What are Atoms | molecules

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Atoms Around Us

If you want to have a language, you will need an alphabet. If you want to build proteins, you will need amino acids. Other examples in chemistry are not any different. If you want to build molecules, you will need elements. Each element is a little bit different from the rest. Those elements are the alphabet to the language of molecules. Why are we talking about elements? This is the section on atoms.


Let's stretch the idea a bit. If you read a book, you will read a language. Letters make up that language. But what makes those letters possible? Ummm... Ink? Yes! You need ink to crate the letters. And for each letter, it is the same type of ink. Confused? Don't be. Elements are like those letters. They have something in common. That's where atoms come in. All elements are made of atoms. While the atoms may have different weights and organization, they are all built in the same way. Electrons, protons, and neutrons make the universe go. If you want to do a little more thinking, start with particles of matter. Matter, the stuff around us, is used to create atoms. Atoms are used to create the elements. Elements are used to create molecules. It just goes on. Everything you see is built by using something else.

You could start really small...

- Particles of matter

- Atoms

- Elements

- Molecules

- Macromolecules

- Cell organelles

- Cells

- Tissues

- Organs

- Systems

- Organisms

- Populations

- Ecosystems

- Biospheres

- Planets

- Planetary Systems with Stars

- Galaxies

- The Universe…

And finish really big. Wow.

All of that is possible because of atoms.
ATOMS = BUILDING BLOCKS
Atoms are the basis of chemistry. They are the basis for everything in the Universe. You should start by remembering that matter is composed of atoms. Atoms and the study of atoms are a world unto themselves. We're going to cover basics like atomic structure and bonding between atoms. As you learn more, you can move to the biochemistry tutorials and see how atoms form compounds that help the biological world survive.

SMALLER THAN ATOMS?
Are there pieces of matter that are smaller than atoms? Sure there are. You'll soon be learning that atoms are composed of pieces like neutrons, electrons, and protons. But guess what? There are even smaller particles moving around in atoms. These super-small particles can be found inside the protons and neutrons. Scientists have many names for those pieces, but you may have heard of nucleons and quarks. Nuclear chemists and physicists work together with particle accelerators to discover the presence of these tiny, tiny, tiny pieces of matter.
Even though those super tiny atomic particles exist, there are three basic parts of an atom. The parts are the electrons, protons, and neutrons. What are electrons, protons, and neutrons? A picture works best. You have a basic atom. There are three pieces to an atom. There are electrons, protons, and neutrons. That's all you have to remember. Three things! As you know, there are over 100 elements in the periodic table. The thing that makes each of those elements different is the number of electrons, protons, and neutrons. The protons and neutrons are always in the center of the atom. Scientists call the center of the atom the nucleus. The electrons are always found whizzing around the center in areas called orbitals.
You can also see that each piece has either a "+", "-", or a "0." That symbol refers to the charge of the particle. You know when you get a shock from a socket, static electricity, or lightning? Those are all different types of electric charges. There are even charges in tiny particles of matter like atoms. The electron always has a "-" or negative charge. The proton always has a "+" or positive charge. If the charge of an entire atom is "0", that means there are equal numbers of positive and negative pieces, equal numbers of electrons and protons. The third particle is the neutron. It has a neutral charge (a charge of zero).




As you know, electrons are always moving. They spin very quickly around the nucleus of an atom. As the electrons spin, they can move in any direction, as long as they stay in their shell. Any direction you can imagine - upwards, downwards, or sidewards - electrons can do it. The atomic shell or orbital is the distance from the nucleus that the electron spins. If you are an electron in the first shell you are always closer to the nucleus than the electrons in the second shell.
ORBITAL BASICS

Let's cover some basics of atomic orbitals. 1. A shell is sometimes called an orbital or energy level. 2. Shells are areas that surround the center of an atom. 3. The center of the atom is called the nucleus. 4. Electrons live in something called shells. 5. Each of those shells has a name. There are a couple of ways that atomic orbitals are named. You may have heard of the SPDF system before. Chemists also use letters to name the orbitals around a nucleus. They use the letters "k,l,m,n,o,p, and q". The "k" shell is the one closest to the nucleus and "q" is the farthest away.

Induction in stereochemistry

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CRAMS RULE IN ASYMMETRIC INDUCTION

Asymmetric induction in stereochemistry describes the preferential formation in a chemical reaction of one enantiomer or diastereoisomer over the other as a result of the influence of a chiral feature present in the substrate, reagent, catalyst or environment . Asymmetric induction is a key element in asymmetric synthesis.

Asymmetric induction was introduced by Emil Fischer based on his work on carbohydrates . Several types of induction exist.

Internal asymmetric induction makes use of a chiral center bound to the reactive center through a covalent bond and remains so during the reaction. The starting material is often derived from chiral pool synthesis. In relayed asymmetric induction the chiral information is introduced in a separate step and removed again in a separate chemical reaction. Special synthons are called chiral auxiliaries.In external asymmetric induction chiral information is introduced in the transition state through a catalyst of chiral ligand. This method of asymmetric synthesis is economically most desirable.

Several models exist to describe chiral induction based on a combination of steric and electronic considerations and often in conflict with each other. Models have been devised by Cram (1952), Cornforth (1959), Felkin (1969) and others.


Cram's rule of asymmetric induction

The Cram's rule of asymmetric induction developed by Donald J. Cram in 1952 is an early concept relating to the prediction of stereochemistry in certain acyclic systems. In full the rule is:

In certain non-catalytic reactions that diastereomer will predominate which could be formed by the approach of the entering group from the least hindered side when the rotational conformation of the C-C bond is such that the double bond is flanked by the two least bulky groups attached to the adjacent asymmetric center.

The rule indicates that the presence of an asymmetric center in a molecule induces the formation of an asymmetric center adjacent to it based on steric hindrance.

In his 1952 publication Cram presented a large number of reactions described in the literature for which the conformation of the reaction products could be explained based on this rule and he also described an elaborate experiment (scheme 1) making his case.


induction in stereochemistry














The experiments involved two reactions. In experiment one 2-phenylpropionaldehyde (1, racemic but (R)-enantiomer shown) was reacted with the Grignard reagent of bromobenzene to 1,2-diphenyl-1-propanol (2) as a mixture of diastereomers, predominantly the threo isomer (see for explanation the Fischer projection).
The preference for the formation of the threo isomer can be explained by the rule stated above by having the active nucleophile in this reaction attacking the carbonyl group from the least hindered side (see Newman projection A) when the carbonyl is positioned in a staggered formation with the methyl group and the hydrogen atom, which are the two smallest substituents creating a minimum of steric hindrance, in a gauche orientation and phenyl as the most bulky group in the anti conformation.
The second reaction is the organic reduction of 1,2-diphenyl-1-propanone 2 with lithium aluminum hydride which results in the same reaction product as above but now with preference for the erythro isomer (2a). Now a hydride anion (H-) is the nucleophile attacking from the least hindered side (imagine hydrogen entering from the paper plane).
In the original 1952 publication additional evidence was obtained for the structural assignment of the reaction products by applying them to a Chugaev elimination where the threo isomer reacts to the cis isomer of -α-methyl-stilbene and the erythro isomer to the trans version.

stereochemistry









Felkin model
The Felkin model (1968) named after Hugh Felkin also predicts the stereochemistry of nucleophilic addition reactions to carbonyl groups [4]. Felkin argued that the Cram model suffered a major drawback: an eclipsed conformation in the transition state between the α-carbonyl substituent (the hydrogen atom in aldehydes) and the largest β-carbonyl substituent. He demonstrated that by increasing the steric bulk of the α-substituent from methyl to ethyl to isopropyl to isobutyl, the stereoselectivity also increased which is not predicted by Cram's rule:






The Felkin rules are:
The transition states are reactant-like.
Torsional strain (Pitzer strain) involving partial bonds (in transition states) represents a substantial fraction of the strain between fully-formed bonds, even when the degree of bonding is quite low. The conformation in the TS is staggered and not eclipsed with the substituent R skew with respect to two adjacent groups one of them the smallest in TS A.




