Organics

shared orbitals

2007-11-22T14:51:00.000-08:00

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atomic orbitals

2006-12-31T23:50:00.000-08:00

Atomic orbitals are often represented as electrons spinning around the nucleus (top - carbon). However, orbital shells actually represent the volume in which the wave-form electron is likeliest to be found (shaded).

As such, orbitals are more akin to a cloud around the nucleus (bottom - sp hybrid hydrogen).

The location of electrons within orbitals is described mathematically by the Schrodinger equations. Computer simulations reveal probability distributions for orbitals.

Table of images of orbitals / Scatter plot of probabilities / interactive / virtual text / virtual text orbitals / download audio-anim of H2 bonding / audio-anim of hybridization of s p orbitals / voxel movie of orbital / movie 2 / movie 3 / movie 4 /

Atomic orbitals are distorted in molecular covalent bonds, where atoms share electrons within a molecule.

When electrons are shared between two atoms of the same element, the electrons are shared equally, creating a non-polar covalent bond.

When electrons are shared between atoms of different elements, the electrons are not shared equally. Unequal sharing results in a polar covalent bond in which the increased-probability cloud over one atom has a slightly negative charge compared to a slightly positive charge over the other -- a dipole.

acidic amino acids

2006-11-30T23:50:00.000-08:00

Both aspartic acid and glutamic acid are able to donate a proton from the hydroxyl group of the side chain (Lowry-Bronsted acids).

acidic and basic amino acids

2006-11-30T23:40:00.000-08:00

Several amino acids possess a side chain that adopts a + (basic) or - (acidic) charge at the pH of cells.grey - carbon / white - hydrogen / blue - nitrogen / red - oxygen

basic amino acids

2006-11-30T23:30:00.000-08:00

The amino group on the side chain of Lysine, and Arginine, and the N of Histidine are able to accept a proton (Lowry-Bronsted base).

polar amino acids

2006-11-30T23:10:00.000-08:00

When electrons are shared between atoms of different elements, the electrons are not shared equally, resulting in a polar bond in which the increased-probability cloud over one atom has a slightly negative charge (delta -)while that over the other atom has a slightly positive charge (delta +). This unequal sharing generates a dipole. Molecules with dipoles tend to align positive toward negative.

grey - carbon / white - hydrogen / blue - nitrogen / red - oxygen / yellow - sulphur

non-polar amino acids

2006-11-30T23:00:00.000-08:00

When electrons are shared between two atoms of the same element, the electrons are shared equally, creating a non-polar bond.

grey - carbon / white - hydrogen / blue - nitrogen / red - oxygen / yellow - sulphur

glycerol

2006-08-31T23:48:00.000-07:00

Glycerol is a three carbon substance that is important component of triglycerides (i.e. fats and oils) and of phospholipids. Glycerol forms the backbone of fatty acids in triglycerides.

DNA

2005-11-17T19:45:00.000-08:00

A space-fill model of the DNA double-helix.

grey - carbon / white - hydrogen / blue - nitrogen / red - oxygen

chirality

2005-11-16T18:43:00.000-08:00

Chirality is that property of molecules related to non-superimposability of arrangements of attached groups -- stereoisomers. For amino acids, the CORN law determines naming. CORN is an acronym for the -COOH (caboxylic acid group), the -R group (indicating the side chain) and -NH2 (the amine group).

Moving from the alpha-carbon to the carboxylic acid group, then the -R group, then the -NH2 group spells the acronym CORN. If CORN fits a clockwise arrangement, then the molecule is the L- form, where the amino group is on the L-eft side in its Fisher projection of the compound. This is the form found in all biologically generated amino acids. Conversely, an anti-clockwise CORN arrangement is the D-form. More modern notation refers to R- and S- stereo-isomers or enantiomers.

As depicted below, the molecule can be imagined with the H superimposed on the thumb, and the CORN groups in the palm of the left or right hand.

Stereochemistry

bases

2005-11-16T18:27:00.000-08:00

grey - carbon / white - hydrogen / blue - nitrogen / red - oxygen

adenine
cytosine
guanine
thymine
uracil

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1990-01-01T13:11:00.000-08:00

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• atomic orbitals • acidic amino acids • acidic and basic amino acids • basic amino acids • polar amino acids • non-polar amino acids • glycerol • DNA • chirality • bases

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