🧪 Chemistry and Molecular Dynamics Simulation

Investigate chemical reactions, molecular structures, and physico-chemical processes in an interactive laboratory

🧪 Molecular Visualization

🎛️ Simulation Controls

📊 Chemical Metrics

0.15
Reaction rate (mol/s)
0.85
Equilibrium constant
45.2
Activation energy (kJ/mol)
7.0
Solution pH
125.6
Entropy (J/mol·K)
-285.8
Enthalpy (kJ/mol)

🔬 Chemical Experiments

⚛️ Molecular Structure

🔄 Chemical Reaction

💎 Crystal Lattice

🌡️ States of Matter

⚡ Electronic Orbitals

🧬 Organic Chemistry

📚 Educational Content

Basics
Reactions
Organic
Physical

🧪 Basics of Chemistry

Chemistry is the science of substances, their properties, structure, and transformations:

Atomic Structure

An atom consists of a nucleus (protons + neutrons) and electrons orbiting around the nucleus.

Atom structure:
Nucleus: p⁺ + n⁰
Electrons: e⁻

Periodic Table of Elements

1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne

Types of Chemical Bonds

  • Ionic: Transfer of electrons between atoms
  • Covalent: Sharing of electrons
  • Metallic: "Sea" of free electrons
  • Hydrogen: Weak bond through hydrogen

🔄 Chemical Reactions

Chemical reactions are processes of transforming one substance into another:

Types of Reactions

  • Synthesis: A + B → AB
  • Decomposition: AB → A + B
  • Replacement: A + BC → AC + B
  • Exchange: AB + CD → AD + CB
Example reaction for methane combustion:
CH₄ + 2O₂ → CO₂ + 2H₂O + energy

Factors affecting the reaction rate

  • Temperature: Increasing by 10°C doubles the rate
  • Concentration: More reactants = faster reaction
  • Catalyst: Accelerates the reaction without being consumed
  • Surface area: Larger surface area = faster reaction

Equilibrium in chemical reactions

Chemical equilibrium is a state where the rates of forward and reverse reactions are equal.

Equilibrium constant:
K = [C]ᶜ[D]ᵈ / [A]ᵃ[B]ᵇ

🧬 Organic Chemistry

Organic chemistry studies carbon compounds and their properties:

Main classes of organic compounds

  • Alkanes: CₙH₂ₙ₊₂ (saturated hydrocarbons)
  • Alkenes: CₙH₂ₙ (unsaturated with a double bond)
  • Alkynes: CₙH₂ₙ₋₂ (unsaturated with a triple bond)
  • Alcohols: R-OH (hydroxyl group)
  • Carboxylic Acids: R-COOH
Examples of Organic Molecules:
Methane: CH₄
Ethane: C₂H₆
Ethylene: C₂H₄
Ethylene: C₂H₂

Functional Groups

  • Hydroxyl (-OH): Alcohols
  • Carbonyl (C=O): Aldehydes and Ketones
  • Carboxyl (-COOH): Carboxylic acids
  • Amino Group (-NH₂): Amines

⚗️ Physical Chemistry

Physical chemistry studies the physical principles of chemical phenomena:

Thermodynamics

  • First Law: ΔU = Q - W (conservation of energy)
  • Second Law: ΔS ≥ 0 (entropy increase)
  • Third Law: S → 0 when T → 0
Gibbs Free Energy Equation:
ΔG = ΔH - TΔS
ΔG < 0: spontaneous reaction
ΔG = 0: equilibrium
ΔG > 0: non-spontaneous reaction

Kinetics

Studies the rates of chemical reactions and mechanisms of their occurrence.

Arrhenius equation:
k = A·e^(-Ea/RT)
de: k - rate constant
A - pre-exponential factor
Ea - activation energy
R - gas constant
T - temperature

Electrochemistry

Studying the interaction of electricity and chemistry:

  • Oxidation: Loss of electrons
  • Reduction: Acceptance of electrons
  • Galvanic cells: Conversion of chemical energy to electrical
  • Electrolysis: Conversion of electrical energy to chemical

❓ Frequently Asked Questions

What is a mole?

+

Mole is a unit of substance amount in the SI system. One mole contains 6.022×10²³ particles (Avogadro number). This is the amount of atoms in 12 grams of carbon-12.

How does a catalyst work?

+

A catalyst lowers the activation energy of a reaction, creating an alternative pathway for transforming reactants into products. It is not consumed in the reaction and can catalyze many cycles.

What is pH?

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pH is a measure of acidity or basicity of a solution. pH = -log[H⁺]. A value of 7 is neutral, less than 7 is acidic, more than 7 is basic. The scale is logarithmic, so pH 6 is ten times more acidic than pH 7.

How does a buffer solution work?

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A buffer solution contains a weak acid and its conjugate base (or a weak base and its conjugate acid). It resists changes in pH upon addition of small amounts of acid or base.

What is enthalpy?

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Enthalpy (H) is a thermodynamic function that characterizes the heat content of a system at constant pressure. The change in enthalpy (ΔH) indicates how much heat is absorbed or released during a reaction.

How does Le Chatelier's principle work?

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Le Chatelier's principle states that if an external influence acts on a system at equilibrium, the system will adjust to counteract this influence. For example, increasing temperature shifts the equilibrium towards an endothermic reaction.

What is electronegativity?

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Electronegativity is the ability of an atom to attract electrons in a chemical bond. Pauling scale: F (4.0) - most electronegative, Cs (0.7) - least electronegative. The difference in electronegativity defines the type of bond.

How does chromatography work?

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Chromatography is a method of separating mixtures based on the different rates of movement through a stationary phase. Components with greater affinity for the stationary phase move more slowly.

What is stereochemistry?

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Stereochemistry studies the three-dimensional arrangement of atoms in molecules and its effect on chemical properties. Includes isomerism, chirality, and conformation of molecules.

How do enzymes work?

+

Enzymes are biological catalysts that lower the activation energy of reactions. They have an active site where the substrate binds and is transformed. Enzymes work on a 'lock-and-key' principle or induced fit.

🆘 System Help

🚀 Quick Start

  • Adjust temperature, pressure, and concentration
  • Click 'Run' to start the chemical simulation
  • Add different molecules for experiments
  • Observe chemical reactions in real time

🔧 Detailed functions

  • Temperature: Affects reaction rate
  • Pressure: Affects equilibrium of gas reactions
  • Concentration: Affects both rate and equilibrium
  • Catalyst: Speeds up the reaction without being consumed

❓ Problem solving

  • If the reaction is slow, increase temperature
  • For gas reactions, increase pressure
  • Use a catalyst to speed up
  • Check if all parameters are set correctly

📚 Resources and links

  • IUPAC: International Chemical Standards
  • ACS: American Chemical Society
  • RSC: Royal Society of Chemistry
  • Chemical databases: PubChem, ChemSpider