AP Biology · Unit 1 · Chemistry of life

Water, adhesion, and how a tree drinks

Four stages, from a cut stem down to a single molecule and back out again. The molecular stages are a real molecular-dynamics simulation — exact geometry, published partial charges, hydrogen bonds that form because of the physics rather than because a script drew them.

  • 2-minute guided tour
  • Real molecular dynamics
  • Jurin's law, live
  • Keyboard and screen-reader friendly
1 · The stem

A tree is a standing column of water

A mature oak moves something like 400 litres a day from its roots to its leaves, and spends no ATP lifting any of it. There is no pump, no valve and no moving part anywhere in the path. The stem is cut across here so you can see the pipes: the ring of vascular bundles, and inside each one the wide, dead, open tubes of the xylem.

Click any glowing xylem vessel to fall through its wall and into the water itself.

AP Bio concept breakdown

The chemistry and biology behind each stage, with the numbers. This is the same text the panel beside the simulation shows — collected here so it can be read straight through, printed, or searched.

1

The stem — A tree is a standing column of water

Life size · ≈ 3 mm across

Cohesion–tension theory

Water evaporates from the wet cell walls inside a leaf and escapes through the stomata. Losing it curves the remaining water into tiny menisci, and a curved water surface pulls: the pressure just under it drops below zero. Because the water in the xylem is one continuous, hydrogen-bonded thread all the way to the root, that negative pressure is transmitted straight down the column, and water is pulled — not pushed — out of the soil. The theory is named for the two properties doing the work: cohesion holds the thread together, and tension is what the thread is under.

Driving energy
Sunlight, at the leaf
ATP spent lifting
None
Typical xylem tension
−0.5 to −2 MPa
Water taken up that is then transpired
≈ 97 %
Xylem is a pipe; phloem is not

Xylem conducting cells — tracheids and vessel elements — are dead at maturity. Their end walls are perforated or gone, their cytoplasm is cleared out, and their side walls are reinforced with lignin so they cannot be crushed by the tension inside them. What is left is an open, rigid, water-filled tube. Phloem, running just outside the xylem in the same bundle, is alive, and it moves sugar the other way by a completely different mechanism (pressure flow, which costs ATP). Only one of the two is plumbing.

Vessel diameter
10 – 500 µm
Tracheid diameter
10 – 15 µm
Sap velocity
1 – 45 m/h
Tallest measured tree
115.55 m (coast redwood)
Why the path has to be continuous

Every part of cohesion–tension depends on there being no break anywhere between the soil and the stomata. A single gas bubble in a vessel and the tension on either side of it is no longer connected: that vessel stops conducting. This is why the stage you are about to reach matters — the entire mechanism is a claim about how strongly water molecules hold on to each other and to the wall, and that claim can be checked at the scale where it is made.

2

The vessel wall — The wall is a carpet of hydroxyl groups

×1 000 000 · ≈ 5 nm across

Cellulose, and where the −OH groups come from

Cellulose is a polymer of β-glucose linked carbon 1 to carbon 4. Every second monomer is flipped 180°, which is what makes the chain a flat ribbon rather than a helix (compare amylose, which is α-linked and coils). Each glucose keeps free hydroxyl groups at C2, C3 and C6, and on the ribbon's surface those point outward into the vessel lumen. So the surface a water molecule meets is a regular array of δ− oxygens and δ+ hydrogens spaced a few tenths of a nanometre apart.

Linkage
β-1,4 glycosidic
Free −OH per glucose
3 (C2, C3, C6)
Sheet stacking distance
≈ 0.39 nm
Surface
Strongly hydrophilic
Adhesion is hydrogen bonding to something that is not water

There is no separate adhesion force. The same δ+ hydrogen that would have hydrogen-bonded to a neighbouring water molecule bonds instead to a hydroxyl oxygen in the wall, and the wall's own δ+ hydrogens bond to water's lone pairs. Cohesion and adhesion are the same interaction with different partners — which is exactly why water wets cellulose so completely, and why the contact angle of water on clean cellulose is close to 0°.

