Lecture 1: Atoms, Chemical Bonds, and Hydrocarbons (2025-2024) PDF

Mustansiriyah University College of Medicine Chemistry and Biochemistry Department Medical Chemistry (Organic) / Lecturer. Dr. Tamara Sami Naji Lecture 1: Atoms, Chemical bonds and Hydrocarbons 1.1 Composition of the Atom  The basic structural unit of an element is the atom.  The nucleus is...

Mustansiriyah University College of Medicine Chemistry and Biochemistry Department Medical Chemistry (Organic) / Lecturer. Dr. Tamara Sami Naji Lecture 1: Atoms, Chemical bonds and Hydrocarbons 1.1 Composition of the Atom  The basic structural unit of an element is the atom.  The nucleus is the very small and very dense core at the center of the atom containing: 1. Protons: positively charged particles. The number of protons is indicated by the atomic number, Z. 2. Neutrons: neutral particles. The number of neutrons is calculated from the mass number minus the atomic number, A–Z. 3. Electrons are negatively charged particles that are located in a diffuse region. For a neutral atom, The number of electrons equals the number of protons.  Isotopes are atoms of the same element that have a different number of neutrons. Isotopes of the same element have the same chemical properties. For example, all of the following are isotopes of hydrogen:  The atomic mass is the weighted average of the masses of the isotopes of an element in atomic mass units; 1 amu = 1.66 * 10-24 grams (g). 1.2 The Periodic Law and the Periodic Table  The periodic law relates the structure of elements to their chemical and physical properties. The modern periodic table groups the elements according to these properties.  Periods are horizontal rows, numbered 1 through 7 from top to bottom. The lanthanide series is part of period 6; the actinide series is part of period 7.  Vertical columns are referred to as groups or families. 2025-2024 1 Mustansiriyah University College of Medicine Chemistry and Biochemistry Department Medical Chemistry (Organic) / Lecturer. Dr. Tamara Sami Naji Figure (1.1): The periodic table (‫(الجدول الدوري لألطالع فقط‬ 1.3 Chemical Bonding Chemical bonding: is the attractive force between atoms in a compound can be classified as  Covalent, atoms sharing electrons  Polar covalent and nonpolar covalent  Ionic, consisting of cations and anions Electronegativity is a measure of the ability of an atom to attract electrons in a chemical bond, and the difference in electronegativity is used in classifying chemical bonds. Difference of 0.5 and less—nonpolar covalent Difference between 0.5 and 2.0—polar covalent Difference of 2.0 or larger—ionic 1.4 Naming Compounds and Writing Formulas of Compounds The system for naming compounds (nomenclature) is different for ionic and covalent compounds 2025-2024 2 Mustansiriyah University College of Medicine Chemistry and Biochemistry Department Medical Chemistry (Organic) / Lecturer. Dr. Tamara Sami Naji 1. Ionic compounds: name cation followed by the anion. Some examples follow: With many elements, such as transition metals, several ions of different charge may exist. Fe2+, Fe3+ and Cu+, Cu2+ are two common examples. Clearly, an ambiguity exists if we use the name iron for both Fe2+ and Fe3+ or copper for both Cu+ and Cu2+. Two systems have been developed to avoid this problem: the Stock system and the common nomenclature system. Monatomic ions are ions consisting of a single atom. The ions that are particularly important in biological systems are highlighted in red. Polyatomic ions, such as the hydroxide ion, OH-, are composed of two or more atoms bonded together. These ions, although bonded to other ions with ionic bonds, are themselves held together by covalent bonds. 2025-2024 3 Mustansiriyah University College of Medicine Chemistry and Biochemistry Department Medical Chemistry (Organic) / Lecturer. Dr. Tamara Sami Naji )‫(الجدول لالطالع فقط‬ )‫)الجدول لالطالع فقط‬ 2025-2024 4 Mustansiriyah University College of Medicine Chemistry and Biochemistry Department Medical Chemistry (Organic) / Lecturer. Dr. Tamara Sami Naji 2. Covalent compounds: name first element first and then second element (with -ide ending). Use prefixes of di-, tri-, etc., to denote the number of atoms of each element in the compound Example: Name the covalent compound N2O4 The name is dinitrogen tetroxide. A Medical Perspective: Kidney stones most often result from the combination of calcium cations (Ca2+) with anions such as oxalate (C2O42- ) and phosphate (PO43-). Calcium oxalate and calcium phosphate are ionic compounds that are only sparingly soluble in water. They grow in a three- dimensional crystal lattice. When the crystals become large enough to inhibit the flow of urine in the kidney or bladder, painful symptoms necessitate some strategy to remove the stones. 1.5 Properties of Ionic and Covalent Compounds Properties Ionic compound Covalent compound Physical State All ionic compounds (for Covalent compounds may be example, NaCl, KCl, and solids (glucose), liquids NaNO3) are solids at (water, ethanol), or gases room (carbon dioxide, methane). Melting and Boiling Ionic compounds have higher melting points and boiling Points points than covalent compounds. Structure of Ionic solids are Covalent solids may either be Compounds in the crystalline, characterized crystalline or have no regular by a regular structure, structure. In the latter case, Solid State they are said to be amorphous Solutions of Ionic When ionic compounds When covalent compounds and Covalent dissolve in water, the ions dissolve in water, the dissociate and the solution compound does not Compounds conducts electricity. dissociate. They are These compounds are nonelectrolytes. electrolytes. 1.6 The Chemistry of Carbon  Organic chemistry is the study of carbon-containing compounds.  All organic compounds are classified as hydrocarbons or substituted hydrocarbons. 2025-2024 5 Mustansiriyah University College of Medicine Chemistry and Biochemistry Department Medical Chemistry (Organic) / Lecturer. Dr. Tamara Sami Naji  Hydrocarbons contain only carbon and hydrogen atoms and may be aliphatic (alkanes, alkenes, and alkynes) or aromatic (containing a benzene ring).  Aliphatic hydrocarbons may be saturated (only C—C and C—H single bonds) or unsaturated (at least one C=C double or triple bond). 1. Alkanes  Alkanes are saturated hydrocarbons with the general formula CnH2n+2.  Alkanes are nonpolar, water-insoluble, and have low melting and boiling points.........(Molecular formulas) Structural formulas  Two organic molecules with the same molecular formula but different bonding patterns have different physical and chemical properties. Such molecules are structural or constitutional (Isomers). 2025-2024 6 Mustansiriyah University College of Medicine Chemistry and Biochemistry Department Medical Chemistry (Organic) / Lecturer. Dr. Tamara Sami Naji  Cycloalkanes are organic molecules having C—C single bonds in a ring structure. 2. Alkenes and Alkynes  Alkenes and alkynes are unsaturated hydrocarbons because they have at least one C=C double bond (alkenes) or triple bond (alkynes). Alkenes have the general formula CnH2n and alkynes have the general formula CnH2n- 2. 2025-2024 7