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Organic
Organic Chemistry Animations Introduction
Nucleophilic Addition to C=O
Borohydride reduction
Cyanide addition
Hemiacetal formation
Organometallic reagents
Grignard addition
Organolithium addition
Diastereoselective ketone reduction
Nucleophilic Substitution at C=O
Ester hydrolysis and transesterification
Amide formation from acid chloride
Acid Chloride Formation – Thionyl Chloride
Acid chloride formation-Phosphorus Pentachloride
Addition to C=O - loss of carbonyl oxygen
Acetal formation
Cyclic acetal formation
Spiroketal Formation
Enamine formation
Wittig reaction
Imine formation
Oxime formation
Hydrazone formation
Wolff-Kishner Reduction
Stereochemistry
Stereochemistry Home Page
Chiral Cyanohydrins – Configuration
Achiral cyanohydrins - Symmetry
Chiral molecules R or S
Chiral or achiral?
Molecules with a Plane of Symmetry
Molecules with a Plane of Symmetry – Feist’s Acid
Chiral Allenes Without Stereogenic Centres
BINAP C2 Axis of Symmetry
Diamides Showing a Centre of Symmetry
Non-superimposable Spiro Amides
Achiral Diastereoisomers
Symmetry of Epoxide Diastereoisomers
Conformation vs Configuration
Conformations of ethane – Newman projection
Conformations of Butane
Conformations of Butane - Newman
Conformations of Butane – energetics
Conformational Analysis – Pea Moth Pheromone
Tartaric acid – Newman projections
Cyclohexane conformations
Decalin conformations
Cis-Decalin conformations
Nucleophilic substitution
Simple S
N
2 reaction
S
N
1 and S
N
2
Substrate structure controls substitution mechanism S
N
1 or S
N
2
Stability and structure of carbocations
S
N
2 examples
S
N
2 Reaction: Allyl Chloride with HS
–
S
N
2 Reaction: Benzyl Chloride with HS
–
S
N
2 Reaction: 2
o
Benzyl Chloride with HS
–
S
N
2' Mechanism
Mitsunobu Reaction
Elimination
E2 to form cyclohexadiene
E2 stereoselective for E alkenes
E2 Stereospecific from diastereoisomers
E2 Regioselective Elimination to Menthenes A
E2 Regioselective Elimination to Menthenes B
E1 unimolecular
E1cB unimolecular conjuagte base
Nitrile Oxide Synthesis Via Oxime
Formation of Nitrosonium Ion
Formation of Diazonium Salt – Diazotization
Electrophilic addition to alkenes
Ethylene and Bromine
Stereospecific addition
Regioselective addition
Racemic mixture formation
Racemate formation - acyclic
Unsymmetrical alkenes - HBr
Epoxidation peracid
Epoxidation of E-Allyl Silanes
Butadiene bromination
Electrophilic aromatic substitution
Nitration of benzene
Friedel-Crafts alkylation
Friedel-Crafts acylation
Sulfonation of benzene
Azo-dye Synthesis
Electrophilic alkenes
Benzyne formation
Benzyne formation – Diazotization-decarboxylation
S
N
Ar Addition-Elimination
S
N
Ar Two Nitro Groups
Oxidation
Jones Oxidation
Swern Oxidation
Allylic Oxidation SeO
2
Oxidation of dihydropyridine by DDQ
Syn-dihydroxylation of alkenes OsO
4
Periodate Cleavage of 1,2-Diols
Glycol Oxidative Cleavage Pb(OAc)
4
Ozonolysis
Sulfoxide - -oxidation to enones
Sharpless Asymmetric Epoxidation
Epoxidation of Z-Allyl Silanes
Enols and Enolates as nucleophiles
Cyclopentanone aldol - acid cat.
