Organic chemistry and instrumental analysis Flashcards
When do Molecular orbitals form?
When atomic orbitals combine
The number of molecular orbitals is equal to..?
the number of atomic orbitals that combine
The combination of two
atomic orbitals results in the formation of…?
a bonding molecular orbital and an antibonding orbital.
The bonding molecular orbital encompasses…?
both nuclei
Sigma bonds
Molecular orbitals that form by end-on overlap of atomic orbitals along the axis of the covalent bond are called sigma (σ ) molecular orbitals or sigma bonds.
pi bonds
Molecular orbitals that form by side-on overlap of parallel atomic orbitals that lie
perpendicular to the axis of the covalent bond are called pi (π ) molecular orbitals or
pi bonds.
electron config of an isolated carbon
The electronic configuration of an isolated carbon atom cannot explain the number of
bonds formed by carbon atoms in molecules. The bonding and shape of molecules of carbon can be explained by hybridisation.
Hybridisation
Hybridisation is the process of mixing atomic orbitals within an atom to generate a set of new atomic orbitals called hybrid orbitals. These hybrid orbitals are degenerate.
Hybridisation in alkanes
the 2s orbital and the three 2p orbitals of carbon hybridise to form four degenerate sp3 hybrid orbitals. These adopt a tetrahedral arrangement. The sp3 hybrid
orbitals overlap end-on with other atomic orbitals to form σ bonds.
Hybridisation in alkenes
The bonding in alkenes can be described in terms of sp2 hybridisation. The 2s orbital and
two of the 2p orbitals hybridise to form three degenerate sp2 hybrid orbitals. These adopt a trigonal planar arrangement. The hybrid sp2 orbitals overlap end-on to form σ bonds. The
remaining 2p orbital on each carbon atom of the double bond is unhybridised and lies
perpendicular to the axis of the σ bond. The unhybridised p orbitals overlap side-on to
form π bonds.
Hybridisation in benzene
The bonding in benzene and other aromatic systems can be described in terms of sp2
hybridisation. The six carbon atoms in benzene are arranged in a cyclic structure with σ
bonds between the carbon atoms. The unhybridised p orbitals on each carbon atom
overlap side-on to form a π molecular system, perpendicular to the plane of the σ bonds.
This π molecular system extends across all six carbon atoms. The electrons in this
system are delocalised.
Hybridisation in alkynes
The bonding in alkynes can be described in terms of sp hybridisation. The 2s orbital and
one 2p orbital of carbon hybridise to form two degenerate hybrid orbitals. These adopt a
linear arrangement. The hybrid sp orbitals overlap end-on to form σ bonds. The remaining
two 2p orbitals on each carbon atom lie perpendicular to each other and to the axis of the
σ bond. The unhybridised p orbitals overlap side-on to form two π bonds.
HOMO
The highest bonding molecular orbital containing electrons is called the highest occupied molecular orbital
LUMO
The lowest antibonding molecular orbital is
called the lowest unoccupied molecular orbital (LUMO).
What happens to electrons when radiation is absorbed?
Absorption of electromagnetic energy can cause electrons to be promoted from HOMO to
LUMO.
Why do most organic molecules appear colourless?
Most organic molecules appear colourless because the energy difference between HOMO
and LUMO is relatively large. This results in absorption of light from the ultraviolet region of
the spectrum.
What is a chromophore and where do they exist?
A chromophore is a group of atoms within
a molecule that is responsible for absorption of light in the visible region of the spectrum.
Light can be absorbed when electrons in a chromophore are promoted from the HOMO to
the LUMO. Chromophores exist in molecules containing a conjugated system
Conjugated system
a system of adjacent
unhybridised p orbitals that overlap side-on to form a molecular orbital across a number of
carbon atoms. Electrons within this conjugated system are delocalised. Molecules with
alternating single and double bonds, and aromatic molecules have conjugated systems.
The more atoms in a conjugated system the smaller…?
