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Water Structure and Science Site Map

Water structure = H2O


'...of all known liquids, water is probably the most studied and least understood.”'

Felix Franks, 1972




The water molecule


The structure of the water molecule

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

Easier introduction to the water molecule

ortho-water and para-water

H2COW [Plug-in, ActiveX] animation

The molecular orbitals of water, H2O

Hydrogen bonding

Hydrogen bonds

Hydrogen bonding in water (1)

Water hydrogen bonds
Water hydrogen bond length
Water hydrogen bond direction

Hydrogen bonding and information transfer (2)

Hydrogen bond cooperativity

Quantum effects
Rearranging hydrogen bonds
Bifurcated hydrogen bonds
Information transfer
Hydrogen bonds and solubility
Water dimerand small clusters

Water dimer inside fullerene C70

Comparison with trimer, tetramer and pentamer

Small clusters

(H2O)2 COW [Plug-in, ActiveX] animation

 All-cis (H2O)5, COW [Plug-in, ActiveX] animation

 Global minimum, COW [Plug-in, ActiveX] animation

The molecular orbitals of a water dimer, (H2O)2

The molecular orbitals of a water cyclic pentamer, (H2O)5

The Phase Diagram of water

Phase diagrams

The phase diagram of water
Triple points

Density change

Supercritical water
Ice phases

Known ices

Very high pressure ices

Ice 0 Jmol animation

Computer ices (ice 0)

Vonnegut's ice-nine
Ice crystal data

ice Ih Jmol animation

Hexagonal ice

Ice nucleation and growth
Is ice slippery?

Ice IJmol animation

Stacking disordered ice (Ice Isd) Jmol animation

Ice II Jmol animation

Ice III Jmol animation

Ice IV Jmol animation

Ice V Jmol animation

Ice VI Jmol animation

Ice VII Jmol animation

Ice VIII Jmol animation

Ice IX Jmol animation

Ice X Jmol animation

Ice XI Jmol animation

Ice XII Jmol animation

Ice XIII Jmol animation

Ice XIV Jmol animation

Ice XV Jmol animation

 Ice XVI Jmol animation

Cubic ice (Ic/XIc)

Stacking disordered ice; Ice Isd















Ultra low density ices

Clathrate s-III (ice XVII?)

Amorphous ice and glassy water

Supercooled water

Cold metastable glassy water
Ultraviscous water and the glass transition temperature
Low-density amorphous ice (LDA)
High-density amorphous ice (HDA)
Very-high density amorphous ice (VHDA)

Clathrate ices I, II and H

 Clathrate ice I, Jmol animation

 Clathrate ice II, Jmol animation

 Clathrate ice H, Jmol animation

CS-I clathrate
CS-II clathrate
HS-III clathrate
Other structures

Molecular vibration and absorption of water

Water and the atmosphere

Absorption and penetration

Absorption spectra of gaseous, liquid and solid water
The vibrational spectra of liquid water
The visible and UV spectra of liquid water

The spectrum of the Zundel cation
Absorption and penetration

Water dissociation, 2H2O = H3O+ + OH-

The ionic product, Kw


Variation in Kw with temperature and pressure

Acidity and basicity
Hydrogen ions
Hydroxide ions
Grotthuss mechanism
Diffusion of hydrogen ions
Diffusion of hydroxyl ions

H3O+ COW [Plug-in, ActiveX] animation

OH- COW [Plug-in, ActiveX] animation

The molecular orbitals of the H3O+ and OH- ions

H3O2- COW [Plug-in, ActiveX] animation

 Asymmetric H5O2+, COW [Plug-in, ActiveX]

 Symmetric H5O2+, COW [Plug-in, ActiveX]

The molecular orbitals of the hydrated hydroxide ion, H3O2-

The molecular orbitals of the dihydronium ions, H5O2+

Water at interfaces and nanobubbles

Confined water

Hydrophobic confinement

Hydrophilic confinement

Water molecules confined in beryl nanovoids


Capillary rise
Venturi effect

Interfacial water and water-gas interfaces

The surface of water
Zeta potential
Thermodynamics of the liquid-gas surface for water

Nanobubbles (ultrafine bubbles)


Evidence for nanobubbles

Nanobubbles preparation and use
Rationale for nanobubble stability

Seventy two anomalous properties of water

The range of anomalous properties of water

Phase anomalies P1-P13

Water has unusually high melting point
Water has unusually high boiling point
Water has unusually high critical point
Solid water exists in a wide variety of stable structures
The thermal conductivity, shear modulus and transverse sound velocity of ice reduce with increasing pressure
The structure of liquid water changes at high pressure
Supercooled water has two phases
Liquid water is easily supercooled but glassified with difficulty
A liquid water phase exists at very low temperatures
Liquid water may be easily superheated
Hot water freezes faster than cold water; the Mpemba effect
Warm water vibrates longer than cold water
Water molecules shrink as the temperature rises and expand as the pressure increases