Intramolecular aldol reactions
Knoevenagel condensation
Lithium enolates
Mannich reaction
Enolate alkylation
Claisen ester condensation
Enamine Acylation
Wittig Reaction
Acid-Catalysed Bromination
Base-Catalysed Bromination
Enolisation and formation of syn aldol product
Enolisation and formation of anti aldol product
Simple Diastereoselectivity - cis gives syn aldol
Simple Diastereoselectivity - trans gives anti aldol
Conjugate addition
Conjugation changes reactivity
Robinson annelation
Conjugate addition with enols
Conjugate Addition Examples
Conjugate Addition of MeSH to an Unsaturated Aldehyde
Conjugate Addition of Diethylamine to an Unsaturated Nitrile (Acrylonitrile)
Conjugate Addition of Diethylamine to an Unsaturated Ester
Conjugate Addition of Enamine to Unsaturated Imine
Conjugate addition of enolates
Robinson annelation
Dimedone synthesis
Conjugate addition of peroxide to form epoxides
Baylis-Hillman Reaction
Enantioselective Conjugate Addition
Diels-Alder reactions
Diels-Alder reaction Overview
Identifying a Diels-Alder Reaction
s-cis v s-trans conformation
Regioselectivity 2-methoxybuta-1,3-diene and acrylonitrile
Regioselectivity 1,1-dimethylbutadiene and methyl acrylate
Stereochemistry of the Diene Z,Z
Stereochemistry of Diene E,Z
Stereochemistry of Diene E,E
Stereochemistry of the dienophile - diesters
Stereochemistry of the dienophile - dinitrile
Endo vs exo
Endo vs exo again
Orbital explanation for the endo rule
Working out which product is
endo
The Woodward Hoffman description of the Diels-Alder
Intramolecular Diels-Alder (E)-3-Methyldeca-1,3,9-triene
Intramolecular Diels-Alder – 1,3,9-decatrien-8-one
2,3-Dimethylbutadiene and Acrolein(propenal)
Quinone as Dienophile – Steroid Framework
Intramolecular Diels-Alder – Regioselectivity reversal
8-Phenylmenthol auxiliary-controlled Diels-Alder
DA benzyne-anthracene
Pyrone Diels-Alder
Aromatic Heterocycles - Structures
Pyrrole structure
Pyridine structure
Pyridine N-Oxide structure
Tautomerism of Hydroxy Pyridine
Aromatic Heterocycles - Synthesis
Hantzsch pyridine synthesis
Paal-Knorr pyrrole synthesis via hemiaminal
Paal-Knorr pyrrole synthesis via enamine
Knorr Pyrrole Synthesis
Thiophene ring formation
Thionation of a Ketone
Lawesson's reagent
Thiazole Formation
Pyridazine synthesis
Pyrazole synthesis
Pyrimidine synthesis
Olefin Metathesis - Pyrrole formation
1,2,3-Triazole formation
Aromatic Heterocycles - Reactions
Pyridine – Nucleophilic Substitution
Pyridine – Nucleophilic Catalyst
Vilsmeier Reaction
Mannich Reaction
Oxidation of dihydropyridine by DDQ
Ritter reaction
Friedel-Crafts Alkylation
Furan Hydrolysis
Pyrrole decarboxylation
Indole Alkylation
Indole – Mannich and Substitution
Pyridine N-Oxide – Nucleophilic Substitution
Pyridine N-Oxide – Remote Oxidation And Rearrangement
Pericyclic reactions
Introduction to Pericyclic Reactions
Cycloadditions
Ozonolysis 1,3-dipolar
1,3-dipolar cycloadditions - nitrone
1,3-Dipolar Cycloaddition Isoxazole from nitrile oxide
[4+3] Oxyallyl Cycloaddition
[4+6] Thermal Cycloaddition
1,2,3-Triazole formation
Tetrazole formation
Intramolecular carbonyl ene
Syn-dihydroxylation of alkenes OsO
4
Periodate Cleavage of 1,2-Diols
Sigmatropic rearrangements
[3,3]-Claisen rearrangement - aromatic
[3,3]-Claisen rearrangement - acyclic
[3,3]-Ireland-Claisen
[2,3]-shift sulfoxide
[1,5]-H shift
[1,7]-H shift
[3,3]-Fischer indole
Citral tandem Claisen-Cope
Electrocyclic reactions
Electrocyclic reactions are stereospecific
Conrotatory ring closure/opening - cyclobutene
Disrotatory ring closure/opening - hextriene
Endiandric Acid Cascade
Nazarov Cyclization
Norcaradiene Ring Opening
Stereospecific Cheleotropic Reactions SO
2
Rearrangements
Benzilic Acid
Neighbouring Group Migration
Pinacol
Semipinacol rearrangements of diazonium salts
Ring expansion means rearrangement
Wagner-Meerwein rearrangement
Payne rearrangement
Beckmann rearrangement
Favorskii rearrangement
Tiffeneau-Demjanov Rearrangement
Rearrangements with different nucleophiles
Retention of stereochemistry can indicate neighbouring group participation
Which Group Migrates?
