Atoms can interact to form molecules by

Formation of sodium fluoride : The transfer of electrons and subsequent attraction of oppositely charged ions. To determine the chemical formulas of ionic compounds, the following two conditions must be satisfied:.

This is because Mg has two valence electrons and it would like to get rid of those two ions to obey the octet rule. Fluorine has seven valence electrons and usually forms the F — ion because it gains one electron to satisfy the octet rule. Therefore, the formula of the compound is MgF 2. The subscript two indicates that there are two fluorines that are ionically bonded to magnesium. On the macroscopic scale, ionic compounds form crystalline lattice structures that are characterized by high melting and boiling points and good electrical conductivity when melted or solubilized.

Fluorine has seven valence electrons and as such, usually forms the F — ion because it gains one electron to satisfy the octet rule. Covalent bonds are a class of chemical bonds where valence electrons are shared between two atoms, typically two nonmetals. The formation of a covalent bond allows the nonmetals to obey the octet rule and thus become more stable. For example:. Covalent bonding requires a specific orientation between atoms in order to achieve the overlap between bonding orbitals.

Sigma bonds are the strongest type of covalent interaction and are formed via the overlap of atomic orbitals along the orbital axis. The overlapped orbitals allow the shared electrons to move freely between atoms. Pi bonds are a weaker type of covalent interactions and result from the overlap of two lobes of the interacting atomic orbitals above and below the orbital axis. Unlike an ionic bond, a covalent bond is stronger between two atoms with similar electronegativity.

For atoms with equal electronegativity, the bond between them will be a non- polar covalent interaction. In non-polar covalent bonds, the electrons are equally shared between the two atoms. For atoms with differing electronegativity, the bond will be a polar covalent interaction, where the electrons will not be shared equally. Ionic solids are generally characterized by high melting and boiling points along with brittle, crystalline structures.

Covalent compounds, on the other hand, have lower melting and boiling points. Unlike ionic compounds, they are often not soluble in water and do not conduct electricity when solubilized. Privacy Policy. Carbon, the most common isotope of carbon, contains six protons and six neutrons. Therefore, it has a mass number of 12 six protons and six neutrons and an atomic number of 6 which makes it carbon. Carbon contains six protons and eight neutrons. Therefore, it has a mass number of 14 six protons and eight neutrons and an atomic number of 6, meaning it is still the element carbon.

These two alternate forms of carbon are isotopes. Some isotopes are unstable and will lose protons, other subatomic particles, or energy to form more stable elements. These are called radioactive isotopes or radioisotopes. Carbon 14 C is a naturally occurring radioisotope that is created in the atmosphere by cosmic rays.

This is a continuous process, so more 14 C is always being created. As a living organism develops, the relative level of 14 C in its body is equal to the concentration of 14 C in the atmosphere. When an organism dies, it is no longer ingesting 14 C, so the ratio will decline. After approximately 5, years, only one-half of the starting concentration of 14 C will have been converted to 14 N.

The time it takes for half of the original concentration of an isotope to decay to its more stable form is called its half-life.

Because the half-life of 14 C is long, it is used to age formerly living objects, such as fossils. Using the ratio of the 14 C concentration found in an object to the amount of 14 C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined.

Based on this amount, the age of the fossil can be calculated to about 50, years. Isotopes with longer half-lives, such as potassium, are used to calculate the ages of older fossils. Through the use of carbon dating, scientists can reconstruct the ecology and biogeography of organisms living within the past 50, years.

To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this site and run the simulation. How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus. The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be filled.

Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons; therefore, it can completely fill the lowest shell with its two electrons.

If you look at the periodic table, you will see that hydrogen and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and helium are the only two elements that have the lowest shell and no other shells.

The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in each pair is filled with an electron before any pairs are completed. Looking at the periodic table again, you will notice that there are seven rows. These rows correspond to the number of shells that the elements within that row have.

The elements within a particular row have increasing numbers of electrons as the columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled with electrons.

If you look at the second row of the periodic table, you will find lithium Li , beryllium Be , boron B , carbon C , nitrogen N , oxygen O , fluorine F , and neon Ne.

These all have electrons that occupy only the first and second shells. Lithium has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled with eight electrons, as is the case with neon.

Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical bonds , or interactions between two or more of the same or different elements that result in the formation of molecules.

To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom.

Because the outermost shells of the elements with low atomic numbers up to calcium, with atomic number 20 can hold eight electrons, this is referred to as the octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule. Atoms with a positive charge will be attracted to negatively charged atoms to form a molecule.