Density anomalies D1-D22

The density of ice increases on heating (up to 70 K)
Water expands on freezing
Pressure reduces ice's melting point
Liquid water has a high density that increases on heating
The surface of water is denser than the bulk
Pressure reduces the temperature of maximum density
There is a minimum in the density of supercooled water
Water has a low thermal expansivity
Water's thermal expansivity reduces at low temperatures
Water's thermal expansivity increases with increased pressure
The number of nearest neighbors increases on melting
Nearest neighbors increases with temperature
Water has unusually low compressibility
The compressibility drops as temperature increases
The compressibility-temperature maximum
The speed of sound increases with temperature up to 74 °C
The speed of sound may show a minimum
'Fast sound' is found at high frequencies
NMR relaxation time is very small at low temperatures
The NMR shift increases to a maximum at low (supercool) temperatures
The refractive index of water has a maximum value
The change in volume as liquid changes to gas is very large

Material anomalies M1-M16

No aqueous solution is ideal
D2O and T2O differ significantly from H2O
Liquid H2O and D2O differ significantly in their phase behavior
H2O and D 2O ices differ significantly in their quantum behavior
The mean kinetic energy of water's hydrogen atoms increases at low temperature
Solutes have varying effects on water's properties
Non-polar gases solubility decreases with temperature
The dielectric constant of water and ice are high
The relative permittivity shows a temperature maximum
Proton and hydroxide ion mobilities are anomalously fast
The electrical conductivity of water rises to a maximum
The electrical conductivity of water rises with frequency
Acidity constants of weak acids show temperature minima
X-ray diffraction shows an unusually detailed structure
Under high pressure water molecules move apart
Water adsorption may cause negative electrical resistance

Thermodynamic anomalies T1-T11

The heat of fusion of water exhibits a maximum at -17 °C
Water has higher specific heat capacity than ice or steam
The specific heat capacity (CP and CV) is unusually high
The specific heat capacity CP has a minimum at 36°
The specific heat capacity (CP) has a maximum
The specific heat capacity (CP) has a pressure minimum
The heat capacity (CV) has a maximum
High heat of vaporization
High heat of sublimation
High entropy of vaporization
The thermal conductivity of water is high

Physical anomalies F1-F10

Water has unusually high viscosity
Large viscosity and Prandtl number increase as the temperature is lowered
Water's viscosity decreases with pressure below 33 °C
Large diffusion decrease as the temperature is lowered
The self-diffusion of water increases with the density
The thermal diffusivity rises to a maximum at about 0.8 GPa
Water has unusually high surface tension
Some salts give a surface tension minimum; the Jones-Ray effect
Some salts prevent the coalescence of small bubbles
The molar ionic volumes of salts show maxima with respect to temperature

Properties of water and its isotopologues

Short properties list for liquid H2O

Changes in some properties with temperature (-30 °C - 100 °C)

Changes in some further properties with temperature (0 °C - 373 °C)

Water-related molecules; comparative data

Important constants and conversion factors

Periodic Table

Unexpected properties of water

Vapor pressure-Temperature behavior

Pressure-Temperature-Density behavior

Volume-Temperature behavior

Temperature-viscosity behavior

Temperature-enthalpy of vaporization relationship

Logarithmic relationships emanating from 228 K

Water molecular models

Water model parameterization

Water model descriptions
Water model properties

Water clustering in liquid water

 (H2O)8 equilibria animation

Overview of the structuring in liquid water

Water clustering
Cluster and H-bond lifetimes are independent
Icosahedral water cluster

Introduction to water clustering

Water's two-state cluster history

Icosahedral clustering and the two-state mixture model?

Outline of methods for investigating water structure

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

Osmotic stress
Physical properties
Vibrational spectra
Terahertz (THz) absorption spectroscopy
Microwave (GHz) absorption spectroscopy
Sum frequency generation (SFG)
X-Ray spectroscopy

(H2O)100 and (H2O)280 clusters Jmol animation

(H2O)280 cluster equilibria Jmol animation

Tetrahedral (H2O)14 cluster Jmol animation

The icosahedral (H2O)280 water clusters

Tetrahedral units
Icosahedral clusters
Cluster equilibria
Cluster density
Sub-structures of the icosahedral water cluster
Connectivity map of the water icosahedron
Solid geometry of the icosahedral cluster (Java)