Baeyer-Villiger
Neighbouring group participation: alpha-lactone formation
Radical reactions
HBr Addition to Isobutene
Termination Steps
Chlorination of alkanes
Conjugate Addition to Acrylonitrile
Bu
3
SnH reduction of C-Br
Cyclisations exo/endo
Cyclisation Tin Hydride
Pinacol Coupling
Julia Olefination
Radical Copolymerization
Fragmentations
Bond polarization
Ring expansion
Beckmann fragmentation
Fragmentations are controlled by stereochemistry
Controlled by stereochemistry (Cis isomer)
Conformational flexibility (Trans)
Controlled by stereochemistry (Trans – Less severe interactions)
Controlled by stereochemistry (Trans – Severe interactions)
Fragmentation of diastereoisomers (Trans-decalin I)
Fragmentation of diastereoisomers (No ring fragmentation)
Juvenile hormone synthesis
Carbene chemistry
Photolysis of diazomethane to produce a carbene
Methylation of carboxylic acid using diazomethane
Formation
From diazocarbonyl compounds
Via alpha elimination
Thermal decomposition via hydrazone
Carbenes – Reactions
Alkene insertion – Singlet v Triplet
Alkene insertion – Singlet carbene
Alkene insertion – Triplet carbene
O-H bond insertion
C-H bond insertion
Bamford-Stevens reaction
Cyclopropanation of an Alkene by a Carbenoid
Simmons-Smith reaction
Stereoselectivity
Wittig Reaction
Cyclopropanation
Felkin-Anh reduction LiAlH
4
Chelated reduction zinc borohydride
Chelate Cram Addition MeMgBr
Beta-Keto Sulfoxide reduction
Intramolecular carbonyl ene reaction
Cyclohexene epoxide opening axial
Aldol Reaction syn product
Aldol Reaction anti product
Stereoselective Aldol Reaction – Cis gives Syn
Stereoselective Aldol Reaction - Trans gives Anti
Allyic strain - Enolate alkylation
Epoxidation of Z-Allyl Silanes
Epoxidation of E-Allyl Silanes
Baldwin's rules
Classes of cyclization
Classes of cyclization (3-exo-tet)
Classes of cyclization (5-exo-trig)
Classes of cyclization (6-endo-dig)
Endo-trig reactions
Endo-trig reactions (6-endo-trig)
Endo-trig reactions (5-endo-trig)
Endo-trig reactions (5-endo-trig orbital overlap)
Organo-main-group chemistry (B/Si/S)
Asymmetric Sulfoxidation
Sulfonium ylids
Sulfoxonium Ylids
Pummerer rearrangement
Swern Oxidation
Sulfoxide elimination
Julia Olefination
Hydroboration
Hydroboration (Addition of boron hydride to alkenes)
Hydroboration (Oxidation)
Hydroboration of cyclopentadiene Ipc
Crotyl boranes react stereospecifically
Alpine Borane
Vinyl silanes react with electrophiles
The Peterson reaction
Stereospecific Peterson reaction
Stereospecific Peterson reaction (Base )
Silicon alpha anion stabilisation
Epoxidation of Z-Allyl Silanes
Epoxidation of E-Allyl Silanes
Organometallic chemistry
Pd-Suzuki Reaction
Pd-Mizoroki-Heck Reaction
Pd-Kosugi-Migita-Stille Reaction
Pd-Carbonylative Kosugi-Migita-Stille Coupling Reaction
Pd-Butenolide Formation From Carbonylation Of A Vinyl Bromide
Pd-catalysed nucleophilic allylic substitution of functionalised compounds
TMM Pd Catalysed Cycloaddition
Ru-Hydrogenation of Ketones
Ru-Hydroformylation OXO reaction
Ru-Olefin Metathesis macrocycle
Ru-Olefin Metathesis unsaturated pyrrole
Enantioselective auxiliaries
Methylation of an enolate
Benzylation of an enolate
Evans oxazolidinone syn Aldol
Evans ent-oxazolidinone syn Aldol
Evans oxazolidinone Diels-Alder
8-Phenylmenthol Diels-Alder
Asymmetic Alkylation of SAMP Hydrazone
Conjugate Addition - Oppolzer's sultam
Meyers enolate alkylation
Schöllkopf amino acid
Enantioselective reagents
Sparteine controlled deprotonation
Hydroboration of cyclopentadiene Ipc-borane
Ketone Reduction with BINAL-H
Acetylenic Ketone Reduction – Alpine Borane
Enantioselective metal catalysts
Sharpless Asymmetric Epoxidation
Direct Sulfoxidation
Hydrogenation of Ketones – Ru(II) cat.