For comparison TS B is the Cram transition state.
The main steric interactions involve those around R and the nucleophile but not
the carbonyl oxygen atom.
A polar effect or electronic affect stabilizes a transition state with maximum separation between the nucleophile and an electron-withdrawing group. For instance haloketones do not obey Cram's rule and in the example above replacing the electron-withdrawing phenyl group by a cyclohexyl group reduces stereoselectivity considerably.
The Felkin-Anh model is an extension of the Felkin model. A so-called Felkin product is that reaction product that obeys the Felkin-Anh model and an anti-Felkin product obviously does not.































SYNTHESIS OF BETA CAROTENE BY BASF AND ROCHE SYNTHESIS

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Synthesis of Carotenoids by BASF AND ROCHE synthesis

The first total synthesis of beta-carotene were reported in 1950 by Karrer and Eugster, Inhoffen et al and Milas et al . There are now many methods known, and beta-carotene is produced industrially on a large scale.Beta-carotene contains 40 carbon atoms, ie it is a C40 carotenoid. There are numerous methods of joining two or three smaller molecules to give the required carbon skeleton. These can be classified as symmetric or unsymmetric. An example of a symmetric synthesis would be

C16 + C8 + C16 = C 40

whereas an unsymmetric synthesis would be

C25 + C15 = C40

Here are two examples of industrial syntheses. The first was developed by the Badische Anilin- & Soda-Fabrik ( BASF) and is based on the Wittig reaction. The second is a Grignard reaction, elaborated by F. Hoffman-La Roche & Co. Ltd ( Roche) from the original synthesis of Inhoffen et al. They are both symmetrical; the BASF synthesis is C20 + C 20 , and the Roche synthesis is C19 + C2 + C 19 .


BASF Synthesis of Beta Carotene












ROCHE SYNTHESIS




































Nitroglycerin | Medical use of Nitroglycerin

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Nitroglycerin (NG), (US spelling) also known as nitroglycerine, (UK Spelling), trinitroglycerin, trinitroglycerine and glyceryl trinitrate, is a chemical compound. It is a heavy, colorless, oily, explosive liquid obtained by nitrating glycerol. Since the 1860s, it has been used as an active ingredient in the manufacture of explosives, specifically dynamite, and as such is employed in the construction and demolition industries. Similarly, since the 1880s, it has been used by the military as an active ingredient, and a gellatinizer for nitrocellulose, in some solid propellants, such as Cordite and Ballistite. Nitroglycerin is also used medically as a vasodilator to treat heart conditions, such as angina and chronic heart failure.

Chemical formula
C3H5(NO3)3

Molar mass
227.0872 g/mol
Shock sensitivity
Very High

Friction sensitivity
Very high

Density
1.6 g/cm³ at 15 °C

Explosive velocity
7700 m/s

RE factor
1.50

Melting point
13.2 °C (55.76 °F)

Autoignition temperature
Decomposes at 50 to 60 °C (122 to 140 °F)

Appearance
Clear yellow/colorless oily liquid
History
Nitroglycerin was discovered by chemist Ascanio Sobrero in 1846, working under TJ Pelouze at the University of Turin. The best manufacturing process was developed by Alfred Nobel in the 1860s. His company exported a liquid combination of nitroglycerin and gunpowder as 'Swedish Blasting Oil', but it was extremely dangerous as a result of its extreme instability, as shown in numerous "appalling catastrophes," such as the explosion that destroyed a Wells Fargo office in San Francisco in 1866.
Liquid nitroglycerin was widely banned, and this led to the development of dynamite (and similar mixtures, such as blasting gelatine, dualine and lithofracteur), made by mixing the nitroglycerin with inert absorbents; for example, Nobel used kieselguhr. Other nitrated materials, such nitrocellulose gel, were also used.
Instability and desensitization
In its pure form, it is a contact explosive (physical shock can cause it to explode) and degrades over time to even more unstable forms. This makes it highly dangerous to transport or use. In this undiluted form, it is one of the most powerful high explosives, comparable to the newer military explosives RDX and PETN (which are not used in munitions at full concentration because of their sensitivity); as well as the plastic explosive C-4—which contains over 90% RDX, as its active ingredient.
Early in the history of this explosive it was discovered that liquid nitroglycerin can be "desensitized" by cooling to 5 to 10 °C (40 to 50 °F), at which temperature it freezes, contracting upon solidification. However, later thawing can be extremely sensitizing, especially if impurities are present or if warming is too rapid. It is possible to chemically "desensitize" nitroglycerin to a point where it can be considered approximately as "safe" as modern high explosive formulations, by the addition of approximately 10-30% ethanol, acetone, or dinitrotoluene (percentage varies with the desensitizing agent used).
Desensitization requires extra effort to reconstitute the "pure" product. Failing this, it must be assumed that desensitized nitroglycerin is substantially more difficult to detonate, possibly rendering it useless as an explosive for practical application.
A serious problem in the use of nitroglycerin results from its high freezing point 13 °C (55 °F). Solid nitroglycerin is much less sensitive to shock than the liquid, a feature common in explosives; in the past it was often shipped in the frozen state, but this resulted in a high number of accidents during the thawing process by the end user just prior to use. This disadvantage is overcome by using mixtures of nitroglycerin with other polynitrates; for example, a mixture of nitroglycerin and ethylene glycol dinitrate freezes at -29 °C (-20 °F).[1]
Detonation
Nitroglycerin and any or all of the dilutents used can certainly deflagrate or burn. However, the explosive power of nitroglycerin is derived from detonation: energy from the initial decomposition causes a pressure gradient that detonates the surrounding fuel. This can generate a self-sustained shock-wave that propagates through the fuel-rich medium at or above the speed of sound as a cascade of near-instantaneous pressure-induced decomposition of the fuel into gas. This is quite unlike deflagration, which depends solely upon available fuel, regardless of pressure or shock.