Cohesion
H₂O ··· H₂O
Adhesion
H₂O ··· HO–cellulose
Interaction
Hydrogen bond, either way
Contact angle on cellulose
≈ 0° (fully wetting)
The ordered layer

Water touching a hydrophilic surface is not bulk water. The first two or three molecular layers are held at a preferred orientation, with their hydrogens turned toward the surface oxygens, and they exchange with the bulk far more slowly than bulk molecules exchange with each other. The strip along the bottom of the viewport measures the hold itself: for each slice of the liquid it plots the share of molecules still joined to the wall by an unbroken chain of hydrogen bonds. It is near 90 % against the surface and falls to nothing by about two nanometres out. Take the hydroxyls away and the whole profile drops to zero, because there is no longer anything to be joined to — and heat the water and it retreats toward the wall, because the far end of every chain breaks first.

What this does to the column

Adhesion pins the edge of the water to the wall. Cohesion means the middle of the column cannot stay behind while the edge climbs, so surface tension pulls the whole meniscus up together. Capillary rise is that argument repeated all the way up a tube, and it is the subject of the last stage.

3

Molecular sandbox — Everything above comes from one bent molecule

×5 000 000 · ≈ 3 nm across

Polar covalent bonding, and the number that decides it

Electronegativity is how strongly an atom in a bond pulls on the shared pair. Oxygen is 3.44 on the Pauling scale; hydrogen is 2.20. The difference, 1.24, sits squarely in the polar covalent range: the electrons are genuinely shared — this is not an ionic bond — but they spend more of their time near the oxygen. That leaves a partial negative charge on the oxygen and a partial positive charge on each hydrogen. Partial, not full: δ, not +1 and −1.

ΔEN = 3.44 (O) − 2.20 (H) = 1.24

ΔEN < 0.4
Nonpolar covalent
ΔEN 0.4 – 1.7
Polar covalent ← water is here
ΔEN > 1.7
Ionic
O–H bond enthalpy
459 kJ/mol
Shape is doing half the work

Oxygen has four electron domains around it: two bonding pairs and two lone pairs. That is a tetrahedral electron geometry, and it would give 109.5° — but lone pairs are held closer to the nucleus and repel more strongly than bonding pairs, so they squeeze the two O–H bonds down to 104.5°. The molecular shape is therefore bent, the two bond dipoles do not point in opposite directions, and they add up to a net molecular dipole. Carbon dioxide is the control experiment: its C=O bonds are more polar than water's O–H bonds, but the molecule is linear, the two dipoles cancel exactly, and CO₂ is nonpolar.

Electron geometry
Tetrahedral
Molecular shape
Bent
H–O–H angle
104.5°
O–H length
0.0957 nm
Dipole moment
1.85 D
The hydrogen bond

A hydrogen already covalently bonded to nitrogen, oxygen or fluorine is left so exposed and so positive that it is attracted to a lone pair on a nearby N, O or F. That attraction is a hydrogen bond. It is about one twentieth the strength of the O–H covalent bond it hangs off, and in liquid water each bond survives only a picosecond or two before breaking and re-forming somewhere else. What makes it powerful is not any individual bond but that there are always billions of them, and that they are directional: the geometry criterion used in this simulation is an H···O distance under 0.245 nm and an O–H···O angle over 130°, which is the same test used on real molecular-dynamics trajectories.

O—H ··· O donor — hydrogen ··· acceptor

Energy
≈ 21 kJ/mol
Compared with O–H covalent
1/22 as strong
H···O distance
≈ 0.18 nm
Max per molecule
4 — donates 2, accepts 2
Average in liquid water, 25 °C
≈ 3.4
Lifetime
1 – 2 picoseconds
Cohesion and adhesion, stated precisely

Cohesion is the attraction of water to water. Adhesion is the attraction of water to a different substance. Both are hydrogen bonding here. When adhesion to the surface is stronger than cohesion within the liquid, the liquid spreads out and climbs — water on glass or cellulose. When cohesion wins, the liquid beads up and the meniscus curves the other way — mercury in a glass tube, or water on a waxed leaf. Everything the last stage shows is decided by which of the two is larger.

What the simulation is actually computing

The molecules on this stage are not animated along a path. Each one carries three point charges (−0.834 e on the oxygen, +0.417 e on each hydrogen) and a Lennard-Jones core on the oxygen, and every pair of molecules exchanges a Coulomb force between all nine site pairs plus a 12-6 dispersion-repulsion term, integrated with a Langevin thermostat so the temperature control means something. Nothing in the code says 'hydrogen bond': the bonds you see are what falls out of the charges. That includes the equilibrium O···O separation of about 0.28 nm, which nobody put there.

