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Galileo Galilei, the father of modern science

Water structure: Methods

V Why different methods give different water structures?
V Dielectric spectroscopy
V Diffraction methods
V Modeling
V Nuclear Magnetic Resonance (NMR)
V Osmotic stress

V Physical properties
V Vibrational spectra
V Terahertz (THz) absorption spectroscopy

V Microwave (GHz) absorption spectroscopy

V Sum frequency generation

V X-Ray spectroscopy


Water structuring is not easy to study


Several independent methods have been used to investigate the structure of liquid water and aqueous and biomolecular [2729] solutions. Although each method is often promoted as producing accurate results, the different methods produce conflicting conclusions. This not only generates academic disputes but also, and more importantly, causes general confusion and bewilderment leading to scientific disorientation.


Why different methods give different water structures?


Each method produces data but this data does not directly give the structure of water. It has to be interpreted. Any analysis depends on a theoretical base to interpret the data. More importantly, the results are only as good as this theoretical base, however excellent the quality of the data collected. In addition, different methods give information at particular time-, or size-scales and so may naturally differ. a Here I show the principles behind the most important analytical methods (Dielectric spectroscopy, Diffraction methods, Models, Nuclear magnetic resonance, Physical properties, Vibrational spectra, X-Ray spectroscopy) and the main assumptions made to interpret their resulting data.

The size and time scales for the different techniques are given below:


Approximate timescales for different methods
Time and size scales
X-ray absorption ~10-15 s, single molecule
Almost instantaneous
Infrared, Raman ~10-14- 10-13 s, single molecule - local cluster
Vibrationally averaged
Models, Pump-probe laser ~10-12- 10-10 s, single molecule - local cluster
Diffusionally averaged
Neutron scattering, NMR shift ~10-9-10-6 s, local cluster
X-ray diffraction, thermodynamics > s, local cluster


The structuring found depends on the time-scale of the investigating methodology [2712] . Instantaneous structures show the actual positions and orientations of molecules, but these will be disordered relative to each other due to vibrational and linear and rotational diffusional motions; thus they will not show, or will show only poorly, any long term or extensive order in the system. Slow processes, such as diffraction, show 'averaged' structures that may be a very poor representation of any structuring consisting of two rapidly interchanging structures. e Diffraction data shows long term order but cannot determine whether the order is due to the same molecules being present in the same positions throughout or whether there are simply 'favored' positions with the molecules exchanging rapidly between them. [Back to Top to top of page]


Dielectric loss spectrum for ribonuclease

Dielectric spectroscopy

Dielectric spectroscopy [950] measures water tumbling and can detect water quantitatively in different clusters if they are held by different average hydrogen bond strengths. The dielectric loss is determined over a wide frequency range (kHz-GHz). Slow tumbling (~ ns) is due to tightly bound water whereas fast tumbling (~ ps) is due to loosely bound water. Opposite is shown an example spectrum of a protein solution [785], where the non-bulk water dielectric loss spectrum (red) can be divided into three underlying Gaussian peaks. c Difficulty remains in unambiguously assigning the molecular structures that produce these peaks. Dielectric spectroscopy does seem to show that long range interactions (~0.1 mm) are present in water [1630]. [Back to Top to top of page]

Diffraction methods

Braggs law for diffractionDiffraction methods make use of Bragg's law, involving the constructive interference of scattering (wavelength λ ~1 Å, integer n) from regularly spaced atoms (shown as blue dots with spacing d, see right). Neutron diffraction determines nuclear atomic coordinates whereas X-ray diffraction refers to the maxima of the electron density distribution. The time scale of X-ray and neutron scattering is very brief. Thus, diffraction methods [2553] involve the sum of a large number of instantaneous data from the many effectively frozen configurations of the sample. Thus, they measure the time-averaged distances between the atoms of water molecules. However, they cannot directly determine the cluster geometry. Also, the long-range hydrogen bonded structure and correlations in liquid water cannot be determined by diffraction as there is no long-range positional order of molecules in a liquid, so any such conclusions drawn are meaningful only on the short scale (< ~nm).