Manufacturing of Nitroglycerin
The industrial manufacturing process often uses a nearly 50:50 mixture of sulfuric acid and nitric acid. This can be produced by mixing white fuming nitric acid (quite costly pure nitric acid in which oxides of nitrogen have been removed, as opposed to red fuming nitric acid) and concentrated sulfuric acid. More often, this mixture is attained by the cheaper method of mixing fuming sulfuric acid (sulfuric acid containing excess sulfur trioxide) and azeotropic nitric acid (consisting of around 70% nitric acid, the rest being water).
The sulfuric acid produces protonated nitric acid species, which are attacked by glycerin's nucleophilic oxygen atoms. The nitro group is thus added as an ester C-O-NO2 and water is produced. This is different from an aromatic nitration reaction in which nitronium ions are the active species in an electrophilic attack of the molecules ring system.
The addition of glycerin results in an exothermic reaction (i.e., heat is produced), as usual for mixed acid nitrations. However, if the mixture becomes too hot, it results in runaway, a state of accelerated nitration accompanied by the destructive oxidizing of organic materials of nitric acid and the release of very poisonous brown nitrogen dioxide gas at high risk of an explosion. Thus, the glycerin mixture is added slowly to the reaction vessel containing the mixed acid (not acid to glycerin). The nitrator is cooled with cold water or some other coolant mixture and maintained throughout the glycerin addition at about 22 °C, much below which the esterification occurs too slowly to be useful. The nitrator vessel, often constructed of iron or lead and generally stirred with compressed air, has an emergency trap door at its base, which hangs over a large pool of very cold water and into which the whole reaction mixture (called the charge) can be dumped to prevent an explosion, a process referred to as drowning. If the temperature of the charge exceeds about 10 °C (actual value varying by country) or brown fumes are seen in the nitrators vent, then it is immediately drowned.
Because of the great dangers associated with its production, most nitroglycerin production facilities are in offshore rigs or very remote locations.

Use as an explosive and a propellant

The main use of Nitroglycerin, by tonnage, is in explosives such as dynamite and in propellants.
Alfred Nobel developed the use of nitroglycerin as a blasting explosive by mixing the nitroglycerine with inert absorbents particularly kieselguhr. He named this explosive Dynamite and patented it in 1867. It was supplied ready for use in the form of sticks, individually wrapped in grease proof paper. Dynamite and similar explosives were widely adopted for civil engineering tasks, such as building railway tunnels and cuttings; and for quarrying.
Nitroglycerin was also adapted as a military propellant, for use in guns and rifles. Poudre B, invented in France in 1886, was one of the first military propellants to replace gunpowder; but it was based on nitrocellulose, not nitroglycerin. It was later found to be unstable.
Alfred Nobel then developed Ballistite, by combining nitroglycerin and guncotton. He patented it in 1887. Ballistite was adopted by a number of European governments, as a military propellant. Italy was the first to adopt it. However, it was not adopted by the British Government. They, together with the British Commonwealth countries, adopted Cordite, which had been developed by Sir Frederick Abel and Sir James Dewar, in 1889. The original
Cordite Mk I consisting of 58% nitroglycerine, 37% guncotton and 5%
Petroleum jelly. Ballistite and Cordite were both manufactured in the forms of cords.
Smokeless powders were originally developed using nitrocellulose as the sole explosive ingredient; and were therefore known as single base propellants. A range of smokeless powders that contain both nitrocellulose and nitroglycerin, known as double base propellants, were also developed. Smokeless powders were originally supplied only for military use; however they were also soon developed for civilian use and were quickly adopted for sport. Some are known as sporting powders.
War time production rates
Large quantities of nitroglycerin were manufactured in both World Wars for use in military propellants.

World War I
In World War I HM Factory, Gretna, the largest propellant factory in the United Kingdom was producing 800 tons (812 tonne) of Cordite RDB per week. This required 336 tons of nitroglycerin per week (assuming no losses in production). The Royal Navy had its own factory at Royal Navy Cordite Factory, Holton Heath.
A large cordite factory was also built in Canada in World War I. The Canadian Explosives Limited Cordite factory at Nobel, Ontario was designed to produce 1,500,000 lb (681 tonne) of Cordite per month. It required 286 tonnes of nitroglycerin per month.

Medical use of Nitroglycerin
Nitroglycerin in medicine, where it is generally called glyceryl trinitrate, is used as a heart medication (under the trade names Nitrospan®, Nitrostat®, and Tridil®, amongst others). It is used as a medicine for angina pectoris (ischaemic heart disease) in tablets, ointment, solution for intravenous use, transdermal patches (Transderm Nitro®, Nitro-Dur®), or sprays administered sublingually (Nitrolingual Pump Spray®, Natispray®).
The principal action of nitroglycerin is vasodilation—widening of the blood vessels. Nitroglycerin will dilate veins more than arteries, decreasing cardiac preload and leading to the following therapeutic effects during episodes of angina pectoris:
subsiding of chest pain
decrease of blood pressure
increase of heart rate.
orthostatic hypotension
These effects arise because nitroglycerin is converted to nitric oxide in the body (by a mechanism that is not completely understood), and nitric oxide is a natural vasodilator. Recently, it has also become popular in an off-label use at reduced (0.2%) concentration in ointment form as an effective treatment for anal fissure.
Industrial exposure
Infrequent exposure to high doses of nitroglycerin can cause severe headaches known as "NG head". These headaches can be severe enough to incapacitate some people; however, humans develop a tolerance and dependence to nitroglycerin after long-term exposure. Withdrawal can (rarely) be fatal; withdrawal symptoms include headaches and heart problems; with re-exposure to nitroglycerin, these symptoms may disappear.

For workers in nitroglycerin manufacturing facilities, this can result in a "Monday morning headache" phenomenon for those who experience regular nitroglycerin exposure in the workplace; over the weekend they develop symptoms of withdrawal, which are then countered by re-exposure on the next work day.

Ballistite | Smokeless Powder | Vielle's powder | Nitrocellulose deteriorate

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Smokeless powder is the general name given to a number of propellants used in firearms and artillery which produce negligible smoke when fired, unlike the older (Gunpowder) black powder which they replaced.

Types of smokeless powder include Cordite, Ballistite and, historically, Poudre B. They are classified as single-base, double-base or triple-base powders.

Smokeless powder consists of nitrocellulose (single-base powders), frequently combined with up to 50 percent nitroglycerin (double-base powders), and sometimes nitroglycerin and nitroguanidine (triple-base), corned into small spherical balls or extruded into cylinders or flakes using solvents such as ether. Other minor ingredients, such as stabilizers and ballistic modifiers, are also added. Double-base propellants are common in handgun and rifle ammunition. Triple-base propellants are more common in artillery guns.

The reason that they are smokeless is that the combustion products are mainly gaseous, compared to around 55% solid products for black powder (potassium carbonate, potassium sulfate etc).

