What are Atoms | molecules

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.

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Induction in stereochemistry

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.

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.

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.

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SYNTHESIS OF BETA CAROTENE BY BASF AND ROCHE SYNTHESIS

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

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