1.
Isomer
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An isomer is a molecule with the same molecular formula as another molecule, but with a different chemical structure. That is, isomers contain the number of atoms of each element. Isomers do not necessarily share similar properties, unless they also have the functional groups. There are two forms of isomerism, structural isomerism and stereoisomerism. In structural isomers, sometimes referred to as constitutional isomers, the atoms, Structural isomers have different IUPAC names and may or may not belong to the same functional group. For example, two position isomers would be 2-fluoropropane and 1-fluoropropane, illustrated on the side of the diagram above. In skeletal isomers the main chain is different between the two isomers. This type of isomerism is most identifiable in secondary and tertiary alcohol isomers, tautomers are structural isomers that spontaneously interconvert with each other, even when pure. They have different chemical properties and, as a consequence, distinct reactions characteristic to each form are observed, if the interconversion reaction is fast enough, tautomers cannot be isolated from each other. An example is when they differ by the position of a proton, such as in keto/enol tautomerism, there is, however, another isomer of C3H8O that has significantly different properties, methoxyethane. Unlike the isomers of propanol, methoxyethane has an oxygen connected to two carbons rather than to one carbon and one hydrogen. Methoxyethane is an ether, not an alcohol, because it lacks a hydroxyl group, propadiene and propyne are examples of isomers containing different bond types. Propadiene contains two double bonds, whereas propyne contains one triple bond, in stereoisomers the bond structure is the same, but the geometrical positioning of atoms and functional groups in space differs. This class includes enantiomers which are non-superposable mirror-images of each other, and diastereomers, enantiomers always contain chiral centers and diastereomers often do, but there are some diastereomers that neither are chiral nor contain chiral centers. Another type of isomer, conformational isomers, may be rotamers, diastereomers, for example, ortho- position-locked biphenyl systems have enantiomers. E/Z isomers, which have restricted rotation at a bond, are configurational isomers. They are classified as diastereomers, whether or not they contain any chiral centers, e/Z notation depicts absolute stereochemistry, which is an unambiguous descriptor based on CIP priorities. Cis–trans isomers are used to describe any molecules with restricted rotation in the molecule, for molecules with C=C double bonds, these descriptors describe relative stereochemistry only based on group bulkiness or principal carbon chain, and so can be ambiguous
2.
Stereochemistry
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Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation. An important branch of stereochemistry is the study of chiral molecules, stereochemistry is also known as 3D chemistry because the prefix stereo- means three-dimensionality. The study of stereochemistry focuses on stereoisomers and spans the spectrum of organic, inorganic, biological, physical. This property, the physical property in which the two types of tartrate salts differed, is due to optical isomerism. In 1874, Jacobus Henricus van t Hoff and Joseph Le Bel explained optical activity in terms of the arrangement of the atoms bound to carbon. Cahn–Ingold–Prelog priority rules are part of a system for describing a molecules stereochemistry and they rank the atoms around a stereocenter in a standard way, allowing the relative position of these atoms in the molecule to be described unambiguously. A Fischer projection is a way to depict the stereochemistry around a stereocenter. An often cited example of the importance of stereochemistry relates to the thalidomide disaster, thalidomide is a pharmaceutical drug, first prepared in 1957 in Germany, prescribed for treating morning sickness in pregnant women. The drug was discovered to be teratogenic, causing genetic damage to early embryonic growth and development. Some of the proposed mechanisms of teratogenecity involve a different biological function for the -. In the human body however, thalidomide undergoes racemization, even if one of the two enantiomers is administered as a drug, the other enantiomer is produced as a result of metabolism. Accordingly, it is incorrect to state one of the stereoisomer is safe while the other is teratogenic. Thalidomide is currently used for the treatment of diseases, notably cancer. Strict regulations and controls have been enabled to avoid its use by pregnant women and this disaster was a driving force behind requiring strict testing of drugs before making them available to the public. Torsional strain results from resistance to twisting about a bond
3.