The more atoms in the conjugated system the smaller the energy gap between HOMO and
LUMO. A lower frequency of light (longer wavelength, lower energy) is absorbed by the
compound. When the wavelength of light absorbed is in the visible region, the compound
will exhibit the complementary colour.
What is bond fission?
When an organic reaction takes place, bonds in the reactant molecules are broken and
bonds in the product molecules are made. The process of bond breaking is known as bond
fission.
name the two types of bond fission
homolytic and heterolytic
What is homolytic fission?
♦ results in the formation of two neutral radicals
♦ occurs when each atom retains one electron from the σ covalent bond and the bond
breaks evenly
♦ normally occurs when non-polar covalent bonds are broken
is homolytic fission appropriate for organic synthesis?
no, Reactions involving homolytic fission tend to result in the formation of very complex
mixtures of products, making them unsuitable for organic synthesis.
What is heterolytic fission?
Heterolytic fission:
♦ results in the formation of two oppositely charged ions
♦ occurs when one atom retains both electrons from the σ covalent bond and the bond
breaks unevenly
♦ normally occurs when polar covalent bonds are broken
Is heterolytic fission suitable for organic synthesis?
yes, Reactions involving heterolytic fission tend to result in far fewer products than reactions
involving homolytic fission, and so are better suited for organic synthesis.
two single-headed arrows starting at the middle of a covalent bond indicate…
homolytic
bond fission is occurring
a double-headed arrow starting at the middle of a covalent bond indicates…
heterolytic
bond fission is occurring
What are nucleophiles?
♦ negatively charged ions or neutral molecules that are electron rich, such as
Cl-, Br- , OH- , CN- , NH3 and H2O
♦ attracted towards atoms bearing a partial (δ+) or full positive charge
♦ capable of donating an electron pair to form a new covalent bond
What are electrophiles?
♦ positively charged ions or neutral molecules that are electron deficient, such as H+, NO2+, SO3
♦ attracted towards atoms bearing a partial (δ−) or full negative charge
♦ capable of accepting an electron pair to form a new covalent bond
Name different reactions and their products with monohaloalkanes
Elimination reactions to form alkenes using a strong base like sodium hydroxide in ethanol.
nucleophilic substitution:
aqueous alkali > alcohol
alkoxides > ethers
ethanolic cyanide > nitriles > hydrolysis > carboxylic acids
SN1
SN1 is a nucleophilic substitution reaction with one species in the rate determining step and occurs in a minimum of two steps via a trigonal planar carbocation intermediate.
SN2
SN2 is a nucleophilic substitution reaction with two species in the rate determining step and
occurs in a single step via a single five-centred, trigonal bipyramidal transition state.
steric hindrance
when atoms or groups are too close to each other, they may not be able to interact properly, or they may even block each other from participating in reactions. This can influence the stability, reactivity, and shape of a molecule.
Alcohols can be prepared from?
♦ haloalkanes by substitution
♦ alkenes by acid-catalysed hydration (addition)
♦ aldehydes and ketones by reduction using a reducing agent such as lithium aluminium
hydride
Name the reactions for alcohols and their products
♦ dehydration to form alkenes using aluminium oxide, concentrated sulfuric acid or
concentrated phosphoric acid
♦ oxidation of primary alcohols to form aldehydes and then carboxylic acids and
secondary alcohols to form ketones, using acidified permanganate, acidified
dichromate or hot copper(II) oxide
♦ formation of alcoholic alkoxides by reaction with some reactive metals such as
potassium or sodium, which can then be reacted with monohaloalkanes to form ethers
♦ formation of esters by reaction with carboxylic acids using concentrated sulfuric acid or
concentrated phosphoric acid as a catalyst
formation of esters by reaction with acid chlorides — this gives a faster
reaction than reaction with carboxylic acids, and no catalyst is needed
What are ethers?
Ethers can be regarded as substituted alkanes in which a hydrogen atom is replaced with
an alkoxy functional group, –OR, and have the general structure R’ – O – R’’, where R’ and R’’ are alkyl groups.
