File Name: molecular forces and chemical bonding in polymers .zip
Table of Contents Structure Williams Home. Molecular interactions are attractive or repulsive forces between molecules and between non-bonded atoms. Molecular interactions are important in all aspects of chemistry, biochemistry and biophysics, including protein folding, drug design, pathogen detection, material science, sensors, gecko feet, nanotechnology, separations, and origins of life.
Molecular interactions are also known as noncovalent interactions, intermolecular interactions and non-bonding interactions. Non-Bonding Interactions.
Molecular Interactions are between molecules, or between atoms that are not linked by bonds. Molecular interactions include cohesive attraction between like , adhesive attraction between unlike and repulsive forces between molecules. Molecular interactions change and bonds remain intact when a ice melts, b water boils, c carbon dioxide sublimes, d proteins unfold, e RNA unfolds, f DNA strands separate and g membranes disassemble. Bonding Interactions.
Bonds hold atoms together within molecules. A molecule is a group of atoms that associates strongly enough that it does not dissociate or lose structure when it interacts with its environment. At room temperature two nitrogen atoms can be bonded N 2. Bonds break and form during chemical reactions. In the chemical reaction called fire, bonds of cellulose break while bonds of carbon dioxide and water form. Boiling Points.
When a molecule transitions from the liquid to the gas phase as during boiling , ideally all molecular interactions are disrupted. Ideal gases are the ONLY systems where there are no molecular interactions. Differences in boiling temperatures give good qualitative indications of strengths of molecular interactions in the liquid phase. High boiling liquids have strong molecular interactions. The boiling point of H 2 O is hundreds of degrees greater than the boiling point of N 2 because of stronger molecular interactions in H 2 O liq than in N 2 liq.
The forces between molecules in H 2 O liq are greater than those in N 2 liq. Native states. In biological systems i proteins fold into globular structures called native states, ii ribosomal and transfer RNAs also fold into native globular structures, iii single strands of DNA anneal to form double stranded helices, iv phospholipids form bilayers, and v proteins assemble with bilayers to form membranes , or with DNA, RNA, or with other proteins.
These native states and assemblies are stabilized by molecular interactions of enormous number and complexity. Denatured states. When you unfold a protein or an RNA denature them or separate two strands of DNA melt it , or disassemble and melt the ribosome, then interior regions become exposed to the surroundings, which are mostly water plus ions. Molecular interactions within the native state or assembly are replaced by molecular interactions with aqueous surroundings. Monster truck tug-of-war.
Biological molecules in general are pushed by powerful forces in opposing directions. When you think about the stability of a folded state or an assembled state , always remember that molecular interactions stabilize both the folded state and the random coil and the disassembled state.
Huge numbers of intramolecular interactions within a protein native state are opposed by huge numbers of intermolecular interactions in the denatured state, with surrounding water molecules, ions, etc. On balance, native biological macromolecules and assemblies are marginally stable, near the tipping point. A small perturbation can change the balance from folded state to unfolded state.
A small change in pH or temperature or a single mutation can unfold a protein. Have you ever denatured a protein converted it from the native state to denatured state? You are not breaking bonds when you boil an egg - you are changing and rearranging molecular interactions. The aggregated protein forms large assemblies that scatter light, giving the egg a white appearance.
When you add lemon juice to milk, the pH drops and the proteins denature and aggregate. Have you ever melted DNA? Yes, if you have run a PCR reaction. Sadly for students, and practicing scientists too, the nomenclature is a mess. Molecular interactions, as noted above, are also known as noncovalent or intermolecular or non-bonding or van der Waals interactions.
He noticed that molecules take space and are sticky, like wet jelly beans. The term, 'van der Waals interaction' should be avoided because its modern definitions are so inconsistent and arbitrary that it is effectively meaningless, and because it does not describe interactions in a physically meaningful way.
Terms including 'van der Waals surface' and 'van der Waals radius' are well-defined and are useful see below. All molecular interactions are fundamentally electrostatic in nature and can be described by some variation of Coulombs Law. However, we reserve the term 'electrostatic interaction' to describe interactions between charged species ions. Interactions between partial charges are given other names.
There are many different ways of parsing or classifying molecular interactions. The categories in the Table of Contents are used here because they are the clearest and easiest to understand and are broadly used in the literature. The Lennard-Jones potential is an empirical description of molecular interactions. However, the L-J potential does not account for all molecular interactions. Electrostatic interactions are not included in the L-J potential.
Atoms take space. Force two atoms together and they will push back. When two atoms are close together, the occupied orbitals on the atom surfaces overlap, causing electrostatic repulsion between surface electrons.
This repulsive force between atoms acts over a very short range, but is very large when distances are short. Because this repulsion rises so sharply as distance decreases it is often useful to pretend that atoms are hard spheres, like very small pool balls, with hard surfaces called van der Waals surfaces and well-defined radii called van der Waals radii.
As two atoms approach each other their van der Waals surfaces make contact when the distance between them equals the sum of their van der Waals radii. At this distance the repulsive energy skyrockets. The smallest distance between two non-bonded atoms is the sum of the van der Waals radii of the two atoms. A sulfur atom and a carbon atom can come no closer together than:. Of course we are assuming here that bonds do not form. When two atoms form a bond, they come very close together and their der Waals radii and surfaces are violated.
Short range repulsion is important to you. Very high gravity, as on neutron stars, overwhelms short range repulsion and causes atoms to collapse. Here in earth, with our modest gravity, the van der Waals radius of carbon r C is evident from the spacing between the layers in graphite. The atoms within a graphite layer are covalently linked bonded , which causes interpenetration of van der Waals surfaces. Carbon atoms within a layer are separated by 1.
