Molecular Structure

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Using the protein nomenclature, we could speak in terms of primary, secondary, tertiary and quaternary structures of the molecule:. Deoxyribose, which is a cyclic pentose 5-carbon sugar. Note: the sugar in RNA is a ribose. Carbons in the sugar are noted from 1' to 5'. A nitrogen atom from the nitrogenous base links to C1' glycosidic link , and the phosphate links to C5' ester link to make the nucleotide.

The nucleotide is therefore: phosphate - C5' sugar C1' - base. Aromatic heterocycles; there are purines and pyrimidines. Note: other nitrogenous bases exist, in particular methylated bases derived from the above mentioned; methylation of the bases has a functional role see chapter ad hoc. Glossary: - Nucleoside names: deoxyribonucleosides in DNA: deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine in DNA ribonucleosides in RNA: adenosine, guanosine, cytidine, uridine. Dinucleotides form from a phosphodiester link between 2 mononucleotides.

The phosphate of a mononucleotide in C5' of its sugar being linked to the C3' of the sugar of the previous mononucleotide. The general appearance of the polymere shows a periodicity of 3. The hydrophobic bases are stacked on the inside, there planes are perpendicular to the axis of the double helix. The outside phosphate and sugar are hydrophilic. Hydrogen bounds between the bases of one strand and that of the other strand hold the two strands together dashed lines in the drawing. A purine on one strand shall link to a pyrimidine on the other strand.

As a corollary, the number of purines residues equals the number of pyrimidine residues. A binds T with 2 hydrogen bounds. G binds C with 3 hydrogen bounds: more stable link: 5. One is the template of the other one, and reciprocally: this property will allow exact replication semi-conservative replication: one strand -the template- is conserved, another is newly synthesized, same with the second strand, conserved, allowing another one to be newly synthesized; see chapter ad hoc.

Chemical Bonding and Molecular Structure

Notes: Hydrogen bounds in base pairing are sometimes different from the model of Watson and Crick above described, using the N7 atom of the purine instead of the N1 Hoogsteen model. The double helix is a quite rigid and viscous molecule of an immense length and a small diameter. It presents a major groove and a minor groove.

The major groove is deep and wide, the minor groove is narrow and shallow. Proteins bind at the floor of the DNA grooves, using specific binding: hydrogen bounds, and non specific binding: van der Waals interactions, generalized electrostatic interactions; proteins recognize H-bond donnors, H-bond acceptors, metyl groups hydrophobic , the later being exclusively in the major groove; there are 4 possible patterns of recognition with the major groove, and only 2 with the minor groove see iconography.

Notes: - The 2 strands are called "plus" and "minus" strands, or "direct" and "reverse" strands.

Chapter 6 – Molecular Structure

At a given location where one strand any of the two bears coding sequences, it is unlikely but not impossible that the other strand also bears coding sequences. Because most metals are soluble in mercury, amalgams are used in gold mining, dentistry, and many other applications. A major difficulty when mining gold is separating very small particles of pure gold from tons of crushed rock. One way to accomplish this is to agitate a suspension of the crushed rock with liquid mercury, which dissolves the gold as well as any metallic silver that might be present. The very dense liquid gold—mercury amalgam is then isolated and the mercury distilled away.

An alloy is a solid or liquid solution that consists of one or more elements in a metallic matrix. A solid alloy has a single homogeneous phase in which the crystal structure of the solvent remains unchanged by the presence of the solute. Thus the microstructure of the alloy is uniform throughout the sample. Examples are substitutional and interstitial alloys such as brass or solder. In contrast, a partial alloy solution has two or more phases that can be homogeneous in the distribution of the components, but the microstructures of the two phases are not the same.

