The Kidneys and the Ionic Composition of the Extracellular Fluids January 28, 2010
Posted by sourcez in 71591, Biology 1.Tags: kidneys, ultrafiltration
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The regulation of homeostasis within the body involves the renal system – which comprises of 2 kidneys connected to a urinary bladder by independant ureters. From the bladder, urine passes out of the body via the Urethra.
Urinary System Diagram - From medicalartlibrary.com
The urine from the bladder can tell us many things about the condition of the body – from ionic content to water content to illnesses and disease. There are 4 different properties to look at:
- Colour – eg Red/Black might indicate red blood cells present & therefore Malaria
- Clarity – is it opaque, translucent…
- Odour
- Taste – eg A sweet taste might indicate glucose presence and therefore Diabetes
Kidney Function
The kidney allows homeostatic regulation of the water and ion content in the blood. This iincludes:
- Regulation of extracellular fluid (ECF)
- Regulation of blood osmolarity
- Regulation of ion concentrations – eg keeping Na+, K+, Cl-, Ca2+ within normal ranges.
- Regulation of blood pH with H+/HCO3-
Following the regulation of these systems the waste fluids and substances (such as urea) are excreted. The renal system is also involved in the production of some hormones such as Vitamin D hormone.
To do all of this, the Kidney is highly specialised and first filters substances out of the blood before selectively reabsorbing what is needed by the body. Anything not reabsorbed is excreted.
Kidney Structure
The functional unit within the kidney is the nephron, which spans the cortex and medulla of the kidney.
Diagram of a Kidney with Nephron closeup - From HowStuffWorks
Looking at the Kidney above, we have:
A – Renal Vein
B – Renal Artery
C – Ureter
D – Cortex/Medulla
E – Renal Pelvis
F – Capsule
In fact, this illustration is not great – all of the tissue between the pelvis and capsule forms the medulla and cortex. The medulla surrounds the pelvis with a structure containing Renal Pyramids (shown in red on the picture above). Surrounding this is the thinner cortex which does not share this unique structure.
Spanning the medulla & cortex there are millions of nephrons. And looking at the nephron (listed in the order filtrate passes through):
5 – Renal corpuscle, comprised of the glomerulus and the bowmans capsule
4 – Prominal Convoluted Tubule
2 – Descending loop of Henle
1 – Ascending loop of Henle
6 – Distal Convoluted Tubule
3 – Renal Capillaries – these do surround all of the above but are only illustrated surrounding several areas.
The distal convoluted tubule then leads on to the collecting duct which also has an important role in Kidney function. The collecting duct leads to the ureter.
Filtration
Filtration of substances out of the blood happens at the Renal Corpuscle.
Renal Corpuscle - Modified from original: Gray's Anatomy figure 1130
The entire unit is the renal corpuscle, which areas in red are the glomerulus and pink the bowmans capsule.
A – Afferent Arteriole
B – Efferent Arteriole (leaving the glomerulus)
C – Fenestrated Endothelium of Glomerular Capillary
E – Basal Lamina
D – Bowman’s Capsule Epithelium
F – Beginning of Proximal Convoluted Tubule
The blood enters the glomerulus and molecules/fluid are filtered out of the blood along a net filtration gradient (~17mmHg). This is driven by the high (60mmHg) hydrostatic pressure which is resisted by the capsule fluid pressure and glomerular osmotic pressure. This net filtration pressure forces molecules through 3 barriers:
- Glomerular Capillary Endothelium
- Basal Lamina
- Bowman’s Capsule Epithelium
This means molecules are sieved and have to be able to ‘fit’ through ’slits’ in the bowman’s capsule epithelium – so larger molecules like cells and larger proteins (eg red blood cells) stay in the blood. The standard glomerular filtration rate is 125ml/min or 180L/day.
Autoregulatory systems ensure the hydrostatic pressure remains constant even when blood pressure or heart rate increases by altering blood flow through the glomerular capillaries. Smooth muscle contracts or relaxes depending on the need.
