1.
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
2.
Atomic number
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The atomic number or proton number of a chemical element is the number of protons found in the nucleus of an atom of that element. It is identical to the number of the nucleus. The atomic number identifies a chemical element. In an uncharged atom, the number is also equal to the number of electrons. The atomic number Z, should not be confused with the mass number A and this number of neutrons, N, completes the weight, A = Z + N. Atoms with the atomic number Z but different neutron numbers N. Historically, it was these atomic weights of elements that were the quantities measurable by chemists in the 19th century. Only after 1915, with the suggestion and evidence that this Z number was also the nuclear charge, loosely speaking, the existence or construction of a periodic table of elements creates an ordering of the elements, and so they can be numbered in order. Dmitri Mendeleev claimed that he arranged his first periodic tables in order of atomic weight, however, in consideration of the elements observed chemical properties, he changed the order slightly and placed tellurium ahead of iodine. This placement is consistent with the practice of ordering the elements by proton number, Z. A simple numbering based on periodic table position was never entirely satisfactory and this central charge would thus be approximately half the atomic weight. This proved eventually to be the case, the experimental position improved dramatically after research by Henry Moseley in 1913. To do this, Moseley measured the wavelengths of the innermost photon transitions produced by the elements from aluminum to gold used as a series of movable anodic targets inside an x-ray tube. The square root of the frequency of these photons increased from one target to the next in an arithmetic progression and this led to the conclusion that the atomic number does closely correspond to the calculated electric charge of the nucleus, i. e. the element number Z. Among other things, Moseley demonstrated that the series must have 15 members—no fewer. After Moseleys death in 1915, the numbers of all known elements from hydrogen to uranium were examined by his method. There were seven elements which were not found and therefore identified as still undiscovered, from 1918 to 1947, all seven of these missing elements were discovered. By this time the first four transuranium elements had also been discovered, in 1915 the reason for nuclear charge being quantized in units of Z, which were now recognized to be the same as the element number, was not understood
3.
IUPAC books
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The Compendium of Chemical Terminology is a book published by the International Union of Pure and Applied Chemistry containing internationally accepted definitions for terms in chemistry. Work on the first edition was initiated by Victor Gold, hence its informal name, the first edition was published in 1987 and the second edition, edited by A. D. McNaught and A. Wilkinson, was published in 1997. A slightly expanded version of the Gold Book is also freely searchable online, translations have also been published in French, Spanish and Polish
4.
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
5.
Amino acid
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Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, hydrogen, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids. The other two are selenocysteine, and pyrrolysine, pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can also be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids also play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, cysteine, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids
6.
Conformational isomerism
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In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted exclusively by rotations about formally single bonds. Such isomers are generally referred to as conformational isomers or conformers and, specifically, rotations about single bonds are restricted by a rotational energy barrier which must be overcome to interconvert one conformer to another. Conformational isomerism arises when the rotation about a bond is relatively unhindered. That is, the barrier must be small enough for the interconversion to occur. Conformational isomers are thus distinct from the classes of stereoisomers where interconversion necessarily involves breaking and reforming of chemical bonds. The study of the energetics between different rotamers is referred to as conformational analysis and it is useful for understanding the stability of different isomers, for example, by taking into account the spatial orientation and through-space interactions of substituents. In addition, conformational analysis can be used to predict and explain product selectivity, mechanisms, the types of conformational isomers are related to the spatial orientations of the substituents between two vicinal atoms. The staggered conformation includes the gauche and anti conformations, depending on the orientations of the two substituents. The energy difference between gauche and anti is 0.9 kcal/mol associated with the energy of the gauche conformer. The anti conformer is, therefore, the most stable, the three eclipsed conformations with dihedral angles of 0°, 120°, and 240° are not considered to be rotamers, but are instead transition states of higher energy. While simple molecules can be described by these types of conformations, more specific examples of conformational isomerism are detailed elsewhere, Ring conformation Cyclohexane conformations with chair and boat conformers. Allylic strain – energetics related to rotation about the bond between sp2 and sp3 carbons. Atropisomerism – due to restricted rotation about a bond, a molecule can become chiral, folding of molecules, where some shapes are stable and functional, but others are not. Three isotherms are given in the depicting the equilibrium distribution of two conformers at different temperatures. At a free energy difference of 0 kcal/mol, this gives a constant of 1. The two have equal energy, neither is more stable, so neither predominates compared to the other. A negative difference in free energy means that a conformer interconverts to a more stable conformation. For example, the ΔG of butane from gauche to anti is −0.9 kcal/mol, therefore the equilibrium constant is 4.5, conversely, a positive difference in free energy means the conformer already is the more stable one, so the interconversion is an unfavorable equilibrium
7.
