Chemical Bonds Notes PDF

Chemical bonds Chapter 2 Hello everyone! Hope everyone is doing well. We will start off first with looking at some basics of chemical bonds. Now when you think about bonds what comes to mind? Bonding – something we are attracted to, something that hol...

Chemical bonds Chapter 2 Hello everyone! Hope everyone is doing well. We will start off first with looking at some basics of chemical bonds. Now when you think about bonds what comes to mind? Bonding – something we are attracted to, something that holds two things together. So keeping that in mind let’s review bonding in our cells…  Background chemistry information: Concept 2.1: Matter consists of chemical elements in pure form and in combination called compounds. Concept 2.2: An element’s properties depend on the structure of its atoms  Learning Outcomes The structure and properties of chemicals determine the behavior and functions of molecules in organisms. 2A. Construct stable biological molecules with the atoms, C, H, O, N, S and P through intra-molecular covalent bonds and distinguish between polar and nonpolar covalent bonds. 2B. Compare and contrast covalent bonds with shared electrons with non-covalent bonds and interactions (ionic bonds, hydrogen bonds, dipole & hydrophobic/hydrophilic interactions). 2C. Give examples of how polar regions of different molecules can form hydrogen bonds with each other while structures with nonpolar covalent bonds cannot. Covalent and non-covalent bonds A subset of the periodic table Shown here is a subset of the periodic table. Can you tell which of these are most abundant elements found in organisms? Check out the highlighted elements! Notice these have incomplete valence shells. Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms. This usually results in atoms staying close together, held by attractions called chemical bonds. Also shown here are electrons in valence shells with unpaired electrons indicated in red. An atom is most stable when its valence shell is filled. One way that shells can be filled is through the formation of chemical bonds – strong attractions that bind atoms together. Atoms interact such that both (all) have 8 electrons in outermost orbit  Covalent bonds Intramolecular Bonds between atoms in a molecule  Now let’s look at how atoms can interact with each other to complete their valence shells and be stable. One way is by sharing electrons. These type of bonds that result from sharing electrons are called covalent bonds. These are intramolecular that is between atoms in a molecule. Note some examples of sharing of electrons between hydrogen and other atoms to form different molecules (NH3 and CH4). Note the different number of valence electrons in each element (C and N) requires different number of hydrogen atoms to share electrons with. Intramolecular bonds Formation of H2 1 In each hydrogen atom , the single electr on is held in its or bital by its attraction to the proton in the nucleus. 2 When two hydrogen atom s appr oach each other , the electron of each atom is also attracted to the proton in the other nucleus. 3 The two electrons becom e shared in a covalent bond, forming an H2 molecule. Note: Electrons are shared between two H atoms. Electrons are shared equally!  Shown here is an example of formation of a hydrogen (H2) molecule through formation of covalent bonds. As shown in this example, as each hydrogen atoms approach the other, the electron of each atom is attracted to the nucleus of the other. This sharing of electrons between the two atoms is called a covalent bond, resulting in the formation of a hydrogen molecule, H2.  Electronegativity (EN) Measure of the ability of an atom to attract electrons in the context of a chemical bond – (Pauling scale and Mulliken scale)  Atoms with higher EN values have a greater attraction for electrons. The closer the atoms in their EN values, the more equal their sharing of electrons.  Polar Covalent Bonds: Unevenly matched, but willing to share. education.jlab.org/jsat/powerpoint/chembond.ppt Polar Covalent Bonds in a Water Molecule Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen. − This results in − two regions of partial negative O charge on oxygen and a partial pos- itive charge on each hydrogen. H H + + H2O  Shown here is an example of a water (H2O) molecule. Note the two OH bonds here. Each is polar covalent. Due to difference in EN values between O and H, electrons are pulled slightly toward Oxygen (O) resulting in O having a slight negative charge which is denoted as - while the H then gets a slight positive charge denoted as +. So the H2O molecule as you can see has both partial positive and negative charges. This is a polar molecule. Do you think it will be attracted to other polar molecules? Hmm…We will come back to this in a few slides.  What type of bond is shown here? education.jlab.org/jsat/powerpoint/chembond.ppt Electron Transfer and Ionic Bonding 1 The single valence electron of a 2 2 Each resulting ion has a completed sodium atom is transferred to join the 7 valence shell. An ionic bond can form valence electrons of a chlorine atom. between the oppositely charged ions. Na Cl Na Cl Na Cl Na+ Cl – Sodium atom Chlorine atom Sodium ion Chloride ion (a cation) (an anion) Sodium chloride (NaCl)  Next let’s talk about what would happen if the difference between EN values between two atoms is so high that they cannot share electrons at all. This is exactly what happens when the EN difference between two interacting atoms is greater than 1.5. Let’s look at an example – Sodium Chloride (NaCl). EN value for Na is 0.9, while EN value for Cl is 3.1, so the difference in EN (3.1-0.9) is 2.2 (which is greater than 1.5). So, as Cl has higher EN value than Na, it pulls the lone valence electron from Na to complete its valence shell. So now Cl ends up with an extra electron while Na has one less electrons. Both have their valence shells full, but now each is called an ion. As Na has one less electron it is a cation, while Cl with one more electron is an anion. So Na now has a complete positive charge, while Cl has a complete negative charge. This strong attraction between opposite charges is called an ionic bond.  