Organic Chemistry Fundamentals for Biochem Part 1 (PDF)

Carbon: The chemistry of Life Organic chemistry is Carbon Inorganic chemistry? all the others.. Carbon: The chemistry of Life Carbon is the best example of an actual circular economy WARM...

Carbon: The chemistry of Life Organic chemistry is Carbon Inorganic chemistry? all the others.. Carbon: The chemistry of Life Carbon is the best example of an actual circular economy WARM RECOMMENDATION: GET ONE AND USE IT. IT WILL HELP YOU. Why Carbon? Carbon is in the midway, considering the octet accomplishment This means that we don’t need to remember too many things. WARM RECOMMENDATION: GET ONE AND USE IT. IT WILL HELP YOU. Elements aim at the valence electron configuration of noble gases Ionic Bond: loss and gain of electrons  LEWIS STRUCTURE 1) Non-valence electrons are not counted in Lewis structures. The total number of electrons represented in a Lewis structure is equal to the sum of valence electrons brought by each individual atom. 2) Once the total number of available electrons has been calculated, electrons must be placed into the structure according to these steps: a) The atoms are first connected by single bonds. The central atom is the one that is not hydrogen displaying the lower electronegativity. b) If “t” is the total number of electrons and “n” the number of single bonds, t-2n electrons remain to be placed. These should be placed as lone pairs: one pair of dots for each pair of electrons available. Lone pairs should initially be placed on outer atoms (other THEY DO NOT CONSIDER ATOMIC than hydrogen) until each outer atom reaches the octet in bonding ORBITALS pairs and lone pairs c) extra lone pairs may then be placed on the central atom. When in doubt, lone pairs should be placed on more electronegative atoms first. d) Once all lone pairs are placed, atoms (especially the central atoms) may not have an octet of electrons. In this case, the atoms must form a double bond; a lone pair of electrons is moved to form a second bond between the two atoms. As the bonding pair is shared between the two atoms, the atom that originally had the lone pair still has an octet; the other atom now has two more electrons in its valence shell. REMEMBER THAT LEWIS STRUCTURES ARE USEFUL SIMPLICATIONS! C2H2Cl2 DRAW THE LEWIS STRUCTURE OF THE FOLLOWING MOLECULES  Energy The Madelung rule Electrons fill orbitals starting at the lowest available energy state before filling higher states. Aufbau procedure: Determine number of electrons for the atom of interest. Fill available orbitals starting with the lowest-energy levels first and avoid pairing electrons in a single orbital until it is necessary. In the periodic table orbitals are progressively filled by electrons as a function of their energy level, always going from the left to the right within the periods. When a period is accomplished (noble gases) the filling process proceeds starting from the first group (alkali metals) in the next energy level (period). ATOMIC ORBITALS  Aufbau explain how electrons fill the lowest energy orbitals first, and then move up to higher energy orbitals only after the lower energy orbitals are full. However, there is a problem with this rule. Certainly, 1s orbitals should be filled before 2s orbitals, because the 1s orbitals have a lower value of n, and thus a lower energy. What about filling the three different 2p orbitals? In what order should they be filled? The answer to this question involves Hund's rule. Orbital diagram Hund's rule states that: 1) Every orbital in a sublevel is singly occupied before any orbital is doubly occupied. 2) All of the electrons in singly occupied orbitals must have the same spin (to maximize total spin) Which one of this orbital diagram is incorrect? Why does carbon atom (z=6) capable of forming four covalent bonds where in fact it has only two unpaired electrons available in its outermost shell for bonding? Sp3 hybrid: one of the two electrons located in the 2s orbital will get promoted to the empty 2pz orbital. As a result, carbon now has 4 unpaired valence electrons with which it can form four bonds. However, to form 4 equal bond, electrons must have the same energy or, in other words, being located in identical orbitals. LONE PAIR REPULSION  DRAW THE LEWIS STRUCTURE OF THE FOLLOWING MOLECULES CH3NO C6H6 C5H7+ NO3- How do you attack a castle? Commanders first had to devise an overall strategy for taking the castle identify strengths and weaknesses of a fortification. Similarly, we have to analyze the overall molecular reactivity (identify each group by its reactivity) to propose a reaction mechanism.  Consider who is the carbon «partner» and the way is bound Bottom line: when it is convenient…  Evaluate if it is thermodynamically convenient. Remember that reactive means unstable (high chemical energy) If the leaving group (L) is a weak base or a weak nucleophile (stable, unreactive) the reaction is thermodynamically favored because the products development is accompanied by a lowering of the system energy. On the contrary, if L is a strong nucleophile or a strong base (unstable, reactive) the reaction is not thermodynamically favored. Alternatively, if the leaving group is a stronger nucleophile it can surely displace the entering group (Nu) Maybe this is a better example for AC students!!  In the transition state, Carbon is “pentavalent” because the broken of the C - X bond is contemporary with the formation of the Nu - C bond Nucleophile (Nu-): negatively charged atom or group or a specie bearing an electron doublet  If four different groups of atoms are attached to the same sp3 carbon atom, they can be arranged in space in two different ways that are mirror images of each other, and which lead to so-called left-handed and right-handed versions of the same molecule. Molecules that cannot be superimposed on their own mirror image are said to be chiral like mirror image: enantiomers For many decades, the origin of homochirality in biological systems has aroused the interest of the scientific community, and it has been in a core position in studies on the origin of life Try shaking a someone's left hand with your right hand. It just doesn't work, does it? Your right palm and her or his left palm cannot mesh comfortably because hands are chiral objects, having non-superimposable mirror images.