Smokeless powder burns only on the surfaces of the granules, flakes or cylinders - described as granules for short. Larger granules burn more slowly, and the burn rate is further controlled by flame-deterrent coatings which retard burning slightly. The intent is to regulate the burn rate so that a more or less constant pressure is exerted on the propelled projectile as long as it is in the barrel so as to obtain the highest velocity. Cannon powder has the largest granules, up to thumb-sized cylinders with seven perforations (one central and the other six in a circle halfway to the outside of the cylinder's end faces). The perforations stabilize the burn rate because as the outside burns inward (thus shrinking the burning surface area) the inside is burning outward (thus increasing the burning surface area, but faster, so as to fill up the increasing volume of barrel presented by the departing projectile). Fast-burning pistol powders are made by extruding shapes with more area such as flakes or by flattening the spherical granules. Drying is usually performed under a vacuum.

The solvents are condensed and recycled. The granules are also coated with graphite to prevent static electricity sparks from causing undesired ignitions.



History

Military commanders had been complaining since the Napoleonic Wars about the problems of giving orders on a battlefield that was covered in thick smoke from the gunpowder used by the guns. A major step forward was introduced when guncotton, a nitrocellulose-based material, was first introduced by Christian Friedrich Schönbein in 1846. He also promoted its use as a blasting explosive.


Guncotton was more powerful than gunpowder, but at the same time was somewhat more unstable. This made it unsuitable as a propellant for small firearms: not only was it dangerous under field conditions, but guns that could fire thousands of rounds using gunpowder would be "used up" after only a few hundred with the more powerful guncotton. It did find wide use with artillery. However, within a short time there were a number of massive explosions and fatalities in guncotton factories due to lack of appreciation of its sensitivity and the means of stabilization. Guncotton then went out of use for some twenty years or more until it could be tamed; it was not until the 1880s that it became a viable propellant.

In 1884 Paul Vieille invented a
smokeless gunpowder called Poudre B, made from gelatinized guncotton mixed with ether and alcohol. It was passed through rollers to form thin sheets, which were cut into flakes of the desired size. The resulting propellant, today known as pyrocellulose, contains somewhat less nitrogen than guncotton and is less volatile. A particularly good feature of the propellant is that it will not burn unless it is compressed, making it very safe to handle under normal conditions.

Vieille's powder revolutionized the effectiveness of small guns, for several reasons. First, it gave off almost no smoke. After a few shots, a soldier with black powder ammunition would have his view obscured by a huge pall of smoke unless there was a strong wind. Conversely, a sniper or other hidden shooter would not be given away by a cloud of smoke over the firing position. Further, it was three times more powerful than black powder, which gave more power from less powder. The higher muzzle velocity meant a flatter trajectory and therefore more accurate long range fire, out to perhaps 1000 metres in the first smokeless powder rifles. Since less powder was needed to propel a bullet, the cartridge could be made smaller and lighter. This allowed troops to carry more ammunition for the same weight. Also, it would burn even when wet. Black powder ammunition had to be kept dry and was almost always stored and transported in watertight cartridges.

Vielle's powder was used in the Lebel rifle that was immediately introduced by the French Army to exploit its huge benefits over black powder. Other European countries swiftly followed and started using their own versions of Poudre B, the first being Germany and Austria which introduced new weapons in 1888.

Meanwhile, in Great Britain, in 1887, Alfred Nobel developed
a smokeless gunpowder called Ballistite. A modified form of this was devised by Sir Frederick Abel and James Dewar which eventually became known as Cordite, leading to a lengthy court battle between Nobel and the other two inventors over alleged British patent infringement. In the USA, in 1890, a patent for smokeless powder was obtained by Hudson Maxim.

These newer propellants were more stable and thus safer to handle than Poudre B, and also more powerful. Today, propellants based on nitrocellulose alone are known as single-base, whereas cordite-like mixtures are known as double-base. A triple-base flashless cordite was also developed, primarily for large naval guns, but also used in battle tank ammunition.

Smokeless powder allowed the development of modern semi- and fully automatic firearms. Burnt blackpowder leaves a thick, heavy fouling which is both hygroscopic and corrosive. Smokeless powder fouling exhibits none of these properties. This makes an autoloading firearm with many moving parts feasible (which would jam or seize under heavy blackpowder fouling).

Single and double-base smokeless powders now make up the vast majority of propellants used in firearms. They are so common that most modern references to "gunpowder" refer to a smokeless powder, particularly when referring to small arms ammunition.


Instability and stabilization

Nitrocellulose deteriorates with time, yielding acidic byproducts. Those byproducts catalyze the further deterioration, increasing its rate. The released heat, in case of bulk storage of the powder, or too large blocks of solid propellant, can cause self-ignition of the material. Single-base nitrocellulose propellants are most susceptible to degradation; double-base and triple-base propellants tend to deteriorate more slowly. To neutralize the decomposition products, which could otherwise cause corrosion of metals of the cartridges and gun barrels, calcium carbonate is added to some formulations.
To prevent buildup of the deterioration products, stabilizers are added. 2-Nitrodiphenylamine is one of the most common stabilizers used. Others are 4-nitrodiphenylamine, N-nitrosodiphenylamine, N-methyl-p-nitroaniline, and diphenylamine. The stabilizers are added in the amount of 0.5-2% of the total amount of the formulation; higher amounts tend to degrade its ballistic properties. The amount of the stabilizer is depleted with time. Propellants in storage should be periodically tested on the remaining amount of stabilizer, as its depletion may lead to autoignition of the propellant.

Smokeless propellant components

The propellant formulations may contain various energetic and auxiliary components:

Propellants:
Nitrocellulose, an energetic component of most smokeless propellants
Nitroglycerin, an energetic component of double-base and triple-base formulations
Nitroguanidine, a component of triple-base formulations
Plasticizers, to make the grains less brittle
Dibutyl phthalate
Polyester adipate
Dinitrotoluene (toxic, carcinogen, obsoleted)
Binders, to hold the grain shape
Rosin
Ethyl acetate
Stabilizers, to prevent or slow down self-decomposition
Diphenylamine
2-Nitrodiphenylamine
4-nitrodiphenylamine
N-nitrosodiphenylamine
N-methyl-p-nitroaniline
Decoppering additives, to hinder the buildup of copper residues from the gun barrel rifling
Tin metal and compounds, e.g. tin dioxide
Bismuth metal and compounds, e.g. bismuth trioxide, bismuth subcarbonate, bismuth nitrate, bismuth antimonide; the bismuth compounds are favored as copper dissolves in molten bismuth, forming brittle and easily removable alloy
Lead foil and lead compounds, phased out due to toxicity
Flash reducers, to reduce the brightness of the muzzle flash
Potassium nitrate
Potassium sulfate (both have a disadvantage - production of smoke)
Wear reduction additives, to lower the wear of the gun barrel liners USA 16"/50 (40.6 cm) Mark 7
Wax
Talc
Titanium dioxide
Polyurethane jackets over the powder bags, in large guns

Other additives
Graphite, a lubricant to cover the grains and prevent them from sticking together, and to dissipate static electricity

Calcium carbonate, to neutralize acidic decomposition products
The properties of the propellant are greatly influenced by the size and shape of its grains. The surface of the grains influences the speed of burning, and the shape influences the surface and its change during burning. By selection of the grain shape it is possible to influence the pressure vs time curve as the propellant burns.