Structural isomer
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Structural isomerism, or constitutional isomerism, is a form of isomerism in which molecules with the same molecular formula have bonded together in different orders, as opposed to stereoisomerism. There are multiple synonyms for constitutional isomers, three categories of constitutional isomers are skeletal, positional, and functional isomers. Positional isomers are also called regioisomers, in chain isomerism, or skeletal isomerism, components of the skeleton are distinctly re-ordered to create different structures. Pentane exists as three isomers, n-pentane, isopentane and neopentane, in position isomerism a functional group or other substituent changes position on a parent structure. In the table below, the group can occupy three different positions on an n-pentane chain forming three different compounds. Many aromatic isomers exist because substituents can be positioned on different parts of the benzene ring, only one isomer of phenol or hydroxybenzene exists but cresol or methylphenol has three isomers where the additional methyl group can be placed on three different positions on the ring. Xylenol has one group and two methyl groups and a total of 6 isomers exist. Functional isomers are structural isomers that have the molecular formula. These groups of atoms are called groups, functionalities. Another way to say this is that two compounds with the molecular formula, but different functional groups, are functional isomers. For example, cyclohexane and 1-hexene both have the formula C6H12 and these two are considered functional group isomers because cyclohexane is a cycloalkane and hex-1-ene is an alkene. For two molecules to be functional isomers, they must contain key groups of atoms arranged in particular ways, some of the best examples come from organic chemistry. Depending on how the atoms are arranged, it can represent two different compounds dimethyl ether CH3-O-CH3 or ethanol CH3CH2-O-H, dimethyl ether and ethanol are functional isomers. The carbon chain-oxygen-carbon chain functionality is called an ether, the carbon chain-oxygen-hydrogen functionality is called an alcohol. If the functionalities stay the same, but their locations change, 1-Propanol and 2-propanol are structural isomers, but they are not functional isomers. The functional group is present in both of these compounds, but they are not the same, while some chemists use the terms structural isomer and functional isomer interchangeably, not all structural isomers are functional isomers. Functional isomers are most often identified in chemistry using infrared spectroscopy, infrared radiation corresponds to the energies associated primarily with molecular vibration. The alcohol functionality has a very distinct vibration called OH-stretch that is due to hydrogen bonding, all alcohols in liquid and solid form absorb infrared radiation at certain wavelengths
4.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH
5.
Chirality (chemistry)
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Chirality /kaɪˈrælɪti/ is a geometric property of some molecules and ions. A chiral molecule/ion is non-superposable on its mirror image, the presence of an asymmetric carbon center is one of several structural features that induce chirality in organic and inorganic molecules. The term chirality is derived from the Greek word for hand, the mirror images of a chiral molecule/ion are called enantiomers or optical isomers. Individual enantiomers are often designated as either right- or left-handed, Chirality is an essential consideration when discussing the stereochemistry in organic and inorganic chemistry. The concept is of practical importance because most biomolecules and pharmaceuticals are chiral. Chirality is based on molecular symmetry elements, specifically, a chiral compound can contain no improper axis of rotation, which includes planes of symmetry and inversion center. Chiral molecules are always dissymmetric but not always asymmetric, in general, chiral molecules have point chirality at a single stereogenic atom, which has four different substituents. The two enantiomers of such compounds are said to have different absolute configurations at this center, the stereogenic atom is usually carbon, as in many biological molecules. However chirality can exist in any atom, including metals, phosphorus, Chiral nitrogen is equally possible, although the effects of nitrogen inversion can make many of these compounds impossible to isolate. While the presence of a stereogenic atom describes the great majority of cases, for instance it is not necessary for the chiral substance to have a stereogenic atom. Examples include 1-bromo-1-chloro-1-fluoroadamantane, methylethylphenyltetrahedrane, certain calixarenes and fullerenes, which have inherent chirality, the C2-symmetric species 1, 1-bi-2-naphthol,1, 3-dichloro-allene have axial chirality. -cyclooctene and many ferrocenes have planar chirality, when the optical rotation for an enantiomer is too low for practical measurement, the species is said to exhibit cryptochirality. Even isotopic differences must be considered when examining chirality, illustrative is the derivative of benzyl alcohol PhCHDOH is chiral. The S enantiomer has D = +0. 715°, many biologically active molecules are chiral, including the naturally occurring amino acids and sugars. In biological systems, most of these compounds are of the chirality, most amino acids are levorotatory. Typical naturally occurring proteins, made of L amino acids, are known as left-handed proteins, d-amino acids are very rare in nature and have only been found in small peptides attached to bacteria cell walls. The origin of this homochirality in biology is the subject of much debate, however, there is some suggestion that early amino acids could have formed in comet dust. Enzymes, which are chiral, often distinguish between the two enantiomers of a chiral substrate, one could imagine an enzyme as having a glove-like cavity that binds a substrate
6.
