Water structure and science

water molecule electron shape

Water Molecule Structure

Water consists of small polar V-shaped molecules with molecular formula H2O

< Water's molecular vibrations and absorptions

< Water dimer

< ortho-water and para-water

V Water structure, Introduction

V Water structure, advanced

V Water's lone pairs
V Water electronic structure
V Water models
V Water reactivity

'Water is H2O, hydrogen two parts, oxygen one, but there is also a third thing, that makes it water and nobody knows what it is. '

D H Lawrence (1885-1930) 

Water structure, Introduction

Water is a tiny bent molecule with the molecular formula H2O, consisting of two light hydrogen atoms attached to each 16-fold heavier oxygen atom. Each molecule is electrically neutral but polar, with the center of positive and negative charges located in different places. Each hydrogen atom has a nucleus consisting of a single positively-charged proton surrounded by a 'cloud' of a single negatively-charged electron and the oxygen atom has a nucleus consisting of a eight positively-charged protons and eight uncharged neutrons surrounded by a 'cloud' of a eight negatively-charged electrons. On forming the molecule, the ten electrons pair up into five 'orbitals', one pair closely associated with the oxygen atom, two pairs associated with the oxygen atom as 'outer' electrons and two pairs forming each of the two identical O-H covalent bonds.

The eight outer electrons are often shown as the pairs of dots in    H2O    where the pairs of electrons between the O and H atoms represent the O-H covalent bonds and the other two pairs of electrons represent the so-called 'lone pairs'. These electron pairs form electron 'clouds' that are spread out approximately tetrahedrally around the oxygen nucleus as they repel each other. This is the reason for water's bent structure. The eight positive charges in the oxygen nucleus attract all these electrons strongly relative to the single positive charges on each of the hydrogen atoms. This leaves the hydrogen atoms partially denuded of electrons, and hence partially positively charged, and the oxygen atom partially negatively charged, that is,       .H2O with charges .

Due to the presence of these charges and the bent nature of the molecule, the center of the positive charge (half way between the two hydrogen atoms) does not coincide with the center of the negative charge (on the oxygen atom). In liquid water, this gives a molecular dipole moment from the center of negative charge to the center of positive charge, equivalent to a unit negative charge (that is, one electron) separated from a unit positive charge by 0.061 nm. The presence of this dipole moment in all water molecules causes its polar nature.

Water is much smaller than almost all other molecules. As a result, both liquid and solid water (ice) have high densities of molecules. One liter of water at room temperature (25 °C) weighs almost a kilogram (997 g) and contains about 33 million million million million molecules.

The molecule is V-shaped. It is often shown as    H2O    or    H2O    but is better represented as    H2O    or even    H2O    giving a more accurate idea of its rather rotund shape and also indicating the charge (pink showing negatively charged surface and green showing positively charged surface).

In liquid water, the mean O-H length is about 0.097 nm, the mean H-O-H angle is about 106° and the mean negative charge on the oxygen atom is about 70% of that of an electron with each hydrogen atom positively charged sharing the neutralizing charge. Individual water molecules will have different values for these parameters dependent on their energy and surroundings. The opposite charges on the oxygen and hydrogen atoms causes different water molecules to attract each other. This attraction is particularly strong when the O-H bond from one water molecule points directly at a nearby oxygen atom in another water molecule, that is, when the three atoms O-H O are in a straight line. This is called 'hydrogen bonding' as the hydrogen atoms appear to hold on to both O atoms. This attraction between neighboring water molecules, together with the high-density of molecules due to their small size, produces a great cohesive effect within liquid water that is responsible for water's liquid nature at ambient temperatures.

Heavy water (D2O) has similar, but not identical, properties to H2O. The deuterium atom (D) is a stable isotope of hydrogen that has a neutron alongside the proton in its nucleus, almost doubling its atomic mass.

Water structure, advanced

Water molecules c are tiny, electrically neutral and V-shaped with molecular formula H2O a and molecular diameter about 2.75 Å. g Water is much smaller than almost all other molecules. For example, it has a smaller volume, and is much lighter, than the four other common atmospheric molecules, oxygen (O2), nitrogen (N2), argon (Ar) and carbon dioxide (CO2); the density of water vapor being just 62% the density of dry air [2215].

In the liquid state, in spite of 80% of the electrons in H2O being concerned with bonding, the three atoms do not stay together as the hydrogen atoms are constantly exchanging between water molecules, due to protonation/deprotonation processes. Both acids and bases catalyze this exchange and even when at its slowest (at pH 7), the average time for the atoms in an H2O molecule to stay together is only about a millisecond. As this brief period is, however, much longer than the timescales encountered during investigations into water's hydrogen bonding or hydration properties, water is usually treated as a permanent structure.