Cyclopropanation – allylic alcohols
Dimethyl Zinc addition to aldehydes
Enantioselective organocatalysts
Ketone reduction with CBS
Intermolecular aldol - proline
Intramolecular Aldol - proline
Aldol dimerisation - proline
Intermolecular aldol -proline – hydroxyacetone
Intramolecular S
N
2 Me-proline
Indole Alkylation - Imidazolidinone
Pyrrole - Friedel-Crafts alkylation
Carbonyl Ene - Phosphoramide
Imine Hydrophosphonylation - Phosphate
Medicinal Chemistry at Liverpool
Medicinal Chemistry Research at the University of Liverpool
Inorganic
Solid state Cubic structures
Simple cubic
Body-centred cubic – bcc
CsCl – Caesium chloride
Simple close packed
Hexagonal close packing – hcp
Cubic close packing – ccp
AB structures
NaCl – Sodium chloride
NiAs – Nickel Arsenide
ZnS – Zinc Blende
ZnS – Wurtzite
AB2 structures
CaF
2
– Fluorite
Na
2
O – Antifluorite
CdCl
2
– Cadmium chloride
CdI
2
– Cadmium iodide
TiO
2
– Anatase
TiO
2
– Rutile
AB3 structures
YCl
3
– Yttrium trichloride
BiI
3
– Bismuth triiodide
Li
3
Bi - Lithium Bismuthide
Advanced solid structures
ReO
3
– Rhenium trioxide
CaTiO
3
– Perovskite
MgAl
2
O
4
– Spinel
Mg
2
TiO
4
– Inverse Spinel
Simple Solids
Tungsten bcc
Silicon Sulfide – SiS
2
Iron-Chromium Alloys
Calcium Carbide – CaC
2
Ammonium Chloride (NH
4
Cl)
Cu
3
Au Auricupride
Zirconium Oxide with Calcium Impurity
Calcium Carbonate – CaCO
3
– Polymorphs
DNA/RNA Base Pairs
Lone Pair Orientation
Hydrogen
Li
2
NH (antifluorite) & LiNH
2
(defect antifluorite)
Group 1 Elements
Caesium Superoxide CsO
2
Dipotassium Pentasulfide (K
2
S
5
)
Lithium nitride (Li
3
N)
Na
172
In
192
Pt
2
K
4
Ge
4
[Cs(18-crown-6)
2
]
+
e
–
Group 2 Elements
Calcium Carbonate – CaCO
3
– Polymorphs
Group 14 Elements
Calcium Carbide – CaC
2
Kaolinite Al
2
(OH)
4
Si
2
O
5
Muscovite – KAl
2
(OH)
2
Si
3
AlO
10
Zeolites X & ZSM-5
d-block Elements
Scandium Chloride – Sc
7
Cl
10
Garnet – Y
3
Al
5
O
12
Zirconium Chloride – ZrCl
Zircon – ZrSiO
4
Vanadium Oxide – V
2
O
5
Molybdenum Disulfide – MoS
2
Copper (I) Oxide – Cu
2
O
BISCO Bismuth Strontium Calcium Copper Oxide – BSCCO
HgO-Mercury(II) oxide
Hexatantalate [Ta
6
O
19
]
2-
f-block Elements
Lanthanum(III) chloride – LaCl
3
Cerium Tetrafluoride – CeF
4
Gadolinium Orthoferrite – GdFeO
3
Garnet – Ca
3
Al
2
Si
3
O
12
– Grossular
Uranium (V) Chloride – U
2
Cl
10
Solid State Materials
Defects and Ion Transport
Metal Oxides, Nitrides and Fluorides
Chalcogenides, Intercalation Compounds and Metal-rich phases
Framework Structures
Hydrides and Hydrogen Storage Materials
Inorganic Pigments
Molecular Materials
Bioinorganic Chemistry
Bioinorganic Chemistry Gallery
Metal Organic Frameworks
MOF – home
MOF-5 (or IRMOF-1)
IRMOF-10
IRMOF-16
ZIF
HKUST-1
UiO-66
MIL-53 (Sc)
NOTT-112
AgFe mixed metal [AgFe(dppd)
3
]BF
4
·2DMSO·2H
2
O
Zn(GlySer)
2
ZnGlySer Pore closure animation
ZnGlyThr
Zn-Carnosine
Zn-Carnosine pore animation
Ni-Asp-bipy