Glycine
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Glycine is the amino acid that has a single hydrogen atom as its side chain. It is the simplest possible amino acid, the chemical formula of glycine is NH2‐CH2‐COOH. Glycine is one of the amino acids. Its codons are GGU, GGC, GGA, GGG of the genetic code, Glycine is a colorless, sweet-tasting crystalline solid. It is unique among the amino acids in that it is achiral. It can fit into hydrophilic or hydrophobic environments since it exists as zwitterion at natural pH, Glycine was first isolated from gelatin in 1820. The name comes from the ancient Greek word γλυκύς sweet tasting, Glycine was discovered in 1820, by Henri Braconnot who boiled a gelatinous object with sulfuric acid. Glycine is manufactured industrially by treating chloroacetic acid with ammonia, ClCH2COOH +2 NH3 → H2NCH2COOH + NH4Cl About 15 million kg are produced annually in this way, in the USA and in Japan, glycine is produced via the Strecker amino acid synthesis. Glycine is also cogenerated as an impurity in the synthesis of EDTA, arising from reactions of the ammonia coproduct. In aqueous solution, glycine itself is amphoteric, at low pH the molecule can be protonated with a pKa of about 2.4, the nature of glycine in aqueous solution has been investigated by theoretical methods. In solution the ratio of concentrations of the two isomers is independent of both the concentration and of pH. This ratio is simply the equilibrium constant for isomerization, K = / Both isomers of glycine have been observed by microwave spectroscopy in the gas phase. The solid-state structure has been analyzed in detail and this conversion is readily reversible, CO2 + NH+4 + N5, N10-Methylene tetrahydrofolate + NADH + H+ → Glycine + tetrahydrofolate + NAD+ Glycine is coded by codons GGU, GGC, GGA and GGG. Most proteins incorporate only small quantities of glycine, a notable exception is collagen, which contains about 35% glycine. Glycine is degraded via three pathways, the first step is the reverse of glycine biosynthesis from serine with serine hydroxymethyl transferase. Serine is then converted to pyruvate by serine dehydratase, in the third pathway of glycine degradation, glycine is converted to glyoxylate by D-amino acid oxidase. Glyoxylate is then oxidized by lactate dehydrogenase to oxalate in an NAD+-dependent reaction. The half-life of glycine and its elimination from the body varies significantly based on dose, in one study, the half-life was between 0.5 and 4.0 hours
8.
International Union of Pure and Applied Chemistry
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The International Union of Pure and Applied Chemistry /ˈaɪjuːpæk/ or /ˈjuːpæk/ is an international federation of National Adhering Organizations that represents chemists in individual countries. It is a member of the International Council for Science, IUPAC is registered in Zürich, Switzerland, and the administrative office, known as the IUPAC Secretariat, is in Research Triangle Park, North Carolina, United States. This administrative office is headed by IUPACs executive director, currently Lynn Soby, IUPAC was established in 1919 as the successor of the International Congress of Applied Chemistry for the advancement of chemistry. Its members, the National Adhering Organizations, can be national chemistry societies, national academies of sciences, there are fifty-four National Adhering Organizations and three Associate National Adhering Organizations. IUPACs Inter-divisional Committee on Nomenclature and Symbols is the world authority in developing standards for the naming of the chemical elements. Since its creation, IUPAC has been run by different committees with different responsibilities. These committees run different projects which include standardizing nomenclature, finding ways to bring chemistry to the world, IUPAC is best known for its works standardizing nomenclature in chemistry and other fields of science, but IUPAC has publications in many fields including chemistry, biology and physics. IUPAC is also known for standardizing the atomic weights of the elements through one of its oldest standing committees, the need for an international standard for chemistry was first addressed in 1860 by a committee headed by German scientist Friedrich August Kekulé von Stradonitz. This committee was the first international conference to create an international naming system for organic compounds, the ideas that were formulated in that conference evolved into the official IUPAC nomenclature of organic chemistry. IUPAC stands as a legacy of this meeting, making it one of the most important historical international collaborations of chemistry societies, since this time, IUPAC has been the official organization held with the responsibility of updating and maintaining official organic nomenclature. IUPAC as such was established in 1919, one notable country excluded from this early IUPAC is Germany. Germanys exclusion was a result of prejudice towards Germans by the Allied powers after World War I, Germany was finally admitted into IUPAC during 1929. However, Nazi Germany was removed from IUPAC during World War II, during World War II, IUPAC was affiliated with the Allied powers, but had little involvement during the war effort itself. After the war, East and West Germany were eventually readmitted to IUPAC, since World War II, IUPAC has been focused on standardizing nomenclature and methods in science without interruption. In 2016, IUPAC denounced the use of chlorine as a chemical weapon, the letter stated, Our organizations deplore the use of chlorine in this manner. According to the CWC, the use, stockpiling, distribution, IUPAC is governed by several committees that all have different responsibilities. Each committee is made up of members of different National Adhering Organizations from different countries, the steering committee hierarchy for IUPAC is as follows, All committees have an allotted budget to which they must adhere. Any committee may start a project, if a projects spending becomes too much for a committee to continue funding, it must take the issue to the Project Committee
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
10.
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
11.
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