Reabsorption
Rates of Reactions, Chemical Kinetics & Orders January 12, 2010
Posted by sourcez in Chemistry 1.add a comment
NOTE: Formatting needed–
One of the most important things to note with chemical reactions is that the molar concentrations of the substrates are often proportional to the rate of the reaction.
So if we take the simplest rate constant for an equation:
A + B –> C
We could might find the rate law to be:
Rate = k[A][B]
The coefficient k is called the rate constant and is dependant on temperature – this is independant of the concentrations of the substrates; so the larger the value of k, the faster the rate of the reaction. Also important is that the units of k will convert the product of the concentrations into a rate – so change in concentration per unit of time, often expressed as mol.dm-3.s-1.
While temperature increases increase the rate constant and rate of reaction in most cases, reactions with a large activation energy will have small rate constants as considerable temperature rises may be required for the reaction to occur at all.
Consider this theoretical example:
Rate = k[A][B] where k = 5 dm3 mol^-1; [A] = 1 mol.dm-3; [B] = 2 mol.dm-3
Therefore Rate = 5 dm3.mol-1.s-1 x 2 mol^2.dm^-6
The units all cancel to leave us with a rate of: 10 mol.dm-3.s-1
So the units for k in that example were dm3.mol-1.s-1. In another rate law, eg: Rate = k[A] we would find the units for k to be simply s-1.
Once we know the rate law and rate constant for that reaction we can go on to predict the reaction rate for any concentration of substrates.
- The Order of a Reaction
Reactions can usually be defined as either zero order (0), first order (1) or second order (2). The order of a reagent or the overall reaction depends on the effect varying the concentrations of substrates has on the rate of the reaction. So:
- Zero Order – rate is not related to reactant A – rate is proportional to [A]0
- First Order – rate is doubled as concentration of reagent B doubles – rate is proportional to [B]1
- Second Order – rate is quadrupled as concentartion of reagent C doubles – rate is proportional to [C]2
Combining the above information, rate is proportional to [A]0[B]1[C]2 – therefore Rate = k[B]1[C]2 – so the reaction is 3rd order ( 1+2=3). Third order tells us the reaction is made of several parts.
- Measuring Rate & Integrated Rate Equations
0. Zero Order:
As a zero order reaction has a rate which is independant of any reagents, we can assume that Rate = k.
To identify a zero order reaction plot concentration of a reagent against time and you would see a straight line. The integrated rate equation is:
Which means that the gradient (from y=mx+c) equals -k. This allows us to determine k from the graph.
Another feature of a zero order reaction is a decreasing half life as the reaction continues. The half life equation for zero order reactions is:
Where [A]0 is the initial concentration. Shows a decreasing half life as concentration falls.
1. First Order:
First order reactions have a rate proportional to the concentration of only one reagent. Any other reagents present will not affect the rate.
To identify a first order reaction plot In(concentration) against time to give a straight line. The integrated rate equation is:
Which means that as with zero order, k is the -ve of the gradient.
The half life of a first order reaction is constant thoughout the reaction:
This half life is dependant only on k as the half life remains constant regardless of concentration.
2.Second Order:
Second order reactions have a rate proportional either to 1 or 2 reagents (eg 2 x first order reagents or 1 x second order reagents).
To identify a second order reaction, plot 1/concentration against time to give a +ve straight line. The integrated rate equation is:
Which means that k = gradient (so the opposite of what we find in zero and first order reactions).
The half life of a second order reaction increases throughout the reaction:
Shows an increasing half life with decreasing concentration.
2(1). Psuedo First Order:
Psuedo first order approximation is used when carrying out some second order reactions. It is useful as it is difficult to effectively control the concentrations of more than one reagent at the same time, and the psuedo technique simply places one reagent in excess at a constant level; essentially limiting the reaction rate the other reagent (you only control the concentration of one reagent).
The equation above illustrates that by putting [B] in excess we have essentially removed it from the rate reaction, allowing us to calculate the psuedo rate constant k‘.
Preparation & Reactions of Aldehydes and Ketones, RHO & ROR’ January 8, 2010
Posted by sourcez in Chemistry 1, Sem2.add a comment
A couple of key points:
- Aldehydes and Ketones both contain a carbonyl group, but are also less reactive than acid chlorides.
