Structure of Atoms & Molecules PDF

# ATOMS ## 1. STRUCTURE OF ATOMS, MOLECULES AND CHEMICAL BONDS Atoms (C, H or O) are the building blocks of all matter (examples: O2, H2O, C6H12O6 etc). The term "atom" comes from the Greek word for uncuttable, because the atoms were the smallest things [100 picometers (10-12m)] in the universe an...

# ATOMS ## 1. STRUCTURE OF ATOMS, MOLECULES AND CHEMICAL BONDS Atoms (C, H or O) are the building blocks of all matter (examples: O2, H2O, C6H12O6 etc). The term "atom" comes from the Greek word for uncuttable, because the atoms were the smallest things [100 picometers (10-12m)] in the universe and could not be divided. ### 1.1 STRUCTURE #### a. Subatomic Particles We now know that atoms are made up of three subatomicparticles: - **Protons** - with a positive electrical charge, - **Neutrons** – with a neutral or no charge and - **Electrons** -with a negative charge. #### b. Nucleus An atom is composed of a positively-charged nucleus, with a cloud of negatively-charged electronssurrounding it, bound together by electrostatic force. Almost all of the mass of an atom is located in the nucleus, with a very small contribution from the electron cloud. Protons and neutrons are bound together to form a nucleus by the nuclear force. The number of positively charged protons = the number of negatively charged electrons → the atom is electrically neutral. #### c. Stable and Unstable Atoms The number of protons = the number of neutrons → the atom is stable. The number of protons < (less than) the number of neutrons → the atom is unstable (become (radioactive). The nucleus of such an unstable atom [iosotope] will try to become stable by giving off particles or packets of energy. These emissions are called radioactivity. ## 1.2 PROPERTIES #### a. Atomic Number (Z) | | | | |----|-----|------| | atomic number | 6 | 12.011 | | symbol | C | | | electron configuration | [He]2s22p2 | | | name | carbon | | In the modern periodic table, the elements are listed in order of increasing atomic number. The atomic number is the number of protons in the nucleus of an atom. The number of protons define the identityof an element (i.e., an element with 6 protons is a carbon atom, no matter how many neutrons may be present). The number of protons determines how many electrons surround the nucleus, and it is the arrangement of these electrons that determines most of the chemical behavior of an element. In a periodic table arranged in order of increasing atomic number, elements having similar chemical properties naturally line up in the same column (group). | | | | |------|------|------| | $^{12}$C | $^{13}$C | $^{14}$C | | | | | | 6 | 6 | 6 | An element is a substance that is made entirely from one type of atom. For example, the element Carbon is made from stable atoms containing just 6 protons and 6 electrons (12C). The 13C and 14C isotopes of Carbon element have the same number of protons, but can have different numbers of neutrons. #### b. Atomic Mass (A) The atomic mass of an atom is equal to the sum of the masses of its protons and neutrons. The mass of atoms and subatomic particles is measured in units called daltons (1.66 x 10-27 kg). A proton weighs approximately 1.009 daltons, as does a neutron (1.007 daltons). In contrast, electrons weigh only 1/1840 of a dalton, so their contribution to the overall mass of an atom is negligible. #### c. Ions Electrons always maintained in their orbits by their attraction to the positively charged nucleus. This attraction sometimes overcome by other forces and an atom can loseor gain one or more additional electrons. Atoms in which the number of electrons does not equal the number of protons are known as (ions and they carry a net electrical charge. An atom that has more protons than electrons has a net positive charge and is called a cation. For example, an atom of sodium (Na) that has lost one electron becomes a sodium ion (Na+), with a charge of +1. An atom that has fewer protons than electrons carries a net negative charge and is called an anion. A chlorine atom (Cl) that has gained one electron becomes a chloride ion (Cl-), with a charge of -1. #### d. Levels, Sublevels and Orbitals Electrons exist around the nucleus of an atom in discrete, specific orbits. These orbits are called levels and we number them 1, 2, 3, 4, and so forth with the 1st level being the orbit closest to the nucleus. The levels can be broken down into sublevels (s, p, d, and f). Level one has one sublevel - s. Level 2 has 2 sublevels - s and p. Level 3 has 3 sublevels - s, p, and d. Level 4 has 4 sublevels - s, p, d, and f. The sublevels contain orbitals. Orbitals are spaces that have a high probability of containing an electron. In other words, an orbital is an area where the electrons live. There can be two electrons in one orbital maximum. The s sublevel has just one orbital, so can contain 2 electrons max. The