Boiling points of ethers
Due to the lack of hydrogen bonding between ether molecules, they have lower boiling
points than the corresponding isomeric alcohols.
solubility of ethers
Methoxymethane and methoxyethane are soluble in water. Larger ethers are insoluble in water due to their increased molecular size.
Why are ethers commonly used as solvents?
Ethers are commonly used as solvents since they are relatively inert chemically and will
dissolve many organic compounds.
Alkenes take part in electrophilic addition reactions with…?
♦ hydrogen to form alkanes in the presence of a catalyst
♦ halogens to form dihaloalkanes
♦ hydrogen halides to form monohaloalkanes
♦ water using an acid catalyst to form alcohols
Markovnikov’s rule
states that when a hydrogen halide or water is added to an
unsymmetrical alkene, the hydrogen atom becomes attached to the carbon with the most
hydrogen atoms attached to it already. Markovnikov’s rule can be used to predict major
and minor products formed during the reaction of a hydrogen halide or water with alkenes.
Carboxylic acids can be prepared by…
♦ oxidising primary alcohols using acidified permanganate, acidified dichromate and hot
copper(II) oxide
♦ oxidising aldehydes using acidified permanganate, acidified dichromate, Fehling’s
solution and Tollens’ reagent
♦ hydrolysing nitriles, esters or amides
Reactions of carboxylic acids include…?
♦ formation of salts by reactions with metals or bases
♦ condensation reactions with alcohols to form esters in the presence of concentrated
sulfuric or concentrated phosphoric acid
♦ reaction with amines to form alkylammonium salts that form amides when heated
♦ reduction with lithium aluminium hydride to form primary alcohols
What are amines
Amines are organic derivatives of ammonia in which one or more hydrogen atoms of
ammonia has been replaced by an alkyl group.
Amines can be classified as primary, secondary or tertiary according to the number of alkyl
groups attached to the nitrogen atom.
What is produced when an amine and acid are reacted?
salts
Boiling points in amines
Primary and secondary amines, but not tertiary amines, display hydrogen bonding. As a result, primary and secondary amines have higher boiling points than isomeric tertiary
amines.
Solubility in amines
Primary, secondary and tertiary amine molecules can hydrogen-bond with water molecules,
thus explaining the appreciable solubility of the shorter chain length amines in water.
Why do benzene rings resist addition reactions?
the presence of delocalized electrons
Benzene rings and electrophilic sub reactions
♦ halogenation by reaction of a halogen using aluminium chloride or iron(III) chloride for
chlorination and aluminium bromide or iron(III) bromide for bromination
♦ alkylation by reaction of a haloalkane using aluminium chloride
♦ nitration using concentrated sulfuric acid and concentrated nitric acid
♦ sulfonation using concentrated sulfuric acid
Stereoisomers occur when…
the order of the bonding in the atoms is the same but the
spatial arrangement of the atoms is different in each isomer. There are two types of
stereoisomer, geometric and optical.
geometric isomers
can occur when there is restricted rotation around a carbon-carbon double bond or a
carbon-carbon single bond in a cyclic compound
♦ must have two different groups attached to each of the carbon atoms that make up the
bond with restricted rotation
♦ can be labelled cis or trans according to whether the substituent groups are on the
same side (cis) or on different sides (trans) of the bond with restricted rotation
♦ have differences in physical properties, such as melting point and boiling point
♦ can have differences in chemical properties
Optical isomers
Optical isomers:
♦ occur in compounds in which four different groups are arranged tetrahedrally around a
central carbon atom (chiral carbon or chiral centre)
♦ are asymmetric
♦ are non-superimposable mirror images of each other
♦ can be described as enantiomers
♦ have identical physical properties, except for their effect on plane-polarised light
♦ have identical chemical properties, except when in a chiral environment such as that
found in biological systems (only one optical isomer is usually present)
♦ rotate plane-polarised light by the same amount but in opposite directions and so are
optically active
♦ when mixed in equal amounts are optically inactive because the rotational effect of the
plane-polarised light cancels out — this is called a racemic mixture
Elemental microanalysis
used to determine the masses of C, H, O, S and N in a sample
of an organic compound in order to determine its empirical formula.