Enantiomer
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A single chiral atom or similar structural feature in a compound causes that compound to have two possible structures which are non-superposable, each a mirror image of the other. Each member of the pair is termed an enantiomorph, the property is termed enantiomerism. The presence of multiple features in a given compound increases the number of geometric forms possible. Enantiopure compounds refer to samples having, within the limits of detection and they are sometimes called optical isomers for this reason. Enantiomer members often have different chemical reactions with other enantiomer substances, since many biological molecules are enantiomers, there is sometimes a marked difference in the effects of two enantiomers on biological organisms. Owing to this discovery, drugs composed of one enantiomer can be developed to enhance the pharmacological efficacy. An example is eszopiclone, which is enantiopure and therefore administered in doses that are exactly 1/2 of the older, in the case of eszopiclone, the S enantiomer is responsible for all the desired effects, while the other enantiomer seems to be inactive. A dose of 2 mg of zopiclone must be administered to produce the therapeutic effect as 1 mg of eszopiclone. In chemical synthesis of enantiomeric substances, non-enantiomeric precursors inevitably produce racemic mixtures, in the absence of an effective enantiomeric environment, separation of a racemic mixture into its enantiomeric components is impossible. The R/S system is an important nomenclature system for denoting distinct enantiomers, another system is based on prefix notation for optical activity, - and - or d- and l-. The Latin for left and right is laevus and dexter, respectively, left and right have always had moral connotations, and the Latin words for these are sinister and rectus. The English word right is a cognate of rectus and this is the origin of the D, L and S, R notations, and the employment of prefixes levo- and dextro- in common names. Most compounds that one or more asymmetric carbon atoms show enantiomerism. There are a few compounds that do have asymmetric carbon atoms. An example of such an enantiomer is the sedative thalidomide, which was sold in a number of countries across the world from 1957 until 1961 and it was withdrawn from the market when it was found to cause of birth defects. One enantiomer caused the desirable effects, while the other, unavoidably present in equal quantities. The herbicide mecoprop is a mixture, with the --enantiomer possessing the herbicidal activity. Another example is the antidepressant drugs escitalopram and citalopram, citalopram is a racemate, escitalopram is a pure enantiomer
7.
Mirror image
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A mirror image is a reflected duplication of an object that appears almost identical, but is reversed in the direction perpendicular to the mirror surface. As an optical effect it results from reflection off of such as a mirror or water. It is also a concept in geometry and can be used as a process for 3-D structures. Two-dimensional mirror images can be seen in the reflections of mirrors or other reflecting surfaces, or on a printed surface seen inside out. If we look at an object that is effectively two-dimensional and then turn it towards a mirror, in this example, it is the change in orientation rather than the mirror itself that causes the observed reversal. Another example is when we stand with our backs to the mirror, then we compare the object with its reflection by turning ourselves 180 degrees, towards the mirror. Again we perceive a left-right reversal due to a change in orientation, so, in these examples the mirror does not actually cause the observed reversals. The concept of reflection can be extended to three-dimensional objects, including the inside parts, the term then relates to structural as well as visual aspects. A three-dimensional object is reversed in the perpendicular to the mirror surface. In physics, mirror images are investigated in the subject called geometrical optics, in chemistry, two versions of a molecule, one a mirror image of the other, are called enantiomers if they are not superposable on each other. That is an example of chirality, in general, an object and its mirror image are called enantiomorphs. If a point of an object has coordinates then the image of this point has coordinates, thus reflection is a reversal of the coordinate axis perpendicular to the mirrors surface. In everyday use, a mirror does not reverse right and left, however, there is often a perception of left-right reversal, probably because the left and right of an object are defined by its top and front. Reflection in a mirror does result in a change in chirality, as a consequence, if one looks in a mirror and lets two axes coincide with those in the mirror, then this gives a reversal of the third axis. Similarly, if you stand side-on to a mirror your left and its important to realise there are only two enantiomorphs, the object and its image. So, no matter how the object is oriented towards the mirror, all the images are fundamentally identical. In the photograph of the urn and mirror, the urn is fairly symmetrical front-back, so, its not surprising that no obvious reversal of the urn can be seen in the mirror image. A mirror image appears more obviously three-dimensional if the observer moves and this is because the relative position of objects changes as the observers perspective changes, or is different viewed with each eye
8.