Water symmetry

Water molecules have two mirror planes of symmetry and a 2-fold rotation axis

Water molecules (H2O) are symmetric (point group C) with two mirror planes of symmetry and a 2-fold rotation axis. The hydrogen atoms may possess parallel or antiparallel nuclear spin. The water molecule consists of two light atoms (H) and a relatively heavy atom (O). The approximately 16-fold difference in mass gives rise to its ease of rotation and the significant relative movements of the hydrogen nuclei, which are in constant and significant relative movement even at a temperature of absolute zero (0 K).

Due to the relatively large positive charge on the oxygen atom nucleus (8+) and the closeness of its electrons, the oxygen atom attracts electrons much more strongly (i.e. is much more electronegative) than the hydrogen atoms (1+). This results in a charge transfer from the hydrogen atoms towards the oxygen atom and, hence, the polarity of the water molecule.

Water's lone pairs?

Water, showing tetrahedrally positioned lone pair electrons

Note. This cartoon of water does not represent its actual outline, which is more rotund (see below).

H2OThe water molecule is often described in school and undergraduate textbooks as having four, approximately tetrahedrally arranged, sp3-hybridized electron pairs, two of which are associated with covalent bonds to the hydrogen atoms leaving the two remaining lone pairs. In a perfect tetrahedral arrangement the bond-bond, bond-lone pair and lone pair-lone pair angles would all be 109.47° and such tetrahedral bonding patterns are found in condensed phases such as hexagonal ice.

Lone pairs as smeared electic charge

H2O molecule showing the smeared electic charge

Ab initio calculations on isolated molecules, however, do not confirm the presence of significant directed electron density where lone pairs are expected. The negative charge is more evenly smeared out along the line between where these lone pairs would have been expected, and lies closer to the center of the O-atom than the centers of positive charge on the hydrogen atoms (as left).


Water electrostatic potential

Water structure, showing the electrostatic potential is raised at those tetrahedral positions where lone pair electrons are commonly displayed
Early 5-point molecular models, with explicit negative charge where the lone pairs are purported to be, fared poorly in describing hydrogen bonding, but more recent models show some promise. Although there is no apparent consensus of opinion [116], such descriptions of substantial sp3-hybridized lone pairs in the isolated water molecule should perhaps be avoided [117], as an sp2-hybridized structure (plus a pz orbital) is indicated. This rationalizes the formation of (almost planar) trigonal hydrogen bonding that can be found around some restricted sites in the hydration of proteins and where the numbers of hydrogen bond donors and acceptors are unequal.

Shown opposite is the electrostatic potential associated with the water structure. Although the lone pairs of electrons do not appear to give distinct directed electron density in isolated molecules, there are minima in the electrostatic potential in approximately the expected positions; approximately tetrahedrally placed 1.22 Å out [2137]. The use of minima in such
molecular electrostatic potential has been proposed in the definition of lone pairs [2137].

Water charge distribution

Water structure, showing that the charge distribution is concentrated around the oxygen atom    























Note that the average electron density around the oxygen atom is about 10x that around the hydrogen atoms.

Water electronic structure

Approximate shape and charge distribution of water

         Water structure, showing that the charge distribution is lower around the hydrogen atoms

The electron density distribution for water is shown above right with some higher density contours around the oxygen atom omitted for clarity. As the centers of positive and negative charge lie in different places, the molecule is polar with a dipole moment. The polarizability of the molecule is almost isotropic, centered around the O-atom (1.4146 Å3) with only small polarizabilities centered on the H-atoms (0.0836 Å3) [736]. Parameters using ab initio calculations with the 6-31G** basis set are shown right. b For an isolated H216O, H217O or H218O molecule, the more exact calculated O-H length is 0.957854 Å and the H-O-H angle is 104.500° (D216O, 0.957835 Å, 104.490°) [836]. The charge distribution depends significantly on the atomic geometry and the method for its calculation but is likely to be about -0.7e on the O-atom (with the equal but opposite positive charge equally divided between the H-atoms) for the isolated molecule [778]. d

Energy diagram for water's bend and stretch

Energy diagrams (rom ab initio 6-31G** calculation) and the zero-point vibrational energies for water's bend and stretch
The experimental values for gaseous water molecule are O-H length 0.95718 Å, H-O-H angle 104.474° [64]. These parameters are the thermodynamically most stable, but the bonds exhibit vibrations away from these values. The energy diagrams and the zero-point vibrational energies (shown blue) are given left. The actual values depend on the vibrational state of the molecule with even values of 180° being attainable during high order bend vibrations (v2 >= 7, λ < 900 nm) for the H-O-H angle [860]. Vibrations are asymmetric around the mean positions. In the ground state, the bond angle (104.5°) is much closer to the tetrahedral angle than that of the other Group VI hydrides, H2S (92.1°), H2Se (91°) or H2Te (89°).