Faster-burning propellants generate higher temperatures and higher pressures, however they also increase the wear of the gun barrels.
A Primex powder contains 0-40% nitroglycerin, 0-10% dibutyl phthalate, 0-10% polyester adipate, 0-5% rosin, 0-5% ethyl acetate, 0.3-1.5% diphenylamine, 0-1.5% N-nitrosodiphenylamine, 0-1.5% 2-nitrodiphenylamine, 0-1.5% potassium nitrate, 0-1.5% potassium sulfate, 0-1.5% tin dioxide, 0.02-1% graphite, 0-1% calcium carbonate, and nitrocellulose as the remainder to 100%

Nitrocellulose lacquer | Nitrocellulose uses

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Nitrocellulose lacquer
Nitrocellulose (also: cellulose nitrate, flash paper) is a highly flammable compound formed by nitrating cellulose through exposure to nitric acid or another powerful nitrating agent. When used as a propellant or low-order explosive, it is also known as guncotton.

Uses of Nitrocellulose

Nitrocellulose is a major component of smokeless gunpowder (also see the section on guncotton below).
Early photographic film, especially black-and-white film prior to 1948.
Nitrocellulose membrane or nitrocellulose paper is a sticky membrane used for Western blots and immobilizing DNA.
It is also used for immobilization of proteins, due to its non-specific affinity for amino acids. Nitrocellulose is widely used as support in diagnostic tests where antigen-antibody binding occur, e.g. pregnancy tests, U-Albumin tests and CRP.
When dissolved in ether or other organic solvents, the solution is called collodion, which has been used as a wound dressing and carrier of topical medications since the U.S. Civil War. To this day it is used in Compound W Wart Remover as a carrier of salicylic acid, the active ingredient.
Collodion was also used as the carrier for silver salts in some very early photographic emulsions, particularly spread in thin layers on glass plates.

Magician's "
flash paper", sheets of paper or cloth made from nitrocellulose, which burn almost instantly, with a bright flash, and leave no ash.
Nail polish
Hair coloring
Radon tests for alpha track etches
Nitrocellulose lacquer was used as a finish on guitars for most of the 20th century and is still used on some current applications. Manufactured by (among others) Dupont, the paint was also used on automobiles sharing the same color codes as many guitars, primarily Fender brands of guitars.

Nitrocellulose lacquer is also used as an aircraft dope, painted onto fabric-covered aircraft to tauten and provide protection to the material.
As a transportation medium for one-time pads, thus making the disposal of the pad complete, secure, and efficient.

pH ELECTRODES | GLASS pH ELECTRODES

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pH Meter














pH meter is a device used for potentiometric pH measurements.
pH can be measured using either pH indicators (like phenolophtaleine) - in form of solution or pH strips - or using potentiometric method. Strips are very useful when all you need is 0.5-1 pH unit accuracy. When you need higher precision, pH meter is the only way to go.
In potentiometric methods you measure potential difference between known reference electrode and the measuring pH electrode. The latter depends on the activities of ions you want to measure. This dependence is described by Nernst equation, thus once the potential has been measured you can calculate the activity.
pH meter is nothing else but precise voltmeter, connected to the pH electrode, and scaled in such a way that it displays not the measured potential, but ready pH value.


pH COMBINATION ELECTRODES Vs GLASS pH ELECTRODES






Most often used pH electrodes are glass electrodes. Typical model is made of glass tube ended with small glass bubble. Inside of the electrode is usually filled with buffered solution of chlorides in which silver wire covered with silver chloride is immersed. pH of internal solution varies - for example it can be 1.0 (0.1M HCl) or 7.0 (different buffers used by different producers).


Active part of the electrode is the glass bubble. While tube has strong and thick walls, bubble is made to be as thin as possible. Surface of the glass is protonated by both internal and external solution till equilibrium is achieved. Both sides of the glass are charged by the adsorbed protons, this charge is responsible for potential difference. This potential in turn is described by the Nernst equation and is directly proportional to the pH difference between solutions on both sides of the glass.

The majority of pH electrodes available commercially are combination electrodes that have both glass H+ ion sensitive electrode and additional reference electrode conveniently placed in one housing. For some specific applications separate pH electrodes and reference electrodes are still used - they allow higher precision needed sometimes for research purposes. In most cases combination electrodes are precise enough and much more convenient to use.

Construction of combination electrode is in large part defined by the processes that must take place when measuring pH. We need to measure difference of potentials between sides of glass in the glass electrode. To do so we need a closed circuit.

Circuit is closed through the solutions - internal and external - and the pH meter. However, for correct and stable results of measurements reference electrode must be isolated from the solution so that they will not crosscontaminate - and it is not an easy task to connect and isolate two solutions at the same time.

Connection is made through a small hole in the electrode body. This hole is blocked by porous membrane, or ceramic (asbestous in older models) wick. Internal solution flows very slowly through the junction, thus such electrodes are called flowing electrodes. To slow down the leaking, in gel electrodes internal solution is gelled.



pH GEL ELECTRODE







In flowing electrodes internal solution of KCl slowly flows to the outside through the junction - small hole with porous membrane, or ceramic or - in older models - asbestous wick. While such electrode contaminates solution with KCl it does it very slowly and traces of K+ and Cl- ions released during measurements are in most cases just spectators.
As the internal solution is lost from the flowing electrodes it must must be refilled so that its level is always above the level of the external (measured) solution. This way internal solution should never get contaminated. However, refilling of the combination electrodes adds to their maintenance cost and makes them difficult to use in portable pH meters.
To overcome problems with filling internal solution is sometimes gelled. While this helps slow down leak, it doesn't prevent diffusional ion exchange through junction - thus internal solution gets contaminated by the ions diffusing from the external sources, at the same time
loosing its own ions. As the composition of internal solution changes and can't be restored by refilling, gel electrodes have in general shorter life time, although they are easier to use and maintain.
Other method of prolonging the lifetime of the electrode is use of double junction.
Speed of the flow is one of important electrode parameters. It can't be too fast nor to slow. Flow can be too fast in case of broken membrane or lost (loose) wick, it can be too slow if the membrane/wick was clogged by some chemical precipitate - for example AgCl if the electrode was used to measure pH of solution containing Ag+ ions.





SINGLE AND DOUBLE JUNCTION pH ELECTRODES




































DOUBLE JUNCTION SINGLE JUNCTION
pH ELECTRODE pH ELECTRODE

In classical combined pH electrode reference electrode is separated from the external solution by the junction through which the electrolyte leaks. Lost electrolyte must be periodically refilled through the filling hole, which makes these elctrodes inconvenient to use, especially in field. Methods of slowing down the leak - like gelling of the electrolyte - have a side effect of shortening the lifetime of the electrode, as it is more prone to the changes in electrolyte composition due to contamination and diffusional leak of the ions. Contaminated gel can not be replaced, thus lifetime of gel electrode is rarely longer then several months.
To prolong lifetime of such electrodes double junction is sometimes used. In double junction electrodes additional chamber is introduced between reference electrode and external solution. Before contamination from the external solution can get to the reference electrode it must diffuse through not one junction, but two (hence the name). Additional chamber works as a buffer, slowing down the changes in the composition of the reference electrode electrolyte. Double junction electrodes can work longer, but they are more difficult to make, thus more expensive.
Note, that single or double junction refers only to the way reference electrode is made. While you will often see combination electrodes described as pH double junction, external reference electrode can be made double junction as well.