- They do NOT react with organocopper reagents and weak hydride donors (as these weak reagents are involved in their own synthesis).
- The reactions are addition rather than substitution as there is no leaving group.
- They have one less bond to an electronegative atom than acid chlorides (no chlorine!).
Aldehyde & Ketone
They can be formed through reduction of Acid Chloride:
Aldehyde & ketone synthesised with Bu3SnH and R
If an aromatic ring is being substituted then we must use friedel crafts acylation.
For Acid Chloride to Aldehyde we use Bu3SnH as a source of weak Hydride ions which displace a Cl-. We do not use a more obvious source such as LiAlH4 as this will result in the over reduction of the aldehyde into a primary alcohol.
For Acid Chloride to Ketone we use R’2CuLi as a source of nucleophilic R’ group.
and via reactions with Alcohols:
Simply, Primary alcohols lead to Aldehydes and secondary alcohols lead to Ketones when reacted with PCC. This is oxidation.
Aldehyde & Ketone synthesised from Alcohols
and finally with Alkanes:
Alkanes are just as simple as alcohols – just add O3 then PPh3 for an easy reaction!
Simple alkenes lead to aldehydes and more complex lead to ketones.
Aldehyde Ketone synthesised from Alkenes
Synthesis Summary:
In short:
REDUCTION
From Acid Chloride to Aldehyde – Bu3SnH (as a source of H-)
From Acid Chloride to Ketone – R2CuLi (as a source of R)
OXIDATION
From Alcohol to Aldehyde/Ketone – PCC
From Alkene to Aldehyde/Ketone – O3 then PPh3
- Reactions with Carbon Nucleophiles and Hydride Donors
As mentioned earlier, aldehydes and ketones do not react with weak hydride donors (eh Bu3SnH) or organocopper reagents (eg R2CuLi) – they need more powerful reagents.
These come in the form of Grignard reagents (eg RMgBr) and powerful halide donors (eg LiAlH4).
TBF
DNA Mutations and Genetic Diseases January 7, 2010
Posted by sourcez in Molecules & the Basis of Life.add a comment
As mentioned, chromosomes select characteristics such as sex (Men have different copies of the sex chromosome, X and Y wheras females have two X chromosomes) but also cause diseases through chromosomal abnormalities:
- Downs Syndrome – Caused by 3 copies of chromosome 21. This is referred to as trisomy.
- Turner Syndrome (women) – only 1 X chromosome.
- Klinefelter Syndrome (men) – YXX (trisomy) rather than YX.
- Cystic Fibrosis – 3 nucleotides removed in DELTAF508 gene – stopping production of phenylalanine.
- Sickle Cell Anaemia – A changed to T in gene for haemaglobin.
Materials can be traslocated from one chromosome to another, nucleotides added or removed or bases substituted. These changes can cause diseases and other genetic problems. Usually these are seen during protein synthesis.
- Down’s Syndrome
Downs Syndrome is a genetic disease caused by an extra copy (which may be complete or partial) or chromosome 21 (trisomy 21). The disease is often associated with lessened cognitive ability & physical development and features a common set of facial characteristics. Further implications of Down’s Syndrome vary greatly from one individual to another. Fertility is another affected function, with very few males able to successfully reproduce and only some females when mating with unaffected males. Incidence rates of the disease in their children are much greater at approximately half.
While treatment can be provided to improve a sufferers quality of life there is no cure.
Fig 2 - Trisomy 21 Causing Down's Syndrome (Female Karyotype)
It is estimated 1 in 800-1000 people are born with the disease, with several factors contributing to the likelyhood of a child having it. The most notable of these seems to be the age of the mother, with the chance of the disease increasing as a mother gets older.
The Mutation in Down’s Syndrome
There are several ways Down’s Syndrome has been discovered to occur. About 95% of all cases occur via the first route, Trisomy-21.
- Trisomy 21 – 95% of cases – Where the extra chromosome 21 is added to a gamete in nondisjunction (where either homologous chromosomes fail to come apart in meiosis 1 or sister chromatids fail to come apart during meiosis 2 or mitosis) event during production in the parent; then joining with a gamete from the other parent to produce an embryo with 47 chromosomes. The vast majority (~88%) of this mutation occurs in the mother.