4

Capillary rise — Adhesion grips, cohesion holds, evaporation pulls

Cohesion–tension · 0 – 3.5 m

Jurin's law

The height a liquid climbs in a narrow tube is set by a balance: the upward pull of surface tension acting around the line where water meets wall, against the weight of the column it is holding up. Solve it and the radius ends up on the bottom, so halving the radius doubles the rise. The cos θ on the top is the contact angle — the term that encodes adhesion. When water wets the wall perfectly, θ is 0 and cos θ is 1. Switch adhesion off in the controls and θ goes toward 90°, cos θ goes toward zero, and so does the rise.

h = 2γ·cos θ / (ρ · g · r)

γ, surface tension at 20 °C
0.0728 N/m
ρ, density
998 kg/m³
θ on cellulose
≈ 0°
r = 5 µm
h ≈ 2.97 m
r = 200 µm
h ≈ 7.4 cm
Why narrow tubes win

The wall can only hold water where water touches wall, and that contact is a circle: it scales with the circumference, 2πr. The load being held is the column's weight, and that scales with the cross-sectional area, πr². Divide one by the other and the grip-to-load ratio goes as 1/r. A narrow vessel is not lifting less water because it is narrow — it is lifting far less water for each unit of wall it has to hold on with.

grip / load ∝ 2πr / πr² = 2/r

Capillarity alone cannot reach the top of a tree

Run the slider to its narrowest and the rise tops out around three metres. A coast redwood is 115 metres. Capillary action is not what lifts water up a tall plant — it is what keeps the water gripping the wall and keeps the meniscus curved. The lifting is done by evaporation at the leaves, which puts the entire column under tension, and that tension is only transmissible because cohesion holds the thread together. Take away adhesion and the thread lets go of the wall; take away cohesion and the thread snaps.

Best capillary rise, 10 µm vessel
≈ 3 m
Height of a coast redwood
115.55 m
Tension needed at that height
≈ 2 MPa
Supplied by
Evaporation at the stomata
Tension, cavitation and embolism

Water in xylem is under negative pressure — it is being stretched. Pure water in a clean tube can take a remarkable amount of that, but a real vessel contains nucleation sites, and past a threshold a bubble forms out of nothing, expands to fill the vessel and breaks the column. That is cavitation, and the gas-filled vessel it leaves behind is an embolism: that pipe is out of service. Plants manage the risk structurally. Narrow conduits resist it better, which is why the tallest trees have the narrowest tracheids, and pit membranes between vessels stop a bubble spreading to its neighbours. In the simulation, raise the temperature and the transpiration rate together in a wide vessel and you can make it happen.

Cavitation threshold, typical xylem
−2 to −4 MPa
Effect of a wider vessel
Cavitates more easily
Effect of heat
Lowers the threshold
Result
That vessel stops conducting
What temperature changes

Three things at once, and they all point the same way. Molecules gain kinetic energy, so a given hydrogen bond survives less time before thermal motion breaks it. Surface tension falls — about 0.15 mN/m for every degree — because surface tension is just the hydrogen-bond network resisting being opened up, so a weaker network pulls less hard. And evaporation at the leaf speeds up, raising the tension in the column at exactly the moment the column is least able to take it.

γ(T) ≈ 0.0728 − 0.00015 · (T − 20) N/m

Every bond and force, on one scale

Chemical bonds hold atoms together inside a molecule. Intermolecular forces act between molecules, and they are one to three orders of magnitude weaker — which is exactly why they can be made and broken at body temperature, and therefore why biology uses them for everything that has to be reversible. “Van der Waals forces” is the umbrella term for three of them: dipole–dipole, dipole–induced dipole, and London dispersion. Hydrogen bonding is usually listed separately, because it is stronger and because it is directional.

Nonpolar covalent bondIntramolecularElectrons shared essentially equally. ΔEN below about 0.4.

150 – 1,000 kJ/mol

Two atoms of similar electronegativity share a pair of electrons and neither wins. There are no partial charges worth speaking of, so molecules built only from these bonds have nothing for water to hold on to — which is the structural definition of hydrophobic. The hydrocarbon tails of a phospholipid are nothing but nonpolar covalent bonds, and that is why they turn away from water and form the interior of every membrane you have.

Examples · C–C (348 kJ/mol) · C–H (413) · O=O (498) · N≡N (945)

Polar covalent bondIntramolecularin the simulationShared, but unequally. ΔEN roughly 0.4 to 1.7. This is the O–H bond in water.

