2-MED101_Basic_Concepts_Chemical_Bonds.pptx

MED100 MOLECULAR AND CELLULAR MEDICAL SCIENCES I Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected]  Lecture Presentation...

MED100 MOLECULAR AND CELLULAR MEDICAL SCIENCES I Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected]  Lecture Presentation Basic concepts Chemical bonds Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I In this Chapter; You will learn Chemical Bonds: The Octet Rule Ionic Bonds Covalent Bonds and Lewis Structures How To Write Lewis Structures Exceptions to the Octet Rule Formal Charges and How To Calculate Them A Summary of Formal Charges How To Write and Interpret Structural Formulas More About Dash Structural Formulas Condensed Structural Formulas Rules for Writing Resonance Structures  Chemical Bonds: The Octet Rule 1. Ionic (or electrovalent) bonds are formed by the transfer of one or more electrons from one atom to another to create ions. 2. Covalent bonds result when atoms share electrons. The central idea in their work on bonding is that atoms without the electronic configuration of a noble gas generally react to produce such a configuration because these configurations are known to be highly stable. For all of the noble gases except helium, this means achieving an octet of electrons in the valence shell. The valence shell is the outermost shell of electrons in an atom. The tendency for an atom to achieve a configuration where its valence shell contains eight electrons is called the octet rule. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Chemical Bonds: The Octet Rule 1. Ionic (or electrovalent) bonds are formed by the transfer of one or more electrons from one atom to another to create ions. 2. Covalent bonds result when atoms share electrons. The central idea in their work on bonding is that atoms without the electronic configuration of a noble gas generally react to produce such a configuration because these configurations are known to be highly stable. For all of the noble gases except helium, this means achieving an octet of electrons in the valence shell. The valence shell is the outermost shell of electrons in an atom. The tendency for an atom to achieve a configuration where its valence shell contains eight electrons is called the octet rule. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Ionic Bonds Atoms may gain or lose electrons and form charged particles called ions. An ionic bond is an attractive force between oppositely charged ions. One source of such ions is a reaction between atoms of widely differing electronegativities Electronegativity is a measure of the ability of an atom to attract electrons. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Covalent Bonds and Lewis Structures Covalent bonds form by sharing of electrons between atoms of similar electronegativities to achieve the configuration of a noble gas. Molecules are composed of atoms joined exclusively or predominantly by covalent bonds. Molecules may be represented by electron-dot formulas or, more conveniently, by formulas where each pair of electrons shared by two atoms is represented by a line. A dash structural formula has lines that show bonding electron pairs and includes elemental symbols for the atoms in a molecule. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Covalent Bonds and Lewis Structures 1. Hydrogen, being in group IA of the periodic table, has one valence electron. Two hydrogen atoms share electrons to form a hydrogen molecule, H2. 2. Because chlorine is in group VIIA, its atoms have seven valence electrons. Two chlorine atoms can share electrons (one electron from each) to form a molecule of Cl2. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Consider the following compounds and decide whether the bond in them would be IONIC Por COVALENT. (a) KCl (b) F2 (c) PH3 (d) CBr4 Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Write Lewis Structures Several simple rules allow us to draw proper Lewis structures: 1. Lewis structures show the connections between atoms in a molecule or ion using only the valence electrons of the atoms involved. Valence electrons are those of an atom’s outermost shell. 2. For main group elements, the number of valence electrons a neutral atom brings to a Lewis structure is the same as its group number in the periodic table. Carbon, for example, is in group IVA and has four valence electrons; the halogens (e.g.,fluorine) are in group VIIA and each has seven valence electrons; hydrogen is in group IA and has one valence electron. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Write Lewis Structures 3. If the structure we are drawing is a negative ion (an anion), we add one electron for each negative charge to the original count of valence electrons. If the structure is a positive ion (a cation), we subtract one electron for each positive charge. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Write Lewis Structures 4. In drawing Lewis structures we try to give each atom the electron configuration of a noble gas. To do so, we draw structures where atoms share electrons to form covalent bonds or transfer electrons to form ions. a. Hydrogen forms one covalent bond by sharing its electron with an electron of another atom so that it can have two valence electrons, the same number as in the noble gas helium. b. Carbon forms four covalent bonds by sharing its four valence electrons with four valence electrons from other atoms, so that it can have eight electrons (the same as the electron configuration of neon, satisfying the octet rule). c. To achieve an octet of valence electrons, elements such as nitrogen, oxygen, and the halogens typically share only some of their valence electrons through covalent bonding, leaving others as unshared electron pairs. Nitrogen typically shares three electrons, oxygen two, and the halogens one. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write the Lewis structure of CH3F. 1. We find the total number of valence electrons of all the atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. We use pairs of electrons to form bonds between all atoms that are bonded to each other. We represent these bonding pairs with lines. In our example this requires four pairs of electrons (8 of the 14 valence electrons). Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  3.We then add the remaining electrons in pairs so as to give each hydrogen 2 electrons (a duet) and every other atom 8 electrons (an octet). In our example, we assign the remaining 6 valence electrons to the fluorine atom in three nonbonding pairs. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write a Lewis structure for methylamine (CH3NH2). 1. We find the total number of valence electrons for all the atoms. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. We use one electron pair to join the carbon and nitrogen. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  3. We use three pairs to form single bonds between the carbon and three hydrogen atoms. 4. We use two pairs to form single bonds between the nitrogen atom and two hydrogen atoms. 5. This leaves one electron pair, which we use as a lone pair on the nitrogen atom. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write the Lewis structure of CH3OH. 5. If necessary, we use multiple bonds to satisfy the octet rule (i.e., give atoms the noble gas configuration). The carbonate ion (CO32−) illustrates this: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write the Lewis structure of CH2O (formaldehyde). 