Super cluster ((H2O)280)13 Jmol animation

Super network ((H2O)100)n Jmol animation

Cluster puckering Jmol animation

Tetrahedra cluster Jmol animation

Bicyclo-octamers cluster Jmol animation

Super clusters of water molecules

Water cluster equilibria, puckering and temperature effects

Water icosahedral cluster architecture

Explanation of water cluster equilibria using animated gifs

Spherical coordinates of the icosahedral water clusters

Shell radii and occupancy of the icosahedral water clusters

Superstrand Jmol animation

Alternative icosahedral clusters Jmol animation

Alternative tetrahedral clusters Jmol animation

 Cavities and networks, Jmol animation

 Clathrate-like, Jmol animation

Super clusters of water molecules

Alternative icosahedral clustering of water

Alternative tetrahedral clustering of water

Water cluster architecture, based on gas clathrates

Paper model of an icosahedral water structure

Paper model of an truncated icosahedral water structure

Plain paper model of the layers of a truncated icosahedral water structure

Evidence for icosahedral water clusters

The radial distribution function
Other support from diffraction data

How can a liquid have a structure?

Does the radial distribution peak at about 3.7 Å exist?

Is there fine structure in the radial distribution function?

Do interstitial water molecules exist?
Support from clathrate structures
Evidence from amorphous ice and low density water
Other evidence

Water cluster conclusions


Protein hydration

The contribution of water to protein structure

Water in protein recognition and binding
Water in protein function

Protein folding and denaturation
Protein folding
Protein crystallization
Protein denaturation

Nucleic acid hydration

Hydrogen bonds in the nucleic acids

DNA hydration
DNA processing

Biomembrane hydration
Cholesterol and membrane hydration

Inositol Jmol animation

Cyclodextrin Jmol animation

Sugar hydration

Aqueous properties of the cyclodextrins

Polysaccharide hydration
Alternatives for defining bound and unbound water
Polar effects, for example, α-D-galacturonic acid
Weak hydrogen bonding, for example, α-L-arabinofuranose
Strong hydrogen bonding, for example, β-1-4-linked D-xylose
Hydrophobic effects, for example, β-1-4-linked D-xylose
Effects of other solutes: non-ionic
Effects of other solutes: ionic
Conclusions concerning polysaccharide hydration

Introduction to polysaccharides

Chart showing the furan pseudorotational angles of ribose and deoxyribose

Hydrocolloids and gums

Hydrocolloid polymers


Mixtures of hydrocolloids
Effect on viscosity
Hydrocolloid action

Agar Jmol animation






Alginate Jmol animation





Arabinoxylan Jmol animation





Carrageenan Jmol animation






CMC Jmol animation





Cellulose Jmol animation





Curdlan Jmol animation





Gelatin Jmol animation


Structural unit
Molecular structure


Structural unit
Molecular structure


Structural unit
Molecular structure


Structural unit
Molecular structure, κ-, ι-, λ- carrageenans, Helices


Structural unit
Molecular structure


Sources for cellulose
Structural unit
Molecular structure


Structural unit
Molecular structure


Sources for gelatin
Structural unit
Molecular structure
Functionality and concerns


Structural unit
Molecular structure

β-Glucan Jmol animation


Structural unit
Molecular structure

Gum arabic

Structural unit
Molecular structure
Other similar gums

Guar gum Jmol animation





Locust bean gum Jmol animation





Pectin Jmol animation





Starch Jmol animation





Xanthan gum Jmol animation

Guar gum

Structural unit
Molecular structure

Locust bean gum

Structural unit
Molecular structure


Pectin sources
Pectin structural unit
Molecular structure


Sources for starch
Structural unit
Molecular structure

Xanthan gum

Structural unit
Molecular structure

Hydrocolloid rheology

Structural effects
Further rheological terminology

Hydrocolloids and health (Dietary fiber)

Dietary fiber

The effect of dietary fiber in digestion
The colon
Colonic fermentation
Water-holding capacity (WHC)
Viscosity and gel formation
Binding to bile acids

Ion hydration and aqueous solutions of salts

What is meant by ion hydration

Methods for determining ion hydration

Ion pairs
Water clustering around ions

SO42 cluster Jmol animation

Sulfate and other large anions

The Hofmeister series

H3O+ magic number cluster Jmol animation 

The H3O+ magic number cluster ions

Water clustering around the SO42- cluster

CO2 cluster Jmol animation

Water clustering around the CO2 cluster

Aqueous CO2 equilibria

Kosmotropes and chaotropes 

Definitions of kosmotropes and chaotropes

Ionic kosmotropes and chaotropes
Non-ionic kosmotropes and chaotropes
Trimethylamine N-oxide (TMAO)

Hydrophobic hydration

The hydrophobic effect

Hydrophobic versus hydrophilic interfaces
Extensive hydrophobic interfaces
Solubility effects
Salting-out and salting-in
Alcoholic solutions

Alcoholic tears

Carboxylate link Jmol animation

Intracellular water

Intracellular solutions contain more K+ ions
Membranes help create a tendency towards low density water in cells
The effect of intracellular protein on water structuring
The importance of protein carboxylate groups
The importance of protein mobility
Cooperative conversion of the water structuring
Actin, tubulins and the intermediate filaments

Water and astrobiology


The origin of Earth's water

What is life?

