Calculators

Small interactive tools.

Concentration calculator

Work out the concentration of a species from an MD box size and molecule count.

Box side (nm)

Number of molecules

Concentration:288.3 mM(volume 1,728 nm³)

Energy unit converter

Edit any box and the rest update. Converts between kJ/mol, kcal/mol, eV, hartree, cm⁻¹ and kT.

kJ/molkcal/moleVhartreecm⁻¹kT

Temperature (K, for kT)

kT = 2.4790 kJ/mol at 298.15 K.

ΔG, K and pKa

Free energy to equilibrium constant and pKa, with the pH-dependent protonation fraction.

A reaction's standard free energy ΔG fixes where its equilibrium sits. The two are linked by ΔG = -RT ln K, where R is the gas constant and T the temperature: a more negative ΔG means a larger K and a reaction that lies further towards products.

For an acid dissociating (HA ⇌ A^- + H⁺), that same free energy is the deprotonation ΔG, and K is the acidity constant K_a. Taking -log₁₀ gives pK_a = ΔG / (RT ln 10). A larger pK_a is a weaker acid that holds onto its proton more tightly.

At a given pH, the Henderson–Hasselbalch relation sets how much of the species is protonated: fraction protonated = 1 / (1 + 10^{pH - pKa}). When pH equals the pK_a the species is exactly half protonated; a pH one unit below the pK_a leaves it ~91% protonated, one unit above ~9%.

ΔG (kJ/mol)Temperature (K)pH

Equilibrium constant K:3.157e-5(ΔG = -RT ln K)

pK_a:4.50(treating ΔG as the deprotonation free energy)

Fraction protonated at pH 7:0.3%

Henderson–Hasselbalch assumes the pK_a above; at pH = pK_a the species is 50% protonated.

Hill equation

Draw the protonation curve against pH for a given pKa and Hill coefficient n.

pKanS = 0.997

Hill Equation: S = 1 / (1 + 10^{n(pK_a - pH)}).