SOLID STATE pH ELECTRODE


Commercially available solid state pH electrodes are mainly built around Ion Selective Field Effect Transistors (ISFET).
The basic principle of the ISFET working is the control of the current flowing between two semiconductor elements (drain and souce) by electrostatic field, generated by the protonated oxide gate. Protonation of the gate is in a way identical to the process taking place in glass pH electrode, just the methodology used to measure protonation degree is different. Instead of measuring potential difference on two sides of the glass, we measure the current flowing through the transistor. The lower the pH, the more protonated and charged gate is which changes its electric field - changing in turn current flowing through the transistor. This current is a signal that can be measured to check the pH value.
ISFET electrodes can be very small when compared to the bulky glass bubble of the standard glass electrode. They are also much more sturdy, so they can be easily used in places where fragile glass electrodes will not survive. However, ISFET electrode can't be used with standard pH meters (unless it is connected through special interface) and the pH measurements are generally less precise when compared to glass electrode.



pH ELECTRODE POTENTIAL



Potential measured by pH meter is a sum of all potentials present in the system. Putting aside junction potentials that can be present in the experimental setup, we are left with three sources of electromotive force. First builds up on the glass electrode, thanks to different activities of the H+ ions on both sides of the glass. Second source is the glass electrode silver wire covered with AgCl and immersed in the solution of chlorides, and third is the reference electrode - silver chloride or calomel, depending on the application.
Thus the real potential measured is sum of three potentials:




where



E glass = E'o + 0.0591 pH outside



which finally leads us to the (almost - read on) final equation describing measured potential:


= E''o + 0.0591 pH outside

Where E0'' contains all constants mentioned above and in the Nernst equation section. As you see after taking (almost - read on) all factors into account we can expect perfect linear dependence between measured potential and pH.
One may ask at this point, why do we complicate things adding two additional sources of potential (EAg/AgCl and Eref), instead of measuring just the potential of glass electrode which behaves as the concentration cell? The answer is simple - there is no easy and practical way of measuring the glass electrode potential. We may think of two added reference cells just as of reliable contacts, interfacing metal wires and solution. While they add their own potentials shifting glass electrode potential readouts, it doesn't matter. First of all, we never need absolute values of glass electrode potential, as only difference being proportional to the difference in pH of both sides of the glass counts. Second, even if we will be able to measure absolute potential it will not help us much, as it depends on many additional things - like internal tensions in the glass, or the smoothness of the glass surface. As we already have to compensate for these impredictable factors, additional, constant shift in voltage doesn't change our situation.
Junction potential, that we have ignored in the above equation, in practice can be an important source of error. It was an important issue back in the early eighties of the 20th century. Most modern electrodes are less prone to this effect.
Every electrode has a characteristic pH where its potential is 0 (so called isopotential point). Carefully choosing potentials of both reference electrodes (which can be done with selection of chlorides concentration) it is possible to compensate for all other sources of potential in the electrode so that isopotential point is at pH=7.0. Most modern pH electrodes are made this way.
As it was mentioned above so far we have looked at almost all factors, but some are still left uncommented. Glass electrode potential depends on the presence of other then H+ ions in the solution. While carefull selection of the glass used makes this difference small, it can't be neglected. More on that in electrode selectivity section.



pH ELECTRODE SELECTIVITY


Ideal pH electrode should have potential dependent solely on the activity of the H+. Unfortunately, there is no such thing as ideal pH electrode.
Potential that builds up on the electrode surfaces has its source in the ions attaching themselves to the glass surface. Glass structure is such that only single charged ions are attracted. Depending on the ion this effect can be stronger or weaker, but the result will be always the same - other ions will interfere with the determination of pH.
To describe effect of other ions on the electrode potential we can use slightly simplified version of Nicolsky-Eisenman equation:

E = Eo + 0.0591 log ([H+] + k1[Na+] + k2[K+] +.....)

where ki are so called selectivity coefficients, determined experimentally.

Every glass electrode potential depends not only on pH but on concentrations of all other single charged ions present. Carefull selection of the glass composition is crucial, as glass is solely responsible for the selectivity coefficients values. These can take values from the 10-1 - 10-15 range. The smaller the value the better. Importance of the small selectivity coefficient can be shown with simple example. Let's assume selectivity coefficient H+/Na+ of 10-8 and 0.1M Na+ solution:

Real pH Measured pH

1.00 1.00

7.00 7.00

8.00 7.96

9.00 8.70

10.00 8.96

Measurement will never show pH above 9.00 in this case. This effect is called alkaline error or sodium error, but not only sodium can interfere with pH measurements. Other single charged cations interfere as well. It is especially important in the case of buffers (for example TRIS based) where the concentration of interfering ion can be relatively high. Most commercial pH electrodes have selectivity ceofficients high enough to not allow such situations. Detailed information about selectivity should be available from electrode manufacturer.
It is worth of noting here, that using proper glass one can make glass electrode that can be used for determination of other single charged ions - like Ag+, Na+, K+ and so on.


HOW TO CHOOSE A pH ELECTRODE


There are many types of pH glass electrodes. In some specific applications you should be very carefull when selecting one, but in most cases the selection is easy. Look for other users working in similar environment and ask them about their experience with different types and makes of electrodes, that way you should be able to find the best offer pretty fast.
If you are working with aqueous solutions containing at least 5% water and your solutions doesn't contain any substances reacting with silver, look for general purpose electrodes.
If you work with solutions containing organic material, proteins, TRIS buffers, heavy metals, or with very low ionic strength solutions, look for calomel electrode. Listed substances can react with silver and clog the junction.

Instead of using calomel electrode you may look for double junction electrode, as it will have similar properties.

If you are working with solutions that can clog normal electrode junction (like oils, foods or paints) look for teflon junction electrode. Junction in these electrodes is made of porous teflon, making it resistant to impurities.

Don't forget to check electrode pH range - some electrodes can't work in high pH, and electrode temperature range - especially if you are going to measure pH in solutions above 60°C.

In most cases manufacturers sites contain a wealth of information about available pH electrode
models and their applications.



pH ELECTRODE MAINTENANCE



Handle electrode with care - it is fragile!

Keep electrode always immersed. Use the solution recommended by manufacturer or neutral solution of KCl (3M-4M).

Remember to always keep internal level of filling solution above the level of measured solution.

Fill electrode (the flowing type) with correct filling solution (as recommended by manufacturer - usually KCl solution, 3M to saturated) to not let it dry internally.

If the electrode will be not used for a long period of time, you may store it dry to prevent aging (aging takes place only when the electrode is wet). Don't try it with gel electrodes - these have to be stored in concentrated solution of KCl only.

If dried incidentally, or after storing - soak for at least 24 hours before using.