X-ray diffraction is sensitive to the concentration of electrons (so not sensitive to isotopes). Even though there are twice as many hydrogen atoms as oxygen atoms in water, these electron-poor atoms contribute little (hydrogen atoms have ~1/13 the electron density of the oxygen atoms and 2 ˣ 1/13 ~= 0.15), with ~85% of the data being provided by the gOO(r) radial distribution function and the remainder from the gOH(r) radial distribution function [1024] (H - H interactions being less than 0.6 %). Recently methodology for detecting hydrogen atoms and X-H bonds has been developed and this may be of great use in the future so long as the temperature is below 140 K, and that the resolution is at least 0.6 Å [2604].


Neutron diffraction of hexagonal ice at 220 K, from [154]

Radial distributions in ice Ih by neutron diffraction [154]

Neutron diffraction utilizes the wave property of slow neutrons produced in an atomic reactor (~ 0.1 eV, ≡ ~1 Å). It is sensitive to nuclei (including isotopes) and can be used to determine the positions of light atoms, such as hydrogen. However, for water it needs mixtures of D2O, HDO and H2O as H atoms are strong incoherent scatterers whereby the scatter contains no structural information. Such mixtures produce data with less precision and accuracy as such mixtures structure water differently from pure H2O.

first radial distances

Neutron diffraction gives gOO(r), gOD(r) and gDD(r) radial distribution data, which does allow some, if incomplete, orientation information to be extracted for neighboring water molecules. The results generally need much interpretation and help from modeling [2405]. Thus even crystalline ice Ih gives rise to artifactual peaks, see the O···O peaks at 2.43 Å and 3.45 Å opposite. Also, the widths of the peaks are greater than might be expected for a crystalline structure. The major drawback of neutron diffraction is the cost of the nuclear reactor facility with its intrinsic risk and poor accessibility for research.


Electron diffraction can only be used on thin films due to its strong scattering. Recent wide-angle X-ray diffraction has confirmed the existence of two distinctly different hydrogen-bonded environments in liquid water [1755].


The use of diffraction methods for studying the hydration structure of alkali ions has been reviewed [1062]. Diffraction data may be refined by fitting water model simulations [1245]. The resulting fit, however, is insensitive to the model chosen [888] such that optimizing the model to the fit does not, perforce, produce a better model. Diffraction results are discussed further elsewhere. Diffraction methods give data little different from bulk water beyond the first hydration shell where other methods indicate changed structure [1427].


Diffraction methods are excellent for testing models of water structure but less good for delivering the real structure of water due to the difficulty in obtaining orientation information and correlations at intermediate distances. [Back to Top to top of page]


Many molecular models for water are described on another page of this site. An underlying assumption for these models is that the structure of liquid water may be modeled using just two-body effects (that is, molecule A affects molecule B independently of molecule C affecting molecule B) and do not include any contribution from any covalency in their interaction. Models for liquid water have, so far, proved to be poor predictors for physical and molecular properties outside those used in their development and parameterization. Modeling studies may result in a picture of an 'average' liquid water molecule, which may be misleading as such 'average' structures do not exist in most ice phases and may not be relevant to liquid water. [Back to Top to top of page]

Nuclear Magnetic Resonance (NMR)

Water contains three isotopes of use in NMR. d


Properties of hydrogen nuclei
NMR, H2O atoms
Spin states
+1/2, -1/2
1, 0, -1
5/2, 3/2, 1/2, -1/2, -3/2, -5/2
Relative sensitivity at natural abundance
1.4 ˣ 10-6
1.1 ˣ 10-5
Gyromagnetic ratio, rad ˣ T-1 ˣ s-1 *
26.7522 ˣ 107
4.1066 ˣ 107
-3.6281 ˣ 107
Frequency at 2.3488 T (MHz) *

* data from WebElements.


The 1H and 2H NMR spectra can be used to quantify the deuterium atom content of H2O, HDO, D2O mixtures from the natural abundance to nearly 100% [1817]. As it has been reported that magnetic fields may alter the clustering of water ([192, 485, 647]), then the results of NMR must be considered with this possibility in mind. Another possible weakness to the use of NMR is that only ortho-water is NMR-active, para-water having no intrinsic magnetic moment [835]. However, all unpaired protons are NMR-active (not just ortho-water) and the exchange of protons may be a rapid compared with gathering the NMR signal [2118].