- Mosiac Down’s Syndrome – 1-2% of cases – Where some of the cells in the embryo (and later body) have Trisomy-21 and some are normal. This can occur as Trisomy-21 above followed by a reversion to normal cells during cell division in the embryo; or the other way around where cell division in a normal embryo somehow change to Trisomy-21.
- Robertson Translocation – 2-3% of cases – In the karyotype of one of the parents, the long arm of chromosome 21 is attached to another chromosome (often 14) and following normal disjunctions during cell replication there is a high possibility of a child receiving the extra chromosome. This is also known as familial Down’s syndrome, as it is passed directly down and the parents show a normal phenotype – with this type there is no age effect and males are as likely as females to cause the disease in their offspring.
A final, very rare occurance is the duplication of a portion of chromosome 21, meaning that there are copies of some of the genes. If these are the genes responsible for the effects seen in Down’s syndrome then these effects will be expressed but otherwise the phenotype will be normal.
- Sickle Cell Anaemia
Sickle cell anaemia affects the red blood cells in the body, by producing cells which hold a rigid sickle shape rather than the usual doughnut. As this is a genetic disease based on a recessive allele there is a possibility for offspring to be carriers, suffer the disease or not carry it at all, depending on their parents. Sickle cell disease is caused by having both recessive alleles (SS) while people can also have sickle cell trait which means they are a carrier but do not show the effects of the disease (HbS).
As the cells are more rigid than normal, and combined with their unusual shape there are many complications which can occur within the body. These include blockages of blood vessels, increased destruction of blood cells (and so reduced oxygen capacity), problems with the spleen and a host of other blood & circulation related problems.
A sickled red blood cell sits among normal cells
It is interesting to note that the disease is found in higher levels in areas where Malaria is more common, as being a carrier (so the sickle cell trait rather than sickle cell disease) is a benefit as sickling of blood cells as they are attacked by malaria halts its spread.
Sickle cell disease is caused by a mutation on the haemoglobin gene – where A is changed to T at position 17 in a base substitution (mis-sense). This changes a glutamic acid on the protein (GAG) to a valine (GTG).
- Types of Mutation in DNA
Fig 1 - Showing different types of chromosomal mutation
Wild Type = Normal Sequence of DNA
- Point Mutations – Single nucleotide changes in the DNA strand which result in different codons.
- Miss-sense = Resulting in a different amino acid.
- Non-sense = Resulting in a STOP codon and possible termination of protein chain.
- Silent = Codon codes for the same amino acid as wild type so the protein is the same.
- Frameshift Base Insertions or Deletions = One nucleotide added or removed, resulting in the change of most of the following amino acids.
5- Classification & Taxonomy January 15, 2009
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The Five Kingdoms
There are 5 kingdoms in the classification system. Organisms are classified according to their evolutionary relationships (their phylogeny).
Phylogeny is the study of the evolutionary history of organisms, and gives us an insight as to how to group them and their extinct relatives. The base hierarchy in the classification system is the Kindom.
Generally, we can order the Kingdoms by increasing complexity. To help remember the names of the kingdoms, I was taught:
Pretty Polly Finds Parrots Attractive – Prokaryote, Protoctista, Fungi, Plantae, Animalia.
| Prokaryotes | Protoctista | Fungi | Plantae | Animalia | |
| Cell Structure | Unicellular; no membrane bound organelles | Eukaryotes, Unicellular & Multicellular | Eukaryotes, Unicellular & Multicellular (Yeast) | Eukaryotic, Multicellular; Large Vacuoles | Eukaryotic, Multicellular |
| Cell Wall | Murein | Sometimes Polysaccharide | Chitin | Cellulose | None |
| Nutrition | Autotrophic, Aerobic Heterotrophic | Autotrophic, Hetrotrophic | Heterotrophic | Autotrophic (Photosynthetic) | Heterotrophic, Digestive System |
| Reproduction | Binary Fission | Fission | Spores | Seeds/Spores, Some asexual while some sexual | Develop from embryo |
| Example | Bacteria | Algae, Protozoa | Penicillin | Mosses, Ferns | Humans, Animals |
NOTE
Q. What’s a photosynthetic organism?
A. An organism that gets its energy by absorbing light.
Q. What’s a autotrophic organism?
A. An organism which gets it’s energy from light (photosynthesis) or from chemical interaction (chemosynthesis).
Q. What’s a heterotrophic organism?
A. An organism that relies on complex organic matter for food.
Remember that 4 of the 5 kingdoms feature Eukaryotes! Only Prokaryotae contains Prokaryotes (no surprise there!).
