore the minor components of three-center bonds with H N>201 A

were excluded from the survey. 304 OH N bonds

) mean 2.06 2.02

) mean 1.96 1.93

) mean 1.87 1.83 1.89

) mean 1.96 1.99

. Including one major component of 3-center bond =2.84 A

(Llamas-Saiz et al., 1992) showed a broad

respectively (Ku ppers and Jessen, 1993).

. There are roughly linear relationships between pairs of

H N hydrogen bond. This is the

either side of the mean plane resulting in a

(Einspar et al., 1973). In the many

(H) N separations range from 2.55 to 2.65 A

N separations are rela-

, see Table III. Some of the bonds are disor-

and the tetrahydrate, there

. In the tetrahydrate, where the N

3,4-furan-dicarboxylate, the transfer of the proton

H N bond between a cation and a molecule,

bond with N H=1.317 (1) A

2.562(x) (1.31 m 1.31) 159 a

2.554(5) (1.31 m 1.31) 153(3) b

(triclinic) 2.574() 1.46() 1.17() 159() d

2.555(3) 1.49(2) 1.11(2) 162(2) g

2.577(3) 1.50(3) 1.22(3) 140(3) h

2.583(2) 1.59(2) 1.08(2) 157(2) k

2.621(3) 1.62(3) 1.06(2) 155(2) l

H disordered over two sites in 0.66:0.34 ratio

complex. Bottom: Symmetrical