As a liquid solution of lead and tin is cooled, for example, different crystalline phases form at different cooling temperatures. Alloys usually have properties that differ from those of the component elements. The covalent bonds that hold the network or lattice together are simply too strong to be broken under normal conditions. They are certainly much stronger than any conceivable combination of intermolecular interactions that might occur in solution. Most metals are insoluble in virtually all solvents for the same reason: the delocalized metallic bonding is much stronger than any favorable metal atom—solvent interactions.

Many metals react with solutions such as aqueous acids or bases to produce a solution.

Interactions in Liquid Solutions

However, as we saw in Section Solids with very strong intermolecular bonding tend to be insoluble. Table 4. Ionic substances are generally most soluble in polar solvents; the higher the lattice energy, the more polar the solvent must be to overcome the lattice energy and dissolve the substance. Because of its high polarity, water is the most common solvent for ionic compounds. Many ionic compounds are soluble in other polar solvents, however, such as liquid ammonia, liquid hydrogen fluoride, and methanol.

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Because all these solvents consist of molecules that have relatively large dipole moments, they can interact favorably with the dissolved ions. Because the dipole moment of acetone 2. This apparent contradiction arises from the fact that the dipole moment is a property of a single molecule in the gas phase. By definition, the dielectric constant of a vacuum is 1. In essence, a solvent with a high dielectric constant causes the charged particles to behave as if they have been moved farther apart.

This behavior is in contrast to that of molecular substances, for which polarity is the dominant factor governing solubility. Note how the cation is nestled within the central cavity of the molecule and interacts with lone pairs of electrons on the oxygen atoms. Cryptands solvate cations via lone pairs of electrons on both oxygen and nitrogen atoms. Crown ethers are named using both the total number of atoms in the ring and the number of oxygen atoms. Thus crown-6 is an membered ring with six oxygen atoms part a in Figure The cation is stabilized by interacting with lone pairs of electrons on the surrounding oxygen atoms.

Thus crown ethers solvate cations inside a hydrophilic cavity, whereas the outer shell, consisting of C—H bonds, is hydrophobic. The availability of crown ethers with cavities of different sizes allows specific cations to be solvated with a high degree of selectivity. However, upon addition of crown ether soluble colored complex is formed. The number in the name of the cryptand is the number of oxygen atoms in each strand of the molecule.

Like crown ethers, cryptands can be used to prepare solutions of ionic compounds in solvents that are otherwise too nonpolar to dissolve them. The solubility of a substance is the maximum amount of a solute that can dissolve in a given quantity of solvent; it depends on the chemical nature of both the solute and the solvent and on the temperature and pressure. When a solution contains the maximum amount of solute that can dissolve under a given set of conditions, it is a saturated solution.

Otherwise, it is unsaturated. Supersaturated solutions, which contain more dissolved solute than allowed under particular conditions, are not stable; the addition of a seed crystal, a small particle of solute, will usually cause the excess solute to crystallize. A system in which crystallization and dissolution occur at the same rate is in dynamic equilibrium. The solubility of a substance in a liquid is determined by intermolecular interactions, which also determine whether two liquids are miscible.

Solutes can be classified as hydrophilic water loving or hydrophobic water fearing. Vitamins with hydrophilic structures are water soluble, whereas those with hydrophobic structures are fat soluble. Many metals dissolve in liquid mercury to form amalgams. Covalent network solids and most metals are insoluble in nearly all solvents. Solutions of many ionic compounds in organic solvents can be dissolved using crown ethers, cyclic polyethers large enough to accommodate a metal ion in the center, or cryptands, compounds that completely surround a cation. The strength of intramolecular bonding determines the solubility of a solute in a given solvent.

London dispersion forces increase with increasing atomic mass.

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  8. Iodine is a solid while bromine is a liquid due to the greater intermolecular interactions between the heavier iodine atoms. Iodine is less soluble than bromine in virtually all solvents because it requires more energy to separate I2 molecules than Br2 molecules.