NMR analysis generally gives reduced information due to proton exchange and movement of water between environments. The average proton residence time on a water molecule is about a millisecond at 25 °C and pH 7, being less than that at other pHs or higher temperatures. Therefore, only single, population weighted averaged, 1H, 2H or 17O NMR peaks are generally seen in aqueous solutions. The exception to this is where separate non- (or very slowly) exchanging pools of water molecules are found.


Water's NMR chemical shifts (17O and 1H) are affected by ions in solution with increasing ionic radius generally causing an increased deshielding effect on the water oxygen atoms but a decreased deshielding effect on the water's protons [781]. The effects are linearly concentration dependent with a change in slope above the concentration that causes a minimum in the specific heat (~ 2-3 M) [556]. Here, the charge density effect (greater charge density causing greater deshielding), as seen in the division of ions into kosmotropes and chaotropes is less important than the ionic size effect [781]. As larger ionic size results in an increased number of first shell water molecules interacting with the ion's field within the clathrate surroundings, the apparent shielding change may be due to an increased effect on the average shift.


Both 1H and 17O NMR peaks shift to downfield (greater ppm) with increasing hydrogen bond strength; in the case of 17O, the donor O shift increasing greater than the acceptor O reduces. However, only ‘averaged’ water environments may be obtained. Where several aqueous environments exist, the 1H NMR spectrum (mainly just one broad peak) may be deconvoluted into Gaussian sub-bands due to differing degrees of hydrogen-bonded water with greater chemical shift (that is, ppm) indicating stronger hydrogen bonding and greater tetrahedrality of the water clustering [851].


The changes in the motion of interfacial water molecules on thawing, detected using NMR, can characterize the dynamic structure of proteins so adding considerably to the information available from protein 3-D structural determination [2249] . NMR has been used to estimate changes in water's hydrogen bond lengths and strengths [458]. Such investigation makes use ab initio calculations to interpret changes in the longitudinal relaxation T1 (see below) of HDO in D2O solution by assuming (somewhat incorrectly) that this mixture has a similar structure to pure H2O.


The NMR signal undergoes two relaxation processes; spin-lattice (longitudinal) relaxation resulting in the decay of the spin distribution (T1) and spin-spin (transverse) relaxation (T2) resulting in the loss of the spin coherence. T2 is inversely proportional to the width (at half height) of the NMR peak. T1 is 3.6 s at 25 °C due mostly to dipole-dipole couplings [430]. As T1 reduces with increasing dissolved molecular oxygen concentration (due to its paramagnetic nature) [782] and dissolved oxygen concentrations are expected to be greater in more hydrophobic environments near hydrophobic surfaces, dissolved oxygen is capable of giving rise to artifacts in the NMR spectra of water. Such affects may change over a period of several days [294].

Variation of NMR relaxation times with order in liquid water; from [581]


Shorter T2 values indicate less molecular mobility; the 1H T2 of water at 25 °C, viscous water and ice at 0 °C are about 3 s, ~1 ms and ~5 μs respectively. However, the T2 relaxation times are also reduced by exchange reactions, with for example, proteins carboxyl, hydroxyl and amine groups. Generally only single, population weighted averaged, 1H, 2H or 17O relaxation rates are seen in aqueous solutions. The exception to this is where separate non- (or very slowly) exchanging pools of water molecules exist such as occur in porous media including biological tissue and many foodstuffs. T1 and T2 are approximately equal for liquid water, both dropping with increased hydrogen-bonded clustering (for example, increased viscosity) under normal conditions. However, as the degree of tetrahedral clustering increases further, T1 increases as T2 decreases [581]. T1 thus shows a minimum at intermediate viscosity (rotational correlation time), f at the NMR resonant frequency, whereas T2 decreases continuously with increasing viscosity. Note that NMR relaxation is a non-equilibrium kinetic event and cannot give thermodynamic quantities such as water activity.