Taxonomy (Breaking it down)
We break down organisms into a total of 7 hierarchical classes (including Kingdom above). That’s a lot of possible choices for organisms, and is know as Taxonomy, or Alpha Taxonomy.
The 7 levels are Kingdom, Phylum, Class, Order, Family, Genus and Species. You could remember this as:
King Penguins Climb Over Frozen Grassy Slopes
Here’s an example of two organisms and their taxonomy:
| Humans | Large White Butterfly | |
| Kingdom | Animalia | Animalia |
| Phylum | Chordata | Arthropoda |
| Class | Mammalia | Insecta |
| Order | Primates | Lepidoptera |
| Family | Hominidae | Pieridae |
| Genus | Homo | Pieris |
| Species | sapiens | brassica |
As you can see, humans are sapiens of the Genus Homo. AKA Homo sapiens (I bet you’ve heard that before!).
The only similarity between these two examples is that they are both in the Animalia kingdom. This means they share a great number of common traits, and so actually tells us a lot about the organisms.
It is also worth bearing in mind that Protoctista is often the ‘Other’ category where organisms who have no clear Kingdom are put. For example, Slime Moulds have fungi characteristics, yet are not quite suitable for classification in the Fungi Kingdom.
The Species
Species is the final tier on the taxonomy hierarchy; and is a group of organisms with similar traits. These include:
- Morphology (The outside appearance of an organism, including shape, colour, structure and pattern)
- Physiology (The way in which an organisms works, by looking at it’s biochemical, mechanical and physics functions)
- Behaviour
BUT most importantly, we can class two organisms as the same species if they can naturally breed together and produce fertile offspring.
The fertility point is an important one, as there are several organisms that can breed together, but produce a sterile offspring which cannot breed any further – such as a horse and a zebra which can produce a hybrid. This hybrid is sterile, so we know what the horse and the zebra are different species.
The Chemistry of Acid Chlorides, ROCl August 24, 2008
Posted by sourcez in Sem2.4 comments
Acid Chlorides:
Highly Reactive Carboxylic Acid Derivatives such as Acid Chlorides can be easily formed:
Easy preparation of acid halides from Carboxylic Acids
Acid Chlorides are:
- Highly reactive functional groups.
- Mainly involved in nucleophilic substitution reactions.
- Have identical reactions to acid bromides and acid anhydrides (so I will only focus on the Chlorides).
Acid Chlorides undergo a fair number of useful reactions. Below is a table illustrating them:
Paths to common, useful products of Acid Chlorides
The mechanism for all of these substitution reactions begins with the addition of Nu- or :NuH to the δ+ carbon atom of the carbonyl. This then creates an tetrahedral intermediate which then collapses to eject the chlorine (Cl-). The only difference with :NuH is an additional step where a base (such as pyridine) removes the H+ from the nucleophile.
Nucleophilic Substitution using Nu- and :NuH on Acid Chloride
Acid Chlorides can be converted into Ketones using organocopper reagents such as Me2CuLi and Ph2CuLi. This can be extremely useful in increasing chain length, amongst other things. The reason we used organocopper reagents instead of Grignard reagents (which we already know work) is down to how far the reaction goes. Grignard reagents are capable of converting Ketones into tertiary alcohols, and so tend to follow this route to completion.
The reactions involving Hydride ions are all run using weaker sources of H- than LiAlH4 (which would normally be the obvious choice). This is because the LiAlH4 will continue the conversion from an Aldehyde to a primary alcohol.
