Atomic Structure I PDF

ATOMIC STRUCTURE I Dr. Alya A. Arabi Department of Biochemistry College of Medicine and Health Sciences 1 2 H2O is a molecule It has two atoms of the element Hydrogen (H) and one atom of the element oxygen (O) 3 ELEMENT ➢At present, scientist have identified 118 elements. 98 are known to oc...

ATOMIC STRUCTURE I Dr. Alya A. Arabi Department of Biochemistry College of Medicine and Health Sciences 1 2 H2O is a molecule It has two atoms of the element Hydrogen (H) and one atom of the element oxygen (O) 3 ELEMENT ➢At present, scientist have identified 118 elements. 98 are known to occur in nature. ➢For example, Carbon is an element with symbol C. 4 ELEMENT ➢ 25 elements are essential for life • 4 elements make up about 96% of the mass of most living organisms (O, C, H, N) • Trace elements are less than 0.01% of human weight 5 Percentages by mass http://science.jrank.org 6 Major elements of importance to plants and animals Name Symbol Carbon C Constituent of protein, CH, fat. Meat, fruit and vegetables Hydrogen H Body fluid, essential for protein, CH, fat. Water Oxygen O Essential for respiration, body fluid,… Air and water Nitrogen N Constituent of proteins, nucleic acids. Meat and fish Phosphorus P Essential for ATP, phospholipids, … Meat and milk Sulfur S Component of proteins. Meat, fish and eggs Chlorine Cl Ion balance across membranes, stomach acid. Table salt, salted foods Sodium Na Ion balance across membranes. Table salt, salted foods Potassium K Anion-cation balance across membranes, nerve impulses. Meat, green vegetables Ca Component of bones, teeth, invertebrate shells, essential for blood clotting. Hard water, milk Calcium Role in living organisms Source used by man 7 Trace elements of importance to plants and animals Name Symbol Role in living organisms Source used by man Fluorine F Constituent of teeth and bones Hard water, milk Iodine I Essential for thyroxin in thyroid Drinking water, sea food, iodized table salt. Selenium Se Removal of active oxygen species by glutathione peroxidase Fruit and vegetables Manganese Mn Growth of bone Present in a range of foods Iron Fe Oxygen carrier in myoglobin and hemoglobin, cofactor in many redox (reduction/oxidation) reactions Liver, red meat, spinach Cobalt Co Essential for Vit. B12 promoting red Liver, red meat cell development Zinc Zn Essential in carbonic anhydrase for carbon dioxide transport in blood Present in a range of foods 8 Metal deficiency Provide iron as Fe(II) salt, it is more soluble than Fe(III) salt, and therefore, better absorbed. 9 Atom – The nucleus: a very small, dense, positively charged part of the atom. – Electron cloud • 10-10 m = 1 Å (Ångström) • Diameter of C is ~1.5 Å. If an atom could be expanded to the size of a football stadium, the nucleus would be the size of a single blueberry. 10 Subatomic Particles of an Atom Within the atom are three basic subatomic particles: protons (p+) Nucleus 0 neutrons (n ) electrons (e–) Mass in kg Mass in amu Charge proton 1.67262×10-27 1 +1 neutron 1.67493×10-27 1 0 electron 0.00091×10-27 0.00055 (~0) -1 11 12 protons neutrons electrons C 6 6 6 C+ 6 6 5 C- 6 6 7 13 Electron Distribution and Electron Configuration 14 Pauli Exclusion Principle ➢ The two electrons in each orbital must have opposite spin (usually indicated by one up-arrow and one down-arrow). 15 Hund’s rule ➢ When orbitals of equal energy are present, electrons occupy each orbital first before pairing in any one. 2p 16 Aufbau’s Principle ➢ Lowest-energy subshells (and their orbitals) fill first: 1s → 2s → 2p → 3s → 3p → 4s → 3d 1s < 2s < 2p < 3s < 3p < 4s < 3d < 4p < 5s < 4d < 5p < 6s 17 1s 2s 2p 3s 3p 4s 3d 4p 5s 4d 5p 6s 4f 5d 6p 7s 5f 6d 7p 18 Subshells: s, p, d, f, etc. s subshell has 1 orbital p subshell has 3 orbitals d subshell has 5 orbitals f subshell has 7 orbitals 19 https://chemistry.stackexchange.com/questions/31189/what-is-spdf-configuration Node: zero probability of finding an electron 1s 2s 2p 3p 20 21 Each orbital can fit 2 electrons Subshell # of orbitals Max. # of electrons s 1 2 p 3 6 d 5 10 f 7 14 22 1s2 2s2 2p6 3s2 3p6 4s2 3d10 4p6 5s2 4d10 5p6 6s2 4f14 5d10 6p6 7s2 5f14 6d10 7p6 23 In red are exceptions due to the added stability associated with half-filled and filled subshells. Shorthand Notation 24 Example in Medicine: In MRI Metal ions possessing one or more unpaired electrons are paramagnetic. This magnetic moment will interact strongly with any magnetic fields to which it is exposed, and it helps creating a better contrast in MRI. Among the high-spin metal ions, Fe3+, Cr3+, Mn2+ and Gd3+, the one with the highest number of unpaired electrons will have the largest magnetic moment, and therefore will be the best enhancing the MRI imaging. Which of these metal ions will have the best contrast? The ions have 5, 3, 5 and 7 unpaired electrons, respectively, so Gd3+ would have the largest magnetic moment and will have the best 25 contrast. Shells Shell Shell quantum number (n) # of Type of subshells Subshells maximum # of electrons (2n2) K 1 1 1s 2 L 2 2 2s,2p 8 M 3 3 3s,3p,3d 18 N 4 4 4s,4p,4d,4f 32 26 # of valence electrons 27 28 Lewis Dot structure Valence electrons are drawn around the sides of the element symbol. lone pair C N Al Ar 4 ve- 5 ve- 3 ve- 8 ve- 1s2 2s2 2p2 1s2 2s2 2p3 1s2 2s2 2p6 3s2 3p1 1s2 2s2 2p6 3s2 3p6 Octet rule (8 electrons in the valence shell) 29 30 Draw the Lewis structure of NF3 Octet rule (8 electrons in the valence shell) 31 http://www.green-planet-solar-energy.com/lewis-dot-structure.html