Comparison of the widths of the 17O-NMR peak at 25C and 400C

17O has been used to estimate water clustering by
means of NMR line-width measurement where
strongly clustered water gives broader peaks.
However this reasoning is faulty and the data is often imprecise and probably affected by dissolved O2 and pH; see also Paul Shin's critique of this method.


Shown opposite are the 17O NMR peaks for water at widely different temperatures, showing how little the width changes even under so different conditions [783].


Nuclear Overhauser effects (NOEs) may be used to identify relatively static water molecules within the first hydration shell (<~0.5 nm) around biological molecules [784].


Apparent diffusion rates of water are measured using magnetic field gradients [652,2112] and may be incorporated into magnetic resonance images (MRI). As diffusion is restricted in more extensive aqueous clusters, this method can differentiate different pools of water by their mean diffusion rates. NMR relaxation measurements can give the rotational diffusion coefficients using the natural 17O abundance [652, 2112]. [Back to Top to top of page]

Osmotic stress

Osmotic stress [2006, 2113] is complementary to other physical techniques in that it probes the changes in hydration that accompanies biologically relevant processes from their dependence on osmotic pressure (water activity). For example, the number of thermodynamically unique water molecules associated with the double helix and released from the single strands upon melting may be determined from the depression of melting temperature upon decreasing the water activity [2113]. [Back to Top to top of page]

Physical properties

Physical properties such as viscosity, compressibility, speed of sound, heat capacity, refractive index, thermal conductivity and surface tension can all be used to gather information concerning the structure of water. The interpretation of this data is not clear-cut, however. Note that only the surface properties, not the bulk properties, are discovered using surface tension. The surface structure of water is very different from the bulk structure and may mislead. [Back to Top to top of page]


The OH stretch peak of water at about 3400 cm-1, divided into three underlying gaussian peaks The OH stretch peak of water at about 3400 cm-1, divided into four underlying gaussian peaks The OH stretch peak of water at about 3400 cm-1, divided into five underlying gaussian peaks The OH stretch peak of water at about 3400 cm-1, divided into six underlying gaussian peaks, see ref. 1318

Vibrational spectra

Water gives complex infrared and Raman spectra [1738, 2627]. Analysis of these, together with changes caused by variations in temperature and/or pressure, or the presence of solutes, is thought capable of providing detailed information concerning liquid water structuring. Liquid water spectra reportedly corresponds to linear mixtures of just two contributing forms [1738]. b Due to peak broadening caused by the varying interactions between neighboring molecules, the spectra may be analyzed by supposing a number of Gaussian-shaped c vibrational absorptions underlying the complex peaks. Difficulties in the analysis concern determining how many absorption peaks are present and what are the molecular origins for these vibrations. Clearly the more vibrations that are thought to contribute to a complex absorption peak, the better may be any produced fit.


The peak at about 3400 cm-1, mainly due to symmetric and asymmetric stretching, has received considerable attention. It appears to consist of a small number of overlapping peaks but may be far more complex. The assignment of symmetric, asymmetric stretch and bending overtone is usually discarded in favor of the assumption of combined stretch absorptions shifted due to local hydrogen bonding arrangements. However and importantly, there is no consensus as to the number of underlying absorptions with different researchers using three, four or five absorptions, as are shown indicatively opposite.


More confusion in the analysis is due to the lack of a consensus view as to what these underlying absorptions represent. It is unclear whether the number of hydrogen bonds are important [786], or is it the type of hydrogen bond (single, bifurcated or trifurcated) [573], or is it the hydrogen bond bending angles [439], or perhaps the nature of the formed or broken donor and acceptor hydrogen bonds [699b], or the length of the hydrogen bonds [1318]. Each of these has been clearly argued (for example, see below) but the contributing vibrational peaks must contain all of these (and other) contributions. It is now believed that analysis involving individual water molecules and gaussian peaks may be inherently flawed as the absorption bands also reflect coherent vibrational transfer involving several to many water molecules [2003].

Further confusion of the Raman spectroscopy is that the peaks in the 3000-3700 cm-1 range are affected by the Raman excitation wavelength [1536]. In particular, the component at ~3200 cm-1 is in resonance with visible red light from a vibrational overtone.