As explained in other sections of this document vdw surfaces are also violated when molecules form hydrogen bonds. The coordinates of graphite are here [coordinates]. Electrostatic interactions are between and among cations and anions, species with charge of Electrostatic interactions can be either attractive or repulsive, depending on the signs of the charges.
Like charges repel. Unlike charges attract. Favorable electrostatic interactions cause the vapor pressure of sodium chloride and other salts to be very low. A very very long time; electrostatic interactions are very very strong.
The electrostatic interactions within a sodium chloride crystal are called ionic bonds. But when a single cation and a single anion are close together, within a protein, or within a folded RNA, those interactions are considered to be non-covalent electrostatic interactions.
Non-covalent electrostatic interactions can be strong, and act at long range. As explained later in this document, electrostatic interactions are highly attenuated dampened by water. Favorable electrostatic interactions between paired anionic and cationic amino acid sidechains are reasonably frequent in proteins. Ion Pairs, sometimes called Salt Bridges, are formed when the charged group of a cationic amino acid like lysine or arginine is around 3.
The charged groups in an ion pair are generally linked by hydrogen bonds, in addition to electrostatic interactions. It reflects the tendency of the medium to shield charged species from each other.
Water is very efficient at shielding charges, reducing electrostatic forces between ions. The problem of calculating electrostatic effects in biological systems is complex in part because of non-uniformity of the dielectric environment. The dielectric micro-environments are complex and variable, with less shielding of charges in regions of hydrocarbon sidechains and greater shielding in regions of polar sidechains. The electrostatic energy is given by:. One can crudely estimate the energetics of a charge-charge interaction in a protein.
This rough approximation is around fold greater than the values determined experimentally. A note on nomenclature. Species with charge We use other terms dipole-dipole The naming scheme is confusing because ALL molecular interactions are between electrons and electrons and between electrons and nuclei, and are actually electrostatic in nature.
It might have been better to use different names that make more sense. However, by convention we have to restrict the term electrostatic to interactions between charged species. Before you can understand dipolar interactions, you have to know about electronegativity.
Electrons are not shared equally in a molecule with unlike atoms.
Molecules cohere even though their ability to form chemical bonds has been satisfied. The evidence for the existence of these weak intermolecular forces is the fact that gases can be liquefied, that ordinary liquids exist and need a considerable input of energy for vaporization to a gas of independent molecules, and that many molecular compounds occur as solids. The role of weak intermolecular forces in the properties of gases was first examined theoretically by the Dutch scientist Johannes van der Waals , and the term van der Waals forces is used synonymously with intermolecular forces. Under certain conditions, weakly bonded clusters of molecules such as an argon atom in association with a hydrogen chloride molecule can exist; such delicately bonded species are called van der Waals molecules. There are many types of intermolecular forces; the repulsive force and four varieties of attractive force are discussed here. In general, the energy of interaction varies with distance, as shown by the graph in Figure Attractive forces dominate to the distance at which the two molecules come into contact, then strong repulsive forces come into play and the potential energy of two molecules rises abruptly.
Molecular forces & chemical bonding in polymers. Lecture Note-1 If a n molecules of a monomer units, they form a polymer. MONOMER.
When many molecules of a simple compound join together, the product is termed a polymer and the process polymerization. The simple compounds whose molecules join together to form the polymers are called monomers. The polymer is a chain of atoms, providing a backbone, to which atoms or groups of atoms are joined. This unit provides an overview of the main types of polymers characterised by how they are made, how their structures govern their general properties and how these properties can be refined by their formulation using a range of additives.
Intramolecular bonds are the bonds that hold atoms to atoms and make compounds. There are 3 types of intramolecular bonds: covalent, ionic, and metallic. Ionic Bond: a bond that holds atoms together in a compound; the electrostatic attraction between charged ions. Ionic compounds are formed between atoms that differ significantly in electronegativity.
In molecular physics , the Van der Waals force , named after Dutch physicist Johannes Diderik van der Waals , is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds , these attractions do not result from a chemical electronic bond; they are comparatively weak and therefore more susceptible to disturbance. The Van der Waals force quickly vanishes at longer distances between interacting molecules. Van der Waals force plays a fundamental role in fields as diverse as supramolecular chemistry , structural biology , polymer science , nanotechnology , surface science , and condensed matter physics. It also underlies many properties of organic compounds and molecular solids , including their solubility in polar and non-polar media. If no other force is present, the distance between atoms at which the force becomes repulsive rather than attractive as the atoms approach one another is called the Van der Waals contact distance ; this phenomenon results from the mutual repulsion between the atoms' electron clouds.
Table of Contents Structure Williams Home. Molecular interactions are attractive or repulsive forces between molecules and between non-bonded atoms. Molecular interactions are important in all aspects of chemistry, biochemistry and biophysics, including protein folding, drug design, pathogen detection, material science, sensors, gecko feet, nanotechnology, separations, and origins of life. Molecular interactions are also known as noncovalent interactions, intermolecular interactions and non-bonding interactions. Non-Bonding Interactions. Molecular Interactions are between molecules, or between atoms that are not linked by bonds.
Carbon forms a huge variety of both synthetic and natural molecules. A 'family' of organic compounds with the same functional group is called a homologous series. The properties of organic molecules depend on their structure being made of simple molecules. The atoms in an individual molecule are joined together by strong covalent bonds. The intermolecular forces between molecules are weaker. The intermolecular forces vary between molecules, so different organic compounds have different melting points and boiling points. Simple molecular substances have no overall charge, and their electrons are not free to move.
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