If you are using the electrode in solution containing substances able to clog the junction or stick to the glass bubble, clean the electrode as soon as possible after use.

Don't put electrode in solutions that can dissolve glass - hydrofluroic acid (or acidified fluroide solution), concentrated alkalies.

Don't put electrode into dehydrating solution such as ethanol, sulfuric acid, etc.

Don't rub or wipe electrode bulb, to reduce chance of error due to polarization.

Don't use organic solvents for cleaning of the electrode with epoxy body.



HOW TO STORE pH ELECTRODES

Electrodes with liquid electrolytes (not gel types) may be stored either wet or dry.

A wet stored electrode allows an immediate use and a short response time, which is not true for dry stored ones. Unfortunately, the wet stored electrode is aging faster, because the process of aging (changing of the structure in the membrane) proceeds also in the case of non-use.
Keeping electrodes wet should preferably be made in KCl solution (3M-4M). Most electrodes have a protective cap that can be filled with storage solution before placing.

To store pH electrode dry you must first remove internal solution, rinse the electrode in DI/RO water, and let it dry.

Note that you can't store dry combination electrodes and gel electrodes. In fact electrodes that can be stored dry are getting more and more rare.

If electrode is stored wet, don't forget to cover fill hole to prohibit evaporation of reference fill solution.

Gel type electrodes can be stored only wet, soaked in the KCl solution (3M-4M). Never store them in DI/RO water.

Check your electrode owners manual for details, as these may depend on the electrode make.

HOW TO CALIBRATE pH ELECTRODES


Before measuring pH you have to calibrate (standardize) electrode. To calibrate the electrode you need at least two solutions of known pH. Most commonly used commercially available calibration buffers have pH of 4.01, 7.00 and 10.00.

Details of the calibration procedure depend on the pH meter model. First step is usually related to temperature correction. Some models will measure temperature by itself, others need external temperature probe, or you will have to enter temperature measured by others means using dials or buttons. Note that this setting changes only slope of the calibration curve and doesn't take into account fact, that buffer pH changes with temperature.

Next step is to put the electrode into pH 7.00 buffer. Rinse the electrode with distilled water from a wash bottle into an empty beaker before immersing it into new solution. You should do it every time electrode is moved from one solution to other to minimise contamination. Check if the working part of the electrode is completely immersed in the buffer. Take care to not hit bottom of the baker with the electrode. Wait for the reading to stabilize (it takes seconds usually, up to a minute sometimes).

Modern pH meter models working in calibration mode often recognize the buffer automatically and take necessary action by themselves. In case of older pH meters you will probably have to turn one of calibration knobs so that the pH meter shows 7.00.

Sometimes pH readings will oscillate. If the oscillations are small try to find out the best position of the knob so that 7.00 is a mean displayed value. If the oscillations are large and erratic, they may be caused by faulty junction (check all), faulty cable (check them), faulty electrode (try other electrode) or faulty pH meter. Sometimes also static electricity can be a reason of erratic readings - consider changing clothes, grounding yourself or shielding pH meter, cables and electrode. If you are using magnetic stirrer check if switching it off doesn't stop oscillations.

Next steps will depend on the solution you want to measure pH of. If you plan to measure pH in acidic solutions, use pH=4.01 buffer. If you plan to measure high pH use pH=10.00 buffer. If you want to be able to measure pH in the wider range, you may want to proceed with three point calibration and you will need both buffers. Remember that high pH buffers tend to absorb atmospheric CO2 thus they should be used as fresh as possible - don't left the bottle open and do the calibration immediately after filling the beaker with the buffer.

Rinse the electrode and move it to the second buffer. Once again pH meter will either act on itself, or you will have to use a knob (probably different from the one used in the previous step). Repeat the action for the third buffer if needed (using third knob - if present).

After that you are ready to take measurements.

Please remember, that above outline is very general. Different pH meters may require slightly different operating procedures. You should consult your manual to be sure how to proceed and how to maintain the electrode.



STANDARD CALIBRATION BUFFERS FOR pH ELECTRODES

In general you will probably use commercially available calibration buffers, sold either as ready solutions or as tablets to dissolve in deionized water. However, it may be interesting to look at the table of standard solutions that can be used for the electrode calibration. pH given is for 25°C:

Standard calibration buffers
_________________________________________________

substance(s) concentration pH
______________________________________________________
hydrochloric acidHCl 0.1000M 1.094

potassium trihydrogen
oxalateKH3C4O8 0.05000m 1.679

potassium hydrogen
phthalateKHC8H4O4 0.05000m 4.005

potassium hydrogen
tartrateKHC4H4O6 saturated in 25°C 3.557

disodium hydrogen
phosphateNa2HPO4
potassium dihydrogen
phosphateKH2PO4 0.02500m
0.02500m 6.865

disodium hydrogen
phosphateNa2HPO4
potassium dihydrogen
phosphateKH2PO4 0.03043m
0.008695m 7.413

disodium tetraborate
Na2B4O7 0.01000m 9.180


sodium hydrogen
carbonateNaHCO3
sodium carbonateNa2CO3 0.02500m
0.02500m 10.012

calcium hydroxide
Ca(OH)2 saturated in 25°C 12.45



TESTING PARAMETERS OF pH ELECTRODE


To ensure your electrode works correctly you may want to measure its parameters.
example correct pH electrode parameters

Property Value

Isopotential point ± 15 mV original value

Slope 55 - 61 mV/pH unit

Glass membrane resistance 20-100 MΩ

Electrolyte leak rate 0.2 to 1.5 mL/24 hours



Note that values presented can be wrong in case of specific electrode (for example electrolyte leak rate in electrodes with sleeve junction can be much faster). Consult owners manual if in doubt.

To test isopotential point and slope, switch your pH meter to display results in mV, not as pH units. If not possible, you have to use other pH meter or laboratory voltmeter able to work with pH electrodes.

Isopotential point of most general use electrodes is set at pH=7.00. To measure it put the electrode into pH 7 buffer and measure the electrode potential. Remember to take the measurements in the temperature electrode was originally calibrated in.

To check the slope move electrode to the pH 4 buffer. When potential stabilizes, read the value.

The difference between previous reading and current reading should be in the 166-184 mV range.

Measurements of the electrode resistance and electrolyte leak rate are more difficult. Glass membrane resistance measurements require electrode test stand. To check electrolyte leak rate fill the electrode wil filling solution. Use a waterproof pen to mark the initiall fill level. Suspend the electrode in a beaker of pH 7 or pH 4 buffer so that the lower electrode plug is level with the water. Wait for 24 hours. Refill the electrode using a serological pipet, noting the volume of filling solution required. Amount of solution added divided by 24 is a flow rate.

















































































































































































































































































































































































































































































Mass Spectrometry

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Mass Spectrometry

1. The Mass Spectrometer
In order to measure the characteristics of individual molecules, a mass spectrometer converts them to ions so that they can be moved about and manipulated by external electric and magnetic fields. The three essential functions of a mass spectrometer, and the associated components, are:
1. A small sample of compound is ionized, usually to cations by loss of an electron.
The Ion Source

2. The ions are sorted and separated according to their mass and charge.
The Mass Analyzer

3. The separated ions are then detected and tallied, and the results are displayed on a chart.
The Detector
Because ions are very reactive and short-lived, their formation and manipulation must be conducted in a vacuum. Atmospheric pressure is around 760 torr (mm of mercury). The pressure under which ions may be handled is roughly 10-5 to 10-8 torr (less than a billionth of an atmosphere).
Each of the three tasks listed above may be accomplished in different ways. In one common procedure, ionization is effected by a high energy beam of electrons, and ion separation is achieved by accelerating and focusing the ions in a beam, which is then bent by an external magnetic field. The ions are then detected electronically and the resulting information is stored and analyzed in a computer.