This bonding between atoms is the key to how molecules interact with each other. The positioning of atoms in a molecule may give it polarity. If two positively charged atoms are near each other in a molecule, that area may carry a slighty positive charge, while elsewhere the charge may be slightly negative. H 2 O is one of the most common molecules we encounter, and the position of the positively charged hydrogen atoms is critical in how it changes state, from solid as ice to liquid to gas as steam.

Fizzy drinks are carbonated, an example of a chemical reaction between carbon dioxide and water that only occurs under pressure. We invite you to discuss this subject, but remember this is a public forum. Please be polite, and avoid your passions turning into contempt for others.

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If you enjoyed this, why not follow a feed to find out when we have new things like it? Choose an RSS feed from the list below. Don't know what to do with RSS feeds? 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. The tendency of any atom to pull electrons towards itself, and away from other atoms, is characterized by a quantity called electronegativity.

Fluorine is the most electronegative atom 4. In general, electronegativity increases with nuclear charge while holding number of core electrons constant i. Electronegativity increases as nuclear shielding decreases from bottom to top in a column of the periodic table. Partial Charges. A greater difference in the electronegativities of two bonded atoms causes the bond between them to be more polar, and the partial charges on the atoms to be larger in magnitude.

In biological systems, oxygen is generally the most electronegative atom, carrying the largest partial negative charge. In methanol CH 3 OH , the electronegative oxygen atom pulls electron density away from the carbon and hydrogen atoms.

In water H 2 O , the electronegative oxygen atom pulls electron density away from both hydrogen atoms. The oxygen atom of water carries a partial negative charge. The hydrogen atoms carry partial positive charges. This phenomena of charge separation is called polarity. Methanol and water are polar molecules. N 2 is a non-polar molecule because the two nitrogen atoms have equal electronegativities and so they share electrons equally.

Hydrocarbon CH 3 CH CH 2 CH 3 is non-polar because the electronegativies of carbon and hydrogen are similar. Dipole moments. A dipole moment is determined by the magnitudes of the partial charges and by the distances between them. To quantitate dipole moments, charges are expressed in esu's and distances in centimeters. The dipole moment of water is 1. The orientation of the dipole moment of a peptide is approximately parallel to the N-H bond and is around 3.

The large dipole moment of a peptide bond should lead one to expect that dipolar interactions are important in protein conformation and interactions. They are. A dipole is surrounded by an electric field, which causes force-at-a-distance on nearby charged and partially charged species. Dipoles also interact with other dipoles Dipole-Dipole Interactions , and induce charge redistribution polarization in surrounding molecules Dipole-Induced Dipole Interactions. We will discuss each of these interactions separately in the sections below.

Two dipoles feel each other at a distance. The positive end of the first dipole is attracted to the negative end of the second dipole and is repelled by positive end. The strength of a dipole-dipole interaction depends on the size of both dipoles and on their proximity and orientations.

The net interaction energy between two dipoles can be either positive or negative. Parallel end to end dipoles attract while antiparallel end to end dipoles repel.

In liquids the orientations of molecular dipoles change rapidly as molecules tumble about. However, dipole moments tend to orient favorably. Therefore, in liquid acetone for example, favorable dipole-dipole interactions outweigh unfavorable dipole-dipole interactions. A polarizable molecule tumbling in a solution of polar molecules is like a wind sock buffeted by shifting winds.

The electron density of a polarizable molecule is shifted and deformed by the electric fields of the surrounding polar molecules. Any molecule with a dipole moment or any ion is surrounded by an electrostatic field. This electrostatic field shifts the electron density alters the dipole moments nearby molecules. A change in the dipole moment of one molecule by another or by any external electric field is called polarization. The ease with which electron density is shifted by an electronic field is called polarizability.

Large atoms like xenon are more polarizable than small atoms like helium. Dipole-induced dipole interactions are important even between molecules with permanent dipoles. A permanent dipole is perturbed by an adjacent dipole. For example, in liquid water where molecules are close together , all water molecules are polarized. The permanent dipole of each water molecule polarizes all adjacent water molecules. The dipole of a water molecule induces change in the dipoles of all nearby water molecule.

Dipole-induced dipole interactions are always attractive and can contribute as much as 0. The resulting interactions, called charge-induced dipole interactions or ion-induced dipole interactions. These interactions are important, for example in protein structure, but are not broken out into a separate section in this document.

A molecule with a permanent dipole can interact favorably with cations and anions. This type of interaction is called a charge-dipole or ion-dipole interaction. Charge-dipole interactions are why sodium chloride, composed cationic sodium ions and anionic chloride ions, and other salts tend to interact well with water, and are very soluble in water, which has a strong dipole. Fluctuating dipolar interactions Dispersive interactions, London Forces. We can see resonance all around us.