1. Find the total number of valence electrons of all the atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. (a) Use pairs of electrons to form single bonds. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  (b) Determine which atoms already have a full valence shell and which ones do not, and how many valence electrons we have used so far. In this case, we have used 6 valence electrons, and the valence shell is full for the hydrogen atoms but not for the carbon and oxygen atoms. (c) We use the remaining electrons as bonds or unshared electron pairs, to fill the valence shell of any atoms whose valence shell is not yet full, taking care not to exceed the octet rule. In this case 6 of the initial 12 valence electrons are left to use. We use 2 electrons to fill the valence shell of the carbon by another bond to the oxygen, and the remaining 4 electrons as two unshared electron pairs with the oxygen, filling its valence shell. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write a Lewis structure for the toxic gas hydrogen cyanide (HCN). 1. We find the total number of valence electrons on all of the atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. We use one pair of electrons to form a single bond between the hydrogen atom and the carbon atom, and we use three pairs to form a triple bond between the carbon atom and the nitrogen atom. This leaves two electrons. We use these as an unshared pair on the nitrogen atom. Now each atom has the electronic structure of a noble gas. The hydrogen atom has two electrons (like helium) and the carbon and nitrogen atoms each have eight electrons (like neon). Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exceptions to the Octet Rule Elements of the second period of the periodic table can have a maximum of four bonds (i.e., have eight electrons around them) because these elements have only one 2s and three 2p orbitals available for bonding. Each orbital can contain two electrons, and a total of eight electrons fills these orbitals. The octet rule, therefore, only applies to these elements, and even here, as we shall see in compounds of beryllium and boron, fewer than eight electrons are possible. Elements of the third period and beyond have d orbitals that can be used for bonding. These elements can accommodate more than eight electrons in their valence shells and therefore can form more than four covalent bonds. Examples are compounds such as PCl5 and SF6. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exceptions to the Octet Rule Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write a Lewis structure for the sulfate ion (SO42−) 1. We find the total number of valence electrons including the extra 2 electrons needed to give the ion the double negative charge: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. We use four pairs of electrons to form bonds between the sulfur atom and the four oxygen atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  3.We add the remaining 24 electrons as unshared pairs on oxygen atoms and as double bonds between the sülfür atom and two oxygen atoms. This gives each oxygen 8 electrons and the sulfur atom 12: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Formal Charges and How To Calculate Them Many Lewis structures are incomplete until we decide whether any of their atoms have a formal charge. Calculating the formal charge on an atom in a Lewis structure is simply a bookkeeping method for its valence electrons. First, we examine each atom and, using the periodic table, we determine how many valence electrons it would have if it were an isolated atom. This is equal to the group number of the atom in the periodic table. For hydrogen this number equals 1, for carbon it equals 4, for nitrogen it equals 5, and for oxygen it equals 6. Next, we examine the atom in the Lewis structure and we assign the valence electrons in the following way: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Formal Charges and How To Calculate Them We assign to each atom half of the electrons it is sharing with another atom and all of its unshared (lone) electron pairs. Then we do the following calculation for the atom: Formal charge = number of valence electrons − 1/2 number of shared electrons − number of unshared electrons or F = Z − (1/2)S − U the number of unshared electrons formal charge group number of the element the number of shared electrons It is important to note, too, that the arithmetic sum of all the formal charges in a molecule or ion will equal the overall charge on the molecule or ion. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Formal Charges of Ammonium Ion o r Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Nitrate Ion or Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Water or Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Ammonia or Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  A Summary of Formal Charges Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Write and Interpret Structural Formulas Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  More About Dash Structural Formulas Dash structural formulas have lines that show bonding electron pairs, and include elemental symbols for all of the atoms in a molecule.  Condensed Structural Formulas In condensed formulas all of the hydrogen atoms that are attached to a particular carbon are usually written immediately after the carbon Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Condensed Structural Formulas The condensed formula for isopropyl alcohol can be written in four different ways: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Rules for Writing Resonance Structures 1. Resonance structures exist only on paper. Although they have no real existence of their own, resonance structures are useful because they allow us to describe molecules and ions for which a single Lewis structure is inadequate. We write two or more Lewis structures, calling them resonance structures or resonance contributors. We connect these structures by double-headed arrows (←→ ), and we say that the real molecule or ion is a hybrid of all of them. 2. We are only allowed to move electrons in writing resonance structures. The positions of the nuclei of the atoms must remain the same in all of the structures. Structure 3 is not a resonance structure of 1 or 2, for example, because in order to form it we would have to move a hydrogen atom and this is not permitted: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Rules for Writing Resonance Structures Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  3. All of the structures must be proper Lewis structures. We should not write structures in which carbon has five bonds, for example: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  4. The energy of the resonance hybrid is lower than the energy of any contributing structure. Resonance stabilizes a molecule or ion. This is especially true when the resonance structures are equivalent. Chemists call this stabilization resonance stabilization. If the resonance structures are equivalent, then the resonance stabilization is large. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  5. The more stable a structure is (when taken by itself ), the greater is its contribution to the hybrid. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I