Assignments from different authors
Peak a
Water's assigned hydrogen bond molecular linkages
unlinked 1 bifurcated b, 1 trifurcated c 2 H-bond, donors broken 3636 cm-1, unlinked
1 H-bond 2 bifurcated 2 H-bond, acceptors broken 3572 cm-1, 3 H-bond, acceptor broken
2 H-bond 1 O-H H-bonded, 1 bifurcated 3 H-bond, donor broken 3430 cm-1,2 H-bond, acceptor and donor broken
3 H-bond Both O-H are weakly H-bonded 3 H-bond, acceptor broken 3220 cm-1, 4 H-bond
4 H-bond Both O-H are strongly H-bonded 4 H-bond 3014 cm-1, 3 H-bond, donor broken
a From high to low wavenumber; 0 = greatest wavenumber.
b The O-H hydrogen bond is shared between two accepting water molecules.
c The O-H hydrogen bond is shared between three accepting water molecules.


A thorough and careful analysis of the combination band centered at about 5260 cm-1 failed to distinguish the substructures that correlate with the vibrational sub-bands [909].


The use of a pump-probe laser using 70-fs pulses at 3350 cm-1 (O-H stretch) and detecting the resultant molecular vibrations within the hydrogen-bonded clusters over a range of frequencies with time shows efficient energy redistribution [750]. However, this method is not yet able to show structuring details.


Two-dimensional Raman spectroscopy has been shown to provide information concerning water's intermolecular dynamics and may eventually provide data on the hydrogen bond network rearrangements responsible for water's anomalies [1097].

Terahertz (THz) absorption spectroscopy

Terahertz (THz) spectroscopy and two-dimensional Raman-THz spectroscopy [2050] (0.3 - 20 THz = 10 - 600 cm-1) may be used to investigate hydrogen bond network resonances and water dynamics on the picosecond timescale. THz absorption spectroscopy probes the reorientation of permanent and induced dipole moments of clusters and, from the time-dependence of these fluctuations, it is able to determine the frequency and strength of the cluster motions [1783].. In particular, the librational resonances of liquid water, that reflect water's hydrogen bonding, can be studied. Such spectroscopy can also be used to investigate the hydration layers around biomolecules [1196, 1427] and how they change during biological processes [2237]. This spectroscopy is powerful for examining changes in water mobility and shows changes in the water structuring at greater distances from biomolecules than those found using NMR or diffraction methods [1368, 1811]. The hydration state of solutions may be examined using terahertz time-domain attenuated total reflection spectroscopy, which makes use of the complete complex dielectric function; both the dielectric loss, due to relaxation motion of water, and the changes in the real part of the relative permittivity (dielectric constant) [1437]. [Back to Top to top of page]

Microwave (GHz) absorption spectroscopy

Rotational spectroscopy can be used in the gas phase for small water clusters. For example, broadband rotational spectroscopy has unambiguously identified the cage, prism, and book isomers of the water hexamer (H2O)6 [2260].

Sum frequency generation

SFG; the output visible light signal (vis out) is due to the sum of the input visible beam (vis) and a resonant infrared beamSum frequency generation (SFG) and second harmonic generation (SHG) surface spectra are spectroscopic methods for investigating the surface of water without interference from the bulk liquid [2627]. The output spectra derive from a combination of input beams when the infrared frequency is in resonance with a vibration within the interface (for example the O-H vibration of water, see right). As both the bulk aqueous solution and the gas phase are isotropic, they are not active in this spectroscopy, leaving just the anisotropic interfacial layer to provide the spectra, due to a net orientation of surface molecular dipoles. The depth of this anisotropy governs the depth probed. As the spectra are acquired over periods of seconds, it is of interest that the surface monolayer may be exchanged millions of time during this period [2408]. It is thus surprising that any spectral features remain from within this ever-changing environment. Any surface-active ions must continue with unchanging spectra even though the surface is in continual flux.

X-Ray spectroscopy (~500 eV)

mechanism for XAS and XESX-ray-based techniques can be used to study the hydrogen-bond network of liquid water [1965, 2623]. As the techniques have attosecond timescales, they reflect the instantaneous molecular configuration of the water molecules. Difficulties in the interpretation of these techniques are due to the lack of a robust theoretical understanding [2623].