Addition of Aromatic Rings (Friedel Crafts Acylation):
Aromatic rings have no direct route for attack. They are poor nucleophiles (due to their stability) and as such require the Acid Chloride to be activated (made into a better electrophile) so they can be pulled in.
This activation can be achieved by using a Lewis acid such as AlCl3 or FeBr3. This reaction type is know as a Friedel Crafts Acylation. The animation below shows the mechanism and reaction scheme for this activation, and joining.
Friedel Crafts Acylation Mechanism - Addition of an Aromatic Ring to form Ketone. Click to launch animation.
If you’re wondering why the product does not reach further, simply consider the properties of the carbonyl group. The carbonyl group has electron withdrawing properties and as such reduces the available of electrons in the aromatic ring…requiring stonger conditions to instigate a second acylation reaction.
The Carbonyl, >C=O August 24, 2008
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One of the most important functional groups is the Carbonyl group.
Source: Wikipedia. Shows C=O and two additional atoms.
A couple of points about the carbonyl group:
- It is Planar (flat).
- Bond angles are 120 degrees.
- The Carbon = Oxygen double bond is the result of overlapping Pi and s orbitals.
- Both the Oxygen and Carbon atoms are sp2 hybridised.
- Oxygen has 2 lone pairs of electrons not involved in bonding.
- Oxygen is electronegative relative to Carbon and therefore the bond is polarised.
There are 2 ways to represent the polarisation of the carbonyl. Delta-notation to show partial charges, or Resonance forms to show the individual structures which contribute to the bonding sturture.
Resonance Forms
Reactivity:
There are three main loci of reactivity – with electrophiles, nucleophiles and bases.
- Reactions with Electrophiles, E+
The Oxygen atom is electron rich and interacts with the Electrophile. One lone pair is used to form a new Sigma bond.
- Reactions with Nucleophiles, Nu-
The carbon atom is electron deficient and so attracts the nucleophile.
- Reactions with Bases, BASE-
A hydrogen on a neighbouring carbon is removed by strong bases, creating a resonance stabilised anion.
The reactivity of carbonyl compounds is influenced by the atoms attached.
Nucleophilic Substitution Reactions – Sn1 & Sn2 Stereochemistry August 24, 2008
Posted by sourcez in Sem1, Sem2.2 comments
- Nuclephilic Substitution Reactions
The viability of nucleophilic substitution over a single bond is determined by the bond polarity. A nucleophile (Nu-) will attack the δ+ atom in a polar bond and replace the existing δ- atom.
A good example of this is the haloalkanes, where the halogens are more electronegative than the Carbon atom. As the the halogen has a higher affinity for -ve charge, the bonding electrons are found closer to the halogen than the carbon, shifting the dipole charges in the molecule.
Nuleophilic Substitution of Iodine with Cyanide in Iodomethane
As you can see the nucleophile (which likes +ve charge) attacks the δ+ carbon atom, and this essentially severs the C-I bond, releasing I-.
There are a large number of other suitable nucleophiles, including the following. I’ve included products too, excuse the lack of correct punctuation. This allows conversion of an Alkyl Halide into many different compounds.
| Starting Material | Reacts With | Produces | AKA |
| RX | PPh3 | RP+Ph3X- | Phophodium Salt |
| RX | R’S- | RSR’ | Thioester |
| RX | Na2S | RSH | Thiol |
| RX | NC- | RCN | Nitrile |
| RX | HCC- | HCCR | Alkyne |
| RX | MeCOO-Ag+ | MeCOOR | Ester |
| RX | EtO- | ROEt | Ether |
| RX | HO- | ROH | Alcohol |
| RX | N3- | RN3 | Alkyl Azide |
| RN3 | H2 / PdC | RNH2 | Amide |
| RX | NH3 | RNH3+X- | Ammonium Salt |
| RNH3+X- | HO- | RNH2 | Amide |
The ones in GREY at the bottom are the amide chain – there are two routes to an Amide. One is through an alkyl azide and the other through an ammonium salt.
*******************************************************************
A special note: Hydride (H-) reducing agents such as LiAlH4 can be used as sources of nucleophilic hydride ions which will replace the halogen group. This allows conversion of an alkyl halide into an alkane.