Mass spectrometry
can be used to determine the accurate gram formula mass (GFM) and
structural features of an organic compound.
mass spec method
In mass spectrometry, a small sample of an organic compound is bombarded by
high-energy electrons. This removes electrons from the organic molecule generating
positively charged molecular ions known as parent ions. These molecular ions then break
into smaller positively charged ion fragments. A mass spectrum is obtained showing a plot
of the relative abundance of the ions detected against the mass-to-charge (m/z) ratio.
The mass-to-charge ratio of the parent ion can be used to determine the GFM of the
molecular ion, and so a molecular formula can be determined using the empirical formula.
The fragmentation data can be interpreted to gain structural information.
Infrared spectroscopy
used to identify certain functional groups in an organic compound
infrared spec method
When infrared radiation is absorbed by organic compounds, bonds within the molecule
vibrate (stretch and bend). The wavelengths of infrared radiation that are absorbed depend
on the type of atoms that make up the bond and the strength of the bond.
In infrared spectroscopy, infrared radiation is passed through a sample of the organic
compound and then into a detector that measures the intensity of the transmitted radiation
at different wavelengths.
Proton nuclear magnetic resonance spectroscopy
can give
information about the different chemical environments of hydrogen atoms (protons or 1H) in an organic molecule, and about how many hydrogen atoms there are in each of these
environments.
H NMR method
1
H nuclei behave like tiny magnets and in a strong magnetic field some align with the field
(lower energy), whilst the rest align against it (higher energy). Absorption of radiation in the
radio frequency region of the electromagnetic spectrum causes the 1
H nuclei to ‘flip’ from
the lower to the higher energy alignment. As they fall back from the higher to the lower
energy alignment the emitted radiation is detected and plotted on a spectrum.
The area under the peak is related to…
the number of 1
H atoms in that environment and is
often given by an integration curve on a spectrum. The height of an integration curve is
proportional to the number of 1
H atoms in that environment, and so a ratio of 1
H atoms in
each environment can be determined
The standard reference substance used in 1H NMR spectroscopy is…?
tetramethylsilane (TMS), which is assigned a chemical shift value equal to zero.
1H NMR spectra can be obtained using…?
low-resolution or high-resolution NMR.
High-resolution 1H NMR uses…?
higher radio frequencies than those used in low-resolution
1H NMR and provides more detailed spectra.
High resolution H NMR method
In a high-resolution 1
H NMR an interaction with 1
H atoms on neighbouring carbon atoms
can result in the splitting of peaks into multiplets. The number of 1
H atoms on neighbouring
carbon atoms will determine the number of peaks within a multiplet and can be determined
using the n+1 rule, where n is the number of 1
H atoms on the neighbouring carbon atom.
What are drugs?
Drugs are substances that alter the biochemical processes in the body
what do most medicines contain?
usually contains the drug plus other ingredients such as fillers to add bulk or
sweeteners to improve the taste.
How do drugs work?
Drugs generally work by binding to specific protein molecules. These protein molecules
can be found on the surface of a cell (receptor) or can be specific enzyme molecules within
a cell.
agonists
An agonist mimics the natural compound and binds to the receptor molecules to
produce a response similar to the natural active compound.
antagonist
An antagonist prevents the natural compound from binding to the receptor, and so
blocks the natural response from occurring.
How do enzyme inhibitors work?
Many drugs that act on enzymes are classified as enzyme inhibitors and act by binding to
the active site of the enzyme and blocking the reaction normally catalysed there.
What interactions form between the drug and receptor
The types of interactions formed can include van der
Waals forces and/or ionic bonds.
What is a difference between a bonding and antibonding molecular orbital?
Anti-bonding has higher energy
Anti-bonding is unfilled and bonding is filled