150 – 1,000 kJ/mol

The more electronegative atom pulls the shared pair closer, so it carries a partial negative charge and its partner a partial positive one. In water, ΔEN is 1.24 and the result is δ− on oxygen, δ+ on each hydrogen. Every other interaction on this page is downstream of that: the partial charges are what make water polar, and water's polarity is what makes it cohesive, adhesive, a solvent for ions, and the reason a tree can drink.

Examples · O–H (459 kJ/mol) · N–H (391) · C–O (358) · C=O (799)

Drawn as the red-to-white gradient along each O–H bond.

Ionic bondIntramolecularElectrons transferred, not shared. ΔEN above about 1.7.

600 – 4,000 kJ/mol

One atom takes the electron outright and the two resulting ions are held together electrostatically in a lattice. The lattice energies are enormous — and yet table salt dissolves in a glass of water in seconds, because water surrounds each ion with a shell of its own dipoles and the sum of those ion–dipole interactions beats the lattice. That is not the ionic bond being weak; it is water being extraordinary.

Examples · NaCl lattice (787 kJ/mol) · MgO (3795) · K⁺ and Cl⁻ across a neuron's membrane

Hydrogen bondIntermolecularin the simulationA δ+ hydrogen on N, O or F attracted to a lone pair on another N, O or F. Strong, and directional.

10 – 40 kJ/mol

Usually treated as its own category rather than as a van der Waals force, for two reasons: it is several times stronger than an ordinary dipole–dipole attraction, and it is directional — it wants the donor, the hydrogen and the acceptor roughly in a line. That directionality is what lets water build an open tetrahedral network instead of packing as tightly as possible, which is why ice is less dense than liquid water and why lakes freeze from the top down. In this simulation it is also cohesion and adhesion: same bond, different partner.

Examples · Water to water (cohesion) · water to cellulose (adhesion) · the two strands of DNA · the α-helix of a protein

Cohesion in teal, adhesion in amber. Detected by distance and angle, not scripted.

Dipole–dipole (Keesom force)van der Waalsin the simulationTwo permanent dipoles turning to face each other, plus to minus.

5 – 25 kJ/mol

Any molecule with a permanent dipole attracts any other, because on average the positive end of one spends more time near the negative end of another. It is the weakest of the three named van der Waals forces to matter for polar molecules, and hydrogen bonding is essentially this interaction taken to an extreme by a hydrogen atom that is small enough and exposed enough to let the two molecules get unusually close.

Examples · HCl to HCl · acetone to acetone · the reason polar molecules boil higher than nonpolar ones of the same mass

Yes — the Coulomb term between the molecules' partial charges is exactly this force.

Dipole–induced dipole (Debye force)van der WaalsA permanent dipole distorts a neighbour's electron cloud, then attracts what it made.

2 – 10 kJ/mol

Bring a polar molecule near a nonpolar one and its field pushes the neighbour's electrons to one side. The neighbour now has a dipole it did not have a moment ago, oriented so that the two attract. It is how a little oxygen dissolves in blood plasma at all, and how nonpolar anaesthetics interact with the polar surfaces of a protein.

Examples · O₂ dissolved in water · a noble gas near a polar solvent · induced polarisation at a membrane surface

London dispersion forcevan der Waalsin the simulationInstantaneous dipole–induced dipole. Present between every pair of atoms in the universe, including ones with no charge at all.

0.05 – 40 kJ/mol

Electrons move. At any instant a perfectly nonpolar atom has more of them on one side than the other, which makes a fleeting dipole, which induces a matching one next door, which attracts. Any single event is negligible; there are simply a very large number of them. Dispersion strength grows with the number of electrons and with how much surface two molecules can lay against each other, which is why longer fatty-acid tails make stiffer membranes, why iodine is a solid and fluorine a gas, and why a gecko can hang from glass. Some textbooks use the phrase 'van der Waals force' to mean this one alone; the fuller convention is that van der Waals covers all three of the forces on this list.

Examples · Lipid tail packing in a membrane · gecko setae on glass · noble gases liquefying at all

Yes — the attractive −(σ/r)⁶ half of the Lennard-Jones term is the dispersion force.

Ion–dipole interactionIntermolecularA full charge against a partial one — much stronger than dipole–dipole.

40 – 600 kJ/mol

Drop sodium chloride into water and each Na⁺ is immediately surrounded by water molecules turning their δ− oxygens inward, while each Cl⁻ collects a shell of δ+ hydrogens. Those hydration shells are what makes water the solvent biology is built around, and they are the reason ion channels are selective: to move an ion through a membrane, a channel has to offer it something as attractive as the water shell it must first give up.