Nucleophilic Substitution of Halide with Hydride via LiAlH4
*******************************************************************
A stable molecule is a good leaving group, such that H2O is better than HO-. In haloalkanes, reactivity goes from RI > RF (travelling down the group).
This can be explained better when we look at the basicity and nucleophilicity of the atom/molecule. Note that while Nucleophilicity is a kinetic property determining the rate of reaction with a Carbon atom (how fast the reaction progresses), Basicity is a thermodynamic property determining an atom/ion/molecul’s ability to accept a proton.
Nucleophilicity (rate of reaction): NC- > I- > RO- > HP- > Br- > Cl- > ROH > H2O
Basicity (ability to accept proton): RO- > HO- > NC- > H2O > ROH > Cl- > Br- > I-
- The Reaction Pathway – Sn1 and Sn2 Reactions
There are two main pathways that a nucleophilic substitution reaction can follow:
Sn1 (Substitution, Nucleophilic, Unimolecular):
- Substrate ionises to form a planar intermediate carbocation in the rate determining step.
- The intermediate cation then rapidly reacts with the nucleophile. This means there are two transition states.
- This is a 1st order reaction as rate = k[substrate]. It is a unimolecular process.
- Favoured in polar solvents – this aids ionisation.
- Favoured Tertiary > Secondary > Primary as the two state process allows access to the carbon centre without steric hindrance (see Sn2 below).
Sn1 Substitution
Sn1 creates a racemic product (an equal amount of left and right enantiomers) which as a result is optically inactive. This means it will not rotate polarised light.
Sn2 (Substitution, Nucleophilic, Bimolecular):
- Reaction occurs completely within one transition state.
- This is a second order reaction as rate = k[substrate][nucleophile]
- Reaction favoured in polar aprotic solvents (solvents which have high polarity but cannot dissociate a H+) such as DMF (Dimethylformamide) and DMSO (Dimethyl Sulfoxide).
- Steric hindrance slows or stops reaction progression in tertiary systems as steric crowding stops attack by the nucleophile (aka there isn’t room!) and tertiary cations are quite stable. In this case we would expect Sn1. Note that the “back route” must be clear else the reaction will proceed by Sn1.
- Favoured Primary > Secondary > Tertiary.
Sn2 Substitution
Sn2 creates a product with an inverted stereo structure to that of the substrate. Essentially the Nucleophile attaches to the opposite side from the leaving group, inverting the molecule’s original stereochemistry.
- Alcohols
Alcohols are extremely important for synthesising new molecules:
Synthesising new molecules from Alcohols (In this case Propanol)
It is especially useful when you consider that we can already use the Alkyl Halide table from above to form a variety of molecules that way.
Hybridisation – Mixing Up Orbitals with sp, sp2, sp3 August 22, 2008
Posted by sourcez in Sem1.7 comments
Essentially, hybridisation is the mixing of standard atomic orbitals to form new orbitals – which can be used to describe bonding in molecules.
Most importantly we have sp3, sp2 and sp hybridisation.
sp3 Hybridisation in Methane (CH4):
The best way I can describe sp3 hybridisation is in Methane (also the most basic choice!). This is simplified for expression. Remember that Carbon has 6 electrons.
- In methane (CH4), 1 Carbon binds with 4 Hydrogens. The carbon atom itself has only 2 electrons available for bonding in the 2p subshell.
Carbon - Ground (normal) electron states. 1s2, 2s2, 2p1 2p1.
- In order for 4 hydrogens to bind there need to be 4 electrons available for bonding, which cannot be achieved at the moment. The pull of a hydrogen nucleus results in an electron being excited from the 2s subshell into the 2p subshell, where it is available for bonding.
Carbon - An electron has been excited to the 2p orbital.
- This excitation changes the forces on the valence (bonding) electrons as the nucleus now exerts a stronger effective core portential upon them. This and other factors leads to the creation of a new ‘hybridised orbital’, called sp3.
Carbon - Hybridisation forms sp3 orbital.