Polarization (waves)
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Polarization is a parameter applying to transverse waves that specifies the geometrical orientation of the oscillations. In a transverse wave the direction of the oscillation is transverse to the direction of motion of the wave, a simple example of a polarized transverse wave is vibrations traveling along a taut string for example in a musical instrument like a guitar string. Depending on how the string is plucked, the vibrations can be in a direction, horizontal direction. Transverse waves that exhibit polarization include electromagnetic waves such as light and radio waves, gravitational waves, in some types of transverse waves the wave displacement is limited to a single direction, so these also dont exhibit polarization. For example, in waves in liquids the wave displacement of the particles is always in a vertical plane. In linear polarization the fields oscillate in a single direction, in circular or elliptical polarization the fields rotate at a constant rate in a plane as the wave travels. Polarized light can be produced by passing unpolarized light through a polarizing filter, some of these are used to make polarizing filters. Light is also partially polarized when it reflects from a surface, according to quantum mechanics, electromagnetic waves consist of particles called photons. When viewed in this way, the polarization of a wave is determined by a quantum mechanical property of photons called their spin. A photon has one of two spins, it can either spin in a right hand sense or a left hand sense about its direction of travel. Circularly polarized electromagnetic waves are composed of photons with one type of spin. Linearly polarized waves consist of numbers of right and left hand spinning photons. Polarization is an important parameter in areas of science dealing with transverse waves, such as optics, seismology, radio, especially impacted are technologies such as lasers, wireless and optical fiber telecommunications, and radar. And incoherent states can be modeled stochastically as a combination of such uncorrelated waves with some distribution of frequencies, phases. Considering a monochromatic wave of optical frequency f, let us take the direction of propagation as the z axis. Being a transverse wave the E and H fields must then contain components only in the x and y directions whereas Ez=Hz=0. Using complex notation, we understand the instantaneous electric and magnetic fields to be given by the real parts of the complex quantities occurring in the following equations. Here ex, ey, hx, and hy are complex numbers, in the second more compact form, as these equations are customarily expressed, these factors are described using the wavenumber k =2 π n / λ and angular frequency ω =2 π f
9.
Optical rotation
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Optical rotation or optical activity is the rotation of the plane of polarization of linearly polarized light as it travels through certain materials. Optical activity occurs only in chiral materials, those lacking microscopic mirror symmetry, unlike other sources of birefringence which alter a beams state of polarization, optical activity can be observed in fluids. This can include gases or solutions of chiral molecules such as sugars, molecules with helical secondary structure such as some proteins and it can also be observed in chiral solids such as certain crystals with a rotation between adjacent crystal planes or metamaterials. The rotation of the plane of polarization may be either clockwise, to the right, for instance, sucrose and camphor are d-rotary whereas cholesterol is l-rotary. For a given substance, the angle by which the polarization of light of a wavelength is rotated is proportional to the path length through the material and proportional to its concentration. The rotation is not dependent on the direction of propagation, unlike the Faraday effect where the rotation is dependent on the direction of the applied magnetic field. Optical activity is measured using a source and polarimeter. Modulation of a liquid crystals optical activity, viewed between two polarizers, is the principle of operation of liquid-crystal displays. The rotation of the orientation of polarized light was first observed in 1811 in quartz by French physicist François Jean Dominique Arago. Jean Baptiste Biot also observed the rotation of the axis of polarization in certain liquids, simple polarimeters have been used since this time to measure the concentrations of simple sugars, such as glucose, in solution. In fact one name for D-glucose, is dextrose, referring to the fact that it causes linearly polarized light to rotate to the right or dexter side. In a similar manner, levulose, more known as fructose. Fructose is even more strongly levorotatory than glucose is dextrorotatory, in 1849, Louis Pasteur resolved a problem concerning the nature of tartaric acid. Pasteur noticed that the crystals come in two forms that are mirror images of one another. Sorting the crystals by hand gave two forms of the compound, Solutions of one form rotate polarized light clockwise, while the other form rotate light counterclockwise, an equal mix of the two has no polarizing effect on light. If the 4 neighbors are all different, then there are two possible orderings of the neighbors around the tetrahedron, which will be mirror images of each other and this led to a better understanding of the three-dimensional nature of molecules. Optical activity occurs due to molecules dissolved in a fluid or due to the fluid itself only if the molecules are one of two stereoisomers, this is known as an enantiomer, the structure of such a molecule is such that it is not identical to its mirror image. In mathematics, this property is known as chirality