p sublevel has 3 orbitals, so can contain 6 electrons max. The d sublevel has 5 orbitals, so can contain 10 electrons max. And the 4 sublevel has 7 orbitals, so can contain 14 electrons max. In the picture, the orbitals are represented by the boxes. You can put two electrons in each box. Some things to notice. Level 1 does not have a p or d or f sublevel, only an s sublevel. So there is no such thing as 1p or 1d or 1f. To distinguish between the different s sublevels, we call them 1s, 2s, 3s, and 4s. The p sublevels are called 2p, 3p, and 4p. There is no d sublevel until the 3rd level. The d sublevels are called 3d and 4d. The only f sublevel we study is the 4f. #### e. Atomic Energy Levels The number of energy states an electron can occupy around a nucleus and different states of the same energy are known as 'shells'. The electrons of an atom belong to different shells (K, L, M and N) characterised by their energies. The K shell, which feels the strongest attraction from the nucleus, is the first to fill up completely. Two electrons at most can fill this layer, and an atom's third electron would have to go into the 2nd L shell. Electrons in the outer shells are more weakly attracted to the nucleus. When an electron absorbs energy, it moves to higher energy levels farther from the nucleus. When an electron releases energy, it falls to lower energy levels closer to the nucleus. # 2. ELEMENTS Elements consist of only one kind of atom and cannot be decomposed into simpler substances. Our planet is made up of some 90 elements. The most abundant elements are oxygen (60.4%), silicon (20.4%) and aluminum (6.3%), followed by hydrogen (2.9%), sodium (2.6%), calcium (1.9%), iron (1.9%), magnesium (1.8%), potassium (1.4%), and titanium (0.2%). These ten elements comprise 99.8% of the lithosphere. # 3. MOLECULES & CHEMICAL BONDS Though the periodic table has only 118 or more elements, there are obviously more substances in nature than 118 pure elements. This is because atoms can react with one another to form new substances called molecules, which are formed by the joining of two or more atoms. The two important chemical bonds are: - covalent bond(strong) and - noncovalentinteractions(weak). ## 3.1 COVALENT BONDS Covalent bonds involve the sharing of a pair of electrons by two atoms. Such bonds lead to stable molecules if they share electrons in such a way as to create a noble gas configuration for each atom and satisfy the Octet Rule. For example H2 gas forms the simplest covalent bond in the diatomic hydrogen molecule. The halogens such as Cl2 also exist as diatomic gases by forming covalent bonds. The nitrogen and oxygen which makes up the bulk of the atmosphere also exhibits covalent bonding in forming diatomic molecules. Examples of Covalent Bonds: Single (H2, F2and I₂), double(O2, CO2 and H2CO) and triple (C₂H₂ and N₂) covalent bonds. The covalent bond dissociation energies are typically between 150-400 kJ/mol for single bonds. Types of Covalent Bonds: There are 2 types of covalent bonds: polar and nonpolar. In a polar covalent bond, the electrons are unequally shared by the atoms and are attracted more to one nucleus than the other. Because of the unequal distribution of electrons between the atoms of different elements, a slightly positive (8+) or slightly negative (8-) charge develops. This partial charge is an important property of water and accounts for many of its characteristics. Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge. Oxygen is highly electrophilic (electron loving). Even though oxygen in water is bound to each of the hydrogens by a covalent bond (due to sharing of electrons), the oxygen "pulls" the shared electrons closer to itself. This unequal sharing of the electrons in the O-H bond causes the hydrogens to have a partial positive charge (positive dipole), and the oxygen has a partial negative charge (negative dipole). Jonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. or example, molecular O₂ is nonpolar because the electrons will be equally distributed between the two oxygen atoms. nother example is methane (CH4). Carbon has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one, making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same electronegativity but are similar; thus, nonpolar bonds form. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent molecule. ## Covalent Bonds in Biomolecules hese bonds are stronger and much more common than ionic bonds in the molecules of living organisms. he phosphodiester bond [-O-P-, in nucleic acids, 419 kJ/mole], peptide bond [-C-N-, in proteins, 293 kJ/mole]and glycosidic ond [-O-N-, in polysaccharides, 352 kJ/mole], are important covalent bonds in biological systems. he disulfide bond between two cysteine residues in protein is also covalent bond. More disulfide bonds in proteins give more thermo-stability. or non covalent interactions, please refer 1C.