A child on a swing, the tides in the Bay of Fundy and the strings on a violin all illustrate the natural resonant frequencies of physical systems. The Tacoma Narrows Bridge is one of the most famous examples of resonance. Molecules resonate too. Electrons, even in a spherical atom like Helium or Xenon, fluctuate over time according to the natural resonant frequency of that atom.

Even though chemists describe atoms like Helium and Xenon as spherical, if you could take a truly instantaneous snapshot of a spherical atom, you would always catch it in a transient non-spherical state.

Xenon is spherical on average, but not at any instantaneous timepoint. As electron density fluctuates, dipole moments also fluctuate. Therefore, all molecules and atoms contain oscillating dipoles.

In all molecules that are close together in any liquid or a solid, but not in a perfect gas the oscillating dipoles sense each other and couple. They oscillate in synchrony, like the strings of a violin. The movements of electrons in adjacent molecules are correlated.

Electrons in one molecule tend to flee those in the next, because of electrostatic repulsion. Coupled fluctuating dipoles experience favorable electrostatic interaction known as dispersive interactions. Dispersive interactions are always attractive and occur between any pair of molecules or non-bonded atoms , polar or non-polar, that are nearby to each other.

Dispersive interactions increase with polarizability, which explains the trend of increasing boiling points i. Dispersive interactions are the only attractive forces between atoms in these liquids. Without dispersive interactions there would be no liquid state for the Nobles. Dispersive interactions are especially strong for aromatic systems, which are very polarizable.

The total number of pairwise atom-atom dispersive interactions within a folded protein is enormous, so that dispersive interactions can make large contributions to stability. The strength of this interaction is related to polarizability. Tryptophan, tyrosine, phenylalanine and histidine are the most polarizable amino acid sidechains, and form the strongest dipsersive interactions in proteins. What about water? Even molecules with permanant dipoles, like water, experience dispersive interactions.

The table on the left shows gas phase interaction enthalpies, which are on the same order as the hydration enthalpies for these cations. Electron withdrawing groups on the ring system weaken cation interactions while electron donating groups strengthen them. Tryptophan and arginine can form extended coplaner assemblies. Hydrogen Bonding. The idea that a single hydrogen atom could interact simultaneously with two other atoms was proposed in by Latimer and Rodebush and their advisor, G.

Maurice Huggins, who was also a student in Lewis' lab, describes the hydrogen bond in his dissertation. A hydrogen bond is a favorable interaction between an atom with a basic lone pair of electrons a Lewis Base and a hydrogen atom that has been partially stripped of its electrons because it is covalently bound to an electronegative atom N, O, or S. In a hydrogen bond, the Lewis Base is the hydrogen bond acceptor A and the partially exposed proton is bound to the hydrogen bond donor H-D.

Why hydrogen? Hydrogen is special because it is the only atom that i forms covalent sigma bonds with electronegative atoms like N, O and S, and ii uses the inner shell 1S electron s in that covalent bond. When its electronegative bonding partner pulls the bonding electrons away from hydrogen, the hydrogen nucleus a proton is exposed on the back side distal from the bonding partner.

The unshielded face of the proton is exposed, attracting the partial negative charge of an electron lone pair. Hydrogen is the only atom that exposes its nucleus this way.

Other atoms have inner shell non-bonding electrons that shield the nucleus. However, the strength of a hydrogen bond correlates well with the acidity of donor H-D and the basicity of acceptor A.

The H-D bond remains intact. The most common hydrogen bonds in biological systems involve oxygen and nitrogen atoms as A and D. In traversing the Period Table, increasing the electronegativity of atom D strips electron density from the proton in H-D , increasing its partial positive charge, and increasing the strength of any hydrogen bond. Thiols -SH can can both donate and accept hydrogen bonds but these are generally weak, because sulfur is not sufficiently electronegative.

Hydrogen bonds involving carbon, where H-D equals H-C, are observed, although these are weak and infrequent. C is insufficiently electronegative to form good hydrogen bonds.

Hydrogen bonds are essentially electrostatic in nature, although the energy can be decomposed into additional contributions from polarization, exchange repulsion, charge transfer, and mixing.

Hydrogen bond strengths form a continuum. A hydrogen bond is not a bond. It is a molecular interaction a non-bonding interaction. The unfortunate name given to this molecular interaction long ago has caused and will continue to cause all kinds of confusion. Do not confuse hydrogen bonds with real bonds.

