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Water structure = H2O

Water Structure and Science, Site Map


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

Felix Franks, 1972   



 The water molecule

 Water: a brief early History of its Science

 The beginnings of water science
 The discovery of hydrogen bonds

 Liquid water


 Water structure, Introduction

 What is in 'water'?

 Water structure, advanced

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

 Pure water and solubility

 Pure water


 Solubility of gases

 Solubility; organic; inorganic


 Henry's constant Henry's volatility constant

 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

 Van der Waals interactions

 Hydrogen bonding in water

 Water hydrogen bonds
 Water hydrogen bond length
 Water hydrogen bond direction


 Entropy-enthalpy compensation

 Hydrogen-bonding and information transfer

 Hydrogen bond cooperativity

 Quantum effects
 Rearranging hydrogen bonds

 Hydrogen bonding and molecular recognition
 Bifurcated hydrogen bonds
 Information transfer
 Hydrogen bonds and solubility
 Water dimer and small clusters

 Water dimer and trimer inside fullerenes

 The water 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

 The Clausius Clapeyron equation

 Density change

 Steam and airborne water

 Water vapor

 The Leidenfrost effect

 Airborne water

 Hexagonally-patterned microdroplets

 Ideal gas

 Supercritical water

 Supercooled water
 Ice phases

 Known ices

 Very high-pressure ices including superionic ice

 Ice 0 Jmol animation

 Computer ices (ice 0, ice χ)

 Vonnegut's ice-nine

 The 'ice-rules' and ice crystal imperfections
 Ice crystal data

 ice Ih Jmol animation

 Hexagonal ice

 Ice nucleation and growth

 Zero-point entropy

 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

 Cubic ice (Ic/XIc)

 Stacking disordered ice; Ice Isd















 Other ice XVs; ice XIX

 Ice XVI Jmol animation

 Ice-sixteen and other ultra low-density ices

 Negative pressure

 Ice XVII Jmol animation


 Very high pressure ices


 Ice-nineteen : Ice-twenty

 Amorphous ice and glassy water

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

 The glassy state

 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

 Humidity units

 Water dissociation, 2H2O = H3O+ + OH

 The ionic product, Kw


 Variation in Kw with temperature and pressure

 Acidity, basicity and the pKa of water

 Weak acids

 Ionic strength
 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

 Mixed confinement

 Water molecules confined in beryl nanovoids


 Capillary rise
 Capillary condensation

 Cavity filling
 Venturi effect
 Capillary flow cause of ring stains

 Interfacial water and water-gas interfaces

 The surface of liquid water

 The surface of ice (Why is ice slippery?)

 Metal interfaces
 Silica interfaces

 Surface potential
 Zeta potential

 Surface charge profile

 Surface charge changes with pH
 Evaporation and condensation

 Thermodynamics of the liquid-gas surface for water

 Nanobubbles (ultrafine bubbles)


 Surface nanobubbles

 Bulk nanobubbles

 Rationale for nanobubble stability

 Nanobubble detection and characterization

 Nanobubbles, preparation, and use

 Seventy-four anomalous properties of water

 The range of anomalous properties of water

 Rationale for the low-temperature anomalies of liquid 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
 A liquid-liquid transition occurs at about 330 K.

 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
 Cold liquid water has a high-density that increases on warmining
 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-M18

 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 (nuclear isotope effect)
 The mean kinetic energy of water's hydrogen atoms increases at low temperature (disputed)
 Solutes have varying effects on water's properties
 nonpolar gases solubility decreases with temperature
 The dielectric constant of water and ice are high
 The relative permittivity shows a temperature maximum

 The relative permittivity shows a 'kink' in its behavior with temperature at 60 °C
 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

 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

 Properties of water and its isotopologues

 Physicochemical data

 Vienna Standard Mean Ocean Water


 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

 Thermodynamics, introduction

 The temperature scale and absolute zero>
 The Zeroth Law of Thermodynamics
 The First Law of Thermodynamics
 The Second Law of Thermodynamics
 The Third Law of Thermodynamics

 Chemical potential
 Internal energy

 Heat capacity and specific heat

 Helmholtz free energy

 Boltzmann constant


 Important constants and conversion factors

 Greek letters and symbols

 Periodic Table

 Water molecular models

 Water model parameterization

 Water model descriptions
 Water model properties

 The Lennard-Jones relationship

 Water clustering in liquid water

  (H2O)8 equilibria animation

 Overview of the structuring in liquid water

 Water clustering
 Cluster lifetimes and hydrogen-bond lifetimes are independent
 Icosahedral water cluster
 The lifetime of the clusters

 Introduction to water clustering

 Water's two-state cluster history

 Is liquid water one liquid or two?