This leaves 4 valence electrons which will each overlap with the s orbital of a Hydrogen to form a σ (sigma) bond. These hydrogens space themselves as far apart as possible, leading to the tetrahedral structure of methane.
3D animation of methane. Produced on ChemSketch.
Each of the bonds in the image above are σ-bonds.
Methane Hybridisation. Shows the S orbits of H overlapping with sp3 orbitals of C. Note 2 electrons in each bond, one from carbon and one from hydrogen. Image by K. Aainsqatsi, released into public domain.
sp2 Hybridisation in Ethene (C2H4):
This is similar to sp3 hybridisation, except there are only 2 hydrogen nuclei pulling on the bonding electrons (which need an electron each) and the other 2 electrons are required for the π (pi) bond (double bond) between the two Carbons.
A molecule of Ethene.
The electron configuration in carbon starts the same:
Carbon - Ground (normal) state of electrons
then:
Carbon - An electron has been excited to the 2p orbital.
but the resulting spread is different:
Carbon hybridisation in Ethene (sp2)
Only 2 of the 2p orbitals are used in sp2 hybridisation; in contrast to the 3 used in sp3 hybridisation (you should be seeing where the numbers come from!).
This leaves us with 3 sp3-orbitals and 1 p-orbital to bond with. 2 of the sp3 orbitals are used for forming σ-bonds with the 2 hydrogens, while the remaining sp3 orbital binds with the other carbon to form a σ-bond and the p-orbital bonds with a p-orbital from the other carbon to form a π-bond.
Every double bond (regardless of what atoms it joins) consists of a π-bond and a σ-bond.
Shows seperate carbon atoms in sp2 hybridisation, then combined to form ethene.
sp Hybridisation in Ethyne (C2H2):
This can occur on an atom with a triple bond such as the alkynes. Ethyne is the simplest.
Ethyne. Triple bonded Carbon with 2 hydrogens.
In this case we only have 1 hydrogen attached to a carbon, and three bonds between each carbon. That’s 1 hybridised bond between the carbon and hydrogen with another hybridised bond between the carbons. The other two p-orbitals form two more bonds between the carbons.
Ethyne - sp Hybridisation
This essentially means that the triple bond consists of 1 σ-bond and 2 π-bonds.
Summary:
Essentially, the hybridisation of the carbon atom is based on the number of bonds to other carbons or identical atoms.
sp3 = single bond
sp2 = double bond
sp = triple bond
Drawing Chemical Formulae on your PC August 19, 2008
Posted by sourcez in IT.2 comments
You will undoubtedly need to draw an equation out on your computer at some point, and there are several ways to do this.
- Load up Paint and spend hours perfecting a drawing.
- Use an Office suite and spend equally long hours trying to get all the lines in the right place.
- Use a specialist application to do it in seconds.
Assuming you chose option 3, we’d like to introduce you to MDL ISIS DRAW 2.5. Best of all, it’s free for personal use!
A couple of the templates provided by ISIS DRAW
You must register first but you can then download ISIS draw through their site here. I believe they are working on replacing it as MDL has now become Symyx, so I am unsure whether it will stay free when they release the next version. The current version (just updated) now works better with Vista.
You could also use an application called ChemSketch. This can be downloaded from their website here.
These applications are very useful for drawing accurate molecules, checking them (for over bonded atoms etc) and naming. They can also generate 3D images of the molecules you make.
I’m not going to go into how to use them here, I’m just introducing you!
How about 3D?
There are quite a few notable molecular visualisation applications and I’ve just included some of the easier to use here.
You can also use the above programs to render in 3D, the easiest to use (I think) is ChemSketch. Simply draw a molecule in the standard view and click copy to 3D – done!
Another choice is Jmol. Jmol is a java applet which means it runs in your browser without installing (there is a stand-alone downloadable version also available). You can check that out here if you need added functuality over ChemSketch. There’s also a host of demonstrations and guides through the link. Like the rest of the applications on this page, it’s free!
The final example is Polyview – you simply fill in a form here and it pumps out a very nice 3D image or animation that can be put into presentations etc easily.
For more information on any of this and more I would suggest checking out this site, there is a huge number of resources for Jmol and other tools.