They are not the same thing at all. The geometry of a hydrogen bond can be described by three quantities, the D to H distance, the H to A distance, and the D to H to A angle. The distances depend on the atom types of A and D. Two-center hydrogen bonds are generally shorter, more linear, and stronger than three- or four-center hydrogen bonds. Three-center bonds are sometimes called bifurcated while four centered hydrogen bonds are sometimes called trifurcated.

Hydrogen atoms are not observable by x-ray crystallography as applied to proteins and nucleic acids. So a geometric description of hydrogen bonding that is dependent on the hydrogen position is not always practical. In these cases one is usually limited to analysis of the D to A distance. It is common to ascribe a hydrogen bond if a distance between A and D is less than the sum of their van der Waal radii.

However this limit is probably too conservative. The best criteria for an H-bond is a distance of less than 3. In biological systems, hydrogen bonds are frequently cooperative and are stabilized by resonance involving multiple hydrogen bonds. In systems with multiple hydrogen bonds, the strength of one hydrogen bond is increased by a adjacent hydrogen bond. For example in the hydrogen-bonded systems below the acetic acid dimer , the top hydrogen bond increases both the acidity of the hydrogen, and the basicity of the oxygen in the bottom hydrogen bond.

Each hydrogen bond makes the other stronger than it would be in isolation. Cooperativity of hydrogen bonding is observed in base pairing and in folded proteins. Water, the most abundant compound on the surface of the Earth and probably in the universe, is the medium of biology. Water is also the most frequent chemical actor in biochemistry. Between a third and a half of known biochemical reactions involve consumption or production of water.

In a cell, a given water molecule frequently and repeatedly serves as a reaction substrate, intermediate, cofactor, and product. Essentially all biological molecules, large and small, are products of or substrates for biochemical reactions that chemically transform water.

Water is never absent from or physically separated from biological macromolecules, organic cofactors, and metals, but readily combines with, withdraws from, and intercedes in their transformations.

In biological systems, water is fully integrated into processes of bond making and bond breaking. For biological water, there is no meaningful distinction between medium and chemical participant.

The use of water as a metabolite is seen in biopolymer formation. All biopolymers are formed by condensation dehydration reactions, which link small building blocks and chemically produce water shown here.

Specifically, a peptide bond in a protein is formed by condensation of amino acids. In the net reaction, two amino acids join together and produce one water molecule to form a peptide bond. Water is a product in the chemical reaction of peptide bond formation. In the reverse reactions, biopolymers are degraded by hydrolysis reactions, which chemically consume water. Water is a reactant in the chemical reaction of peptide bond breaking.

Triglycerides and phospholipids are formed by condensation of glycerol with fatty acids and other molecules. Cellulose, the most abundant polymer in the biosphere, is formed by condensation of glucose.

In sum: Water is the medium of biology the solvent and is fully integrated into the most basic and universal chemical reactions of biology. Stay hydrated. Water is intrinsically self-complementary. In liquid or solid water, all the atoms of every water molecule, utilizing the entire surface of the molecule, engage in ideal hydrogen bonding interactions with surrounding water molecules.

All the HB donor and acceptor sites of any water molecule find perfect geometric matches in the HB donors and acceptors of surrounding water molecules.

Liquid and solid water have the highest density of ideal hydrogen bonds per volume of any material. In condensed phases liquid or solid of water, the hydrogen bonding groups of each water molecule are complementary to the hydrogen bonding groups of the watery surroundings. Water has a balanced number of hydrogen bond donors and acceptors two of each.

In condensed phases, every water molecule acts as a donor in two hydrogen bonds and an acceptor in two hydrogen bonds, each with ideal geometry. The self-complementarity of water is emergent on the condensed phase. Isolated or small clusters of water molecules do participate in self-complementary interactions.

Strong self-complementary forces between water molecules cause very high melting temperature, boiling temperature, heat of vaporization, heat of fusion and surface tension. Water puffs up increases volume when it freezes; Ice floats.

Water is a powerful solvent for ions and polar substances and is a poor solvent for non-polar substances. Water causes certain amphipathic molecules with both polar and non-polar functionalities to spontaneously form compartments. In water, membranes assemble and proteins fold.

Water has a unique ability to shield charged species from each other. Electrostatic interactions between ions are highly attenuated in water. The electrostatic force between two ions in solution is inversely proportional to the dielectric constant of the solvent.

The dielectric constant of water It is over twice that of methanol Water is a good solvent for salts because the attractive forces between cations and anions are minimized by water.

A water molecule H 2 O can form strong hydrogen bonds, with either hydrogen bond donors or acceptors. Figure 22 illustrates hydrogen bonding between two water molecules.

The hydrogen bonds are short, linear and strong.