 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 (Raman and infrared)
 Terahertz (THz) absorption spectroscopy
 Microwave (GHz) absorption spectroscopy
 Sum frequency generation (SFG)
 X-Ray spectroscopy

 Gaussian and Lorentzian curves

 (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 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

 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 a 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 a 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
 The fragile to strong transition

 Water cluster conclusions


 Protein hydration

 The contribution of water to protein structure

 Water in protein recognition and binding
 Water in protein and enzyme function

 Enzymic reactions in biphasic liquid systems

 Antifreeze proteins

 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

 Phospholipid hydration

 Cholesterol and membrane hydration

 Triacylglyceride hydration

 Surfactants and nanoemulsions

 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 pseudo-rotational angles of ribose and deoxyribose

 Hydrocolloids and gums

 Hydrocolloid polymers


 Mixtures of hydrocolloids
 Effect on viscosity
 Hydrocolloid action

 The DLVO theory

 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

 Interaction with water

 Microcrystalline cellulose


 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


 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


 H3O+ magic number cluster Jmol animation 

 SO42 cluster Jmol animation

 CO2 cluster Jmol animation

 Sulfate and other large anions

 The H3O+ magic number cluster ions

 Water clustering around the SO42− cluster

 The CO2-water cluster

 Carbon dioxide

 Carbon dioxide hydration and equilibria

 Carbon dioxide compared with carbon monoxide

 CO2 and CO clathrate hydrates

 Carbonic acid (H2CO3)

 Aqueous ammonia


 Aqueous ammonia

 Nitrogen oxides | N2O | NO | NO2

 Nitrous and nitric acid

 Aqueous H2S


 Hydrogen sulfide

 Aqueous H2S

 Sulfur dioxide

 Aqueous SO2

 Sulfur trioxide

 Sulfuric acid

 Aqueous hydrogen halides

 The hydrohalic acids

 Hydrogen fluoride

 Why is hydrofluoric acid a weak acid?

 Aqueous borates

 Boron trioxide

 Boric acid

 The closo-dodecaborate anion

 Aqueous phosphate


 Orthophosphoric acid

 Phosphorous acid

 Phosphinic acid

 Hydroxyapatite and bone

 Aqueous silicates


 Orthosilicic acid
 Silica interfaces

 The Hofmeister series

 Thermodynamic properties
 Effect on physical properties
 Effect on solubility; ion-pairs
 Stabilization of proteins
 Hydrophobic and hydrophilic associations

 The effect on biphasic partitioning

 The Jones-Dole expression

 Kosmotropes and chaotropes 

 Definitions of kosmotropes and chaotropes

 Ionic kosmotropes and chaotropes
 Non-ionic kosmotropes and chaotropes

 Trimethylamine N-oxide (TMAO)
 Hyaluronic acid

 Hydrophobic hydration

 The hydrophobic effect

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

 Young's equation
 Alcoholic solutions

 Alcoholic tears

 Carboxylate link Jmol animation

 Intracellular water

 Water transfer across membranes
 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


 Water in the solar system

 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
 Water and global warming

 Water cycle

 Water availability

 Water use

 The Practical Salinity Scale

 Hard water and descaling

 Hard water

 Calcium carbonate equilibria
 Water softening
 Magnetic descaling

 Solubility product

 Definition of hardness


 Reverse osmosis

 Forward osmosis


 Pressure retarded osmosis

 Membrane distillation

 Solar powered water harvesting

 Treatment of contaminated water

 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


 Introduction to electrolysis

 Electrolysis compartments

 What is less well understood?

 Commercial systems

 Water powered cars

 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

 Temperature and pressure
 Polarization and polarizability
 Refractive index

 The complex dielectric permittivity behavior of water

 The complex dielectric permittivity

 Effect of oxygen on water

 Peroxide and oxygen radicals


 Reaction of water with ionizing radiation

 Redox reactions of O2

 Water activity

 Definition of 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 , %w/v and % v/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
 Osmotic flux

 Relation of osmotic pressure to vapor pressure lowering

 Osmotic pressure of polymers
 Osmotic potential


 Reverse osmosis


 Pressure retarded osmosis

 Solar powered water harvesting

 Treatment of contaminated water


 Brownian motion

 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

 Similarities of EZ-water to osmotically-generated surface water

 Osmotic pressure stabilizes nanobubbles

 The Nernst and Knudsen layers


 Aqueous biphasic systems

 Introduction to aqueous biphasic systems

 Ionic liquids

 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

 The giant Mo240 hollow opening dodecahedra

 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 the fullerenes 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?
 The placebo effect

 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, EZ-water and other Waters


 EZ water

 Strange Waters
 Clustered and 'declustered' water

 Fullerane Jmol animation

 Novel fulleranes and carbons
 Novel fulleranes
 C18 and other 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

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

 Aqueous systems at elevated temperatures and pressures

 References  1 - 100 (currently 5392 including multiple references in entries; + ~400 external website references)

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 Visitor's Book archive, 2000-2003

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This page was established in 2006 and last updated by Martin Chaplin on 5 September, 2022

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