Examples · Na⁺ hydration shell · Cl⁻ hydration shell · selectivity filters in ion channels

The hydrophobic effectNot a bondNonpolar groups clustering — not because they attract each other, but because water's network excludes them.

3 – 20 kJ/mol

There is no hydrophobic force pulling oil droplets together. Water molecules next to a nonpolar surface cannot hydrogen-bond in every direction, so they order themselves into a cage, and ordering costs entropy. Push the nonpolar groups together and the total caged surface area falls, entropy goes back up, and the process runs itself. This is the effect that folds proteins, assembles the lipid bilayer, and seats a nonpolar substrate in an enzyme's active site — and it is driven almost entirely by what water wants, not by what the oil wants.

Examples · Protein folding · lipid bilayer assembly · oil separating from vinegar

What the simulation actually computes, and what it exaggerates

A simulation a student is asked to reason from should say which parts are real.

The molecules are real physics

Stages 2 and 3 run rigid three-site water in two dimensions with TIP3P parameters: charges of −0.834 e on the oxygen and +0.417 e on each hydrogen, a Lennard-Jones core with σ = 0.315 nm and ε = 0.636 kJ/mol, an O–H length of 0.0957 nm and an H–O–H angle of 104.5°. Every pair of molecules within 0.85 nm exchanges a Coulomb force across all nine site pairs plus the Lennard-Jones term, integrated with a Langevin thermostat at 2 fs per step. Nothing in the code places a hydrogen bond; the 0.28 nm oxygen–oxygen spacing you can measure on screen is an output.

The hydrogen bonds are detected, not drawn

A bond is counted when the H···O distance is under 0.245 nm and the O–H···O angle is over 130° — the same geometric criterion used to analyse real molecular-dynamics trajectories. The counter beside the viewport is therefore a measurement of the simulation, and it lands near the textbook figure of about 3.4 hydrogen bonds per molecule in liquid water.

The capillary numbers are analytic

Stage 4 does not simulate a metre of water molecule by molecule — that is roughly 10²⁵ molecules. The rise is Jurin’s law evaluated on the live slider values, with surface tension corrected for temperature at −0.15 mN/m per degree, and the cavitation threshold rising as the vessel narrows. The molecules drawn in the column are illustrative; the height, the tension and the contact angle are not.

Two things are deliberately exaggerated

Time, and temperature. Real water reorganises on a picosecond scale, so the molecular stages run many orders of magnitude slower than life. And real liquid water only loses about half a hydrogen bond per molecule across the whole range from freezing to boiling — true, and invisible — so the temperature control drives an amplified thermal energy in the molecular view. The slider says °C; the label says it is exaggerated.

It is two-dimensional

Real water is tetrahedral and each molecule can hold four hydrogen bonds arranged in three dimensions. A flat simulation can show the geometry, the directionality and the network, but a student should know that the picture is a slice. The bond angle, bond length, charges and energies quoted are all the real three-dimensional values.

Nothing is sent anywhere

The page runs entirely in the browser. There is no account, no tracking of what you move, and no network request once the page has loaded. It can be run from a projector in a classroom with the wifi switched off.

Using it in a lesson

Two minutes, projected

Open the simulation, press Play the 2-minute tour and let it run. It narrates all four stages and drives the controls itself, including the two demonstrations worth stopping on: removing the wall hydroxyls, and snapping the column with heat and transpiration. Press T to pause it at any point and take a question.

Four minutes, in their hands

Three questions that need the simulation to answer: what happens to the ordered layer when you remove the hydroxyls, and why; why a narrower vessel lifts water higher when it clearly holds less water; and what combination of diameter, temperature and transpiration rate causes an embolism — and what that tells you about why the tallest trees have the narrowest conduits.

Where it sits in the course

AP Biology Unit 1, Topic 1.1 — the structure of water and hydrogen bonding — and the properties that follow from it: cohesion, adhesion, surface tension and capillary action. It also reaches forward to water transport in plants, and the bond library covers the full set of intramolecular and intermolecular forces the course expects students to distinguish.

Access

Every control is a real form element, so the whole simulation is operable from the keyboard: ← and → move between stages, R resets. The viewport carries a live description of what it is showing, and every number on screen is also in the readout as text. With reduced motion requested, the camera cuts instead of diving.