Lithium Ion Batteries
Lithium Ion Battery Materials – Home
Cathode (Positive electrode) material examples
Lithium Iron Phosphate-LiFePO
4
– Conduction animation
Lithium Cobalt Oxide – LiCoO
2
Lithium Manganese Oxide – LiMn
2
O
4
Anode (Negative electrode) Material Examples
Graphite anode
Lithium titanate-Li
4
Ti
5
O
12
– Conduction animation
Silicon Anode
LISICON – Solid Electrolyte example
Structure and Bonding
Atomic Orbitals
s-orbitals
p-orbitals
3d-orbitals
4f-orbitals
Compare shape and size of 1s, 2s and 2p orbitals
Molecular Orbitals
Hydrogen
Nitrogen
Fluorine
Ammonia
Methane
Ethylene (Ethene)
Acetylene (Ethyne)
Allene
Formaldehyde(Methanal)
Acrolein
Carbon Monoxide
Hydrogen Fluoride
Allyl Anion
Butadiene
Benzene
Aromaticity of cyclic polyenes - Frost
Animated Molecular Orbitals
Spectroscopy
Introduction
Symbols, Terminology and Constants
Orbitals
Vibrational spectroscopy
Water
Hydrogen Chloride
Carbon Dioxide
Rotational Introduction
Rotational Examples
Ultraviolet/Visible UV/Vis
Translations
Molecular vibrations-IR
Water
Hydrogen Cyanide
Carbon Dioxide
Ammonia
Boron Trifluoride
Methane
Ethylene (Ethene)
Phophorus Pentafluoride
Sulfur hexafluoride
Nickel Tetracarbonyl
Iron Pentacarbonyl
Benzene
cis-[PdCl
2
(NH
3
)
2
]
trans-[PdCl
2
(NH
3
)
2
UV - conjugation
Ultraviolet/Visible UV/Vis Spectroscopy
Ethylene (Ethene) and Butadiene
Linear Polyenes
Colour of Dyes
Aniline Yellow
Disperse Orange 1
Oil Red O
Janus Green B
Azo-dye Synthesis
Dipoles and Electrostatic surfaces
Small polar molecules
Unsaturated Molecules
Lone Pair Conjugation
Hydration of Carbonyl Compounds
XeF
4
, ClF
3
and CCl
3
Br
Introductory Organic Structures
Linoleic acid
Amino Acids
Carbon Allotropes (Diamond, Graphite, C
60
)
Cyclooctatetraene
Cyclophanes and Annulenes
Selected Polycyclic Structures
Sucrose
Shapes of molecules VSEPR
H
2
O Water
NH
3
Ammonia
CH
4
Methane
PF
5
Phosphorus Pentafluoride
SF
4
Sulfur Tetrafluoride
ClF
3
Chlorine Trifluoride
SF
6
Sulfur Hexafluoride
XeF
4
, ClF
3
and CCl
3
Br
Organometallics (Metal-Ligand Bonding)
Carbon Monoxide
Phosphine
Hydrogen
Ethylene
Cyclobutadiene
Butadiene
Benzene
Allyl
Cyclopentadienyl
Carbene
Symmetry
Symmetry Operations
C
nh
| C
nv
| S
2n
| C
n
Point groups
D
nh
| D
nd
| D
n
Point groups
C
s
| C
i
| C
1
Point groups
T
d
| O
h
| I
h
Point groups
Symmetry Decision Tree
Orbital-orbital Interactions and Symmetry Adapted Linear Combinations
Metal reaction mechanisms
Point groups of polyhedral structures
Distortions of a regular Octahedron
Distortions of a octahedral complex with chelating ligands
Berry pseudorotation
Octahedral [Ru(en)
3
]
2+
enantiomers
Delta v lambda M(L-L)
3
Ligand Substitution Square Planar Complex
Ligand Substitution mechanisms
Bailar and Ray-Dutt twists
Inner Sphere Electron Transfer Mechanism
Outer Sphere Electron Transfer Mechanism
Bent metallocenes
Jahn-Teller distortion