A mass spectrometer operating in this fashion is outlined in the following diagram.
Mass Spectrometry



















The heart of the spectrometer is the ion source. Here molecules of the sample (black dots) are bombarded by electrons (light blue lines) issuing from a heated filament. This is called an EI (electron-impact) source. Gases and volatile liquid samples are allowed to leak into the ion source from a reservoir (as shown), but non-volatile solids and liquids may be introduced directly. Cations formed by the electron bombardment (red dots) are pushed away by a charged repellor plate (anions are attracted to it), and accelerated toward other electrodes, having slits through which the ions pass as a beam. Some of these ions fragment into smaller cations and neutral fragments. When the ion beam experiences a strong magnetic field perpendicular to its direction of motion, the ions are deflected in an arc whose radius is inversely proportional to the mass of the ion. Lighter ions are deflected more than heavier ions. By varying the strength of the magnetic field, ions of different mass can be focused progressively on a detector fixed at the end of a curved tube (also under a high vacuum).

When a high energy electron collides with a molecule it often ionizes it by knocking away one of the molecular electrons (either bonding or non-bonding). This leaves behind a molecular ion (colored red in the following diagram). Residual energy from the collision may cause the molecular ion to fragment into neutral pieces (colored green) and smaller fragment ions (colored pink and orange). The molecular ion is a radical cation, but the fragment ions may either be radical cations (pink) or carbocations (orange), depending on the nature of the neutral fragment. An animated display of this ionization process will appear if you click on the ion source of the mass spectrometer diagram.
Mass Spectrometry





The Nature of Mass Spectra
A mass spectrum will usually be presented as a vertical bar graph, in which each bar represents an ion having a specific mass-to-charge ratio (m/z) and the length of the bar indicates the relative abundance of the ion. The most intense ion is assigned an abundance of 100, and it is referred to as the base peak. Most of the ions formed in a mass spectrometer have a single charge, so the m/z value is equivalent to mass itself. Modern mass spectrometers easily distinguish (resolve) ions differing by only a single atomic mass unit (amu), and thus provide completely accurate values for the molecular mass of a compound. The highest-mass ion in a spectrum is normally considered to be the molecular ion, and lower-mass ions are fragments from the molecular ion, assuming the sample is a single pure compound.

The following diagram displays the mass spectra of three simple gaseous compounds, carbon dioxide, propane and cyclopropane. The molecules of these compounds are similar in size, CO2 and C3H8 both have a nominal mass of 44 amu, and C3H6 has a mass of 42 amu. The molecular ion is the strongest ion in the spectra of CO2 and C3H6, and it is moderately strong in propane. The unit mass resolution is readily apparent in these spectra (note the separation of ions having m/z=39, 40, 41 and 42 in the cyclopropane spectrum). Even though these compounds are very similar in size, it is a simple matter to identify them from their individual mass spectra. By clicking on each spectrum in turn, a partial fragmentation analysis and peak assignment will be displayed. Even with simple compounds like these, it should be noted that it is rarely possible to explain the origin of all the fragment ions in a spectrum. Also, the structure of most fragment ions is seldom known with certainty.
Since a molecule of carbon dioxide is composed of only three atoms, its mass spectrum is very simple. The molecular ion is also the base peak, and the only fragment ions are CO (m/z=28) and O (m/z=16). The molecular ion of propane also has m/z=44, but it is not the most abundant ion in the spectrum. Cleavage of a carbon-carbon bond gives methyl and ethyl fragments, one of which is a carbocation and the other a radical. Both distributions are observed, but the larger ethyl cation (m/z=29) is the most abundant, possibly because its size affords greater charge dispersal. A similar bond cleavage in cyclopropane does not give two fragments, so the molecular ion is stronger than in propane, and is in fact responsible for the the base peak. Loss of a hydrogen atom, either before or after ring opening, produces the stable allyl cation (m/z=41). The third strongest ion in the spectrum has m/z=39 (C3H3). Its structure is uncertain, but two possibilities are shown in the diagram. The small m/z=39 ion in propane and the absence of a m/z=29 ion in cyclopropane are particularly significant in distinguishing these hydrocarbons.

Most stable organic compounds have an even number of total electrons, reflecting the fact that electrons occupy atomic and molecular orbitals in pairs. When a single electron is removed from a molecule to give an ion, the total electron count becomes an odd number, and we refer to such ions as radical cations. The molecular ion in a mass spectrum is always a radical cation, but the fragment ions may either be even-electron cations or odd-electron radical cations, depending on the neutral fragment lost. The simplest and most common fragmentations are bond cleavages producing a neutral radical (odd number of electrons) and a cation having an even number of electrons. A less common fragmentation, in which an even-electron neutral fragment is lost, produces an odd-electron radical cation fragment ion. Fragment ions themselves may fragment further. As a rule, odd-electron ions may fragment either to odd or even-electron ions, but even-electron ions fragment only to other even-electron ions.The masses of molecular and fragment ions also reflect the electron count, depending on the number of nitrogen atoms in the species.
Ions with no nitrogen
or an even # N atoms
odd-electron ions
even-number mass
even-electron ions
odd-number mass
Ions having an odd # N atoms
odd-electron ions
odd-number mass
even-electron ions
even-number mass.

This distinction is illustrated nicely by the follwing two examples. The unsaturated ketone, 4-methyl-3-pentene-2-one, on the left has no nitrogen so the mass of the molecular ion (m/z = 98) is an even number. Most of the fragment ions have odd-numbered masses, and therefore are even-electron cations. Diethylmethylamine, on the other hand, has one nitrogen and its molecular mass (m/z = 87) is an odd number. A majority of the fragment ions have even-numbered masses (ions at m/z = 30, 42, 56 & 58 are not labeled), and are even-electron nitrogen cations. The weak even -electron ions at m/z=15 and 29 are due to methyl and ethyl cations (no nitrogen atoms). The fragmentations leading to the chief fragment ions will be displayed by clicking on the appropriate spectrum.



Mass Spectrometry
Mass Spectrometry










When non-bonded electron pairs are present in a molecule (e.g. on N or O), fragmentation pathways may sometimes be explained by assuming the missing electron is partially localized on that atom. A few such mechanisms are shown above. Bond cleavage generates a radical and a cation, and both fragments often share these roles, albeit unequally.

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