These values are not maintained in liquid water, where ab initio (O-H length 0.991 Å, H-O-H angle 105.5° [90]) and diffraction studies (O-H length 1.01 Å, O-D length 0.98 Å [1485]; O-H length 0.990 Å, O-D length 0.985 Å [1884]; O-D length 0.970 Å, D-O-D angle 106° [91]) f suggest slightly greater values, which are caused by the hydrogen bonding weakening the covalent bonding and reducing the repulsion between the electron orbitals. These bond lengths and angles are likely to change, due to polarization shifts, in different hydrogen-bonded environments and when the water molecules are bound to solutes and ions. Commonly used molecular models use O-H lengths of between 0.957 Å and 1.00 Å and H-O-H angles of 104.52° to 109.5°. [Back to Top to top of page]

The molecule H2O has 10 electrons associated, 8 from the oxygen atom and one each from the two hydrogen atoms. Its electronic structure has been proposed as 1sO2.00 2sO1.82 2pxO1.50 2pzO1.12 2pyO2.00 1sH10.78 1sH20.78 [71], with the inner 1sO pair of electrons unhybridized. However it now appears that the 2s orbital may also be effectively unhybridized with the bond angle expanded from the (then) expected angle of 90° due to the steric and ionic repulsion between  the partially-positively charged hydrogen atoms (as proposed by Pauling over 50 years ago [99]). The molecular orbitals of water, (1a1)2(2a1)2(1b2)2(3a1)2(1b1)2(4a1)0(2b2)0 are shown on another page.

Van der Waals radii [206]

van der Waals volume of water


The mean van der Waals diameter of water has been reported as identical with that of isoelectronic neon (2.82 Å) [112]. Molecular model values and intermediate peak radial distribution data indicates however that it is somewhat greater (~3.2Å). The molecule is clearly not spherical, however, with about a ±5% variation in van der Waals diameter dependent on the axis chosen; approximately tetrahedrally placed slight indentations being apparent opposite the (putative) electron pairs. The H-O···O angle (0°) shown here (representing non-hydrogen-bonded close-packed water molecules) has been found by neutron diffraction in liquid water as a minor arrangement [2405].


A novel state of the water molecule has been described where single molecules sit within the voids in the beryl crystal and hydrogen atoms are spread into rings (see elsewhere) [2547]. [Back to Top to top of page]

Water models

Simplified models for the water molecule have been developed to agree with particular physical properties (for example, agreement with the critical parameters) but they are not robust and resultant data are often very sensitive to the precise model parameters [206]. Models are still being developed and are generally more complex than earlier but they still appear to have poor predictive value outside the conditions and physical parameters for which they were developed. [Back to Top to top of page]

Water reactivity

Although not often perceived as such, water is a very reactive molecule available at a high concentration. This reactivity, however, is greatly moderated in the liquid at ambient temperatures due to the extensive hydrogen bonding. Water molecules each possess a strongly nucleophilic oxygen atom that enables many of life‘s reactions, as well as dissociating to produce reactive hydrogen ions and hydroxide ions. Reduction of the hydrogen bonding at high temperatures, or due to electro-magnetic fields, results in greater reactivity of the water molecules.


This reactivity is particularly noted in the gas phase within our atmosphere, where water molecules are important reactants, complexing agents, surface-active reagents and catalysts [3063]. [Back to Top to top of page]


a It has been suggested that H1.5O may better reflect the formula at very small (attosecond) timescales when some of the H-atoms appear invisible to neutron and electron interaction [515]. The experimental results have since been questioned [630] and described as erroneous [796], but have been more recently confirmed and thought due to a failure of the Born-Oppenheimer approximation (this assumes that the electronic motion and the nuclear motion in molecules can be separated) [1134]. Thus the formula H1.5O is incorrect but such suggestions do, however, add support to the view that observations concerning the structure of water should be tempered by the timescale used. In charged droplets the water formula may be given as between H2.00000000045 Oδ+ and H1.999 999 9986 Oδ- [2661]. [Back]

b More exact parameters are given in the text. These parameters are given mainly for comparison with the hydrogen and hydroxide ions. In reality, no distance or angle is exact as the molecules are not rigid structures and are vibrating. [Back]

c Liquid water consists of a mixture of molecules [1377] and ions, including H2O, HDO (~10-2 %), H3O+ and OH- (~10-6 %), H2O2 (~10-7 %), CO2 (~10-4 %), O2 (~10-4 %) and N2 (~10-3 %). A 'standard' water (Vienna Standard Mean Ocean Water) has been proposed. 'Pure liquid water', meaning consisting of just H2O molecules, only exists in computer simulations. Even 'just H2O' consists of a mixture of 'ortho' and 'para' forms. Avoiding this complexity, 'water' is normally taken to mean H2O molecules, without consideration over its magnetic state. H2O is also known as 'light water' with D2O being heavy water (D2O density = 111% H2O density, 25 °C) and T2O being super heavy water (T2O density = 122% H2O density, 25 °C). The properties of H2O, D2O and T2O are different. Even though the amount of deuterium in commonly-found water is low (~16 mM) the properties of such water are different to water containing protium (1H) only [2063]. [Back]

Atomic charges of the first row hydrides

Atomic charges of the hydrides across the first row of the periodic table -0.022 -0.724 (c) Martin Chaplin 15 October, 2017
(printed 20 January 2018)