Protein Folding Kinetics
Framework Model of Protein Folding
Hairpin Folding from Chain
Folding Process of Myoglobin
Gold Nanoparticles
Introduction
PVP encapsulation
Possible morphologies of Au Nanoparticles
Au
25
(SEt)
18
, Thiolate-Protected Au
25
Cluster
(p-MBA)-protected Au
102
nanoparticle
Fluorination of medicinal compounds
Introduction
Amide Mimetic
Halex Reaction
Conformation Effects
Uracil and 5-Fluorouracil
A Level
Atomic Orbitals
s-orbitals
p-orbitals
3d-orbitals
Comparison of 1s, 2s and 2p orbitals
Organic Reaction Mechanisms
Organic Chemistry Introduction
Electrophilic Addition Addition of bromine to an alkene
Electrophilic addition to alkenes – Symmetrical and Unsymmetrical
Reaction of carbonyl compounds with HCN
Nucleophilic Addition Addition of Hydride
Cyanohydrin Formation – Nucleophilic addition to the carbonyl group
Nucleophilic Substitution at Saturated Carbon
Nucleophilic Substitution Cyanide + Ethyl Bromide
Elimination
Elimination – E2 Stereoselective for E alkenes
Amide formation
Formation of Ethyl Ethanoate
Hydrolysis of ethanoyl chloride
Nitration of Benzene
Friedel-Crafts acylation
Friedel-Crafts alkylation
Radical Reactions Synthesis of Chloroalkanes
Radical Reactions – Initiation Step
Radical Reactions – Propagation Steps
Radical Reactions – Termination Steps
Radical Reactions CFCs and the Ozone Layer
Crystal Structures
Carbon (Diamond, Graphite C
60
)
Ice
I
2
– Iodine
Magnesium
NaCl – Sodium chloride
Proton NMR Introduction
Ethanol Proton NMR
Propanone Proton NMR
Ethyl Acetate Proton NMR
Ethyl Benzene Proton NMR
Ethanol D
2
O exchange
Ethyl Amine (D
2
O) Proton Exchange
Shapes of molecules VSEPR
H
2
O Water
NH
3
Ammonia
CH
4
Methane
SF
6
Sulfur Hexafluoride
SF
4
Sulfur Tetrafluoride
PF
5
Phosphorus Pentafluoride
ClF
3
Chlorine Trifluoride
Medicinal Chemistry at Liverpool
Medicinal Chemistry Research at the University of Liverpool
Polymers A Level
Terylene polyester PET
Polyvinyl Chloride Poly(chloroethene) PVC
Nylon 6,6 - polyamide
Polystyrene (PS)
DNA/RNA Base Pairs
cis-Platin and DNA
Polymers
Polymer Chemistry
Poly(ether ketone)
Polyethylene Polythene (PE)
Natural Rubber
Polystyrene (PS)
Polyethylene terephthalate PET
Bisphenol A (polycarbonate)
Nylon 6,6
Poly(methyl methacrylate)
Kapton
Polyphenylene I
Polyphenylene II
Polyphenylene III
PAMAM Dendrimer (Polyamidoamines)
Polyvinyl Chloride PVC
Polypyrrole
Polythiophene PT
Poly(ether sulfone) PES
Poly(phenylene sulfone) PPSF or PPSU
Polydimethylsiloxane PDMS
Radical Copolymerization
360° Lab Safety
Apparatus/Equipment
Reflux Exercise
Dean-Stark Exercise
Distillation Exercise
Column Chromatography Exercise
"Bad Lab" Scenes
Analytical Chemistry Lab Exercise
Titration Exercise
General Chemistry Lab Exercise
Synthetic Chemistry Lab A Exercise
Synthetic Chemistry Lab B Exercise
Synthetic Chemistry Lab C Exercise
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