    In dental amalgam, the mercury atoms are locked in a solid phase that does not undergo corrosion under physiological conditions; hence, the mercury atoms cannot readily diffuse to the surface where they could vaporize or undergo chemical reaction. Dissolve the mixture of A and B in a solvent in which they are both soluble when hot and relatively insoluble when cold, filter off any undissolved B, and cool slowly.

    Pure A should crystallize, while B stays in solution. If B were less soluble, it would be impossible to obtain pure A by this method in a single step, because some of the less soluble compound B will always be present in the solid that crystallizes from solution. Factors Affecting Solubility The maximum amount of a solute that can dissolve in a solvent at a specified temperature and pressure is its solubility.

    Note The solubility of most solids increases with increasing temperature. Interactions in Liquid Solutions The interactions that determine the solubility of a substance in a liquid depend largely on the chemical nature of the solute such as whether it is ionic or molecular rather than on its physical state solid, liquid, or gas.

    Journal of Molecular Structure

    Solutions of Molecular Substances in Liquids The London dispersion forces, dipole—dipole interactions, and hydrogen bonds that hold molecules to other molecules are generally weak. Image used with permission from Wikipedia The solubilities of simple alcohols in water are given in Table Solid Solutions Solutions are not limited to gases and liquids; solid solutions also exist.

    Note Solids with very strong intermolecular bonding tend to be insoluble. Solubilities of Ionic Substances in Liquids Table 4. Summary The solubility of a substance is the maximum amount of a solute that can dissolve in a given quantity of solvent; it depends on the chemical nature of both the solute and the solvent and on the temperature and pressure. Key Takeaway The strength of intramolecular bonding determines the solubility of a solute in a given solvent. Conceptual Problems If a compound is only slightly soluble in a particular solvent, what are the relative strengths of the solvent—solvent and solute—solute interactions versus the solute—solvent interactions?

    Predict whether each of the following sets of conditions favors formation of a solution:. Arrange the following liquids in order of increasing solubility in water: t-butanol [ CH3 3COH], benzene, ammonia, and heptane. Justify your answer. Which compound in each pair will be more soluble in water? Explain your reasoning in each case. When the stirring is stopped and the mixture is allowed to stand, two layers are formed. At this point, each layer contains only one of the two original compounds.

    Identify the compound that is present in each layer following the addition of HCl. Explain your reasoning. How can the original compounds be recovered from the toluene solution? A solution is made by mixing Which is the solute, and which is the solvent? Is it valid to assume that the volume of the resulting solution will be mL? Explain your answer. Why is sodium iodide so much more soluble in water? Do you expect KCl to be more soluble or less soluble in water than NaCl? When water is mixed with a solvent with which it is immiscible, the two liquids usually form two separate layers.

    If the density of the nonaqueous solvent is 1. If you were not sure of the density and the identity of the other liquid, how might you be able to identify which is the aqueous layer?

    When two liquids are immiscible, the addition of a third liquid can occasionally be used to induce the formation of a homogeneous solution containing all three. Why does adding a third solvent produce a homogeneous solution? Methanol and n-hexane are immiscible. Which of the following solvents would you add to create a homogeneous solution—water, n-butanol, or cyclohexane? Justify your choice. Some proponents of vitamin therapy for combating illness encourage the consumption of large amounts of fat-soluble vitamins.

    Why can this be dangerous? Would it be as dangerous to consume large amounts of water-soluble vitamins? Why or why not? Why are most metals insoluble in virtually all solvents? Because sodium reacts violently with water, it is difficult to weigh out small quantities of sodium metal for a reaction due to its rapid reaction with small amounts of moisture in the air.

    Will it be more or less sensitive to moisture than solid Na or K?

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    Dental amalgams often contain high concentrations of Hg, which is highly toxic. Arrange acetone, chloroform, cyclohexane, and 2-butanol in order of increasing dielectric constant. Dissolving a white crystalline compound in ethanol gave a blue solution. Evaporating the ethanol from the solution gave a bluish-crystalline product, which slowly transformed into the original white solid on standing in the air for several days.

    Explain what happened.