X-Ray absorption spectroscopy (XAS) involves the absorption of high-energy photons to excite core (1s, 2s) electrons to unoccupied p-character valence levels. (see the molecular orbital energy levels left). The energies required are sensitive to the local environment mostly providing information concerning the hydrogen bond donating orbitals of the absorbing molecule at very short timescales (~ 10-18s) [373, 690a, 1757].


The energies given left are those calculated for isolated molecules using the Restricted Hartree-Fock wave function (RHF) using the 6-31G** basis set. Some electron movements are forbidden, such as 2a1 to half-empty1a1 Hydrogen bonding affects the energy levels.


XAS has been used to investigate the hydration of concentrated salt solutions [2170]. At high photon energy, expelled electrons have sufficient energy to escape from their atom (to the continuum) and at higher energies these escaped electrons may produce signals due to backscattering. Care must be taken to avoid artifacts at the water-air surface due to desorption [1440]. X-ray Raman scattering (XRS) gives similar results to XAS and involves the inelastic scattering of x-rays from the core electrons.

X-ray absorption spectrum of liquid water, showing possible underlying gaussian contributionsShown right is the O K-edge (1s) XAS of liquid water (red) with possible underlying Gaussian (blue) and continuum (green) contributions.


The first peak in the X-Ray absorption spectrum (right) at about 535 eV is due to excitation from the 1s orbital to the vacant O-H 4a1 antibonding orbital. Assignment of these gaussian peaks to electron transitions depends heavily on the underlying theory (for example, see the current dispute) as there is little structure in the experimental spectrum, this spectrum varies from run to run [690c], between methods and between different energies of the X-rays.


Thus, data fitting is error-prone. An interesting discussion of these differences has been published [834].


X-ray emission spectrum of water, showing possible underlying gaussian contributionsRelated to XAS is the X-ray emission spectra (XES, shown right, [1757]) involving transitions from the three outermost occupied molecular orbitals 1b1, 3a1 and 1b2 to fill the vacancy (produced as above) in the 1a1 (1s) orbital [411]; peaks occurring in the 520-528 eV range and corresponding to instantaneous local structuring (~ 10-15s). Recent X-ray emission spectroscopy shows the presence in liquid water of two well-separated peaks (split from the lone-pair non-bonding 1b1 peak) that interconvert but do not broaden with changes in temperature [1639]. This strongly supports a two-state network model such as presented here, although it has been proposed that it may be alternatively due to ultrafast dynamics during the core-hole lifetime [2196].


Another recently improved X-ray technique is small-angle X-ray scattering (SAXS, [1757]) which is sensitive to density inhomogeneities in the nm-range has confirmed the existence of two distinctly different hydrogen-bonded environments in liquid water [1757].


a Consider, for example, the very different photographs obtained at night of cars on the road between the use of fast flash and a natural light long exposure. Short exposures show the cars but not the roads; long exposures show the roads but not the cars. [Back]


b There is evidence, however, that the spectra may be due to a continuous variation in the hydrogen bonding and not due to discrete but overlapping populations [875]. [Back]

Normal distribution curve with W=1 and centered on lambda max


c A Gaussian curve (normal distribution curve) may be represented by the relationship:


therefore, for vibrational peaks,

Amplitude = maximum amplitude x exp(-0.5 x {(wavenumber -  wavenumber of peak)/(2.355 x width at half height)}squared)


where A is the amplitude, Amax is the peak height, λ is the wave number , λmax is the wavenumber at the peak and W is the width of the peak at half height, and the standard deviation (s) of the distribution s = W/(2 ˣ Ö(2 ˣ Ln (2)).


It should be noted that although there is no theoretical reason why the actual sub-peaks should correspond exactly with Gaussian-shaped peaks, they generally fit well. [Back, 2]


d 16O and 18O have no nuclear spin. [Back]


e As an example of this, consider the 'average' structure of a person; nothing like a man or a woman, but somewhere in between. [Back]


f The rotational correlation time is the time it takes the average molecule to rotate one radian. It may be determined by dielectric spectroscopy .[Back]




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