How life originated

How many planets have life in the Universe

Life on Mars?

Water on Earth
Water in the mantle
Salt water (seawater)
Water and global warming

Water cycle
Water availability
Water use

Hard water, descaling and desalination

Hard water
Water softening
Magnetic descaling

Water and life
Can life exist without water?
Consequences of changes in water’s hydrogen bond strength
Estimating the effect of changes in water hydrogen bond strength
Effect of water hydrogen bond strength on melting and boiling point
Effect of hydrogen bond strength on the temperature of maximum density
Effect of water hydrogen bond strength on kosmotropes and chaotropes
Effect of water hydrogen bond strength on its dissociation
Effect of water hydrogen bond strength on biomolecule hydration
Effect of water hydrogen bond strength on its other physical properties
Conclusions concerning water and life

Water and health

Water content
Water balance
Water requirements
Water roles
Drinking water

Water redox processes
The redox potential of water


Electrolysis compartments

What is less well understood?

Driving cars using water

Magnetic and electric effects on water

Electric effects on water
Magnetic effects on water
Electromagnetic effects on water

Magnetic descaling
Other related effects

Water and microwaves

Dielectric loss
Effect of salt
Electromagnetic penetration

Dielectric constant and polarization

Background information and definitions
Polarization and polarizability
Refractive index

The complex dielectric permittivity behavior of water

The complex dielectric permittivity

Water activity

The effect of salt
The effect of temperature
The control of activity in foodstuffs

Moles, molarity and molality

Moles and mole fraction

Molality and molarity
% w/w and w/v

Colligative properties of water

Overview of colligative properties
Vapor pressure lowering : CaCl2
Freezing point depression : examples : Glucose : Urea : Ethanol : NaCl : CaCl2
Boiling point elevation : Glucose
Osmotic pressure
Osmotic pressure

Relation of osmotic pressure to vapor pressure lowering

Osmotic pressure of polymers
Osmotic potential

Reverse osmosis

Self-generation of osmotic pressure at interfaces

Osmotic pressure of particles and membranes
Exclusion zone (EZ) water
Proposal for the generation of osmotic pressure at aqueous interfaces

Osmotic pressure stabilizes nanobubbles

Aqueous biphasic systems

Aqueous biphasic interfaces

Associative phase separation

Polyoxomolybdate systems

{Mo132} nanodrop Jmol animation

 nanodrop + fullerene, Jmol animation

{Mo154} nanowheel Jmol animation

{Mo132} nanocapsule and aqueous nanodrop

Molybdenum blue {Mo154} nanowheel

How does the {Mo154} nanowheel hydrate?
How do the nanowheels form large spherical clusters?

 Single C60, Jmol animation

(C60)13 cluster, Jmol animation

Aqueous solutions of fuillerenes, C60 and C70

Water surrounding fullerenes
Fullerenes containing water

Frequently asked questions concerning liquid water

How can hot water freeze quicker than cold water?

Can increasing pressure prevent water from freezing?

Is water good for you?

Is water blue?

Why does salt lower the freezing point of water?

Does water have a memory?

Does magnetic descaling of water work?

How can a liquid have a structure?

Does the radial distribution peak at about 3.7 Å exist?

Is there fine structure in the radial distribution function?

Do interstitial water molecules exist?

Icosahedral clustering and the two-state mixture model?

Water-related material


What is homeopathy?

Published evidence for and against homeopathy
Homeopathic solutions
Does homeopathy work?

Memory of water

Does water have memory?

Is water special?
Does the glassware matter?
Is gas important?
Does dilution happen as predicted?
Solutions are more complex than expected
Peroxide and radical production in water
Possible scenarios for the memory effect in homeopathic solutions

'Polywater', declustered water and other waters

Clustered and 'declustered' water

Fullerane Jmol animation

Novel fulleranes and carbons
Novel fulleranes
Novel carbons

Platonic solids Java animation

Platonic solids, water and the golden ratio

Contributed papers

 pdf file

J. G. Watterson, Enzyme function: random events or coherent


Book reviews

Aqueous systems at elevated temperatures and pressures

Handbook of refractive index and dispersion of water for scientists and engineers

References (currently 3203 including multiple references in entries; + ~400 external website references)

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201 - 300

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Visitor's Book, recent postings

Visitor's Book archive, 2000-2003

Visitor's Book archive, 2004-2006

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 Links with animation

 Earlier publications




Water related links

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This page was established in 2006 and last updated by Martin Chaplin on 23 September, 2016

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