Ionic compounds – Compounds formed by ionic bonds – Are often called salts, which may form crystals Na+ Cl– Atoms pack into a crystal structure  Compounds formed by ionic bonds are called ionic compounds or salts. As shown here Na+ and Cl- pack together to form crystals. Crystals of salt found in nature of various sizes and shapes, each an aggregate of vast number. of cations and anions bonded by their electrical attraction arranged in a 3D lattice.  NaCl This is the formation of an ionic bond. + - Na Cl electron transfer and the formation of ions Cl2 This is the formation of a covalent bond. Cl Cl sharing of a pair of electrons and the formation of molecules academic.pgcc.edu/~ssinex/ChemBond.ppt  Note the difference in bonds between Na+ Cl- and between two Cl- atoms. Dipole-dipole interactions Intermolecular interactions  Now moving on to intermolecular (between molecule) forces – an example is dipole-dipole interactions. These are strong interactions that occur between polar molecules. As shown in (a) they are due to the attraction of the + atoms of one molecule to the - atoms of another molecule. Now look at (b) a bunch of these polar molecules can be attracted with each other. Notice the dotted lines denoting attraction (red)? Why are they dotted? It is because these individual attractions are not very strong, they can form and break easily.  A Hydrogen Bond − + − H Water (H2O) O This hydrogen bond H (dotted line) results from + the attraction between the partial positive − charge on a hydrogen atom of water and the partial negative charge Ammonia (NH3) N on the nitrogen atom of ammonia. H H + + H +  As example of dipole-dipole interactions in cells is the hydrogen bond. These are strong dipole-dipole type of interactions that occur among polar covalent molecules containing H directly attached to one of the three small electronegative elements: O, N, or F. Note this is an intermolecular bond, so it is formed between polar molecules. Example shown here is hydrogen bonding between two water molecules. Ion-dipole interactions. We also see attractive forces between ions and polar molecules. These are called ion- dipole interactions. Water molecules orient themselves in a what that the partial negative charge of Oxygen is attracted to the complete positive charge of Na or the partial positive charge of H in H2O is attracted to the full negative charge of Chlorine. When water molecules surround each ion this is referred to as a hydration  Hydrophobic interactions https://chem.libretexts.org/Core/Physical_and_Theoretical_Chemistry/Physical_Properties_ of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Hydrophobic_Interacti ons  Apart from attractive forces found in cells that result in molecules and ions, we also see forces that cause molecules to not want to bond with molecules with other polar molecules. For example when nonpolar molecules (remember they have no partial/complete charges) are placed in water (polar environment), they gather together and shield themselves away from water. This type of ‘huddling together’ is referred to as hydrophobic interaction. Shown in this figure the orange blob is a hydrophobic molecule placed in water. Note how multiple hydrophobic molecules gather together to get away from water. So what is holding the hydrophobic molecules together? Are they sharing electrons? Are they forming hydrogen bonds? No! They are held together by their mutual dislike for water. Van der Waals interactions  A type of weak interaction evident especially in nonpolar molecules is Van der Waals interactions. So what is this attraction? Look at the figure here. Electrons may be distributed asymmetrically in molecules or atoms The resulting regions of positive or negative charge enable all atoms and molecules to stick to one another These weak van der Waals interactions occur only when atoms and molecules are very close together Collectively, such interactions can be strong, as between molecules of a gecko’ s toe hairs and a wall surface, allowing geckos to climb walls or hang from ceiling..:) Models Showing the Shapes of Two Small Molecules Space-Filling Ball-and-Stick Model Model O H H 104.5 Water (H2O) H C H H H Methane (CH4)  Ok so we saw how we form molecules. Now a molecule’s size and shape are key to its function in a cell. Molecular shape determines how biological molecules recognize and respond to one another  A Molecular Mimic a) Structures of endorphin and morphine b) Binding to endorphin receptors © 2017 Pearson Education, Inc.  Biological molecules may bind temporarily to each other through weak interactions if their shapes are complementary. Molecules with similar shapes can have similar biological effects. As show here evaluating the shape of natural endorphin one can design a drug (morphine) that can replicate the binding and the biological effect of a natural endorphin in cells.  Learning Resources Reading in text: Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms. Additional resources: Introduction to Chemistry for biology: Dr. Sata Sathasivan https://www.youtube.com/watch?v=tVxPcZpw- qk&t=35s  Learning Objectives Name the different types of bonds present in biological molecules. In your own words explain the formation of each of the following: polar and nonpolar covalent bonds, ionic bonds, hydrogen bonds, hydrophobic interactions, van der Waals interactions. Rate bonds in the order of their strength from weakest to strongest. What type of bond occurs between O and H, C and H, N and H, Na and Cl?